US20220235367A1 - Isolated polynucleotides and polypeptides and methods of using same for increasing plant yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance of plants and nitrogen use efficiency - Google Patents

Abstract

Provided are isolated polynucleotides comprising a nucleic acid sequence encoding a polypeptide at least 80% identical to SEQ ID NO: 422, 362-421, 423-601, 2429-4085 and 4086, such as a polynucleotide which is at least 80% identical to SEQ ID NO: 260, 1-259, 261-361, 602-2427 and 2428, nucleic acid constructs comprising same, plant cells comprising same, transgenic plants expressing same, and methods of generating thereof for increasing the yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, nitrogen use efficiency and/or abiotic stress tolerance of a plant.

Description

RELATED APPLICATIONS
• This application is a division of U.S. patent application Ser. No. 16/984,195 filed on Aug. 4, 2020, which is a division of U.S. patent application Ser. No. 16/244,197 filed on Jan. 10, 2019, now U.S. Pat. No. 10,815,492, which is a division of U.S. patent application Ser. No. 15/886,868 filed on Feb. 2, 2018, now U.S. Pat. No. 10,253,327, which is a division of U.S. patent application Ser. No. 14/381,596, filed on Aug. 28, 2014, now U.S. Pat. No. 9,920,330, which is a National Phase of PCT Patent Application No. PCT/IL2013/050172 having International Filing Date of Feb. 27, 2013, which claims the benefit of priority under 35 USC § 119(e) of U.S. Provisional Patent Application Nos. 61/604,588 filed on Feb. 29, 2012 and 61/681,252 filed on Aug. 9, 2012.
• The contents of the above applications are all incorporated by reference as if fully set forth herein in their entirety.
SEQUENCE LISTING STATEMENT
• The ASCII file, entitled 91715SequenceListing.txt, created on Apr. 5, 2022, comprising 11,837,140 bytes, submitted concurrently with the filing of this application is incorporated herein by reference.
FIELD AND BACKGROUND OF THE INVENTION
• The present invention, in some embodiments thereof, relates to isolated polypeptides and polynucleotides, nucleic acid constructs comprising same, transgenic cells comprising same, transgenic plants exogenously expressing same and more particularly, but not exclusively, to methods of using same for increasing yield (e.g., seed yield, oil yield), biomass, growth rate, vigor, oil content, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of a plant.
• Yield is affected by various factors, such as, the number and size of the plant organs, plant architecture (for example, the number of branches), grains set length, number of filled grains, vigor (e.g. seedling), growth rate, root development, utilization of water, nutrients (e.g., nitrogen) and fertilizers, and stress tolerance.
• Crops such as, corn, rice, wheat, canola and soybean account for over half of total human caloric intake, whether through direct consumption of the seeds themselves or through consumption of meat products raised on processed seeds or forage. Seeds are also a source of sugars, proteins and oils and metabolites used in industrial processes.
• The ability to increase plant yield, whether through increase dry matter accumulation rate, modifying cellulose or lignin composition, increase stalk strength, enlarge meristem size, change of plant branching pattern, erectness of leaves, increase in fertilization efficiency, enhanced seed dry matter accumulation rate, modification of seed development, enhanced seed filling or by increasing the content of oil, starch or protein in the seeds would have many applications in agricultural and non-agricultural uses such as in the biotechnological production of pharmaceuticals, antibodies or vaccines.
• Vegetable or seed oils are the major source of energy and nutrition in human and animal diet. They are also used for the production of industrial products, such as paints, inks and lubricants. In addition, plant oils represent renewable sources of long-chain hydrocarbons which can be used as fuel. Since the currently used fossil fuels are finite resources and are gradually being depleted, fast growing biomass crops may be used as alternative fuels or for energy feedstocks and may reduce the dependence on fossil energy supplies. However, the major bottleneck for increasing consumption of plant oils as bio-fuel is the oil price, which is still higher than fossil fuel. In addition, the production rate of plant oil is limited by the availability of agricultural land and water. Thus, increasing plant oil yields from the same growing area can effectively overcome the shortage in production space and can decrease vegetable oil prices at the same time.
• Studies aiming at increasing plant oil yields focus on the identification of genes involved in oil metabolism as well as in genes capable of increasing plant and seed yields in transgenic plants. Genes known to be involved in increasing plant oil yields include those participating in fatty acid synthesis or sequestering such as desaturase [e.g., DELTA6, DELTA12 or acyl-ACP (Ssi2; Arabidopsis Information Resource (TAIR; Hypertext Transfer Protocol://World Wide Web (dot) arabidopsis (dot) org/), TAIR No. AT2G43710)], OleosinA (TAIR No. AT3G01570) or FAD3 (TAIR No. AT2G29980), and various transcription factors and activators such as Lec1 [TAIR No. AT1G21970, Lotan et al. 1998. Cell. 26:93(7):1195-205], Lec2 [TAIR No. AT1G28300, Santos Mendoza et al. 2005, FEBS Lett. 579(21):4666-70], Fus3 (TAIR No. AT3G26790), ABI3 [TAIR No. AT3G24650, Lara et al. 2003. J Biol Chem. 278(23): 21003-11] and Wri1 [TAIR No. AT3G54320, Cemac and Benning, 2004. Plant J. 40(4): 575-85].
• Genetic engineering efforts aiming at increasing oil content in plants (e.g., in seeds) include upregulating endoplasmic reticulum (FAD3) and plastidal (FAD7) fatty acid desaturases in potato (Zabrouskov V., et al., 2002; Physiol Plant. 116:172-185); over-expressing the GmDof4 and GmDof11 transcription factors (Wang H W et al., 2007; Plant J. 52:716-29); over-expressing a yeast glycerol-3-phosphate dehydrogenase under the control of a seed-specific promoter (Vigeolas H. et al. 2007, Plant Biotechnol J. 5:431-41; U.S. Pat. Appl. No. 20060168684); using Arabidopsis FAEI and yeast SLC1-1 genes for improvements in erucic acid and oil content in rapeseed (Katavic V. et al., 2000, Biochem Soc Trans. 28:935-7).
• Various patent applications disclose genes and proteins which can increase oil content in plants. These include for example, U.S. Pat. Appl. No. 20080076179 (lipid metabolism protein); U.S. Pat. Appl. No. 20060206961 (the Ypr140w polypeptide); U.S. Pat. Appl. No. 20060174373 [triacylglycerols synthesis enhancing protein (TEP)]; U.S. Pat. Appl. Nos. 20070169219, 20070006345, 20070006346 and 20060195943 (disclose transgenic plants with improved nitrogen use efficiency which can be used for the conversion into fuel or chemical feedstocks); WO2008/122980 (polynucleotides for increasing oil content, growth rate, biomass, yield and/or vigor of a plant).
• A common approach to promote plant growth has been, and continues to be, the use of natural as well as synthetic nutrients (fertilizers). Thus, fertilizers are the fuel behind the “green revolution”, directly responsible for the exceptional increase in crop yields during the last 40 years, and are considered the number one overhead expense in agriculture. For example, inorganic nitrogenous fertilizers such as ammonium nitrate, potassium nitrate, or urea, typically accounts for 40% of the costs associated with crops such as corn and wheat. Of the three macronutrients provided as main fertilizers [Nitrogen (N), Phosphate (P) and Potassium (K)], nitrogen is often the rate-limiting element in plant growth and all field crops have a fundamental dependence on inorganic nitrogenous fertilizer. Nitrogen is responsible for biosynthesis of amino and nucleic acids, prosthetic groups, plant hormones, plant chemical defenses, etc. and usually needs to be replenished every year, particularly for cereals, which comprise more than half of the cultivated areas worldwide. Thus, nitrogen is translocated to the shoot, where it is stored in the leaves and stalk during the rapid step of plant development and up until flowering. In corn for example, plants accumulate the bulk of their organic nitrogen during the period of grain germination, and until flowering. Once fertilization of the plant has occurred, grains begin to form and become the main sink of plant nitrogen. The stored nitrogen can be then redistributed from the leaves and stalk that served as storage compartments until grain formation.
• Since fertilizer is rapidly depleted from most soil types, it must be supplied to growing crops two or three times during the growing season. In addition, the low nitrogen use efficiency (NUE) of the main crops (e.g., in the range of only 30-70%) negatively affects the input expenses for the farmer, due to the excess fertilizer applied. Moreover, the over and inefficient use of fertilizers are major factors responsible for environmental problems such as eutrophication of groundwater, lakes, rivers and seas, nitrate pollution in drinking water which can cause methemoglobinemia, phosphate pollution, atmospheric pollution and the like. However, in spite of the negative impact of fertilizers on the environment, and the limits on fertilizer use, which have been legislated in several countries, the use of fertilizers is expected to increase in order to support food and fiber production for rapid population growth on limited land resources. For example, it has been estimated that by 2050, more than 150 million tons of nitrogenous fertilizer will be used worldwide annually.
• Increased use efficiency of nitrogen by plants should enable crops to be cultivated with lower fertilizer input, or alternatively to be cultivated on soils of poorer quality and would therefore have significant economic impact in both developed and developing agricultural systems.
• Genetic improvement of fertilizer use efficiency (FUE) in plants can be generated either via traditional breeding or via genetic engineering.
• Attempts to generate plants with increased FUE have been described in U.S. Pat. Appl. No. 20020046419 to Choo, et al.; U. S. Pat. Appl. No. 20050108791 to Edgerton et al.; U.S. Pat. Appl. No. 20060179511 to Chomet et al.; Good, A, et al. 2007 (Engineering nitrogen use efficiency with alanine aminotransferase. Canadian Journal of Botany 85: 252-262); and Good A G et al. 2004 (Trends Plant Sci. 9:597-605).
• Yanagisawa et al. (Proc. Natl. Acad. Sci. U.S.A. 2004 101:7833-8) describe Dof1 transgenic plants which exhibit improved growth under low-nitrogen conditions.
• U.S. Pat. No. 6,084,153 to Good et al. discloses the use of a stress responsive promoter to control the expression of Alanine Amine Transferase (AlaAT) and transgenic canola plants with improved drought and nitrogen deficiency tolerance when compared to control plants.
• Abiotic stress (ABS; also referred to as “environmental stress”) conditions such as salinity, drought, flood, suboptimal temperature and toxic chemical pollution, cause substantial damage to agricultural plants. Most plants have evolved strategies to protect themselves against these conditions. However, if the severity and duration of the stress conditions are too great, the effects on plant development, growth and yield of most crop plants are profound. Furthermore, most of the crop plants are highly susceptible to abiotic stress and thus necessitate optimal growth conditions for commercial crop yields. Continuous exposure to stress causes major alterations in the plant metabolism which ultimately leads to cell death and consequently yield losses.
• Drought is a gradual phenomenon, which involves periods of abnormally dry weather that persists long enough to produce serious hydrologic imbalances such as crop damage, water supply shortage and increased susceptibility to various diseases. In severe cases, drought can last many years and results in devastating effects on agriculture and water supplies. Furthermore, drought is associated with increase susceptibility to various diseases.
• For most crop plants, the land regions of the world are too arid. In addition, overuse of available water results in increased loss of agriculturally-usable land (desertification), and increase of salt accumulation in soils adds to the loss of available water in soils.
• Salinity, high salt levels, affects one in five hectares of irrigated land. None of the top five food crops, i.e., wheat, corn, rice, potatoes, and soybean, can tolerate excessive salt. Detrimental effects of salt on plants result from both water deficit, which leads to osmotic stress (similar to drought stress), and the effect of excess sodium ions on critical biochemical processes. As with freezing and drought, high salt causes water deficit; and the presence of high salt makes it difficult for plant roots to extract water from their environment. Soil salinity is thus one of the more important variables that determine whether a plant may thrive. In many parts of the world, sizable land areas are uncultivable due to naturally high soil salinity. Thus, salination of soils that are used for agricultural production is a significant and increasing problem in regions that rely heavily on agriculture, and is worsen by over-utilization, over-fertilization and water shortage, typically caused by climatic change and the demands of increasing population. Salt tolerance is of particular importance early in a plant's lifecycle, since evaporation from the soil surface causes upward water movement, and salt accumulates in the upper soil layer where the seeds are placed. On the other hand, germination normally takes place at a salt concentration which is higher than the mean salt level in the whole soil profile.
• Salt and drought stress signal transduction consist of ionic and osmotic homeostasis signaling pathways. The ionic aspect of salt stress is signaled via the SOS pathway where a calcium-responsive SOS3-SOS2 protein kinase complex controls the expression and activity of ion transporters such as SOS1. The osmotic component of salt stress involves complex plant reactions that overlap with drought and/or cold stress responses.
• Suboptimal temperatures affect plant growth and development through the whole plant life cycle. Thus, low temperatures reduce germination rate and high temperatures result in leaf necrosis. In addition, mature plants that are exposed to excess of heat may experience heat shock, which may arise in various organs, including leaves and particularly fruit, when transpiration is insufficient to overcome heat stress. Heat also damages cellular structures, including organelles and cytoskeleton, and impairs membrane function. Heat shock may produce a decrease in overall protein synthesis, accompanied by expression of heat shock proteins, e.g., chaperones, which are involved in refolding proteins denatured by heat. High-temperature damage to pollen almost always occurs in conjunction with drought stress, and rarely occurs under well-watered conditions. Combined stress can alter plant metabolism in novel ways. Excessive chilling conditions, e.g., low, but above freezing, temperatures affect crops of tropical origins, such as soybean, rice, maize, and cotton. Typical chilling damage includes wilting, necrosis, chlorosis or leakage of ions from cell membranes. The underlying mechanisms of chilling sensitivity are not completely understood yet, but probably involve the level of membrane saturation and other physiological deficiencies. Excessive light conditions, which occur under clear atmospheric conditions subsequent to cold late summer/autumn nights, can lead to photoinhibition of photosynthesis (disruption of photosynthesis). In addition, chilling may lead to yield losses and lower product quality through the delayed ripening of maize.
• Common aspects of drought, cold and salt stress response [Reviewed in Xiong and Zhu (2002) Plant Cell Environ. 25: 131-139] include: (a) transient changes in the cytoplasmic calcium levels early in the signaling event; (b) signal transduction via mitogen-activated and/or calcium dependent protein kinases (CDPKs) and protein phosphatases; (c) increases in abscisic acid levels in response to stress triggering a subset of responses; (d) inositol phosphates as signal molecules (at least for a subset of the stress responsive transcriptional changes; (e) activation of phospholipases which in turn generates a diverse array of second messenger molecules, some of which might regulate the activity of stress responsive kinases; (f) induction of late embryogenesis abundant (LEA) type genes including the CRT/DRE responsive COR/RD genes; (g) increased levels of antioxidants and compatible osmolytes such as proline and soluble sugars; and (h) accumulation of reactive oxygen species such as superoxide, hydrogen peroxide, and hydroxyl radicals. Abscisic acid biosynthesis is regulated by osmotic stress at multiple steps. Both ABA-dependent and -independent osmotic stress signaling first modify constitutively expressed transcription factors, leading to the expression of early response transcriptional activators, which then activate downstream stress tolerance effector genes.
• Several genes which increase tolerance to cold or salt stress can also improve drought stress protection, these include for example, the transcription factor AtCBF/DREB1, OsCDPK7 (Saijo et al. 2000, Plant J. 23: 319-327) or AVP1 (a vacuolar pyrophosphatase-proton pump, Gaxiola et al. 2001, Proc. Natl. Acad. Sci. USA 98: 11444-11449).
• Studies have shown that plant adaptations to adverse environmental conditions are complex genetic traits with polygenic nature. Conventional means for crop and horticultural improvements utilize selective breeding techniques to identify plants having desirable characteristics. However, selective breeding is tedious, time consuming and has an unpredictable outcome. Furthermore, limited germplasm resources for yield improvement and incompatibility in crosses between distantly related plant species represent significant problems encountered in conventional breeding. Advances in genetic engineering have allowed mankind to modify the germplasm of plants by expression of genes-of-interest in plants. Such a technology has the capacity to generate crops or plants with improved economic, agronomic or horticultural traits.
• Genetic engineering efforts, aimed at conferring abiotic stress tolerance to transgenic crops, have been described in various publications [Apse and Blumwald (Curr Opin Biotechnol. 13:146-150, 2002), Quesada et al. (Plant Physiol. 130:951-963, 2002), Holmström et al. (Nature 379: 683-684, 1996), Xu et al. (Plant Physiol 110: 249-257, 1996), Pilon-Smits and Ebskamp (Plant Physiol 107: 125-130, 1995) and Tarczynski et al. (Science 259: 508-510, 1993)].
• Various patents and patent applications disclose genes and proteins which can be used for increasing tolerance of plants to abiotic stresses. These include for example, U.S. Pat. Nos. 5,296,462 and 5,356,816 (for increasing tolerance to cold stress); U.S. Pat. No. 6,670,528 (for increasing ABST); U.S. Pat. No. 6,720,477 (for increasing ABST); U.S. application Ser. Nos. 09/938,842 and 10/342,224 (for increasing ABST); U.S. application Ser. No. 10/231,035 (for increasing ABST); WO2004/104162 (for increasing ABST and biomass); WO2007/020638 (for increasing ABST, biomass, vigor and/or yield); WO2007/049275 (for increasing ABST, biomass, vigor and/or yield); WO2010/076756 (for increasing ABST, biomass and/or yield); WO2009/083958 (for increasing water use efficiency, fertilizer use efficiency, biotic/abiotic stress tolerance, yield and/or biomass); WO2010/020941 (for increasing nitrogen use efficiency, abiotic stress tolerance, yield and/or biomass); WO2009/141824 (for increasing plant utility); WO2010/049897 (for increasing plant yield).
• Nutrient deficiencies cause adaptations of the root architecture, particularly notably for example is the root proliferation within nutrient rich patches to increase nutrient uptake. Nutrient deficiencies cause also the activation of plant metabolic pathways which maximize the absorption, assimilation and distribution processes such as by activating architectural changes. Engineering the expression of the triggered genes may cause the plant to exhibit the architectural changes and enhanced metabolism also under other conditions.
• In addition, it is widely known that the plants usually respond to water deficiency by creating a deeper root system that allows access to moisture located in deeper soil layers. Triggering this effect will allow the plants to access nutrients and water located in deeper soil horizons particularly those readily dissolved in water like nitrates.
• Cotton and cotton by-products provide raw materials that are used to produce a wealth of consumer-based products in addition to textiles including cotton foodstuffs, livestock feed, fertilizer and paper. The production, marketing, consumption and trade of cotton-based products generate an excess of $100 billion annually in the U.S. alone, making cotton the number one value-added crop.
• Even though 90% of cotton's value as a crop resides in the fiber (lint), yield and fiber quality has declined due to general erosion in genetic diversity of cotton varieties, and an increased vulnerability of the crop to environmental conditions.
• There are many varieties of cotton plant, from which cotton fibers with a range of characteristics can be obtained and used for various applications. Cotton fibers may be characterized according to a variety of properties, some of which are considered highly desirable within the textile industry for the production of increasingly high quality products and optimal exploitation of modem spinning technologies. Commercially desirable properties include length, length uniformity, fineness, maturity ratio, decreased fuzz fiber production, micronaire, bundle strength, and single fiber strength. Much effort has been put into the improvement of the characteristics of cotton fibers mainly focusing on fiber length and fiber fineness. In particular, there is a great demand for cotton fibers of specific lengths.
• A cotton fiber is composed of a single cell that has differentiated from an epidermal cell of the seed coat, developing through four stages, i.e., initiation, elongation, secondary cell wall thickening and maturation stages. More specifically, the elongation of a cotton fiber commences in the epidermal cell of the ovule immediately following flowering, after which the cotton fiber rapidly elongates for approximately 21 days. Fiber elongation is then terminated, and a secondary cell wall is formed and grown through maturation to become a mature cotton fiber.
• Several candidate genes which are associated with the elongation, formation, quality and yield of cotton fibers were disclosed in various patent applications such as U.S. Pat. No. 5,880,100 and U.S. patent application Ser. Nos. 08/580,545, 08/867,484 and 09/262,653 (describing genes involved in cotton fiber elongation stage); WO0245485 (improving fiber quality by modulating sucrose synthase); U.S. Pat. No. 6,472,588 and WO0117333 (increasing fiber quality by transformation with a DNA encoding sucrose phosphate synthase); WO9508914 (using a fiber-specific promoter and a coding sequence encoding cotton peroxidase); WO9626639 (using an ovary specific promoter sequence to express plant growth modifying hormones in cotton ovule tissue, for altering fiber quality characteristics such as fiber dimension and strength); U.S. Pat. Nos. 5,981,834, 5,597,718, 5,620,882. U.S. Pat. Nos. 5,521,708 and 5,495,070 (coding sequences to alter the fiber characteristics of transgenic fiber producing plants); U.S. patent applications U.S. 2002049999 and U.S. 2003074697 (expressing a gene coding for endoxyloglucan transferase, catalase or peroxidase for improving cotton fiber characteristics); WO 01/40250 (improving cotton fiber quality by modulating transcription factor gene expression); WO 96/40924 (a cotton fiber transcriptional initiation regulatory region associated which is expressed in cotton fiber); EP0834566 (a gene which controls the fiber formation mechanism in cotton plant); WO2005/121364 (improving cotton fiber quality by modulating gene expression); WO2008/075364 (improving fiber quality, yield/biomass/vigor and/or abiotic stress tolerance of plants).
• WO publication No. 2004/104162 discloses methods of increasing abiotic stress tolerance and/or biomass in plants and plants generated thereby.
• WO publication No. 2004/111183 discloses nucleotide sequences for regulating gene expression in plant trichomes and constructs and methods utilizing same.
• WO publication No. 2004/081173 discloses novel plant derived regulatory sequences and constructs and methods of using such sequences for directing expression of exogenous polynucleotide sequences in plants.
• WO publication No. 2005/121364 discloses polynucleotides and polypeptides involved in plant fiber development and methods of using same for improving fiber quality, yield and/or biomass of a fiber producing plant.
• WO publication No. 2007/049275 discloses isolated polypeptides, polynucleotides encoding same, transgenic plants expressing same and methods of using same for increasing fertilizer use efficiency, plant abiotic stress tolerance and biomass.
• WO publication No. 2007/020638 discloses methods of increasing abiotic stress tolerance and/or biomass in plants and plants generated thereby.
• WO publication No. 2008/122980 discloses genes constructs and methods for increasing oil content, growth rate and biomass of plants.
• WO publication No. 2008/075364 discloses polynucleotides involved in plant fiber development and methods of using same.
• WO publication No. 2009/083958 discloses methods of increasing water use efficiency, fertilizer use efficiency, biotic/abiotic stress tolerance, yield and biomass in plant and plants generated thereby.
• WO publication No. 2009/141824 discloses isolated polynucleotides and methods using same for increasing plant utility.
• WO publication No. 2009/013750 discloses genes, constructs and methods of increasing abiotic stress tolerance, biomass and/or yield in plants generated thereby.
• WO publication No. 2010/020941 discloses methods of increasing nitrogen use efficiency, abiotic stress tolerance, yield and biomass in plants and plants generated thereby.
• WO publication No. 2010/076756 discloses isolated polynucleotides for increasing abiotic stress tolerance, yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, and/or nitrogen use efficiency of a plant.
• WO2010/100595 publication discloses isolated polynucleotides and polypeptides, and methods of using same for increasing plant yield and/or agricultural characteristics.
• WO publication No. 2010/049897 discloses isolated polynucleotides and polypeptides and methods of using same for increasing plant yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance of plants and nitrogen use efficiency.
• WO2010/143138 publication discloses isolated polynucleotides and polypeptides, and methods of using same for increasing nitrogen use efficiency, fertilizer use efficiency, yield, growth rate, vigor, biomass, oil content, abiotic stress tolerance and/or water use efficiency.
• WO publication No. 2011/080674 discloses isolated polynucleotides and polypeptides and methods of using same for increasing plant yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance of plants and nitrogen use efficiency.
• WO2011/015985 publication discloses polynucleotides and polypeptides for increasing desirable plant qualities.
SUMMARY OF THE INVENTION
• According to an aspect of some embodiments of the present invention there is provided a method of increasing yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide at least 80% homologous (e.g., identical) to SEQ ID NO: 362-601, 2429-4085 or 4086, thereby increasing the yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of the plant.
• According to an aspect of some embodiments of the present invention there is provided a method of increasing yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide selected from the group consisting of SEQ ID NOs: 362-601, 2429-4085 and 4086, thereby increasing the yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of the plant.
• According to an aspect of some embodiments of the present invention there is provided a method of producing a crop comprising growing a crop of a plant expressing an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide at least 80% homologous (e.g., identical) to the amino acid sequence selected from the group consisting of SEQ ID NOs: 362-601, 2429-4085 and 4086, wherein the plant is derived from a plant selected for increased yield, increased growth rate, increased biomass, increased vigor, increased oil content, increased seed yield, increased fiber yield, increased fiber quality, increased nitrogen use efficiency, and/or increased abiotic stress tolerance as compared to a control plant, thereby producing the crop.
• According to an aspect of some embodiments of the present invention there is provided a method of increasing yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence at least 80% identical to SEQ ID NO: 1-361, 602-2427 or 2428, thereby increasing the yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of the plant.
• According to an aspect of some embodiments of the present invention there is provided a method of increasing yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant, comprising expressing within the plant an exogenous polynucleotide comprising the nucleic acid sequence selected from the group consisting of SEQ ID NOs:1-361, 602-2427 and 2428, thereby increasing the yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of the plant.
• According to an aspect of some embodiments of the present invention there is provided a method of producing a crop comprising growing a crop of a plant expressing an exogenous polynucleotide which comprises a nucleic acid sequence which is at least 80% identical to the nucleic acid sequence selected from the group consisting of SEQ ID NOs:1-361, 602-2427 and 2428, wherein the plant is derived from a plant selected for increased yield, increased growth rate, increased biomass, increased vigor, increased oil content, increased seed yield, increased fiber yield, increased fiber quality, increased nitrogen use efficiency, and/or increased abiotic stress tolerance as compared to a control plant, thereby producing the crop.
• According to an aspect of some embodiments of the present invention there is provided an isolated polynucleotide comprising a nucleic acid sequence encoding a polypeptide which comprises an amino acid sequence at least 80% homologous (e.g., identical) to the amino acid sequence set forth in SEQ ID NO: 362-601, 24294085 or 4086, wherein the amino acid sequence is capable of increasing yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant.
• According to an aspect of some embodiments of the present invention there is provided an isolated polynucleotide comprising a nucleic acid sequence encoding a polypeptide which comprises the amino acid sequence selected from the group consisting of SEQ ID NOs: 362-601, 2429-4085 and 4086.
• According to an aspect of some embodiments of the present invention there is provided an isolated polynucleotide comprising a nucleic acid sequence at least 80% identical to SEQ ID NO: 1-361, 602-2427 or 2428, wherein the nucleic acid sequence is capable of increasing yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant.
• According to an aspect of some embodiments of the present invention there is provided an isolated polynucleotide comprising the nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-361, 602-2427 and 2428.
• According to an aspect of some embodiments of the present invention there is provided a nucleic acid construct comprising the isolated polynucleotide of some embodiments of the invention, and a promoter for directing transcription of the nucleic acid sequence in a host cell.
• According to an aspect of some embodiments of the present invention there is provided an isolated polypeptide comprising an amino acid sequence at least 80% homologous (e.g., identical) to SEQ ID NO: 362-601, 2429-4085 or 4086, wherein the amino acid sequence is capable of increasing yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant.
• According to an aspect of some embodiments of the present invention there is provided an isolated polypeptide comprising the amino acid sequence selected from the group consisting of SEQ ID NOs: 362-601, 2429-4085 and 4086.
• According to an aspect of some embodiments of the present invention there is provided a plant cell exogenously expressing the polynucleotide of some embodiments of the invention, or the nucleic acid construct of some embodiments of the invention.
• According to an aspect of some embodiments of the present invention there is provided a plant cell exogenously expressing the polypeptide of some embodiments of the invention.
• According to some embodiments of the invention, the nucleic acid sequence encodes an amino acid sequence selected from the group consisting of SEQ ID NOs: 362-601, 2429-4085 and 4086.
• According to some embodiments of the invention, the nucleic acid sequence is selected from the group consisting of SEQ ID NOs: 1-361, 602-2427 and 2428.
• According to some embodiments of the invention, the polynucleotide consists of the nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-361, 602-2427 and 2428.
• According to some embodiments of the invention, the nucleic acid sequence encodes the amino acid sequence selected from the group consisting of SEQ ID NOs: 362-601, 2429-4085 and 4086.
• According to some embodiments of the invention, the plant cell forms part of a plant.
• According to some embodiments of the invention, the method further comprising growing the plant expressing the exogenous polynucleotide under the abiotic stress.
• According to some embodiments of the invention, the abiotic stress is selected from the group consisting of salinity, drought, osmotic stress, water deprivation, flood, etiolation, low temperature, high temperature, heavy metal toxicity, anaerobiosis, nutrient deficiency, nutrient excess, atmospheric pollution and UV irradiation.
• According to some embodiments of the invention, the yield comprises seed yield or oil yield.
• According to an aspect of some embodiments of the present invention there is provided a transgenic plant comprising the nucleic acid construct of some embodiments of the invention or the plant cell of some embodiments of the invention.
• According to some embodiments of the invention, the method further comprising growing the plant expressing the exogenous polynucleotide under nitrogen-limiting conditions.
• According to some embodiments of the invention, the promoter is heterologous to the isolated polynucleotide and/or to the host cell.
• According to an aspect of some embodiments of the present invention there is provided a method of growing a crop, the method comprising seeding seeds and/or planting plantlets of a plant transformed with the isolated polynucleotide of some embodiments of the invention, or the nucleic acid construct of some embodiments of the invention, wherein the plant is derived from plants selected for at least one trait selected from the group consisting of: increased nitrogen use efficiency, increased abiotic stress tolerance, increased biomass, increased growth rate, increased vigor, increased yield, increased fiber yield or quality, and increased oil content as compared to a non-transformed plant, thereby growing the crop.
• According to some embodiments of the invention, the non-transformed plant is a wild type plant of identical genetic background.
• According to some embodiments of the invention, the non-transformed plant is a wild type plant of the same species.
• According to some embodiments of the invention, the non-transformed plant is grown under identical growth conditions.
• Unless otherwise defined, all technical and/or scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention pertains. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of embodiments of the invention, exemplary methods and/or materials are described below. In case of conflict, the patent specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and are not intended to be necessarily limiting.
BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS
• Some embodiments of the invention are herein described, by way of example only, with reference to the accompanying drawings. With specific reference now to the drawings in detail, it is stressed that the particulars shown are by way of example and for purposes of illustrative discussion of embodiments of the invention. In this regard, the description taken with the drawings makes apparent to those skilled in the art how embodiments of the invention may be practiced.
• In the drawings:
• FIG. 1 is a schematic illustration of the modified pGI binary plasmid containing the new At6669 promoter (SEQ ID NO: 4111) and the GUSintron (pQYN 6669) used for expressing the isolated polynucleotide sequences of the invention. RB—T-DNA right border; LB—T-DNA left border; MCS—Multiple cloning sites; RE—any restriction enzyme; NOS pro=nopaline synthase promoter; NPT-II=neomycin phosphotransferase gene; NOS ter=nopaline synthase terminator; Poly-A signal (polyadenylation signal); GUSintron—the GUS reporter gene (coding sequence and intron). The isolated polynucleotide sequences of the invention were cloned into the vector while replacing the GUSintron reporter gene.
• FIG. 2 is a schematic illustration of the modified pGI binary plasmid containing the new At6669 promoter (SEQ ID NO: 4111) (pQFN or pQFNc) used for expressing the isolated polynucleotide sequences of the invention. RB—T-DNA right border; LB—T-DNA left border; MCS—Multiple cloning site; RE—any restriction enzyme; NOS pro=nopaline synthase promoter; NPT-II=neomycin phosphotransferase gene; NOS ter=nopaline synthase terminator; Poly-A signal (polyadenylation signal); The isolated polynucleotide sequences of the invention were cloned into the MCS of the vector.
• FIGS. 3A-3F are images depicting visualization of root development of transgenic plants exogenously expressing the polynucleotide of some embodiments of the invention when grown in transparent agar plates under normal (FIGS. 3A-3B), osmotic stress (15% PEG; FIGS. 3C-3D) or nitrogen-limiting (FIGS. 3E-3F) conditions. The different transgenes were grown in transparent agar plates for 17 days (7 days nursery and 10 days after transplanting). The plates were photographed every 3-4 days starting at day 1 after transplanting. FIG. 3A—An image of a photograph of plants taken following 10 after transplanting days on agar plates when grown under normal (standard) conditions. FIG. 3B—An image of root analysis of the plants shown in FIG. 3A in which the lengths of the roots measured are represented by arrows. FIG. 3C—An image of a photograph of plants taken following 10 days after transplanting on agar plates, grown under high osmotic (PEG 15%) conditions. FIG. 3D—An image of root analysis of the plants shown in FIG. 3C in which the lengths of the roots measured are represented by arrows. FIG. 3E—An image of a photograph of plants taken following 10 days after transplanting on agar plates, grown under low nitrogen conditions. FIG. 3F—An image of root analysis of the plants shown in FIG. 3E in which the lengths of the roots measured are represented by arrows.
• FIG. 4 is a schematic illustration of the modified pGI binary plasmid containing the Root Promoter (pQNa RP) used for expressing the isolated polynucleotide sequences of the invention. RB—T-DNA right border; LB—T-DNA left border; NOS pro=nopaline synthase promoter; NPT-II=neomycin phosphotransferase gene; NOS ter=nopaline synthase terminator; Poly-A signal (polyadenylation signal); the isolated polynucleotide sequences according to some embodiments of the invention were cloned into the MCS (Multiple cloning site) of the vector.
• FIG. 5 is a schematic illustration of the pQYN plasmid.
• FIG. 6 is a schematic illustration of the pQFN plasmid.
• FIG. 7 is a schematic illustration of the pQFYN plasmid.
• FIG. 8 is a schematic illustration of the modified pGI binary plasmid (pQXNc) used for expressing the isolated polynucleotide sequences of some embodiments of the invention. RB—T-DNA right border; LB—T-DNA left border; NOS pro=nopaline synthase promoter; NPT-II=neomycin phosphotransferase gene; NOS ter=nopaline synthase terminator; RE=any restriction enzyme; Poly-A signal (polyadenylation signal); 35S—the 35S promoter (pqfnc; SEQ ID NO: 4107). The isolated polynucleotide sequences of some embodiments of the invention were cloned into the MCS (Multiple cloning site) of the vector.
DESCRIPTION OF SPECIFIC EMBODIMENTS OF THE INVENTION
• The present invention, in some embodiments thereof, relates to isolated polynucleotides and polypeptides, nucleic acid constructs encoding same, cells expressing same, transgenic plants expressing same and methods of using same for increasing yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, nitrogen use efficiency and/or abiotic stress tolerance of a plant.
• Before explaining at least one embodiment of the invention in detail, it is to be understood that the invention is not necessarily limited in its application to the details set forth in the following description or exemplified by the Examples. The invention is capable of other embodiments or of being practiced or carried out in various ways.
• The present inventors have identified novel polypeptides and polynucleotides which can be used to generate nucleic acid constructs, transgenic plants and to increase yield, growth rate, vigor, biomass, oil content, fiber yield, fiber quality, fiber length, nitrogen use efficiency, fertilizer use efficiency, abiotic stress tolerance and/or water use efficiency of a plant.
• Thus, as shown in the Examples section which follows, the present inventors have utilized bioinformatics tools to identify polynucleotides which enhance yield (e.g., seed yield, oil yield, oil content), growth rate, biomass, vigor and/or abiotic stress tolerance of a plant. Genes which affect the trait-of-interest were identified based on expression profiles of genes of several Arabidopsis, tomato, B. juncea, Soghum, Soybean, Brachypodium and cotton ecotypes, varieties and accessions in various tissues and under various growth conditions, homology with genes known to affect the trait-of-interest and using digital expression profile in specific tissues and conditions (Tables 1-53, Examples 1-12). Homologous (e.g., orthologous) polypeptides and polynucleotides having the same function were also identified (Table 54, Example 13). Transgenic plants over-expressing the identified polynucleotides were found to exhibit increased seed yield, oil yield, biomass, vigor, photosynthetic area, dry matter, harvest index, growth rate, rosette area, oil percentage in seed and weight of 1000 seeds (Tables 56-69; Examples 15-17). Altogether, these results suggest the use of the novel polynucleotides and polypeptides of the invention for increasing yield (including oil yield, seed yield and oil content), growth rate, biomass, vigor, fiber yield and/or quality, nitrogen use efficiency and/or abiotic stress tolerance of a plant.
• Thus, according to an aspect of some embodiments of the invention, there is provided method of increasing yield, oil content, growth rate, biomass, vigor, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more say 100% homologous to the amino acid sequence selected from the group consisting of SEQ ID NOs: 362-601, 2429-4085 and 4086, thereby increasing the yield, oil content, growth rate, biomass, vigor, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of the plant.
• As used herein the phrase “plant yield” refers to the amount (e.g., as determined by weight or size) or quantity (numbers) of tissues or organs produced per plant or per growing season. Hence increased yield could affect the economic benefit one can obtain from the plant in a certain growing area and/or growing time.
• It should be noted that a plant yield can be affected by various parameters including, but not limited to, plant biomass; plant vigor; growth rate; seed yield; seed or grain quantity; seed or grain quality; oil yield; content of oil, starch and/or protein in harvested organs (e.g., seeds or vegetative parts of the plant); number of flowers (florets) per panicle (expressed as a ratio of number of filled seeds over number of primary panicles); harvest index; number of plants grown per area; number and size of harvested organs per plant and per area; number of plants per growing area (density); number of harvested organs in field; total leaf area; carbon assimilation and carbon partitioning (the distribution/allocation of carbon within the plant); resistance to shade; number of harvestable organs (e.g. seeds), seeds per pod, weight per seed; and modified architecture [such as increase stalk diameter, thickness or improvement of physical properties (e.g. elasticity)].
• As used herein the phrase “seed yield” refers to the number or weight of the seeds per plant, seeds per pod, or per growing area or to the weight of a single seed, or to the oil extracted per seed. Hence seed yield can be affected by seed dimensions (e.g., length, width, perimeter, area and/or volume), number of (filled) seeds and seed filling rate and by seed oil content. Hence increase seed yield per plant could affect the economic benefit one can obtain from the plant in a certain growing area and/or growing time; and increase seed yield per growing area could be achieved by increasing seed yield per plant, and/or by increasing number of plants grown on the same given area.
• The term “seed” (also referred to as “grain” or “kernel”) as used herein refers to a small embryonic plant enclosed in a covering called the seed coat (usually with some stored food), the product of the ripened ovule of gymnosperm and angiosperm plants which occurs after fertilization and some growth within the mother plant.
• The phrase “oil content” as used herein refers to the amount of lipids in a given plant organ, either the seeds (seed oil content) or the vegetative portion of the plant (vegetative oil content) and is typically expressed as percentage of dry weight (10% humidity of seeds) or wet weight (for vegetative portion).
• It should be noted that oil content is affected by intrinsic oil production of a tissue (e.g., seed, vegetative portion), as well as the mass or size of the oil-producing tissue per plant or per growth period.
• In one embodiment, increase in oil content of the plant can be achieved by increasing the size/mass of a plant's tissue(s) which comprise oil per growth period. Thus, increased oil content of a plant can be achieved by increasing the yield, growth rate, biomass and vigor of the plant.
• As used herein the phrase “plant biomass” refers to the amount (e.g., measured in grams of air-dry tissue) of a tissue produced from the plant in a growing season, which could also determine or affect the plant yield or the yield per growing area. An increase in plant biomass can be in the whole plant or in parts thereof such as aboveground (harvestable) parts, vegetative biomass, roots and seeds.
• As used herein the phrase “growth rate” refers to the increase in plant organ/tissue size per time (can be measured in cm² per day).
• As used herein the phrase “plant vigor” refers to the amount (measured by weight) of tissue produced by the plant in a given time. Hence increased vigor could determine or affect the plant yield or the yield per growing time or growing area. In addition, early vigor (seed and/or seedling) results in improved field stand.
• Improving early vigor is an important objective of modern rice breeding programs in both temperate and tropical rice cultivars. Long roots are important for proper soil anchorage in water-seeded rice. Where rice is sown directly into flooded fields, and where plants must emerge rapidly through water, longer shoots are associated with vigor. Where drill-seeding is practiced, longer mesocotyls and coleoptiles are important for good seedling emergence. The ability to engineer early vigor into plants would be of great importance in agriculture. For example, poor early vigor has been a limitation to the introduction of maize (Zea mays L.) hybrids based on Corn Belt germplasm in the European Atlantic.
• It should be noted that a plant yield can be determined under stress (e.g., abiotic stress, nitrogen-limiting conditions) and/or non-stress (normal) conditions.
• As used herein, the phrase “non-stress conditions” refers to the growth conditions (e.g., water, temperature, light-dark cycles, humidity, salt concentration, fertilizer concentration in soil, nutrient supply such as nitrogen, phosphorous and/or potassium), that do not significantly go beyond the everyday climatic and other abiotic conditions that plants may encounter, and which allow optimal growth, metabolism, reproduction and/or viability of a plant at any stage in its life cycle (e.g., in a crop plant from seed to a mature plant and back to seed again). Persons skilled in the art are aware of normal soil conditions and climatic conditions for a given plant in a given geographic location. It should be noted that while the non-stress conditions may include some mild variations from the optimal conditions (which vary from one type/species of a plant to another), such variations do not cause the plant to cease growing without the capacity to resume growth.
• The phrase “abiotic stress” as used herein refers to any adverse effect on metabolism, growth, reproduction and/or viability of a plant. Accordingly, abiotic stress can be induced by suboptimal environmental growth conditions such as, for example, salinity, water deprivation, flooding, freezing, low or high temperature, heavy metal toxicity, anaerobiosis, nutrient deficiency, atmospheric pollution or UV irradiation. The implications of abiotic stress are discussed in the Background section.
• The phrase “abiotic stress tolerance” as used herein refers to the ability of a plant to endure an abiotic stress without suffering a substantial alteration in metabolism, growth, productivity and/or viability.
• Plants are subject to a range of environmental challenges. Several of these, including salt stress, general osmotic stress, drought stress and freezing stress, have the ability to impact whole plant and cellular water availability. Not surprisingly, then, plant responses to this collection of stresses are related. Zhu (2002) Ann. Rev. Plant Biol. 53: 247-273 et al. note that “most studies on water stress signaling have focused on salt stress primarily because plant responses to salt and drought are closely related and the mechanisms overlap”. Many examples of similar responses and pathways to this set of stresses have been documented. For example, the CBF transcription factors have been shown to condition resistance to salt, freezing and drought (Kasuga et al. (1999) Nature Biotech. 17: 287-291). The Arabidopsis rd29B gene is induced in response to both salt and dehydration stress, a process that is mediated largely through an ABA signal transduction process (Uno et al. (2000) Proc. Natl. Acad. Sci. USA 97: 11632-11637), resulting in altered activity of transcription factors that bind to an upstream element within the rd29B promoter. In Mesembryanthemum crystallinum (ice plant), Patharker and Cushman have shown that a calcium-dependent protein kinase (McCDPK1) is induced by exposure to both drought and salt stresses (Patharker and Cushman (2000) Plant J. 24: 679-691). The stress-induced kinase was also shown to phosphorylate a transcription factor, presumably altering its activity, although transcript levels of the target transcription factor are not altered in response to salt or drought stress. Similarly, Saijo et al. demonstrated that a rice salt/drought-induced calmodulin-dependent protein kinase (OsCDPK7) conferred increased salt and drought tolerance to rice when overexpressed (Saijo et al. (2000) Plant J. 23: 319-327).
• Exposure to dehydration invokes similar survival strategies in plants as does freezing stress (see, for example. Yelenosky (1989) Plant Physiol 89: 444-451) and drought stress induces freezing tolerance (see, for example. Siminovitch et al. (1982) Plant Physiol 69: 250-255; and Guy et al. (1992) Planta 188: 265-270). In addition to the induction of cold-acclimation proteins, strategies that allow plants to survive in low water conditions may include, for example, reduced surface area, or surface oil or wax production. In another example increased solute content of the plant prevents evaporation and water loss due to heat, drought, salinity, osmoticum, and the like therefore providing a better plant tolerance to the above stresses.
• It will be appreciated that some pathways involved in resistance to one stress (as described above), will also be involved in resistance to other stresses, regulated by the same or homologous genes. Of course, the overall resistance pathways are related, not identical, and therefore not all genes controlling resistance to one stress will control resistance to the other stresses. Nonetheless, if a gene conditions resistance to one of these stresses, it would be apparent to one skilled in the art to test for resistance to these related stresses. Methods of assessing stress resistance are further provided in the Examples section which follows.
• As used herein the phrase “water use efficiency (WUE)” refers to the level of organic matter produced per unit of water consumed by the plant, i.e., the dry weight of a plant in relation to the plant's water use, e.g., the biomass produced per unit transpiration.
• As used herein the phrase “fertilizer use efficiency” refers to the metabolic process(es) which lead to an increase in the plant's yield, biomass, vigor, and growth rate per fertilizer unit applied. The metabolic process can be the uptake, spread, absorbent, accumulation, relocation (within the plant) and use of one or more of the minerals and organic moieties absorbed by the plant, such as nitrogen, phosphates and/or potassium.
• As used herein the phrase “fertilizer-limiting conditions” refers to growth conditions which include a level (e.g., concentration) of a fertilizer applied which is below the level needed for normal plant metabolism, growth, reproduction and/or viability.
• As used herein the phrase “nitrogen use efficiency (NUE)” refers to the metabolic process(es) which lead to an increase in the plant's yield, biomass, vigor, and growth rate per nitrogen unit applied. The metabolic process can be the uptake, spread, absorbent, accumulation, relocation (within the plant) and use of nitrogen absorbed by the plant.
• As used herein the phrase “nitrogen-limiting conditions” refers to growth conditions which include a level (e.g., concentration) of nitrogen (e.g., ammonium or nitrate) applied which is below the level needed for normal plant metabolism, growth, reproduction and/or viability.
• Improved plant NUE and FUE is translated in the field into either harvesting similar quantities of yield, while implementing less fertilizers, or increased yields gained by implementing the same levels of fertilizers. Thus, improved NUE or FUE has a direct effect on plant yield in the field. Thus, the polynucleotides and polypeptides of some embodiments of the invention positively affect plant yield, seed yield, and plant biomass. In addition, the benefit of improved plant NUE will certainly improve crop quality and biochemical constituents of the seed such as protein yield and oil yield.
• It should be noted that improved ABST will confer plants with improved vigor also under non-stress conditions, resulting in crops having improved biomass and/or yield e.g., elongated fibers for the cotton industry, higher oil content.
• The term “fiber” is usually inclusive of thick-walled conducting cells such as vessels and tracheids and to fibrillar aggregates of many individual fiber cells. Hence, the term “fiber” refers to (a) thick-walled conducting and non-conducting cells of the xylem; (b) fibers of extraxylary origin, including those from phloem, bark, ground tissue, and epidermis; and (c) fibers from stems, leaves, roots, seeds, and flowers or inflorescences (such as those of Sorghum vulgare used in the manufacture of brushes and brooms).
• Example of fiber producing plants, include, but are not limited to, agricultural crops such as cotton, silk cotton tree (Kapok, Ceiba pentandra), desert willow, creosote bush, winterfat, balsa, kenaf, roselle, jute, sisal abaca, flax, corn, sugar cane, hemp, ramie, kapok, coir, bamboo, spanish moss and Agave spp. (e.g. sisal).
• As used herein the phrase “fiber quality” refers to at least one fiber parameter which is agriculturally desired, or required in the fiber industry (further described hereinbelow). Examples of such parameters, include but are not limited to, fiber length, fiber strength, fiber fitness, fiber weight per unit length, maturity ratio and uniformity (further described hereinbelow.
• Cotton fiber (lint) quality is typically measured according to fiber length, strength and fineness. Accordingly, the lint quality is considered higher when the fiber is longer, stronger and finer.
• As used herein the phrase “fiber yield” refers to the amount or quantity of fibers produced from the fiber producing plant.
• As used herein the term “increasing” refers to at least about 2%, at least about 3%, at least about 4%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, increase in yield, oil content, growth rate, biomass, vigor, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of a plant as compared to a native plant or a wild type plant [i.e., a plant not modified with the biomolecules (polynucleotide or polypeptides) of the invention, e.g., a non-transformed plant of the same species which is grown under the same (e.g., identical) growth conditions].
• The phrase “expressing within the plant an exogenous polynucleotide” as used herein refers to upregulating the expression level of an exogenous polynucleotide within the plant by introducing the exogenous polynucleotide into a plant cell or plant and expressing by recombinant means, as further described herein below.
• As used herein “expressing” refers to expression at the mRNA and optionally polypeptide level.
• As used herein, the phrase “exogenous polynucleotide” refers to a heterologous nucleic acid sequence which may not be naturally expressed within the plant (e.g., a nucleic acid sequence from a different species) or which overexpression in the plant is desired. The exogenous polynucleotide may be introduced into the plant in a stable or transient manner, so as to produce a ribonucleic acid (RNA) molecule and/or a polypeptide molecule. It should be noted that the exogenous polynucleotide may comprise a nucleic acid sequence which is identical or partially homologous to an endogenous nucleic acid sequence of the plant.
• The term “endogenous” as used herein refers to any polynucleotide or polypeptide which is present and/or naturally expressed within a plant or a cell thereof.
• According to some embodiments of the invention, the exogenous polynucleotide of the invention comprises a nucleic acid sequence encoding a polypeptide having an amino acid sequence at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more say 100% homologous to the amino acid sequence selected from the group consisting of SEQ ID NOs: 362-601, 2429-4085 and 4086.
• Homologous sequences include both orthologous and paralogous sequences. The term “paralogous” relates to gene-duplications within the genome of a species leading to paralogous genes. The term “orthologous” relates to homologous genes in different organisms due to ancestral relationship.
• One option to identify orthologues in monocot plant species is by performing a reciprocal blast search. This may be done by a first blast involving blasting the sequence-of-interest against any sequence database, such as the publicly available NCBI database which may be found at: Hypertext Transfer Protocol://World Wide Web (dot) ncbi (dot) nlm (dot) nih (dot) gov. If orthologues in rice were sought, the sequence-of-interest would be blasted against, for example, the 28,469 full-length cDNA clones from Oryza sativa Nipponbare available at NCBI. The blast results may be filtered. The full-length sequences of either the filtered results or the non-filtered results are then blasted back (second blast) against the sequences of the organism from which the sequence-of-interest is derived. The results of the first and second blasts are then compared. An orthologue is identified when the sequence resulting in the highest score (best hit) in the first blast identifies in the second blast the query sequence (the original sequence-of-interest) as the best hit. Using the same rational a paralogue (homolog to a gene in the same organism) is found. In case of large sequence families, the ClustalW program may be used [Hypertext Transfer Protocol://World Wide Web (dot) ebi (dot) ac (dot) uk/Tools/clustalw2/index (dot) html], followed by a neighbor-joining tree (Hypertext Transfer Protocol://en (dot) wikipedia (dot) org/wiki/Neighbor-joining) which helps visualizing the clustering.
• Homology (e.g., percent homology, identity+similarity) can be determined using any homology comparison software computing a pairwise sequence alignment.
• Identity (e.g., percent homology) can be determined using any homology comparison software, including for example, the BlastN software of the National Center of Biotechnology Information (NCBI) such as by using default parameters.
• According to some embodiments of the invention, the identity is a global identity, i.e., an identity over the entire amino acid or nucleic acid sequences of the invention and not over portions thereof.
• According to some embodiments of the invention, the term “homology” or “homologous” refers to identity of two or more nucleic acid sequences; or identity of two or more amino acid sequences; or the identity of an amino acid sequence to one or more nucleic acid sequence.
• According to some embodiments of the invention, the homology is a global homology, i.e., an homology over the entire amino acid or nucleic acid sequences of the invention and not over portions thereof.
• The degree of homology or identity between two or more sequences can be determined using various known sequence comparison tools. Following is a non-limiting description of such tools which can be used along with some embodiments of the invention.
• Pairwise global alignment was defined by S. B. Needleman and C. D. Wunsch, “A general method applicable to the search of similarities in the amino acid sequence of two proteins” Journal of Molecular Biology, 1970, pages 443-53, volume 48).
• For example, when starting from a polypeptide sequence and comparing to other polypeptide sequences, the EMBOSS-6.0.1 Needleman-Wunsch algorithm (available from emboss(dot)sourceforge(dot)net/apps/cvs/emboss/apps/needle(dot)html) can be used to find the optimum alignment (including gaps) of two sequences along their entire length—a “Global alignment”. Default parameters for Needleman-Wunsch algorithm (EMBOSS-6.0.1) include: gapopen=10; gapextend=0.5; datafile=EBLOSUM62; brief=YES.
• According to some embodiments of the invention, the parameters used with the EMBOSS-6.0.1 tool (for protein-protein comparison) include: gapopen=8; gapextend=2; datafile=EBLOSUM62; brief=YES.
• According to some embodiments of the invention, the threshold used to determine homology using the EMBOSS-6.0.1 Needleman-Wunsch algorithm is 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96% 97%, 98%, 99%, or 100%.
• When starting from a polypeptide sequence and comparing to polynucleotide sequences, the OneModel FramePlus algorithm [Halperin, E., Faigler, S. and Gill-More, R. (1999)—FramePlus: aligning DNA to protein sequences. Bioinformatics, 15, 867-873) (available from world wide web (dot)biocceleration(dot)com/Products(dot)html] can be used with following default parameters: model=frame+_p2n.model mode=local.
• According to some embodiments of the invention, the parameters used with the OneModel FramePlus algorithm are model=frame+_p2n.model, mode=qglobal.
• According to some embodiments of the invention, the threshold used to determine homology using the OneModel FramePlus algorithm is 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100 When starting with a polynucleotide sequence and comparing to other polynucleotide sequences the EMBOSS-6.0.1 Needleman-Wunsch algorithm (available from emboss(dot)sourceforge(dot)net/apps/cvs/emboss/apps/needle(dot)html) can be used with the following default parameters: (EMBOSS-6.0.1) gapopen=10; gapextend=0.5; datafile=EDNAFULL; brief=YES.
• According to some embodiments of the invention, the parameters used with the EMBOSS-60.1 Needleman-Wunsch algorithm are gapopen=10; gapextend=0.2; datafile=EDNAFULL; brief=YES.
• According to some embodiments of the invention, the threshold used to determine homology using the EMBOSS-6.0.1 Needleman-Wunsch algorithm for comparison of polynucleotides with polynucleotides is 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%.
• According to some embodiment, determination of the degree of homology further requires employing the Smith-Waterman algorithm (for protein-protein comparison or nucleotide-nucleotide comparison).
• Default parameters for GenCore 6.0 Smith-Waterman algorithm include; model=sw.model.
• According to some embodiments of the invention, the threshold used to determine homology using the Smith-Waterman algorithm is 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90% 91%, 92%, 93%, 94%, 95% 96%, 97%, 98%, 99%, or 100%.
• According to some embodiments of the invention, the global homology is performed on sequences which are pre-selected by local homology to the polypeptide or polynucleotide of interest (e.g., 60% identity over 60% of the sequence length), prior to performing the global homology to the polypeptide or polynucleotide of interest (e.g., 80% global homology on the entire sequence). For example, homologous sequences are selected using the BLAST software with the Blastp and tBlastn algorithms as filters for the first stage, and the needle (EMBOSS package) or Frame+ algorithm alignment for the second stage. Local identity (Blast alignments) is defined with a very permissive cutoff—60% Identity on a span of 60% of the sequences lengths because it is used only as a filter for the global alignment stage. In this specific embodiment (when the local identity is used), the default filtering of the Blast package is not utilized (by setting the parameter “-F F”).
• In the second stage, homologs are defined based on a global identity of at least 80% to the core gene polypeptide sequence.
• According to some embodiments of the invention, two distinct forms for finding the optimal global alignment for protein or nucleotide sequences are used:
• 1. Between Two Proteins (Following the Blastp Filter):
• EMBOSS-6.0.1 Needleman-Wunsch algorithm with the following modified parameters: gapopen=8 gapextend=2. The rest of the parameters are unchanged from the default options listed here:
• Standard (Mandatory) Qualifiers:
• • [-asequence] sequence Sequence filename and optional format, or reference (input USA)
  • [-bsequence] seqall Sequence(s) filename and optional format, or reference (input USA)
  • -gapopen float [10.0 for any sequence]. The gap open penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences. (Floating point number from 1.0 to 100.0)
  • -gapextend float [0.5 for any sequence]. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized.
• Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring. (Floating point number from 0.0 to 10.0)
• • [-outfile] align [*.needle] Output alignment file name
• Additional (Optional) Qualifiers:
• • -datafile matrixf [EBLOSUM62 for protein, EDNAFULL for DNA]. This is the scoring matrix file used when comparing sequences. By default it is the file ‘EBLOSUM62’ (for proteins) or the file ‘EDNAFULL’ (for nucleic sequences). These files are found in the ‘data’ directory of the EMBOSS installation.
• Advanced (Unprompted) Qualifiers:

• 	-[no]brief	boolean	[Y] Brief identity and similarity

• Associated Qualifiers:

• “-asequence” associated qualifiers

  	-sbegin1	integer	Start of the sequence to be used
  	-send1	integer	End of the sequence to be used
  	-sreverse1	boolean	Reverse (if DNA)
  	-sask1	boolean	Ask for begin/end/reverse
  	-snucleotide1	boolean	Sequence is nucleotide
  	-sprotein1	boolean	Sequence is protein
  	-slower1	boolean	Make lower case
  	-supper1	boolean	Make upper case
  	-sformat1	string	Input sequence format
  	-sdbname1	string	Database name
  	-sid1	string	Entryname
  	-ufo1	string	UFO features
  	-fformat1	string	Features format
  	-fopenfile1	string	Features file name

  “-bsequence” associated qualifiers

  	-sbegin2	integer	Start of each sequence to be used
  	-send2	integer	End of each sequence to be used
  	-sreverse2	boolean	Reverse (if DNA)
  	-sask2	boolean	Ask for begin/end/reverse
  	-snucleotide2	boolean	Sequence is nucleotide
  	-sprotein2	boolean	Sequence is protein
  	-slower2	boolean	Make lower case
  	-supper2	boolean	Make upper case
  	-sformat2	string	Input sequence format
  	-sdbname2	string	Database name
  	-sid2	string	Entryname
  	-ufo2	string	UFO features
  	-fformat2	string	Features format
  	-fopenfile2	string	Features file name

  “-outfile” associated qualifiers

  	-aformat3	string	Alignment format
  	-aextension3	string	File name extension
  	-adirectory3	string	Output directory
  	-aname3	string	Base file name
  	-awidth3	integer	Alignment width
  	-aaccshow3	boolean	Show accession number in the header
  	-adesshow3	boolean	Show description in the header
  	-ausashow3	boolean	Show the full USA in the alignment
  	-aglobal3	boolean	Show the full sequence in alignment

• General Qualifiers:

• -auto	boolean	Turn off prompts
  -stdout	boolean	Write first file to standard output
  -filter	boolean	Read first file from standard input, write
  		first file to standard output
  -options	boolean	Prompt for standard and additional values
  -debug	boolean	Write debug output to program.dbg
  -verbose	boolean	Report some/full command line options
  -help	boolean	Report command line options. More information
  		on associated and general qualifiers can be
  		found with -help -verbose
  -warning	boolean	Report warnings
  -error	boolean	Report errors
  -fatal	boolean	Report fatal errors
  -die	boolean	Report dying program messages

• 2. Between a protein sequence and a nucleotide sequence (following the tblastn filter): GenCore 6.0 OneModel application utilizing the Frame+ algorithm with the following parameters: model=frame+_p2n.model mode=qglobal -q=protein.sequence -db=nucleotide.sequence. The rest of the parameters are unchanged from the default options:
Usage:
• om -model=<model_fname>[-q=]query [-db=]database [options]
  -model=<model_fname> Specifies the model that you want to run. All models supplied by Compugen are located in the directory SCGNROOT/models/.
Valid Command Line Parameters:
• -dev=<dev_name> Selects the device to be used by the application.
• Valid devices are:
• • bic—Bioccelerator (valid for SW, XSW, FRAME_N2P, and FRAME_P2N models).
  • xlg—BioXLG (valid for all models except XSW).
  • xlp—BioXLP (valid for SW, FRAME+_N2P, and FRAME_P2N models).
  • xlh—BioXU/H (valid for SW, FRAME+_N2P, and FRAME_P2N models).
  • soft—Software device (for all models).
    -q=<query> Defines the query set. The query can be a sequence file or a database reference.
• You can specify a query by its name or by accession number. The format is detected automatically. However, you may specify a format using the -qfmt parameter. If you do not specify a query, the program prompts for one. If the query set is a database reference, an output file is produced for each sequence in the query.
• -db=<database name> Chooses the database set. The database set can be a sequence file or a database reference. The database format is detected automatically. However, you may specify a format using -dfmt parameter.
  -qacc Add this parameter to the command line if you specify query using accession numbers.
  -dacc Add this parameter to the command line if you specify a database using accession numbers.
  -dfmt/-qfmt=<format_type> Chooses the database/query format type. Possible formats are:
• • fasta—fasta with seq type auto-detected.
  • fastap—fasta protein seq.
  • fastan—fasta nucleic seq.
  • gcg—gcg format, type is auto-detected.
  • gcg9seq—gcg9 format, type is auto-detected.
  • gcg9seqp—gcg9 format protein seq.
  • gcg9seqn—gcg9 format nucleic seq.
  • nbrf—nbrf seq, type is auto-detected.
  • nbrfp—nbrf protein seq.
  • nbrfn—nbrf nucleic seq.
  • embl—embl and swissprot format.
  • genbank—genbank format (nucleic).
  • blast—blast format.
  • nbrf_gcg—nbrf-gcg seq, type is auto-detected.
  • nbrf_gcgp—nbrf-gcg protein seq.
  • nbrf_gcgn—nbrf-gcg nucleic seq.
  • raw—raw ascii sequence, type is auto-detected.
  • rawp—raw ascii protein sequence.
  • rawn—raw ascii nucleic sequence.
  • pir—pir codata format, type is auto-detected.
  • profile—gcg profile (valid only for -qfmt in SW, XSW, FRAME_P2N, and FRAME+_P2N).
    -out=<out_fname> The name of the output file.
    -suffix=<name> The output file name suffix.
    -gapop=<n> Gap open penalty. This parameter is not valid for FRAME+. For FrameSearch the default is 12.0. For other searches the default is 10.0.
    -gapext=<n> Gap extend penalty. This parameter is not valid for FRAME+. For FrameSearch the default is 4.0. For other models: the default for protein searches is 0.05, and the default for nucleic searches is 1.0.
    -qgapop=<n> The penalty for opening a gap in the query sequence. The default is 10.0. Valid for XSW.
    -qgapext=<n> The penalty for extending a gap in the query sequence. The default is 0.05. Valid for XSW.
    -start=<n> The position in the query sequence to begin the search.
    -end=<n> The position in the query sequence to stop the search.
    -qtrans Performs a translated search, relevant for a nucleic query against a protein database.
    The nucleic query is translated to six reading frames and a result is given for each frame.
• Valid for SW and XSW.
• -dtrans Performs a translated search, relevant for a protein query against a DNA database.
  Each database entry is translated to six reading frames and a result is given for each frame.
• Valid for SW and XSW.
• Note: “-qtrans” and “-dtrans” options are mutually exclusive.
  -matrix=<matrix_file> Specifies the comparison matrix to be used in the search. The matrix must be in the BLAST format. If the matrix file is not located in $CGNROOT/tables/matrix, specify the full path as the value of the -matrix parameter.
  -trans=<transtab_name> Translation table. The default location for the table is $CGNROOT/tables/trans.
  -onestrand Restricts the search to just the top strand of the query/database nucleic sequence.
  -list=<n> The maximum size of the output hit list. The default is 50.
  -docalign=<n> The number of documentation lines preceding each alignment. The default is 10.
  -thr_score=<score name> The score that places limits on the display of results. Scores that are smaller than -thr_min value or larger than -thr_max value are not shown. Valid options are: quality.
• • zscore.
  • escore.
    -thr_max=<n> The score upper threshold. Results that are larger than -thr_max value are not shown.
    -thr_min=<n> The score lower threshold. Results that are lower than -thr_min value are not shown.
    -align=<n> The number of alignments reported in the output file.
    -noalign Do not display alignment.
    Note: “-align” and “-noalign” parameters are mutually exclusive.
    -outfmt=<format_name> Specifies the output format type. The default format is PFS. Possible values are:
  • PFS—PFS text format
  • FASTA—FASTA text format
  • BLAST—BLAST text format
    -nonorm Do not perform score normalization.
    -norm=<norm_name> Specifies the normalization method. Valid options are:
  • log—logarithm normalization.
  • std—standard normalization.
  • stat—Pearson statistical method.
    Note: “-nonorm” and “-norm” parameters cannot be used together.
    Note: Parameters -xgapop, -xgapext, -fgapop, -fgapext, -ygapop, -ygapext, -delop, and -delext apply only to FRAME+.
    -xgapop=<n> The penalty for opening a gap when inserting a codon (triplet). The default is 12.0.
    -xgapext=<n> The penalty for extending a gap when inserting a codon (triplet). The default is 4.0.
    -ygapop=<n> The penalty for opening a gap when deleting an amino acid. The default is 12.0.
    -ygapext=<n> The penalty for extending a gap when deleting an amino acid. The default is 4.0.
    -fgapop=<n> The penalty for opening a gap when inserting a DNA base. The default is 6.0.
    -fgapext=<n> The penalty for extending a gap when inserting a DNA base. The default is 7.0.
    -delop=<n> The penalty for opening a gap when deleting a DNA base. The default is 6.0.
    -delext=<n> The penalty for extending a gap when deleting a DNA base. The default is 7.0.
    -silent No screen output is produced.
    -host=<host_name> The name of the host on which the server runs. By default, the application uses the host specified in the file $CGNROOT/cgnhosts.
    -wait Do not go to the background when the device is busy. This option is not relevant for the Parseq or Soft pseudo device.
    -batch Run the job in the background. When this option is specified, the file “$CGNROOT/defaults/batch.defaults” is used for choosing the batch command. If this file does not exist, the command “at now” is used to run the job.
    Note: “-batch” and “-wait” parameters are mutually exclusive.
    -version Prints the software version number.
    -help Displays this help message. To get more specific help type:
  • “om -model=<model_fname>-help”.
• According to some embodiments the homology is a local homology or a local identity.
• Local alignments tools include, but are not limited to the BlastP, BlastN, BlastX or TBLASTN software of the National Center of Biotechnology Information (NCBI). FASTA, and the Smith-Waterman algorithm.
• A tblastn search allows the comparison between a protein sequence to the six-frame translations of a nucleotide database. It can be a very productive way of finding homologous protein coding regions in unannotated nucleotide sequences such as expressed sequence tags (ESTs) and draft genome records (HTG), located in the BLAST databases est and htgs, respectively.
• Default parameters for blastp include: Max target sequences: 100; Expected threshold: e⁻⁵; Word size: 3; Max matches in a query range: 0; Scoring parameters: Matrix—BLOSUM62; filters and masking: Filter—low complexity regions.
• Local alignments tools, which can be used include, but are not limited to, the tBLASTX algorithm, which compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database. Default parameters include: Max target sequences: 100; Expected threshold: 10; Word size: 3; Max matches in a query range: 0; Scoring parameters: Matrix—BLOSUM62; filters and masking: Filter—low complexity regions.
• According to some embodiments of the invention, the exogenous polynucleotide of the invention encodes a polypeptide having an amino acid sequence at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more say 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOs:362-601, 2429-4085 and 4086.
• According to some embodiments of the invention, the method of increasing yield, oil content, growth rate, biomass, vigor, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of a plant, is effected by expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide at least at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more say 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOs:362-601, 2429-4085 and 4086, thereby increasing the yield, oil content, growth rate, biomass, vigor, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of the plant.
• According to some embodiments of the invention, the exogenous polynucleotide encodes a polypeptide consisting of the amino acid sequence set forth by SEQ ID NO:362-601, 2429-4085 or 4086.
• According to an aspect of some embodiments of the invention, the method of increasing yield, oil content, growth rate, biomass, vigor, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of a plant, is effected by expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs:362-601, 24294085 and 4086, thereby increasing the yield, oil content, growth rate, biomass, vigor, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of the plant.
• According to an aspect of some embodiments of the invention, there is provided a method of increasing yield, oil content, growth rate, biomass, vigor, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide selected from the group consisting of SEQ ID NOs: 362-601, 24294085 and 4086, thereby increasing the yield, oil content, growth rate, biomass, vigor, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of the plant.
• According to some embodiments of the invention, the exogenous polynucleotide encodes a polypeptide consisting of the amino acid sequence set forth by SEQ ID NO: 362-601, 2429-4085 or 4086.
• According to some embodiments of the invention the exogenous polynucleotide comprises a nucleic acid sequence which is at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, e.g., 100% identical to the nucleic acid sequence selected from the group consisting of SEQ ID NOs:1-361, 602-2427 and 2428.
• According to an aspect of some embodiments of the invention, there is provided a method of increasing yield, oil content, growth rate, biomass, vigor, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, e.g., 100% identical to the nucleic acid sequence selected from the group consisting of SEQ ID NOs:1-361, 602-2427 and 2428, thereby increasing the yield, oil content, growth rate, biomass, vigor, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of the plant.
• According to some embodiments of the invention the exogenous polynucleotide is at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, e.g., 100% identical to the polynucleotide selected from the group consisting of SEQ ID NOs:1-361, 602-2427 and 2428.
• According to some embodiments of the invention the exogenous polynucleotide is set forth by SEQ ID NO:1-361, 602-2427 or 2428.
• As used herein the term “polynucleotide” refers to a single or double stranded nucleic acid sequence which is isolated and provided in the form of an RNA sequence, a complementary polynucleotide sequence (cDNA), a genomic polynucleotide sequence and/or a composite polynucleotide sequences (e.g., a combination of the above).
• The term “isolated” refers to at least partially separated from the natural environment e.g., from a plant cell.
• As used herein the phrase “complementary polynucleotide sequence” refers to a sequence, which results from reverse transcription of messenger RNA using a reverse transcriptase or any other RNA dependent DNA polymerase. Such a sequence can be subsequently amplified in vivo or in vitro using a DNA dependent DNA polymerase.
• As used herein the phrase “genomic polynucleotide sequence” refers to a sequence derived (isolated) from a chromosome and thus it represents a contiguous portion of a chromosome.
• As used herein the phrase “composite polynucleotide sequence” refers to a sequence, which is at least partially complementary and at least partially genomic. A composite sequence can include some exonal sequences required to encode the polypeptide of the present invention, as well as some intronic sequences interposing therebetween. The intronic sequences can be of any source, including of other genes, and typically will include conserved splicing signal sequences. Such intronic sequences may further include cis acting expression regulatory elements.
• Nucleic acid sequences encoding the polypeptides of the present invention may be optimized for expression. Examples of such sequence modifications include, but are not limited to, an altered G/C content to more closely approach that typically found in the plant species of interest, and the removal of codons atypically found in the plant species commonly referred to as codon optimization.
• The phrase “codon optimization” refers to the selection of appropriate DNA nucleotides for use within a structural gene or fragment thereof that approaches codon usage within the plant of interest. Therefore, an optimized gene or nucleic acid sequence refers to a gene in which the nucleotide sequence of a native or naturally occurring gene has been modified in order to utilize statistically-preferred or statistically-favored codons within the plant. The nucleotide sequence typically is examined at the DNA level and the coding region optimized for expression in the plant species determined using any suitable procedure, for example as described in Sardana et al. (19%, Plant Cell Reports 15:677-681). In this method, the standard deviation of codon usage, a measure of codon usage bias, may be calculated by first finding the squared proportional deviation of usage of each codon of the native gene relative to that of highly expressed plant genes, followed by a calculation of the average squared deviation. The formula used is: 1 SDCU=n=1 N [(Xn−Yn)/Yn]2/N, where Xn refers to the frequency of usage of codon n in highly expressed plant genes, where Yn to the frequency of usage of codon n in the gene of interest and N refers to the total number of codons in the gene of interest. A Table of codon usage from highly expressed genes of dicotyledonous plants is compiled using the data of Murray et al. (1989, Nuc Acids Res. 17:477-498).
• One method of optimizing the nucleic acid sequence in accordance with the preferred codon usage for a particular plant cell type is based on the direct use, without performing any extra statistical calculations, of codon optimization Tables such as those provided on-line at the Codon Usage Database through the NIAS (National Institute of Agrobiological Sciences) DNA bank in Japan (Hypertext Transfer Protocol://World Wide Web (dot) kazusa (dot) or (dot) jp/codon/). The Codon Usage Database contains codon usage tables for a number of different species, with each codon usage Table having been statistically determined based on the data present in Genbank.
• By using the above Tables to determine the most preferred or most favored codons for each amino acid in a particular species (for example, rice), a naturally-occurring nucleotide sequence encoding a protein of interest can be codon optimized for that particular plant species. This is effected by replacing codons that may have a low statistical incidence in the particular species genome with corresponding codons, in regard to an amino acid, that are statistically more favored. However, one or more less-favored codons may be selected to delete existing restriction sites, to create new ones at potentially useful junctions (5′ and 3′ ends to add signal peptide or termination cassettes, internal sites that might be used to cut and splice segments together to produce a correct full-length sequence), or to eliminate nucleotide sequences that may negatively effect mRNA stability or expression.
• The naturally-occurring encoding nucleotide sequence may already, in advance of any modification, contain a number of codons that correspond to a statistically-favored codon in a particular plant species. Therefore, codon optimization of the native nucleotide sequence may comprise determining which codons, within the native nucleotide sequence, are not statistically-favored with regards to a particular plant, and modifying these codons in accordance with a codon usage table of the particular plant to produce a codon optimized derivative. A modified nucleotide sequence may be fully or partially optimized for plant codon usage provided that the protein encoded by the modified nucleotide sequence is produced at a level higher than the protein encoded by the corresponding naturally occurring or native gene. Construction of synthetic genes by altering the codon usage is described in for example PCT Patent Application 93/07278.
• According to some embodiments of the invention, the exogenous polynucleotide is a non-coding RNA.
• As used herein the phrase ‘non-coding RNA’ refers to an RNA molecule which does not encode an amino acid sequence (a polypeptide). Examples of such non-coding RNA molecules include, but are not limited to, an antisense RNA, a pre-miRNA (precursor of a microRNA), or a precursor of a Piwi-interacting RNA (piRNA).
• A non-limiting example of a non-coding RNA polynucleotide is provided in SEQ ID NO: 731.
• Thus, the invention encompasses nucleic acid sequences described hereinabove; fragments thereof, sequences hybridizable therewith, sequences homologous thereto, sequences encoding similar polypeptides with different codon usage, altered sequences characterized by mutations, such as deletion, insertion or substitution of one or more nucleotides, either naturally occurring or man induced, either randomly or in a targeted fashion.
• The invention provides an isolated polynucleotide comprising a nucleic acid sequence at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, e.g., 100% identical to the polynucleotide selected from the group consisting of SEQ ID NOs:1-361, 602-2427 and 2428.
• According to some embodiments of the invention the nucleic acid sequence is capable of increasing yield, oil content, growth rate, biomass, vigor, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of a plant.
• According to some embodiments of the invention the isolated polynucleotide comprising the nucleic acid sequence selected from the group consisting of SEQ ID NOs:1-361, 602-2427 and 2428.
• According to some embodiments of the invention the isolated polynucleotide is set forth by SEQ ID NO:1-361, 602-2427 or 2428.
• The invention provides an isolated polynucleotide comprising a nucleic acid sequence encoding a polypeptide which comprises an amino acid sequence at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more say 100% homologous to the amino acid sequence selected from the group consisting of SEQ ID NO: 362-601, 24294085 or 4086.
• According to some embodiments of the invention the amino acid sequence is capable of increasing yield, oil content, growth rate, biomass, vigor, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of a plant.
• The invention provides an isolated polynucleotide comprising a nucleic acid sequence encoding a polypeptide which comprises the amino acid sequence selected from the group consisting of SEQ ID NOs:362-601, 2429-4085 and 4086.
• According to an aspect of some embodiments of the invention, there is provided a nucleic acid construct comprising the isolated polynucleotide of the invention, and a promoter for directing transcription of the nucleic acid sequence in a host cell.
• The invention provides an isolated polypeptide comprising an amino acid sequence at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more say 100% homologous to an amino acid sequence selected from the group consisting of SEQ ID NO: 362-601, 2429-4085 or 4086.
• According to some embodiments of the invention, the polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs:362-601, 2429-4085 and 4086.
• According to some embodiments of the invention, the polypeptide is set forth by SEQ ID NO: 362-601, 2429-4085 or 4086.
• The invention also encompasses fragments of the above described polypeptides and polypeptides having mutations, such as deletions, insertions or substitutions of one or more amino acids, either naturally occurring or man induced, either randomly or in a targeted fashion.
• The term “plant” as used herein encompasses whole plants, ancestors and progeny of the plants and plant parts, including seeds, shoots, stems, roots (including tubers), and plant cells, tissues and organs. The plant may be in any form including suspension cultures, embryos, meristematic regions, callus tissue, leaves, gametophytes, sporophytes, pollen, and microspores. Plants that are particularly useful in the methods of the invention include all plants which belong to the superfamily Viridiplantae, in particular monocotyledonous and dicotyledonous plants including a fodder or forage legume, ornamental plant, food crop, tree, or shrub selected from the list comprising Acacia spp., Acer spp., Actinidia spp., Aesculus spp., Agathis australis, Albizia amara, Alsophila tricolor, Andropogon spp., Arachis spp, Areca catechu, Astelia fragrans, Astragalus cicer, Baikiaea plurijuga, Betula spp., Brassica spp., Bruguiera gymnorrhiza, Burkea africana, Butea frondosa, Cadaba farinosa, Calliandra spp, Camellia sinensis, Canna indica, Capsicum spp., Cassia spp., Centroema pubescens, Chacoomeles spp., Cinnamomum cassia, Coffea arabica, Colophospermum mopane, Coronillia varia, Cotoneaster serotina, Crataegus spp., Cucumis spp., Cupressus spp., Cyathea dealbata. Cydonia oblonga, Cryptomeria japonica, Cymbopogon spp., Cynthea dealbata, Cydonia oblonga, Dalbergia monetaria, Davallia divaricata, Desmodium spp., Dicksonia squarosa, Dibeteropogon amplectens, Dioclea spp, Dolichos spp., Dorycnium rectum, Echinochloa pyramidalis, Ehraffia spp., Eleusine coracana, Eragrestis spp., Erythrina spp., Eucalypfus spp., Euclea schimperi, Eulalia vi/losa, Pagopyrum spp., Feijoa sellowlana, Fragaria spp., Flemingia spp, Freycinetia banksli, Geranium thunbergii, Ginkgo biloba, Glycine javanica, Gliricidia spp, Gossypium hirsutum, Grevillea spp., Guibourtia coleosperma, Hedysarum spp., Hemaffhia altissima, Heteropogon contoffus, Hordeum vulgare, Hyparrhenia rufa, Hypericum erectum, Hypeffhelia dissolute, Indigo incamata, Iris spp., Leptarrhena pyrolifolia, Lespediza spp., Lettuca spp., Leucaena leucocephala, Loudetia simplex, Lotonus bainesli, Lotus spp., Macrotyloma axillare, Malus spp., Manihot esculenta. Medicago saliva, Metasequoia glyptostroboides, Musa sapientum, Nicotianum spp., Onobrychis spp., Omithopus spp., Oryza spp., Peltophorum africanum, Pennisetum spp., Persea gratissima, Petunia spp., Phaseolus spp., Phoenix canariensis, Phormium cookianum, Photinia spp., Picea glauca, Pinus spp., Pisum sativam, Podocarpus totara, Pogonarthria fleckii, Pogonaffhria squarrosa, Populus spp., Prosopis cineraria, Pseudotsuga menziesii, Pterolobium stellatum, Pyrus communis, Quercus spp., Rhaphiolepsis umbellata, Rhopalostylis sapida, Rhus natalensis, Ribes grossularia, Ribes spp., Robinia pseudoacacia, Rosa spp., Rubus spp., Salix spp., Schyzachyrium sanguineum, Sciadopitys veflicillata, Sequoia sempervirens, Sequoiadendron giganteum, Sorghum bicolor, Spinacia spp., Sporobolus fimbriatus, Stiburus alopecuroides, Stylosanthos humilis, Tadehagi spp, Taxodium distichum, Themeda triandra, Trifolium spp., Triticum spp., Tsuga heterophylla, Vaccinium spp., Vicia spp., Vitis vinifera, Watsonia pyramidata, Zantedeschia aethiopica, Zea mays, amaranth, artichoke, asparagus, broccoli, Brussels sprouts, cabbage, canola, carrot, cauliflower, celery, collard greens, flax, kale, lentil, oilseed rape, okra, onion, potato, rice, soybean, straw, sugar beet, sugar cane, sunflower, tomato, squash tea, maize, wheat, barely, rye, oat, peanut, pea, lentil and alfalfa, cotton, rapeseed, canola, pepper, sunflower, tobacco, eggplant, eucalyptus, a tree, an ornamental plant, a perennial grass and a forage crop. Alternatively algae and other non-Viridiplantae can be used for the methods of the present invention.
• According to some embodiments of the invention, the plant used by the method of the invention is a crop plant such as rice, maize, wheat, barley, peanut, potato, sesame, olive tree, palm oil, banana, soybean, sunflower, canola, sugarcane, alfalfa, millet, leguminosae (bean, pea), flax, lupinus, rapeseed, tobacco, poplar and cotton.
• According to some embodiments of the invention the plant is a dicotyledonous plant.
• According to some embodiments of the invention the plant is a monocotyledonous plant.
• According to some embodiments of the invention, there is provided a plant cell exogenously expressing the polynucleotide of some embodiments of the invention, the nucleic acid construct of some embodiments of the invention and/or the polypeptide of some embodiments of the invention.
• According to some embodiments of the invention, expressing the exogenous polynucleotide of the invention within the plant is effected by transforming one or more cells of the plant with the exogenous polynucleotide, followed by generating a mature plant from the transformed cells and cultivating the mature plant under conditions suitable for expressing the exogenous polynucleotide within the mature plant.
• According to some embodiments of the invention, the transformation is effected by introducing to the plant cell a nucleic acid construct which includes the exogenous polynucleotide of some embodiments of the invention and at least one promoter for directing transcription of the exogenous polynucleotide in a host cell (a plant cell). Further details of suitable transformation approaches are provided hereinbelow.
• As mentioned, the nucleic acid construct according to some embodiments of the invention comprises a promoter sequence and the isolated polynucleotide of the invention.
• According to some embodiments of the invention, the isolated polynucleotide is operably linked to the promoter sequence.
• A coding nucleic acid sequence is “operably linked” to a regulatory sequence (e.g., promoter) if the regulatory sequence is capable of exerting a regulatory effect on the coding sequence linked thereto.
• As used herein, the term “promoter” refers to a region of DNA which lies upstream of the transcriptional initiation site of a gene to which RNA polymerase binds to initiate transcription of RNA. The promoter controls where (e.g., which portion of a plant) and/or when (e.g., at which stage or condition in the lifetime of an organism) the gene is expressed.
• According to some embodiments of the invention, the promoter is heterologous to the isolated polynucleotide and/or to the host cell.
• As used herein the phrase “heterologous promoter” refers to a promoter from a different species or from the same species but from a different gene locus as of the isolated polynucleotide sequence.
• Any suitable promoter sequence can be used by the nucleic acid construct of the present invention. Preferably the promoter is a constitutive promoter, a tissue-specific, or an abiotic stress-inducible promoter.
• According to some embodiments of the invention, the promoter is a plant promoter, which is suitable for expression of the exogenous polynucleotide in a plant cell.
• Suitable promoters for expression in wheat include, but are not limited to, Wheat SPA promoter (SEQ ID NO: 4087; Albanietal, Plant Cell, 9: 171-184, 1997, which is fully incorporated herein by reference), wheat LMW (SEQ ID NO: 4088 (longer LMW promoter), and SEQ ID NO: 4089 (LMW promoter) and HMW glutenin-1 (SEQ ID NO: 4090 (Wheat HMW glutenin-1 longer promoter); and SEQ ID NO: 4091 (Wheat HMW glutenin-1 Promoter); Thomas and Flavell, The Plant Cell 2:1171-1180; Furtado et al., 2009 Plant Biotechnology Journal 7:240-253, each of which is fully incorporated herein by reference), wheat alpha, beta and gamma gliadins [e.g., SEQ ID NO: 4092 (wheat alpha gliadin, B genome, promoter); SEQ ID NO: 4093 (wheat gamma gliadin promoter); EMBO 3:1409-15, 1984, which is fully incorporated herein by reference], wheat TdPR60 [SEQ ID NO: 4094 (wheat TdPR60 longer promoter) or SEQ ID NO: 4095 (wheat TdPR60 promoter); Kovalchuk et al., Plant Mol Biol 71:81-98, 2009, which is fully incorporated herein by reference], maize Ub1 Promoter [cultivar Nongda 105 (SEQ ID NO: 4096); GenBank: DQ141598.1; Taylor et al., Plant Cell Rep 1993 12: 491-495, which is fully incorporated herein by reference; and cultivar B73 (SEQ ID NO: 4097); Christensen, A H, et al. Plant Mol. Biol. 18 (4), 675-689 (1992), which is fully incorporated herein by reference]; rice actin 1 (SEQ ID NO: 4098; Mc Elroy et al. 1990, The Plant Cell, Vol. 2, 163-171, which is fully incorporated herein by reference), rice GOS2 [SEQ ID NO: 4099 (rice GOS2 longer promoter) and SEQ ID NO: 4100 (rice GOS2 Promoter); De Pater et al. Plant J. 1992; 2: 837-44, which is fully incorporated herein by reference], Arabidopsis Pho1 [SEQ ID NO: 4101 (Arabidopsis Pho1 Promoter); Hamburger et al., Plant Cell. 2002; 14: 889-902, which is fully incorporated herein by reference], ExpansinB promoters, e.g., rice ExpB5 [SEQ ID NO: 4102 (rice ExpB5 longer promoter) and SEQ ID NO: 4103 (rice ExpB5 promoter)] and Barley ExpB1 [SEQ ID NO: 4104 (barley ExpB1 Promoter), Won et al. Mol Cells. 2010; 30:369-76, which is fully incorporated herein by reference], barley SS2 (sucrose synthase 2) [(SEQ ID NO: 4105), Guerin and Carbonero, Plant Physiology May 1997 vol. 114 no. 1 55-62, which is fully incorporated herein by reference], and rice PG5a [SEQ ID NO:4106, U.S. Pat. No. 7,700,835, Nakase et al., Plant Mol Biol. 32:621-30, 1996, each of which is fully incorporated herein by reference].
• Suitable constitutive promoters include, for example, CaMV 35S promoter [SEQ ID NO: 4107 (CaMV 35S (QFNC) Promoter); SEQ ID NO: 4108 (PJJ 35S from Brachypodium); SEQ ID NO: 4109 (CaMV 35S (OLD) Promoter) (Odell et al., Nature 313:810-812, 1985)], Arabidopsis At6669 promoter (SEQ ID NO: 4110 (Arabidopsis At6669 (OLD) Promoter); see PCT Publication No. WO04081173A2 or the new At6669 promoter (SEQ ID NO: 4111 (Arabidopsis At6669 (NEW) Promoter)); maize Ub1 Promoter [cultivar Nongda 105 (SEQ ID NO:4096); GenBank: DQ141598.1; Taylor et al., Plant Cell Rep 1993 12: 491-495, which is fully incorporated herein by reference; and cultivar B73 (SEQ ID NO:4097); Christensen, A H, et al. Plant Mol. Biol. 18 (4), 675-689 (1992), which is fully incorporated herein by reference]; rice actin 1 (SEQ ID NO: 4098, McElroy et al., Plant Cell 2:163-171, 1990); pEMU (Last et al., Theor. Appl. Genet. 81:581-588, 1991); CaMV 19S (Nilsson et al., Physiol. Plant 100:456-462, 1997); rice GOS2 [SEQ ID NO: 4099 (rice GOS2 longer Promoter) and SEQ ID NO: 4100 (rice GOS2 Promoter), de Pater et al, Plant J November; 2(6):837-44, 1992]; RBCS promoter (SEQ ID NO:4112); Rice cyclophilin (Bucholz et al, Plant Mol Biol. 25(5):837-43, 1994); Maize H3 histone (Lepetit et al, Mol. Gen. Genet. 231: 276-285, 1992); Actin 2 (An et al, Plant J. 10(1); 107-121, 1996) and Synthetic Super MAS (Ni et al., The Plant Journal 7: 661-76, 1995). Other constitutive promoters include those in U.S. Pat. Nos. 5,659,026, 5,608,149; 5,608,144; 5,604,121; 5,569,597; 5,466,785; 5,399,680; 5,268,463; and 5,608,142.
• Suitable tissue-specific promoters include, but not limited to, leaf-specific promoters [e.g., AT5G06690 (Thioredoxin) (high expression, SEQ ID NO: 4113), AT5G61520 (AtSTP3) (low expression, SEQ ID NO: 4114) described in Buttner et al 2000 Plant, Cell and Environment 23, 175-184, or the promoters described in Yamamoto et al., Plant J. 12:255-265, 1997; Kwon et al., Plant Physiol. 105:357-67, 1994; Yamamoto et al., Plant Cell Physiol. 35:773-778, 1994; Gotor et al., Plant J. 3:509-18, 1993; Orozco et al., Plant Mol. Biol. 23:1129-1138, 1993; and Matsuoka et al., Proc. Natl. Acad. Sci. USA 90:9586-9590, 1993; as well as Arabidopsis STP3 (AT5G61520) promoter (Buttner et al., Plant, Cell and Environment 23:175-184, 2000)], seed-preferred promoters [e.g., Napin (originated from Brassica napus which is characterized by a seed specific promoter activity; Stuitje A. R. et. al. Plant Biotechnology Journal 1 (4): 301-309; SEQ ID NO: 4115 (Brassica napus NAPIN Promoter) from seed specific genes (Simon, et al., Plant Mol. Biol. 5. 191, 1985; Scofield, et al., J. Biol. Chem. 262: 12202, 1987; Baszczynski, et al., Plant Mol. Biol. 14: 633, 1990), rice PG5a (SEQ ID NO: 4106; U.S. Pat. No. 7,700,835), early seed development Arabidopsis BAN (AT1G61720) (SEQ ID NO: 4116, US 2009/0031450 A1), late seed development Arabidopsis ABI3 (AT3G24650) (SEQ ID NO: 4117 (Arabidopsis ABI3 (AT3G24650) longer Promoter) or 4118 (Arabidopsis ABI3 (AT3G24650) Promoter)) (Ng et al., Plant Molecular Biology 54: 25-38, 2004), Brazil Nut albumin (Pearson’ et al., Plant Mol. Biol. 18: 235-245, 1992), legumin (Ellis, et al. Plant Mol. Biol. 10: 203-214, 1988), Glutelin (rice) (Takaiwa, et al., Mol. Gen. Genet. 208: 15-22, 1986; Takaiwa, et al., FEBS Letts. 221: 43-47, 1987), Zein (Matzke et al Plant Mol Biol, 143). 323-32 1990), napA (Stalberg, et al, Planta 199: 515-519, 1996), Wheat SPA (SEQ ID NO: 4087; Albanietal, Plant Cell, 9: 171-184, 1997), sunflower oleosin (Cummins, et al., Plant Mol. Biol. 19: 873-876, 1992)], endosperm specific promoters [e.g., wheat LMW (SEQ ID NO: 4088 (Wheat LMW Longer Promoter), and SEQ ID NO: 4089 (Wheat LMW Promoter) and HMW glutenin-1 [(SEQ ID NO: 4090 (Wheat HMW glutenin-1 longer Promoter)); and SEQ ID NO: 4091 (Wheat HMW glutenin-1 Promoter), Thomas and Flavell, The Plant Cell 2:1171-1180, 1990; Mol Gen Genet 216:81-90, 1989; NAR 17:461-2), wheat alpha, beta and gamma gliadins (SEQ ID NO: 4092 (wheat alpha gliadin (B genome) promoter); SEQ ID NO: 4093 (wheat gamma gliadin promoter); EMBO 3:1409-15, 1984), Barley ltrl promoter, barley B1, C, D hordein (Theor Appl Gen 98:1253-62, 1999; Plant J 4:343-55, 1993; Mol Gen Genet 250:750-60, 1996), Barley DOF (Mena et al, The Plant Journal, 116(1): 53-62, 1998), Biz2 (EP99106056.7), Barley SS2 (SEQ ID NO: 4105 (Barley SS2 Promoter); Guerin and Carbonero Plant Physiology 114: 1 55-62, 1997), wheat Tarp60 (Kovalchuk et al., Plant Mol Biol 71:81-98, 2009), barley D-hordein (D-Hor) and B-hordein (B-Hor) (Agnelo Furtado, Robert J. Henry and Alessandro Pellegrineschi (2009)], Synthetic promoter (Vicente-Carbajosa et al., Plant J. 13: 629-640, 1998), rice prolamin NRP33, rice -globulin Glb-1 (Wu et al, Plant Cell Physiology 39(8) 885-889, 1998), rice alpha-globulin REB/OHP-1 (Nakase et al Plant Mol. Biol. 33: 513-S22, 1997), rice ADP-glucose PP (Trans Res 6:157-68, 1997), maize ESR gene family (Plant J 12:235-46, 1997), sorgum gamma-kafirin (PMB 32:1029-35, 1996)], embryo specific promoters [e.g., rice OSH1 (Sato et al, Proc. Natl. Acad. Sci. USA, 93: 8117-8122), KNOX (Postma-Haarsma ef al, Plant Mol. Biol. 39:257-71, 1999), rice oleosin (Wu et at, J. Biochem., 123:386, 1998)], and flower-specific promoters [e.g., AtPRP4, chalene synthase (chsA) (Van der Meer, et al., Plant Mol. Biol. 15, 95-109, 1990), LAT52 (Twell et al Mol. Gen Genet. 217:240-245; 1989), Arabidopsis apetala-3 (Tilly et al., Development. 125:1647-57, 1998), Arabidopsis APETALA 1 (AT1G69120, API) (SEQ ID NO: 4119 (Arabidopsis (AT1G69120) APETALA 1)) (Hempel et al., Development 124:3845-3853, 1997)], and root promoters [e.g., the ROOTP promoter [SEQ ID NO: 4120]; rice ExpB5 (SEQ ID NO:4103 (rice ExpB5 Promoter); or SEQ ID NO: 4102 (rice ExpB5 longer Promoter)) and barley ExpB1 promoters (SEQ ID NO:4104) (Won et al. Mol. Cells 30: 369-376, 2010); Arabidopsis ATTPS-CIN (AT3G25820) promoter (SEQ ID NO: 4121; Chen et al., Plant Phys 135:1956-66, 2004); arabidopsis Pho1 promoter (SEQ ID NO: 4101, Hamburger et al., Plant Cell. 14: 889-902, 2002), which is also slightly induced by stress].
• Suitable abiotic stress-inducible promoters include, but not limited to, salt-inducible promoters such as RD29A (Yamaguchi-Shinozalei et al., Mol. Gen. Genet. 236:331-340. 1993); drought-inducible promoters such as maize rab17 gene promoter (Pla et. al., Plant Mol. Biol. 21:259-266, 1993), maize rab28 gene promoter (Busk et. al., Plant J. 11:1285-1295, 1997) and maize Ivr2 gene promoter (Pelleschi et. al., Plant Mol. Biol. 39:373-380, 1999); heat-inducible promoters such as heat tomato hsp80-promoter from tomato (U.S. Pat. No. 5,187,267).
• The nucleic acid construct of some embodiments of the invention can further include an appropriate selectable marker and/or an origin of replication. According to some embodiments of the invention, the nucleic acid construct utilized is a shuttle vector, which can propagate both in E. coli (wherein the construct comprises an appropriate selectable marker and origin of replication) and be compatible with propagation in cells. The construct according to the present invention can be, for example, a plasmid, a bacmid, a phagemid, a cosmid, a phage, a virus or an artificial chromosome.
• The nucleic acid construct of some embodiments of the invention can be utilized to stably or transiently transform plant cells. In stable transformation, the exogenous polynucleotide is integrated into the plant genome and as such it represents a stable and inherited trait. In transient transformation, the exogenous polynucleotide is expressed by the cell transformed but it is not integrated into the genome and as such it represents a transient trait.
• There are various methods of introducing foreign genes into both monocotyledonous and dicotyledonous plants (Potrykus, I., Annu. Rev. Plant. Physiol., Plant. Mol. Biol. (1991) 42:205-225; Shimamoto et al., Nature (1989) 338:274-276).
• The principle methods of causing stable integration of exogenous DNA into plant genomic DNA include two main approaches:
• (i) Agrobacterium-mediated gene transfer: Klee et al. (1987) Annu. Rev. Plant Physiol. 38:467-486; Klee and Rogers in Cell Culture and Somatic Cell Genetics of Plants, Vol. 6, Molecular Biology of Plant Nuclear Genes, eds. Schell, J., and Vasil, L. K., Academic Publishers, San Diego. Calif. (1989) p. 2-25; Gatenby, in Plant Biotechnology, eds. Kung, S. and Amtzen, C. J., Butterworth Publishers, Boston, Mass. (1989) p. 93-112.
• (ii) Direct DNA uptake: Paszkowski et al., in Cell Culture and Somatic Cell Genetics of Plants, Vol. 6, Molecular Biology of Plant Nuclear Genes eds. Schell, J., and Vasil, L. K., Academic Publishers, San Diego, Calif. (1989) p. 52-68; including methods for direct uptake of DNA into protoplasts, Toriyama. K. et al. (1988) Bio/Technology 6:1072-1074. DNA uptake induced by brief electric shock of plant cells: Zhang et al. Plant Cell Rep. (1988) 7:379-384. Fromm et al. Nature (1986) 319:791-793. DNA injection into plant cells or tissues by particle bombardment, Klein et al. Bio/Technology (1988) 6:559-563; McCabe et al. Bio/Technology (1988) 6:923-926; Sanford, Physiol. Plant. (1990) 79:206-209; by the use of micropipette systems: Neuhaus et al., Theor. Appl. Genet. (1987) 75:30-36; Neuhaus and Spangenberg, Physiol. Plant. (1990) 79:213-217; glass fibers or silicon carbide whisker transformation of cell cultures, embryos or callus tissue, U.S. Pat. No. 5,464,765 or by the direct incubation of DNA with germinating pollen, DeWet et al. in Experimental Manipulation of Ovule Tissue, eds. Chapman, G. P. and Mantell, S. H. and Daniels, W. Longman, London, (1985) p. 197-209; and Ohta, Proc. Natl. Acad. Sci. USA (1986) 83:715-719.
• The Agrobacterium system includes the use of plasmid vectors that contain defined DNA segments that integrate into the plant genomic DNA. Methods of inoculation of the plant tissue vary depending upon the plant species and the Agrobacterium delivery system. A widely used approach is the leaf disc procedure which can be performed with any tissue explant that provides a good source for initiation of whole plant differentiation. See, e.g., Horsch et al. in Plant Molecular Biology Manual A5, Kluwer Academic Publishers, Dordrecht (1988) p. 1-9. A supplementary approach employs the Agrobacterium delivery system in combination with vacuum infiltration. The Agrobacterium system is especially viable in the creation of transgenic dicotyledonous plants.
• There are various methods of direct DNA transfer into plant cells. In electroporation, the protoplasts are briefly exposed to a strong electric field. In microinjection, the DNA is mechanically injected directly into the cells using very small micropipettes. In microparticle bombardment, the DNA is adsorbed on microprojectiles such as magnesium sulfate crystals or tungsten particles, and the microprojectiles are physically accelerated into cells or plant tissues.
• Following stable transformation plant propagation is exercised. The most common method of plant propagation is by seed. Regeneration by seed propagation, however, has the deficiency that due to heterozygosity there is a lack of uniformity in the crop, since seeds are produced by plants according to the genetic variances governed by Mendelian rules. Basically, each seed is genetically different and each will grow with its own specific traits. Therefore, it is preferred that the transformed plant be produced such that the regenerated plant has the identical traits and characteristics of the parent transgenic plant. Therefore, it is preferred that the transformed plant be regenerated by micropropagation which provides a rapid, consistent reproduction of the transformed plants.
• Micropropagation is a process of growing new generation plants from a single piece of tissue that has been excised from a selected parent plant or cultivar. This process permits the mass reproduction of plants having the preferred tissue expressing the fusion protein. The new generation plants which are produced are genetically identical to, and have all of the characteristics of, the original plant. Micropropagation allows mass production of quality plant material in a short period of time and offers a rapid multiplication of selected cultivars in the preservation of the characteristics of the original transgenic or transformed plant. The advantages of cloning plants are the speed of plant multiplication and the quality and uniformity of plants produced.
• Micropropagation is a multi-stage procedure that requires alteration of culture medium or growth conditions between stages. Thus, the micropropagation process involves four basic stages: Stage one, initial tissue culturing; stage two, tissue culture multiplication; stage three, differentiation and plant formation; and stage four, greenhouse culturing and hardening. During stage one, initial tissue culturing, the tissue culture is established and certified contaminant-free. During stage two, the initial tissue culture is multiplied until a sufficient number of tissue samples are produced to meet production goals. During stage three, the tissue samples grown in stage two are divided and grown into individual plantlets. At stage four, the transformed plantlets are transferred to a greenhouse for hardening where the plants' tolerance to light is gradually increased so that it can be grown in the natural environment.
• According to some embodiments of the invention, the transgenic plants are generated by transient transformation of leaf cells, meristematic cells or the whole plant.
• Transient transformation can be effected by any of the direct DNA transfer methods described above or by viral infection using modified plant viruses.
• Viruses that have been shown to be useful for the transformation of plant hosts include CaMV, Tobacco mosaic virus (TMV), brome mosaic virus (BMV) and Bean Common Mosaic Virus (BV or BCMV). Transformation of plants using plant viruses is described in U.S. Pat. No. 4,855,237 (bean golden mosaic virus; BGV), EP-A 67,553 (TMV), Japanese Published Application No. 63-14693 (TMV), EPA 194,809 (BV), EPA 278,667 (BV); and Gluzman, Y. et al., Communications in Molecular Biology: Viral Vectors, Cold Spring Harbor Laboratory, New York, pp. 172-189 (1988). Pseudovirus particles for use in expressing foreign DNA in many hosts, including plants are described in WO 87/06261.
• According to some embodiments of the invention, the virus used for transient transformations is avirulent and thus is incapable of causing severe symptoms such as reduced growth rate, mosaic, ring spots, leaf roll, yellowing, streaking, pox formation, tumor formation and pitting. A suitable avirulent virus may be a naturally occurring avirulent virus or an artificially attenuated virus. Virus attenuation may be effected by using methods well known in the art including, but not limited to, sub-lethal heating, chemical treatment or by directed mutagenesis techniques such as described, for example, by Kurihara and Watanabe (Molecular Plant Pathology 4:259-269, 2003), Gal-on et al. (1992). Atreya et al. (1992) and Huet et al. (1994).
• Suitable virus strains can be obtained from available sources such as, for example, the American Type culture Collection (ATCC) or by isolation from infected plants. Isolation of viruses from infected plant tissues can be effected by techniques well known in the art such as described, for example by Foster and Tatlor, Eds. “Plant Virology Protocols: From Virus Isolation to Transgenic Resistance (Methods in Molecular Biology (Humana Pr), Vol 81)”, Humana Press, 1998. Briefly, tissues of an infected plant believed to contain a high concentration of a suitable virus, preferably young leaves and flower petals, are ground in a buffer solution (e.g., phosphate buffer solution) to produce a virus infected sap which can be used in subsequent inoculations.
• Construction of plant RNA viruses for the introduction and expression of non-viral exogenous polynucleotide sequences in plants is demonstrated by the above references as well as by Dawson, W. O. et al., Virology (1989) 172:285-292; Takamatsu et al. EMBO J. (1987) 6:307-311; French et al. Science (1986) 231:1294-1297; Takamatsu et al. FEBS Letters (1990) 269:73-76; and U.S. Pat. No. 5,316,931.
• When the virus is a DNA virus, suitable modifications can be made to the virus itself. Alternatively, the virus can first be cloned into a bacterial plasmid for ease of constructing the desired viral vector with the foreign DNA. The virus can then be excised from the plasmid. If the virus is a DNA virus, a bacterial origin of replication can be attached to the viral DNA, which is then replicated by the bacteria. Transcription and translation of this DNA will produce the coat protein which will encapsidate the viral DNA. If the virus is an RNA virus, the virus is generally cloned as a cDNA and inserted into a plasmid. The plasmid is then used to make all of the constructions. The RNA virus is then produced by transcribing the viral sequence of the plasmid and translation of the viral genes to produce the coat protein(s) which encapsidate the viral RNA.
• In one embodiment, a plant viral polynucleotide is provided in which the native coat protein coding sequence has been deleted from a viral polynucleotide, a non-native plant viral coat protein coding sequence and a non-native promoter, preferably the subgenomic promoter of the non-native coat protein coding sequence, capable of expression in the plant host, packaging of the recombinant plant viral polynucleotide, and ensuring a systemic infection of the host by the recombinant plant viral polynucleotide, has been inserted. Alternatively, the coat protein gene may be inactivated by insertion of the non-native polynucleotide sequence within it, such that a protein is produced. The recombinant plant viral polynucleotide may contain one or more additional non-native subgenomic promoters. Each non-native subgenomic promoter is capable of transcribing or expressing adjacent genes or polynucleotide sequences in the plant host and incapable of recombination with each other and with native subgenomic promoters. Non-native (foreign) polynucleotide sequences may be inserted adjacent the native plant viral subgenomic promoter or the native and a non-native plant viral subgenomic promoters if more than one polynucleotide sequence is included. The non-native polynucleotide sequences are transcribed or expressed in the host plant under control of the subgenomic promoter to produce the desired products.
• In a second embodiment, a recombinant plant viral polynucleotide is provided as in the first embodiment except that the native coat protein coding sequence is placed adjacent one of the non-native coat protein subgenomic promoters instead of a non-native coat protein coding sequence.
• In a third embodiment, a recombinant plant viral polynucleotide is provided in which the native coat protein gene is adjacent its subgenomic promoter and one or more non-native subgenomic promoters have been inserted into the viral polynucleotide. The inserted non-native subgenomic promoters are capable of transcribing or expressing adjacent genes in a plant host and are incapable of recombination with each other and with native subgenomic promoters. Non-native polynucleotide sequences may be inserted adjacent the non-native subgenomic plant viral promoters such that the sequences are transcribed or expressed in the host plant under control of the subgenomic promoters to produce the desired product.
• In a fourth embodiment, a recombinant plant viral polynucleotide is provided as in the third embodiment except that the native coat protein coding sequence is replaced by a non-native coat protein coding sequence.
• The viral vectors are encapsidated by the coat proteins encoded by the recombinant plant viral polynucleotide to produce a recombinant plant virus. The recombinant plant viral polynucleotide or recombinant plant virus is used to infect appropriate host plants. The recombinant plant viral polynucleotide is capable of replication in the host, systemic spread in the host, and transcription or expression of foreign gene(s) (exogenous polynucleotide) in the host to produce the desired protein.
• Techniques for inoculation of viruses to plants may be found in Foster and Taylor, eds. “Plant Virology Protocols: From Virus Isolation to Transgenic Resistance (Methods in Molecular Biology (Humana Pr), Vol 81)”, Humana Press, 1998; Maramorosh and Koprowski, eds. “Methods in Virology” 7 vols, Academic Press, New York 1967-1984; Hill, S. A. “Methods in Plant Virology”, Blackwell, Oxford, 1984; Walkey, D. G. A. “Applied Plant Virology”. Wiley, New York, 1985; and Kado and Agrawa, eds. “Principles and Techniques in Plant Virology”, Van Nostrand-Reinhold, New York.
• In addition to the above, the polynucleotide of the present invention can also be introduced into a chloroplast genome thereby enabling chloroplast expression.
• A technique for introducing exogenous polynucleotide sequences to the genome of the chloroplasts is known. This technique involves the following procedures. First, plant cells are chemically treated so as to reduce the number of chloroplasts per cell to about one. Then, the exogenous polynucleotide is introduced via particle bombardment into the cells with the aim of introducing at least one exogenous polynucleotide molecule into the chloroplasts. The exogenous polynucleotides selected such that it is integratable into the chloroplast's genome via homologous recombination which is readily effected by enzymes inherent to the chloroplast. To this end, the exogenous polynucleotide includes, in addition to a gene of interest, at least one polynucleotide stretch which is derived from the chloroplast's genome. In addition, the exogenous polynucleotide includes a selectable marker, which serves by sequential selection procedures to ascertain that all or substantially all of the copies of the chloroplast genomes following such selection will include the exogenous polynucleotide. Further details relating to this technique are found in U.S. Pat. Nos. 4,945,050; and 5,693,507 which are incorporated herein by reference. A polypeptide can thus be produced by the protein expression system of the chloroplast and become integrated into the chloroplast's inner membrane.
• Since processes which increase yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant can involve multiple genes acting additively or in synergy (see, for example, in Quesda et al., Plant Physiol. 130:951-063, 2002), the present invention also envisages expressing a plurality of exogenous polynucleotides in a single host plant to thereby achieve superior effect on oil content, yield, growth rate, biomass, vigor and/or abiotic stress tolerance.
• Expressing a plurality of exogenous polynucleotides in a single host plant can be effected by co-introducing multiple nucleic acid constructs, each including a different exogenous polynucleotide, into a single plant cell. The transformed cell can then be regenerated into a mature plant using the methods described hereinabove.
• Alternatively, expressing a plurality of exogenous polynucleotides in a single host plant can be effected by co-introducing into a single plant-cell a single nucleic-acid construct including a plurality of different exogenous polynucleotides. Such a construct can be designed with a single promoter sequence which can transcribe a polycistronic messenger RNA including all the different exogenous polynucleotide sequences. To enable co-translation of the different polypeptides encoded by the polycistronic messenger RNA, the polynucleotide sequences can be inter-linked via an internal ribosome entry site (IRES) sequence which facilitates translation of polynucleotide sequences positioned downstream of the IRES sequence. In this case, a transcribed polycistronic RNA molecule encoding the different polypeptides described above will be translated from both the capped 5′ end and the two internal IRES sequences of the polycistronic RNA molecule to thereby produce in the cell all different polypeptides. Alternatively, the construct can include several promoter sequences each linked to a different exogenous polynucleotide sequence.
• The plant cell transformed with the construct including a plurality of different exogenous polynucleotides, can be regenerated into a mature plant, using the methods described hereinabove.
• Alternatively, expressing a plurality of exogenous polynucleotides in a single host plant can be effected by introducing different nucleic acid constructs, including different exogenous polynucleotides, into a plurality of plants. The regenerated transformed plants can then be cross-bred and resultant progeny selected for superior abiotic stress tolerance, water use efficiency, fertilizer use efficiency, growth, biomass, yield and/or vigor traits, using conventional plant breeding techniques.
• According to some embodiments of the invention, the method further comprising growing the plant expressing the exogenous polynucleotide under the abiotic stress.
• Non-limiting examples of abiotic stress conditions include, salinity, osmotic stress, drought, water deprivation, excess of water (e.g., flood, waterlogging), etiolation, low temperature (e.g., cold stress), high temperature, heavy metal toxicity, anaerobiosis, nutrient deficiency, nutrient excess, atmospheric pollution and UV irradiation.
• According to some embodiments of the invention, the method further comprising growing the plant expressing the exogenous polynucleotide under fertilizer limiting conditions (e.g., nitrogen-limiting conditions). Non-limiting examples include growing the plant on soils with low nitrogen content (40-50% Nitrogen of the content present under normal or optimal conditions), or even under sever nitrogen deficiency (0-10% Nitrogen of the content present under normal or optimal conditions).
• Thus, the invention encompasses plants exogenously expressing the polynucleotide(s), the nucleic acid constructs and/or polypeptide(s) of the invention.
• Once expressed within the plant cell or the entire plant, the level of the polypeptide encoded by the exogenous polynucleotide can be determined by methods well known in the art such as, activity assays. Western blots using antibodies capable of specifically binding the polypeptide, Enzyme-Linked Immuno Sorbent Assay (ELISA), radio-immuno-assays (RIA), immunohistochemistry, immunocytochemistry, immunofluorescence and the like.
• Methods of determining the level in the plant of the RNA transcribed from the exogenous polynucleotide are well known in the art and include, for example, Northern blot analysis, reverse transcription polymerase chain reaction (RT-PCR) analysis (including quantitative, semi-quantitative or real-time RT-PCR) and RNA-in situ hybridization.
• The sequence information and annotations uncovered by the present teachings can be harnessed in favor of classical breeding. Thus, sub-sequence data of those polynucleotides described above, can be used as markers for marker assisted selection (MAS), in which a marker is used for indirect selection of a genetic determinant or determinants of a trait of interest (e.g., biomass, growth rate, oil content, yield, abiotic stress tolerance, water use efficiency, nitrogen use efficiency and/or fertilizer use efficiency). Nucleic acid data of the present teachings (DNA or RNA sequence) may contain or be linked to polymorphic sites or genetic markers on the genome such as restriction fragment length polymorphism (RFLP), microsatellites and single nucleotide polymorphism (SNP), DNA fingerprinting (DFP), amplified fragment length polymorphism (AFLP), expression level polymorphism, polymorphism of the encoded polypeptide and any other polymorphism at the DNA or RNA sequence.
• Examples of marker assisted selections include, but are not limited to, selection for a morphological trait (e.g., a gene that affects form, coloration, male sterility or resistance such as the presence or absence of awn, leaf sheath coloration, height, grain color, aroma of rice); selection for a biochemical trait (e.g., a gene that encodes a protein that can be extracted and observed; for example, isozymes and storage proteins); selection for a biological trait (e.g., pathogen races or insect biotypes based on host pathogen or host parasite interaction can be used as a marker since the genetic constitution of an organism can affect its susceptibility to pathogens or parasites).
• The polynucleotides and polypeptides described hereinabove can be used in a wide range of economical plants, in a safe and cost effective manner.
• Plant lines exogenously expressing the polynucleotide or the polypeptide of the invention are screened to identify those that show the greatest increase of the desired plant trait.
• Thus, according to an additional embodiment of the present invention, there is provided a method of evaluating a trait of a plant, the method comprising: (a) expressing in a plant or a portion thereof the nucleic acid construct of some embodiments of the invention, and (b) evaluating a trait of a plant as compared to a wild type plant of the same type (e.g., a plant not transformed with the claimed biomolecules); thereby evaluating the trait of the plant.
• According to an aspect of some embodiments of the invention there is provided a method of producing a crop comprising growing a crop of a plant expressing an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more say 100% homologous (e.g., identical) to the amino acid sequence selected from the group consisting of SEQ ID NOs: 362-601, 2429-4085 and 4086, wherein the plant is derived from a plant selected for increased yield, increased growth rate, increased biomass, increased vigor, increased fiber yield, increased fiber quality, increased fertilizer use efficiency (e.g., nitrogen use efficiency), increased oil content, and/or increased abiotic stress tolerance as compared to a control plant, thereby producing the crop.
• According to an aspect of some embodiments of the invention there is provided a method of producing a crop comprising growing a crop of a plant expressing an exogenous polynucleotide which comprises a nucleic acid sequence which is at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, e.g., 100% identical to the nucleic acid sequence selected from the group consisting of SEQ ID NOs:1-361, 602-2427 and 2428 wherein the plant is derived from a plant selected for increased yield, increased growth rate, increased biomass, increased vigor, increased fiber yield, increased fiber quality, increased fertilizer use efficiency (e.g., nitrogen use efficiency), increased oil content, and/or increased abiotic stress tolerance as compared to a control plant, thereby producing the crop.
• According to an aspect of some embodiments of the invention there is provided a method of growing a crop comprising seeding seeds and/or planting plantlets of a plant transformed with the exogenous polynucleotide of the invention, e.g., the polynucleotide which encodes the polypeptide of some embodiments of the invention, wherein the plant is derived from plants selected for at least one trait selected from the group consisting of: increased yield, increased fiber yield or quality, increased oil content, increased biomass, increased growth rate, increased vigor, abiotic stress tolerance, and/or increased nitrogen use efficiency, as compared to a non-transformed plant.
• According to some embodiments of the invention the method of growing a crop comprising seeding seeds and/or planting plantlets of a plant transformed with an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, e.g., 100% identical to SEQ ID NO: 362-601, 2429-4085 or 4086, wherein the plant is derived from plants selected for at least one trait selected from the group consisting of increased yield, increased fiber yield or quality, increased biomass, increased oil content, increased growth rate, increased vigor, abiotic stress tolerance, and/or increased nitrogen use efficiency as compared to a non-transformed plant, thereby growing the crop.
• According to some embodiments of the invention the method of growing a crop comprising seeding seeds and/or planting plantlets of a plant transformed with an exogenous polynucleotide comprising the nucleic acid sequence at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, e.g., 100% identical to SEQ ID NO: 1-361, 602-2427 or 2428, wherein the plant is derived from plants selected for at least one trait selected from the group consisting of increased yield, increased fiber yield or quality, increased biomass, increased growth rate, increased vigor, increased oil content, increased abiotic stress tolerance, and/or increased nitrogen use efficiency as compared to a non-transformed plant, thereby growing the crop.
• The effect of the transgene (the exogenous polynucleotide encoding the polypeptide) on abiotic stress tolerance can be determined using known methods such as detailed below and in the Examples section which follows.
• Abiotic stress tolerance—Transformed (i.e., expressing the transgene) and non-transformed (wild type) plants are exposed to an abiotic stress condition, such as water deprivation, suboptimal temperature (low temperature, high temperature), nutrient deficiency, nutrient excess, a salt stress condition, osmotic stress, heavy metal toxicity, anaerobiosis, atmospheric pollution and UV irradiation.
• Salinity tolerance assay—Transgenic plants with tolerance to high salt concentrations are expected to exhibit better germination, seedling vigor or growth in high salt. Salt stress can be effected in many ways such as, for example, by irrigating the plants with a hyperosmotic solution, by cultivating the plants hydroponically in a hyperosmotic growth solution (e.g., Hoagland solution), or by culturing the plants in a hyperosmotic growth medium [e.g., 50% Murashige-Skoog medium (MS medium)]. Since different plants vary considerably in their tolerance to salinity, the salt concentration in the irrigation water, growth solution, or growth medium can be adjusted according to the specific characteristics of the specific plant cultivar or variety, so as to inflict a mild or moderate effect on the physiology and/or morphology of the plants (for guidelines as to appropriate concentration see, Bernstein and Kafkafi, Root Growth Under Salinity Stress In: Plant Roots, The Hidden Half 3rd ed. Waisel Y. Eshel A and Kafkafi U. (editors) Marcel Dekker Inc., New York, 2002, and reference therein).
• For example, a salinity tolerance test can be performed by irrigating plants at different developmental stages with increasing concentrations of sodium chloride (for example 50 mM, 100 mM, 200 mM, 400 mM NaCl) applied from the bottom and from above to ensure even dispersal of salt. Following exposure to the stress condition the plants are frequently monitored until substantial physiological and/or morphological effects appear in wild type plants. Thus, the external phenotypic appearance, degree of wilting and overall success to reach maturity and yield progeny are compared between control and transgenic plants.
• Quantitative parameters of tolerance measured include, but are not limited to, the average wet and dry weight, growth rate, leaf size, leaf coverage (overall leaf area), the weight of the seeds yielded, the average seed size and the number of seeds produced per plant. Transformed plants not exhibiting substantial physiological and/or morphological effects, or exhibiting higher biomass than wild-type plants, are identified as abiotic stress tolerant plants.
• Osmotic tolerance test—Osmotic stress assays (including sodium chloride and mannitol assays) are conducted to determine if an osmotic stress phenotype was sodium chloride-specific or if it was a general osmotic stress related phenotype. Plants which are tolerant to osmotic stress may have more tolerance to drought and/or freezing. For salt and osmotic stress germination experiments, the medium is supplemented for example with 50 mM, 100 mM, 200 mM NaCl or 100 mM, 200 mM NaCl, 400 mM mannitol.
• Drought tolerance assay/Osmoticum assay—Tolerance to drought is performed to identify the genes conferring better plant survival after acute water deprivation. To analyze whether the transgenic plants are more tolerant to drought, an osmotic stress produced by the non-ionic osmolyte sorbitol in the medium can be performed. Control and transgenic plants are germinated and grown in plant-agar plates for 4 days, after which they are transferred to plates containing 500 mM sorbitol. The treatment causes growth retardation, then both control and transgenic plants are compared, by measuring plant weight (wet and dry), yield, and by growth rates measured as time to flowering.
• Conversely, soil-based drought screens are performed with plants overexpressing the polynucleotides detailed above. Seeds from control Arabidopsis plants, or other transgenic plants overexpressing the polypeptide of the invention are germinated and transferred to pots. Drought stress is obtained after irrigation is ceased accompanied by placing the pots on absorbent paper to enhance the soil-drying rate. Transgenic and control plants are compared to each other when the majority of the control plants develop severe wilting. Plants are re-watered after obtaining a significant fraction of the control plants displaying a severe wilting. Plants are ranked comparing to controls for each of two criteria: tolerance to the drought conditions and recovery (survival) following re-watering.
• Cold stress tolerance—To analyze cold stress, mature (25 day old) plants are transferred to 4° C. chambers for 1 or 2 weeks, with constitutive light. Later on plants are moved back to greenhouse. Two weeks later damages from chilling period, resulting in growth retardation and other phenotypes, are compared between both control and transgenic plants, by measuring plant weight (wet and dry), and by comparing growth rates measured as time to flowering, plant size, yield, and the like.
• Heat stress tolerance—Heat stress tolerance is achieved by exposing the plants to temperatures above 34° C. for a certain period. Plant tolerance is examined after transferring the plants back to 22° C. for recovery and evaluation after 5 days relative to internal controls (non-transgenic plants) or plants not exposed to neither cold or heat stress.
• Water use efficiency—can be determined as the biomass produced per unit transpiration. To analyze WUE, leaf relative water content can be measured in control and transgenic plants. Fresh weight (FW) is immediately recorded; then leaves are soaked for 8 hours in distilled water at room temperature in the dark, and the turgid weight (TW) is recorded. Total dry weight (DW) is recorded after drying the leaves at 60° C. to a constant weight. Relative water content (RWC) is calculated according to the following Formula I:
• 
  RWC=[(FW−DW)/(TW−DW)]×100  Formula I
• Fertilizer use efficiency—To analyze whether the transgenic plants are more responsive to fertilizers, plants are grown in agar plates or pots with a limited amount of fertilizer, as described, for example, in Yanagisawa et al (Proc Natl Acad Sci USA. 2004; 101:7833-8). The plants are analyzed for their overall size, time to flowering, yield, protein content of shoot and/or grain. The parameters checked are the overall size of the mature plant, its wet and dry weight, the weight of the seeds yielded, the average seed size and the number of seeds produced per plant. Other parameters that may be tested are: the chlorophyll content of leaves (as nitrogen plant status and the degree of leaf verdure is highly correlated), amino acid and the total protein content of the seeds or other plant parts such as leaves or shoots, oil content, etc. Similarly, instead of providing nitrogen at limiting amounts, phosphate or potassium can be added at increasing concentrations. Again, the same parameters measured are the same as listed above. In this way, nitrogen use efficiency (NUE), phosphate use efficiency (PUE) and potassium use efficiency (KUE) are assessed, checking the ability of the transgenic plants to thrive under nutrient restraining conditions.
• Nitrogen use efficiency—To analyze whether the transgenic plants (e.g., Arabidopsis plants) are more responsive to nitrogen, plant are grown in 0.75-3 mM (nitrogen deficient conditions) or 6-10 mM (optimal nitrogen concentration). Plants are allowed to grow for additional 25 days or until seed production. The plants are then analyzed for their overall size, time to flowering, yield, protein content of shoot and/or grain/seed production. The parameters checked can be the overall size of the plant, wet and dry weight, the weight of the seeds yielded, the average seed size and the number of seeds produced per plant. Other parameters that may be tested are: the chlorophyll content of leaves (as nitrogen plant status and the degree of leaf greenness is highly correlated), amino acid and the total protein content of the seeds or other plant parts such as leaves or shoots and oil content. Transformed plants not exhibiting substantial physiological and/or morphological effects, or exhibiting higher measured parameters levels than wild-type plants, are identified as nitrogen use efficient plants.
• Nitrogen Use efficiency assay using plantlets—The assay is done according to Yanagisawa-S. et al. with minor modifications (“Metabolic engineering with Dof1 transcription factor in plants: Improved nitrogen assimilation and growth under low-nitrogen conditions” Proc. Natl. Acad. Sci. USA 101, 7833-7838). Briefly, transgenic plants which are grown for 7-10 days in 0.5×MS [Murashige-Skoog] supplemented with a selection agent are transferred to two nitrogen-limiting conditions: MS media in which the combined nitrogen concentration (NH₄NO₃ and KNO₃) was 0.75 mM (nitrogen deficient conditions) or 6-15 mM (optimal nitrogen concentration). Plants are allowed to grow for additional 30-40 days and then photographed, individually removed from the Agar (the shoot without the roots) and immediately weighed (fresh weight) for later statistical analysis. Constructs for which only T1 seeds are available are sown on selective media and at least 20 seedlings (each one representing an independent transformation event) are carefully transferred to the nitrogen-limiting media. For constructs for which T2 seeds are available, different transformation events are analyzed. Usually, 20 randomly selected plants from each event are transferred to the nitrogen-limiting media allowed to grow for 3-4 additional weeks and individually weighed at the end of that period. Transgenic plants are compared to control plants grown in parallel under the same conditions. Mock-transgenic plants expressing the uidA reporter gene (GUS) under the same promoter or transgenic plants carrying the same promoter but lacking a reporter gene are used as control.
• Nitrogen determination—The procedure for N (nitrogen) concentration determination in the structural parts of the plants involves the potassium persulfate digestion method to convert organic N to NO₃ ⁻ (Purcell and King 1996 Argon. J. 88:111-113, the modified Cd-mediated reduction of NO₃ ⁻ to NO₂ ⁻ (Vodovotz 1996 Biotechniques 20:390-394) and the measurement of nitrite by the Griess assay (Vodovotz 1996, supra). The absorbance values are measured at 550 nm against a standard curve of NaNO₂. The procedure is described in details in Samonte et al. 2006 Agron. J. 98:168-176.
• Germination tests—Germination tests compare the percentage of seeds from transgenic plants that could complete the germination process to the percentage of seeds from control plants that are treated in the same manner. Normal conditions are considered for example, incubations at 22° C. under 22-hour light 2-hour dark daily cycles. Evaluation of germination and seedling vigor is conducted between 4 and 14 days after planting. The basal media is 50% MS medium (Murashige and Skoog, 1962 Plant Physiology 15, 473-497).
• Germination is checked also at unfavorable conditions such as cold (incubating at temperatures lower than 10° C. instead of 22° C.) or using seed inhibition solutions that contain high concentrations of an osmolyte such as sorbitol (at concentrations of 50 mM, 100 mM, 200 mM, 300 mM, 500 mM, and up to 1000 mM) or applying increasing concentrations of salt (of 50 mM, 100 mM, 200 mM, 300 mM, 500 mM NaCl).
• The effect of the transgene on plant's vigor, growth rate, biomass, yield and/or oil content can be determined using known methods.
• Plant vigor—The plant vigor can be calculated by the increase in growth parameters such as leaf area, fiber length, rosette diameter, plant fresh weight and the like per time.
• Growth rate—The growth rate can be measured using digital analysis of growing plants. For example, images of plants growing in greenhouse on plot basis can be captured every 3 days and the rosette area can be calculated by digital analysis. Rosette area growth is calculated using the difference of rosette area between days of sampling divided by the difference in days between samples.
• Evaluation of growth rate can be done by measuring plant biomass produced, rosette area, leaf size or root length per time (can be measured in cm² per day of leaf area).
• Relative growth area can be calculated using Formula II.
• 
  Growth rate area=Regression coefficient of area along time course.  Formula II:
• Thus, the growth rate area is in units of 1/day and length growth rate is in units of 1/day.
• Seed yield—Evaluation of the seed yield per plant can be done by measuring the amount (weight or size) or quantity (i.e., number) of dry seeds produced and harvested from 8-16 plants and divided by the number of plants.
• For example, the total seeds from 8-16 plants can be collected, weighted using e.g., an analytical balance and the total weight can be divided by the number of plants. Seed yield per growing area can be calculated in the same manner while taking into account the growing area given to a single plant. Increase seed yield per growing area could be achieved by increasing seed yield per plant, and/or by increasing number of plants capable of growing in a given area.
• In addition, seed yield can be determined via the weight of 1000 seeds. The weight of 1000 seeds can be determined as follows: seeds are scattered on a glass tray and a picture is taken. Each sample is weighted and then using the digital analysis, the number of seeds in each sample is calculated.
• The 1000 seeds weight can be calculated using formula III:
• 
  1000 Seed Weight=number of seed in sample/sample weight×1000  Formula III:
• The Harvest Index can be calculated using Formula IV
• 
  Harvest Index=Average seed yield per plant/Average dry weight  Formula IV:
• Grain protein concentration—Grain protein content (g grain protein m⁻²) is estimated as the product of the mass of grain N (g grain N m⁻²) multiplied by the N/protein conversion ratio of k-5.13 (Mosse 1990, supra). The grain protein concentration is estimated as the ratio of grain protein content per unit mass of the grain (g grain protein kg⁻¹ grain).
• Fiber length—Fiber length can be measured using fibrograph. The fibrograph system was used to compute length in terms of “Upper Half Mean” length. The upper half mean (UHM) is the average length of longer half of the fiber distribution. The fibrograph measures length in span lengths at a given percentage point (Hypertext Transfer Protocol://World Wide Web (dot) cottoninc (dot) com/ClassificationofCotton/?Pg=4#Length).
• According to some embodiments of the invention, increased yield of corn may be manifested as one or more of the following: increase in the number of plants per growing area, increase in the number of ears per plant, increase in the number of rows per ear, number of kernels per ear row, kernel weight, thousand kernel weight (1000-weight), ear length/diameter, increase oil content per kernel and increase starch content per kernel.
• As mentioned, the increase of plant yield can be determined by various parameters. For example, increased yield of rice may be manifested by an increase in one or more of the following: number of plants per growing area, number of panicles per plant, number of spikelets per panicle, number of flowers per panicle, increase in the seed filling rate, increase in thousand kernel weight (1000-weight), increase oil content per seed, increase starch content per seed, among others. An increase in yield may also result in modified architecture, or may occur because of modified architecture.
• Similarly, increased yield of soybean may be manifested by an increase in one or more of the following: number of plants per growing area, number of pods per plant, number of seeds per pod, increase in the seed filling rate, increase in thousand seed weight (1000-weight), reduce pod shattering, increase oil content per seed, increase protein content per seed, among others. An increase in yield may also result in modified architecture, or may occur because of modified architecture.
• Increased yield of canola may be manifested by an increase in one or more of the following: number of plants per growing area, number of pods per plant, number of seeds per pod, increase in the seed filling rate, increase in thousand seed weight (1000-weight), reduce pod shattering, increase oil content per seed, among others. An increase in yield may also result in modified architecture, or may occur because of modified architecture.
• Increased yield of cotton may be manifested by an increase in one or more of the following: number of plants per growing area, number of bolls per plant, number of seeds per boll, increase in the seed filling rate, increase in thousand seed weight (1000-weight), increase oil content per seed, improve fiber length, fiber strength, among others. An increase in yield may also result in modified architecture, or may occur because of modified architecture.
• Oil content—The oil content of a plant can be determined by extraction of the oil from the seed or the vegetative portion of the plant. Briefly, lipids (oil) can be removed from the plant (e.g., seed) by grinding the plant tissue in the presence of specific solvents (e.g., hexane or petroleum ether) and extracting the oil in a continuous extractor. Indirect oil content analysis can be carried out using various known methods such as Nuclear Magnetic Resonance (NMR) Spectroscopy, which measures the resonance energy absorbed by hydrogen atoms in the liquid state of the sample [See for example, Conway T F. and Earle F R., 1963, Journal of the American Oil Chemists' Society; Springer Berlin/Heidelberg, ISSN: 0003-021X (Print) 1558-9331 (Online)]; the Near Infrared (NI) Spectroscopy, which utilizes the absorption of near infrared energy (1100-2500 nm) by the sample; and a method described in WO/2001/023884, which is based on extracting oil a solvent, evaporating the solvent in a gas stream which forms oil particles, and directing a light into the gas stream and oil particles which forms a detectable reflected light.
• Thus, the present invention is of high agricultural value for promoting the yield of commercially desired crops (e.g., biomass of vegetative organ such as poplar wood, or reproductive organ such as number of seeds or seed biomass).
• Any of the transgenic plants described hereinabove or parts thereof may be processed to produce a feed, meal, protein or oil preparation, such as for ruminant animals.
• The transgenic plants described hereinabove, which exhibit an increased oil content can be used to produce plant oil (by extracting the oil from the plant).
• The plant oil (including the seed oil and/or the vegetative portion oil) produced according to the method of the invention may be combined with a variety of other ingredients. The specific ingredients included in a product are determined according to the intended use. Exemplary products include animal feed, raw material for chemical modification, biodegradable plastic, blended food product, edible oil, biofuel, cooking oil, lubricant, biodiesel, snack food, cosmetics, and fermentation process raw material. Exemplary products to be incorporated to the plant oil include animal feeds, human food products such as extruded snack foods, breads, as a food binding agent, aquaculture feeds, fermentable mixtures, food supplements, sport drinks, nutritional food bars, multi-vitamin supplements, diet drinks, and cereal foods.
• According to some embodiments of the invention, the oil comprises a seed oil.
• According to some embodiments of the invention, the oil comprises a vegetative portion oil (oil of the vegetative portion of the plant).
• According to some embodiments of the invention, the plant cell forms a part of a plant.
• According to another embodiment of the present invention, there is provided a food or feed comprising the plants or a portion thereof of the present invention.
• As used herein the term “about” refers to ±10%.
• The terms “comprises”, “comprising”, “includes”, “including”, “having” and their conjugates mean “including but not limited to”.
• The term “consisting of” means “including and limited to”.
• The term “consisting essentially of” means that the composition, method or structure may include additional ingredients, steps and/or parts, but only if the additional ingredients, steps and/or parts do not materially alter the basic and novel characteristics of the claimed composition, method or structure.
• As used herein, the singular form “a”, “an” and “the” include plural references unless the context clearly dictates otherwise. For example, the term “a compound” or “at least one compound” may include a plurality of compounds, including mixtures thereof.
• Throughout this application, various embodiments of this invention may be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 3, 4, 5, and 6. This applies regardless of the breadth of the range.
• Whenever a numerical range is indicated herein, it is meant to include any cited numeral (fractional or integral) within the indicated range. The phrases “ranging/ranges between” a first indicate number and a second indicate number and “ranging/ranges from” a first indicate number “to” a second indicate number are used herein interchangeably and are meant to include the first and second indicated numbers and all the fractional and integral numerals therebetween.
• As used herein the term “method” refers to manners, means, techniques and procedures for accomplishing a given task including, but not limited to, those manners, means, techniques and procedures either known to, or readily developed from known manners, means, techniques and procedures by practitioners of the chemical, pharmacological, biological, biochemical and medical arts.
• It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the invention, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable subcombination or as suitable in any other described embodiment of the invention. Certain features described in the context of various embodiments are not to be considered essential features of those embodiments, unless the embodiment is inoperative without those elements.
• Various embodiments and aspects of the present invention as delineated hereinabove and as claimed in the claims section below find experimental support in the following examples.
EXAMPLES
• Reference is now made to the following examples, which together with the above descriptions illustrate some embodiments of the invention in a non limiting fashion.
• Generally, the nomenclature used herein and the laboratory procedures utilized in the present invention include molecular, biochemical, microbiological and recombinant DNA techniques. Such techniques are thoroughly explained in the literature. See, for example, “Molecular Cloning: A laboratory Manual” Sambrook et al., (1989); “Current Protocols in Molecular Biology” Volumes I-III Ausubel, R. M., ed. (1994); Ausubel et al., “Current Protocols in Molecular Biology”. John Wiley and Sons, Baltimore, Md. (1989); Perbal, “A Practical Guide to Molecular Cloning”, John Wiley & Sons, New York (1988); Watson et al., “Recombinant DNA”, Scientific American Books, New York; Birren et al. (eds) “Genome Analysis: A Laboratory Manual Series”, Vols. 1-4, Cold Spring Harbor Laboratory Press, New York (1998): methodologies as set forth in U.S. Pat. Nos. 4,666,828; 4,683,202; 4,801,531; 5,192,659 and 5,272,057; “Cell Biology: A Laboratory Handbook”, Volumes I-III Cellis, J. E., ed. (1994): “Current Protocols in Immunology” Volumes I-III Coligan J. E., ed. (1994); Stites et al (eds), “Basic and Clinical Immunology” (8th Edition), Appleton & Lange, Norwalk. Conn. (1994); Mishell and Shiigi (eds), “Selected Methods in Cellular Immunology”, W. H. Freeman and Co., New York (1980); available immunoassays are extensively described in the patent and scientific literature, see, for example, U.S. Pat. Nos. 3,791,932; 3,839,153; 3,850,752; 3,850,578; 3,853,987; 3,867,517; 3,879,262; 3,901,654; 3,935,074; 3,984,533; 3,996,345; 4,034,074; 4,098,876; 4,879,219; 5,011,771 and 5,281,521: “Oligonucleotide Synthesis” Gait, M. J., ed. (1984); “Nucleic Acid Hybridization” Hames, B. D., and Higgins S. J., eds. (1985); “Transcription and Translation” Hames, B. D., and Higgins S. J., Eds. (1984); “Animal Cell Culture” Freshney, R. I., ed. (1986); “Immobilized Cells and Enzymes” IRL Press, (1986); “A Practical Guide to Molecular Cloning” Perbal, B., (1984) and “Methods in Enzymology” Vol. 1-317. Academic Press; “PCR Protocols: A Guide To Methods And Applications”, Academic Press, San Diego, Calif. (1990); Marshak et al., “Strategies for Protein Purification and Characterization—A Laboratory Course Manual” CSHL Press (1996); all of which are incorporated by reference as if fully set forth herein. Other general references are provided throughout this document. The procedures therein are believed to be well known in the art and are provided for the convenience of the reader. All the information contained therein is incorporated herein by reference.
• General Experimental and Bioinformatics Methods
• RNA extraction—Tissues growing at various growth conditions (as described below) were sampled and RNA was extracted using TRizol Reagent from Invitrogen [Hypertext Transfer Protocol://World Wide Web (dot) invitrogen (dot) com/content (dot)cfm?pageid=469]. Approximately 30-50 mg of tissue was taken from samples. The weighed tissues were ground using pestle and mortar in liquid nitrogen and resuspended in 500 μl of TRIzol Reagent. To the homogenized lysate, 100 μl of chloroform was added followed by precipitation using isopropanol and two washes with 75% ethanol. The RNA was eluted in 30 μl of RNase-free water. RNA samples were cleaned up using Qiagen's RNeasy minikit clean-up protocol as per the manufacturer's protocol (QIAGEN Inc. CA USA). For convenience, each micro-array expression information tissue type has received an expression Set ID.
• Correlation analysis—was performed for selected genes according to some embodiments of the invention, in which the characterized parameters (measured parameters according to the correlation IDs) were used as “x axis” for correlation with the tissue transcriptome which was used as the “Y axis”. For each gene and measured parameter a correlation coefficient “R” was calculated (using Pearson correlation) along with a p-value for the significance of the correlation. When the correlation coefficient (R) between the levels of a gene's expression in a certain tissue and a phenotypic performance across ecotypes/variety/hybrid is high in absolute value (between 0.5-1), there is an association between the gene (specifically the expression level of this gene) the phenotypic characteristic (e.g., improved nitrogen use efficiency, abiotic stress tolerance, yield, growth rate and the like).
Example 1 Identification of Genes and Predicted Role Using Bioinformatics Tools
• The present inventors have identified polynucleotides which can increase plant yield, seed yield, oil yield, oil content, biomass, growth rate, fiber yield and/or quality, abiotic stress tolerance, nitrogen use efficiency and/or vigor of a plant, as follows.
• The nucleotide sequence datasets used here were from publicly available databases or from sequences obtained using the Solexa technology (e.g. Barley and Sorghum). Sequence data from 100 different plant species was introduced into a single, comprehensive database. Other information on gene expression, protein annotation, enzymes and pathways were also incorporated. Major databases used include:
• Genomes
• Arabidopsis genome [TAIR genome version 8 (Hypertext Transfer Protocol://World Wide Web (dot) arabidopsis (dot) org/)]:
• Rice genome [build 6.0 (Hypertext Transfer Protocol://rice (dot) plantbiology(dot)msu(dot)edu/index(dot)shtml];
• Poplar [Populus trichocarpa release 1.1 from JGI (assembly release v1.0) (Hypertext Transfer Protocol://World Wide Web (dot) genome (dot) jgi-psf (dot) org/)];
• Brachypodium [JGI 4× assembly. Hypertext Transfer Protocol://World Wide Web (dot) brachypodium (dot) org)]:
• Soybean [DOE-JGI SCP, version Glymal (Hypertext Transfer Protocol://World Wide Web (dot) phytozome (dot) net/)]:
• Grape [French-Italian Public Consortium for Grapevine Genome Characterization grapevine genome (Hypertext Transfer Protocol://World Wide Web (dot) genoscope (dot) cns (dot) fr/)];
• Castobean ITIGR/J Craig Venter Institute 4× assembly [(Hypertext Transfer Protocol://msc (dot) jcvi (dot) org/r communis];
• Sorghum [DOE-JGI SCP, version Sbi1 [Hypertext Transfer Protocol://World Wide Web (dot) phytozome (dot) net/)]:
• Partially assembled genome of Maize [Hypertext Transfer Protocol://maizesequence (dot) org/];
• Expressed EST and mRNA Sequences were Extracted from the Following Databases:
• EST and RNA sequencesfrom NCBI (Hypertext Transfer Protocol://World Wide Web (dot) ncbi (dot) nlm (dot) nih (dot) gov/dbEST/);
• RefSeq (Hypertext Transfer Protocol://World Wide Web (dot) ncbi (dot) nlm (dot) nih (dot) gov/RefSeq/);
• TAIR (Hypertext Transfer Protocol://World Wide Web (dot) arabidopsis (dot) org/):
• Protein and Pathway Databases
• Uniprot [Hypertext Transfer Protocol://World Wide Web (dot) uniprot (dot) org/].
• AraCyc [Hypertext Transfer Protocol://World Wide Web (dot) arabidopsis (dot) org/biocyc/index (dot)jsp].
• ENZYME [Hypertext Transfer Protocol://expasy (dot) org/enzyme/].
• Microarray Datasets were Downloaded from:
• GEO (Hypertext Transfer Protocol://World Wide Web.ncbi.nlm.nih.gov/geo/) TAIR (Hypertext Transfer Protocol://World Wide Web.arabidopsis.org/).
• Proprietary microarray data (See WO2008/122980) and Examples 2-9 below.
• QTL and SNPs Information
• Gramene [Hypertext Transfer Protocol://World Wide Web (dot) gramene (dot) org/qtl/].
• Panzea [Hypertext Transfer Protocol://World Wide Web (dot) panzea (dot) org/index (dot) html].
• Database Assembly—was performed to build a wide, rich, reliable annotated and easy to analyze database comprised of publicly available genomic mRNA, ESTs DNA sequences, data from various crops as well as gene expression, protein annotation and pathway data QTLs, and other relevant information.
• Database assembly is comprised of a toolbox of gene refining, structuring, annotation and analysis tools enabling to construct a tailored database for each gene discovery project. Gene refining and structuring tools enable to reliably detect splice variants and antisense transcripts, generating understanding of various potential phenotypic outcomes of a single gene. The capabilities of the “LEADS” platform of Compugen LTD for analyzing human genome have been confirmed and accepted by the scientific community [see e.g., “Widespread Antisense Transcription”, Yelin, et al. (2003) Nature Biotechnology 21, 379-85; “Splicing of Alu Sequences”, Lev-Maor, et al. (2003) Science 300 (5623), 1288-91: “Computational analysis of alternative splicing using EST tissue information”, Xie H et al. Genomics 2002], and have been proven most efficient in plant genomics as well.
• EST clustering and gene assembly—For gene clustering and assembly of organisms with available genome sequence data (Arabidopsis, rice, castorbean, grape, brachypodium, poplar, soybean, sorghum) the genomic LEADS version (GANG) was employed. This tool allows most accurate clustering of ESTs and mRNA sequences on genome, and predicts gene structure as well as alternative splicing events and anti-sense transcription.
• For organisms with no available full genome sequence data, “expressed LEADS” clustering software was applied.
• Gene annotation—Predicted genes and proteins were annotated as follows: Blast search [Hypertext Transfer Protocol://blast (dot) ncbi (dot) nlm (dot) nih (dot) gov/Blast (dot) cgi] against all plant UniProt [Hypertext Transfer Protocol://World Wide Web (dot) uniprot (dot) org/] sequences was performed. Open reading frames of each putative transcript were analyzed and longest ORF with higher number of homologues was selected as predicted protein of the transcript. The predicted proteins were analyzed by InterPro [Hypertext Transfer Protocol://World Wide Web (dot) ebi (dot) ac (dot) uk/interpro/].
• Blast against proteins from AraCyc and ENZYME databases was used to map the predicted transcripts to AraCyc pathways.
• Predicted proteins from different species were compared using blast algorithm [Hypertext Transfer Protocol://World Wide Web (dot) ncbi (dot) nlm (dot) nih (dot) gov/Blast (dot) cgi] to validate the accuracy of the predicted protein sequence, and for efficient detection of orthologs.
• Gene expression prfiling—Several data sources were exploited for gene expression profiling which combined microarray data and digital expression profile (see below). According to gene expression profile, a correlation analysis was performed to identify genes which are co-regulated under different developmental stages and environmental conditions and which are associated with different phenotypes.
• Publicly available microarray datasets were downloaded from TAIR and NCBI GEO sites, renormalized, and integrated into the database. Expression profiling is one of the most important resource data for identifying genes important for yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance of plants and nitrogen use efficiency.
• A digital expression profile summary was compiled for each cluster according to all keywords included in the sequence records comprising the cluster. Digital expression, also known as electronic Northern Blot, is a tool that displays virtual expression profile based on the EST sequences forming the gene cluster. The tool provides the expression profile of a cluster in terms of plant anatomy (e.g., the tissue/organ in which the gene is expressed), developmental stage (e.g., the developmental stages at which a gene can be found/expressed) and profile of treatment (provides the physiological conditions under which a gene is expressed such as drought, cold, pathogen infection, etc). Given a random distribution of ESTs in the different clusters, the digital expression provides a probability value that describes the probability of a cluster having a total of N ESTs to contain X ESTs from a certain collection of libraries. For the probability calculations, the following is taken into consideration: a) the number of ESTs in the cluster, b) the number of ESTs of the implicated and related libraries, c) the overall number of ESTs available representing the species. Thereby clusters with low probability values are highly enriched with ESTs from the group of libraries of interest indicating a specialized expression.
• Recently, the accuracy of this system was demonstrated by Portnoy et al., 2009 (Analysis Of The Melon Fruit Transcriptome Based On 454 Pyrosequencing) in: Plant & Animal Genomes XVII Conference, San Diego, Calif. Transcriptomic analysis, based on relative EST abundance in data was performed by 454 pyrosequencing of cDNA representing mRNA of the melon fruit. Fourteen double strand cDNA samples obtained from two genotypes, two fruit tissues (flesh and rind) and four developmental stages were sequenced. GS FLX pyrosequencing (Roche/454 Life Sciences) of non-normalized and purified cDNA samples yielded 1,150,657 expressed sequence tags that assembled into 67,477 unigenes (32,357 singletons and 35,120 contigs). Analysis of the data obtained against the Cucurbit Genomics Database [Hypertext Transfer Protocol://World Wide Web (dot) icugi (dot) org/] confirmed the accuracy of the sequencing and assembly. Expression patterns of selected genes fitted well their qRT-PCR data.
Example 2 Production of Arabidopsis Transcriptome and High Throughput Correlation Analysis of Yield, Biomass and/or Vigor Related Parameters Using 44K Arabidopsis Full Genome Oligonucleotide Micro-Array
• To produce a high throughput correlation analysis, the present inventors utilized an Arabidopsis thaliana oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?lPage=50879]. The array oligonucleotide represents about 40,000 A. thaliana genes and transcripts designed based on data from the TIGR ATH1 v.5 database and Arabidopsis MPSS (University of Delaware) databases. To define correlations between the levels of RNA expression and yield, biomass components or vigor related parameters, various plant characteristics of 15 different Arabidopsis ecotypes were analyzed. Among them, nine ecotypes encompassing the observed variance were selected for RNA expression analysis. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test [Hypertext Transfer Protocol://World Wide Web (dot) davidmlane (dot) com/hyperstat/A34739 (dot) html].
• Experimental Procedures
• Analyzed Arabidopsis tissues—Five tissues at different developmental stages including root, leaf, flower at anthesis, seed at 5 days after flowering (DAF) and seed at 12 DAF, representing different plant characteristics, were sampled and RNA was extracted as described hereinabove under “GENERAL EXPERIMENTAL AND BIOINFORMATICS METHODS”. For convenience, each micro-array expression information tissue type has received a Set ID as summarized in Table 1 below.

• TABLE 1
  Tissues used for Arabidopsis transcriptome expression sets

  	Expression Set	Set ID

  	Leaf	1
  	Root	2
  	Seed 5DAF	3
  	Flower at anthesis	4
  	Seed 12DAF	5
  	Table 1: Provided are the identification (ID) digits of each of the Arabidopsis expression sets (1-5). DAF = days after flowering.

• Yield components and vigor related parameters assessment—Eight out of the nine Arabidopsis ecotypes were used in each of 5 repetitive blocks (named A, B, C, D and E), each containing 20 plants per plot. The plants were grown in a greenhouse at controlled conditions in 22° C., and the N:P:K fertilizer (20:20:20; weight ratios) [nitrogen (N), phosphorus (P) and potassium (K)] was added. During this time data was collected, documented and analyzed. Additional data was collected through the seedling stage of plants grown in a tissue culture in vertical grown transparent agar plates. Most of chosen parameters were analyzed by digital imaging.
• Digital imaging in Tissue culture—A laboratory image acquisition system was used for capturing images of plantlets sawn in square agar plates. The image acquisition system consists of a digital reflex camera (Canon EOS 300D) attached to a 55 mm focal length lens (Canon EF-S series), mounted on a reproduction device (Kaiser RS), which included 4 light units (4×150 Watts light bulb) and located in a darkroom.
• Digital Imaging in Greenhouse—The image capturing process was repeated every 3-4 days starting at day 7 till day 30. The same camera attached to a 24 mm focal length lens (Canon EF series), placed in a custom made iron mount, was used for capturing images of larger plants sawn in white tubs in an environmental controlled greenhouse. The white tubs were square shape with measurements of 36×26.2 cm and 7.5 cm deep. During the capture process, the tubs were placed beneath the iron mount, while avoiding direct sun light and casting of shadows. This process was repeated every 3-4 days for up to 30 days.
• An image analysis system was used, which consists of a personal desktop computer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ 1.37, Java based image processing program, which was developed at the U.S National Institutes of Health and is freely available on the internet at Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/. Images were captured in resolution of 6 Mega Pixels (3072×2048 pixels) and stored in a low compression JPEG (Joint Photographic Experts Group standard) format. Next, analyzed data was saved to text files and processed using the JMP statistical analysis software (SAS institute).
• Leaf analysis—Using the digital analysis leaves data was calculated, including leaf number, area, perimeter, length and width. On day 30, 3-4 representative plants were chosen from each plot of blocks A, B and C. The plants were dissected, each leaf was separated and was introduced between two glass trays, a photo of each plant was taken and the various parameters (such as leaf total area, laminar length etc.) were calculated from the images. The blade circularity was calculated as laminar width divided by laminar length.
• Root analysis—During 17 days, the different ecotypes were grown in transparent agar plates. The plates were photographed every 3 days starting at day 7 in the photography room and the roots development was documented (see examples in FIGS. 3A-3F). The growth rate of roots was calculated according to Formula V.
• 
  Growth rate of root coverage=Regression coefficient of root coverage along time course.  Formula V:
• Vegetative growtk rate analysis—was calculated according to Formula VI. The analysis was ended with the appearance of overlapping plants.
• 
  Vegetative growth rate area=Regression coefficient of vegetative area along time course.  Formula VI
• For comparison between ecotypes the calculated rate was normalized using plant developmental stage as represented by the number of true leaves. In cases where plants with 8 leaves had been sampled twice (for example at day 10 and day 13), only the largest sample was chosen and added to the Anova comparison.
• Seeds in siliques analysis—On day 70, 15-17 siliques were collected from each plot in blocks D and E. The chosen siliques were light brown color but still intact. The siliques were opened in the photography room and the seeds were scatter on a glass tray, a high resolution digital picture was taken for each plot. Using the images the number of seeds per silique was determined.
• Seeds average weight—At the end of the experiment all seeds from plots of blocks A-C were collected. An average weight of 0.02 grams was measured from each sample, the seeds were scattered on a glass tray and a picture was taken. Using the digital analysis, the number of seeds in each sample was calculated.
• Olpercentage in seeds—At the end of the experiment all seeds from plots of blocks A-C were collected. Columbia seeds from 3 plots were mixed grounded and then mounted onto the extraction chamber. 210 ml of n-Hexane (Cat No. 080951 Biolab Ltd.) were used as the solvent. The extraction was performed for 30 hours at medium heat 50° C. Once the extraction has ended the n-Hexane was evaporated using the evaporator at 35° C. and vacuum conditions. The process was repeated twice. The information gained from the Soxhlet extractor (Soxhlet, F. Die gewichtsanalytische Bestimmung des Milchfettes, Polytechnisches J. (Dingler's) 1879, 232, 461) was used to create a calibration curve for the Low Resonance NMR. The content of oil of all seed samples was determined using the Low Resonance NMR (MARAN Ultra-Oxford Instrument) and its MultiQuant sowftware package.
• Silique length analysis—On day 50 from sowing, 30 siliques from different plants in each plot were sampled in block A. The chosen siliques were green-yellow in color and were collected from the bottom parts of a grown plant's stem. A digital photograph was taken to determine silique's length.
• Dry weight and seed yield—On day 80 from sowing, the plants from blocks A-C were harvested and left to dry at 30° C. in a drying chamber. The biomass and seed weight of each plot was separated, measured and divided by the number of plants. Dry weight=total weight of the vegetative portion above ground (excluding roots) after drying at 30° C. in a drying chamber; Seed yield per plant=total seed weight per plant (gr).
• Oil yield—The oil yield was calculated using Formula VII.
• 
  Seed Oil yield=Seed yield per plant (gr.)*Oil % in seed.  Formula VII:
• Harvest Inder (seed)—The harvest index was calculated using Formula IV (described above): Harvest Index=Average seed yield per plant/Average dry weight.
• Experimental Results
• Nine different Arabidopsis ecotypes were grown and characterized for 18 parameters (named as vectors).

• TABLE 2
  Arabidopsis correlated parameters (vectors)

  	Correlated parameter with	Correlation ID

  	Seeds per silique (number)	1
  	Harvest Index (value)	2
  	seed yield per plant (gr)	3
  	Dry matter per plant (gr)	4
  	Total Leaf Area per plant (cm2)	5
  	Oil % per seed (percent)	6
  	Oil yield per plant (mg)	7
  	relative root growth (cm/day)	8
  	root length day 7 (cm)	9
  	root length day 13 (cm)	10
  	fresh weight (gr)	11
  	seed weight (gr)	12
  	Vegetative growth rate (cm2/day)	13
  	Lamina length (cm)	14
  	Lamina width(cm)	15
  	Leaf width/length (ratio)	16
  	Blade circularity	17
  	Silique length (cm)	18
  	Table 2. Provided are the Arabidopsis correlated parameters (correlation ID Nos. 1-18). Abbreviations: Cm = centimeter(s); gr = gram(s); mg = milligram(s).

• The characterized values are summarized in Table 3 below.

• TABLE 3
  Measured parameters in Arabidopsis ecotypes

  Trait	Line-1	Line-2	Line-3	Line-4	Line-5	Line-6	Line-7	Line-8	Line-9

  1	45.44	53.47	58.47	35.27	48.56	37.00	39.38	40.53	25.53
  2	0.53	0.35	0.56	0.33	0.37	0.32	0.45	0.51	0.41
  3	0.34	0.44	0.59	0.42	0.61	0.43	0.36	0.62	0.55
  4	0.64	1.27	1.05	1.28	1.69	1.34	0.81	1.21	1.35
  5	46.86	109.89	58.36	56.80	114.66	110.82	88.49	121.79	93.04
  6	34.42	31.19	38.05	27.76	35.49	32.91	31.56	30.79	34.02
  7	118.63	138.73	224.06	116.26	218.27	142.11	114.15	190.06	187.62
  8	0.63	0.66	1.18	1.09	0.91	0.77	0.61	0.70	0.78
  9	0.94	1.76	0.70	0.73	0.99	1.16	1.28	1.41	1.25
  10	4.42	8.53	5.62	4.83	5.96	6.37	5.65	7.06	7.04
  11	1.51	3.61	1.94	2.08	3.56	4.34	3.47	3.48	3.71
  12	0.02	0.02	0.03	0.03	0.02	0.03	0.02	0.02	0.02
  13	0.31	0.38	0.48	0.47	0.43	0.64	0.43	0.38	0.47
  14	2.77	3.54	3.27	3.78	3.69	4.60	3.88	3.72	4.15
  15	1.38	1.70	1.46	1.37	1.83	1.65	1.51	1.82	1.67
  16	0.35	0.29	0.32	0.26	0.36	0.27	0.30	0.34	0.31
  17	0.51	0.48	0.45	0.37	0.50	0.38	0.39	0.49	0.41
  18	1.06	1.26	1.31	1.47	1.24	1.09	1.18	1.18	1.00
  Table 3. Provided are the values of each of the parameters measured in Arabidopsis ecotypes: 3 = Seed yield per plant (gram); 7 = oil yield per plant (mg); 6 = oil % per seed; 12 = 1000 seed weight (gr); 4 = dry matter per plant (gr); 2 = harvest index; 5 = total leaf area per plant (cm); 1 = seeds per silique; 18 = Silique length (cm); 13 = Vegetative growth rate (cm2/day) until 8 true leaves; 8 = relative root growth (cm/day) (day 13); 9 = Root length day 7 (cm); 10 = Root length day 13 (cm); 11 = fresh weight per plant (gr.) at bolting stage; 14. = Lamina length (cm); 15 = Lamina width (cm); 16 = Leaf width/length; 17 = Blade circularity.

• TABLE 4
  Correlation between the expression level of selected genes of some
  embodiments of the invention in various tissues and the phenotypic performance
  under normal conditions across Arabidopsis accessions

  			Set	Corr.				Set	Corr.
  Gene Name	R	P value	ID	Set ID	Gene Name	R	P value	ID	Set ID

  LYD521	0.85	1.65E−02	2	3	LYD521	0.81	2.73E−02	2	6
  LYD521	0.89	6.63E−03	2	7	LYD521	0.84	1.88E−02	2	8
  LYD522	0.76	2.72E−02	5	5	LYD522	0.75	3.22E−02	5	14
  LYD522	0.83	1.02E−02	5	11	LYD522	0.71	5.02E−02	5	13
  LYD524	0.70	5.28E−02	3	3	LYD525	0.84	8.98E−03	1	18
  LYD525	0.86	6.06E−03	5	2	LYD526	0.72	4.42E−02	3	3
  LYD526	0.76	2.90E−02	3	8	LYD526	0.71	5.06E−02	5	3
  LYD526	0.74	3.61E−02	5	7	LYD526	0.75	3.09E−02	5	8
  LYD527	0.75	5.37E−02	2	16	LYD527	0.73	3.81E−02	5	1
  LYD527	0.72	4.43E−02	5	8	LYD528	0.70	7.84E−02	2	15
  LYD528	0.76	4.65E−02	2	5	LYD529	0.80	1.69E−02	1	16
  LYD529	0.76	4.77E−02	2	2	LYD529	0.77	2.48E−02	3	15
  LYD529	0.71	4.92E−02	3	5	LYD529	0.78	2.21E−02	3	3
  LYD529	0.71	5.06E−02	5	2	LYD529	0.74	3.74E−02	4	2
  LYD530	0.71	4.99E−02	1	10	LYD530	0.72	6.54E−02	2	1
  LYD530	0.78	3.97E−02	2	18	LYD530	0.84	1.92E−02	2	8
  LYD530	0.75	3.35E−02	3	1	LYD530	0.73	3.78E−02	5	1
  LYD530	0.88	3.71E−03	4	1	LYD531	0.70	7.71E−02	2	9
  LYD531	0.72	4.55E−02	5	6	LYD531	0.70	5.19E−02	5	7
  LYD533	0.77	4.43E−02	2	17	LYD533	0.73	4.13E−02	5	15
  LYD533	0.74	3.63E−02	4	1	LYD533	0.80	1.66E−02	4	17
  LYD534	0.78	2.38E−02	1	10	LYD534	0.87	1.01E−02	2	3
  LYD534	0.85	1.47E−02	2	7	LYD534	0.70	7.86E−02	2	8
  LYD534	0.74	3.65E−02	3	15	LYD534	0.77	2.53E−02	3	3
  LYD534	0.74	3.49E−02	3	7	LYD534	0.74	3.65E−02	5	18
  LYD534	0.71	4.97E−02	5	8	LYD535	0.82	1.33E−02	1	1
  LYD535	0.85	7.25E−03	3	8	LYD535	0.89	3.39E−03	5	14
  LYD535	0.72	4.50E−02	5	13	LYD536	0.74	3.58E−02	3	6
  LYD536	0.74	3.70E−02	5	8	LYD536	0.85	7.90E−03	4	8
  Table 4. Provided are the correlations (R) between the expression levels of yield improving genes and their homologues in tissues [leaf, flower, seed and root; Expression sets (Exp)] and the phenotypic performance in various yield, biomass, growth rate and/or vigor components [Correlation vector (corr.)] under stress conditions or normal conditions across Arabidopsis accessions. P = p value.

Example 3 Production of Arabidopsis Transcriptome and High Throughput Correlation Analysis of Normal and Nitrogen Limiting Conditions Using 44K Arabidopsis Oligonucleotide Micro-Array
• In order to produce a high throughput correlation analysis, the present inventors utilized an Arabidopsis oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem (dot) agilent (dot) com/Scripts/PDS (dot) asp?lPage=50879]. The array oligonucleotide represents about 44,000 Arabidopsis genes and transcripts. To define correlations between the levels of RNA expression with NUE, yield components or vigor related parameters various plant characteristics of 14 different Arabidopsis ecotypes were analyzed. Among them, ten ecotypes encompassing the observed variance were selected for RNA expression analysis. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test [Hypertext Transfer Protocol://World Wide Web (dot) davidmlane (dot) com/hyperstat/A34739 (dot) html].
• Experimental Procedures
• Two tissues of plants [leaves and stems] growing at two different nitrogen fertilization levels (1.5 mM Nitrogen or 6 mM Nitrogen) were sampled and RNA was extracted as described hereinabove under “GENERAL EXPERIMENTAL AND BIOINFORMATICS METHODS”. For convenience, each micro-array expression information tissue type has received a Set ID as summarized in Table 5 below.

• TABLE 5
  Tissues used for Arabidopsis transcriptome expression sets

  	Expression Set	Set ID

  	Leaves at 1.5 mM Nitrogen fertilization	1
  	Stems at 6 mM Nitrogen fertilization	2
  	Leaves at 6 mM Nitrogen fertilization	3
  	Stems at 1.5 mM Nitrogen fertilization	4
  	Table 5: Provided are the identification (ID) digits of each of the Arabidopsis expression sets.

• Assessment of Arabidopsis yield components and vigor related parameters under different nitrogen fertilization levels—10 Arabidopsis accessions in 2 repetitive plots each containing 8 plants per plot were grown at greenhouse. The growing protocol used was as follows: surface sterilized seeds were sown in Eppendorf tubes containing 0.5× Murashige-Skoog basal salt medium and grown at 23° C. under 12-hour light and 12-hour dark daily cycles for 10 days. Then, seedlings of similar size were carefully transferred to pots filled with a mix of perlite and peat in a 1:1 ratio. Constant nitrogen limiting conditions were achieved by irrigating the plants with a solution containing 1.5 mM inorganic nitrogen in the form of KNO₃, supplemented with 2 mM CaCl₂), 1.25 mM KH₂PO₄, 1.50 mM MgSO₄, 5 mM KCl, 0.01 mM H₃BO₃ and microelements, while normal irrigation conditions (Normal Nitrogen conditions) was achieved by applying a solution of 6 mM inorganic nitrogen also in the form of KNO₃, supplemented with 2 mM CaCl₂), 1.25 mM KH₂PO₄, 1.50 mM MgSO₄, 0.01 mM H₃BO₃ and microelements. To follow plant growth, trays were photographed the day nitrogen limiting conditions were initiated and subsequently every 3 days for about 15 additional days. Rosette plant area was then determined from the digital pictures. ImageJ software was used for quantifying the plant size from the digital pictures [Hypertext Transfer Protocol://rsb (dot) info (dot) nih (dot) gov/ij/] utilizing proprietary scripts designed to analyze the size of rosette area from individual plants as a function of time. The image analysis system included a personal desktop computer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ 1.37 (Java based image processing program, which was developed at the U.S. National Institutes of Health and freely available on the internet [Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/]. Next, analyzed data was saved to text files and processed using the JMP statistical analysis software (SAS institute).
• Data parameters collected are summarized in Table 6, herein below.

• TABLE 6
  Arabidopsis correlated parameters (vectors)

  Correlated parameter with	Correlation ID

  N 6 mM; Seed Yield [gr./plant]	1
  N 6 mM; Harvest Index	2
  N 6 mM; 1000 Seeds weight [gr.]	3
  N 6 mM; seed yield/rosette area day at day 10 [gr./cm2]	4
  N 6 mM; seed yield/leaf blade area [gr./cm2]	5
  N 1.5 mM; Rosette Area at day 8 [cm2]	6
  N 1.5 mM; Rosette Area at day 10 [cm2]	7
  N 1.5 mM; Leaf Number at day 10	8
  N 1.5 mM; Leaf Blade Area at day 10 [cm2]	9
  N 1.5 mM; RGR of Rosette Area at day 3 [cm2/day]	10
  N 1.5 mM; t50 Flowering [day]	11
  N 1.5 mM; Dry Weight [gr./plant]	12
  N 1.5 mM; Seed Yield [gr./plant]	13
  N 1.5 mM; Harvest Index	14
  N 1.5 mM; 1000 Seeds weight [gr.]	15
  N 1.5 mM; seed yield/rosette area at day 10 [gr./cm2]	16
  N 1.5 mM; seed yield/leaf blade area [gr./cm2]	17
  N 1.5 mM; % Seed yield reduction compared to N 6 mM	18
  N 1.5 mM; % Biomass reduction compared to N 6 mM	19
  N 6 mM; Rosette Area at day 8 [cm2]	20
  N 6 mM; Rosette Area at day 10 [cm2]	21
  N 6 mM; Leaf Number at day 10	22
  N 6 mM; Leaf Blade Area at day 10	23
  N 6 mM; RGR of Rosette Area at day 3 [cm2/gr.]	24
  N 6 mM; t50 Flowering [day]	25
  N 6 mM; Dry Weight [gr./plant]	26
  N 6 mM; N level/DW (SPAD unit/gr. plant)	27
  N 6 mM; DW/N level [gr./SPAD unit]	28
  N 6 mM; N level/FW	29
  N 6 mM; Seed yield/N unit [gr./SPAD unit]	30
  N 1.5 mM; N level/FW [SPAD unit/gr.]	31
  N 1.5 mM; N level/DW [SPAD unit/gr.]	32
  N 1.5 mM; DW/N level [gr/SPAD unit]	33
  N 1.5 mM; seed yield/N level [gr/SPAD unit]	34
  Table 6. Provided are the Arabidopsis correlated parameters (vectors). “N” = Nitrogen at the noted concentrations; “gr.” = grams; “SPAD” = chlorophyll levels; “t50” = time where 50% of plants flowered; “gr./SPAD unit” = plant biomass expressed in grams per unit of nitrogen in plant measured by SPAD. “DW” = Plant Dry Weight; “FW” = Plant Fresh weight; “N level/DW” = plant Nitrogen level measured in SPAD unit per plant biomass [gr.]; “DW/N level” = plant biomass per plant [gr.]/SPAD unit; Rosette Area (measured using digital analysis); Plot Coverage at the indicated day [%](calculated by the dividing the total plant area with the total plot area); Leaf Blade Area at the indicated day [cm2] (measured using digital analysis); RGR (relative growth rate) of Rosette Area at the indicated day [cm2/day]; t50 Flowering [day[ (the day in which 50% of plant flower); seed yield/rosette area at day 10 [gr/cm2] (calculated); seed yield/leaf blade [gr/cm2] (calculated); seed yield/N level [gr/SPAD unit] (calculated).

• Assessment of NUE, yield components and vigor-related parameters—Ten Arabidopsis ecotypes were grown in trays, each containing 8 plants per plot, in a greenhouse with controlled temperature conditions for about 12 weeks. Plants were irrigated with different nitrogen concentration as described above depending on the treatment applied. During this time, data was collected documented and analyzed. Most of chosen parameters were analyzed by digital imaging.
• Digital Imaging—Greenhouse Assay
• An image acquisition system, which consists of a digital reflex camera (Canon EOS 400D) attached with a 55 mm focal length lens (Canon EF-S series) placed in a custom made Aluminum mount, was used for capturing images of plants planted in containers within an environmental controlled greenhouse. The image capturing process is repeated every 2-3 days starting at day 9-12 till day 16-19 (respectively) from transplanting.
• The image processing system which was used is described in Example 4 above. Images were captured in resolution of 10 Mega Pixels (3888×2592 pixels) and stored in a low compression JPEG (Joint Photographic Experts Group standard) format. Next, image processing output data was saved to text files and analyzed using the JMP statistical analysis software (SAS institute).
• Leaf analysis—Using the digital analysis leaves data was calculated, including leaf number, leaf blade area, plot coverage, Rosette diameter and Rosette area.
• Relative growth rate area: The relative growth rate area of the rosette and the leaves was calculated according to Formulas VIII and IX, respectively.
• 
  Growth rate of rosette area=Regression coefficient of rosette area along time course.  Formula VIII:
• 
  Growth rate of plant leaf number=Regression coefficient of plant leaf number along time course.  Formula IX
• Seed yield and 1000 seeds weight—At the end of the experiment all seeds from all plots were collected and weighed in order to measure seed yield per plant in terms of total seed weight per plant (gr.). For the calculation of 1000 seed weight, an average weight of 0.02 grams was measured from each sample, the seeds were scattered on a glass tray and a picture was taken. Using the digital analysis, the number of seeds in each sample was calculated.
• Dry weight and seed yield—At the end of the experiment, plant were harvested and left to dry at 30° C. in a drying chamber. The biomass was separated from the seeds, weighed and divided by the number of plants. Dry weight=total weight of the vegetative portion above ground (excluding roots) after drying at 30° C. in a drying chamber.
• Harvest Index (seed)—The harvest index was calculated using Formula IV as described above [Harvest Index=Average seed yield per plant/Average dry weight].
• T₅₀ days to flowering—Each of the repeats was monitored for flowering date. Days of flowering was calculated from sowing date till 50% of the plots flowered.
• Plant nitrogen level—The chlorophyll content of leaves is a good indicator of the nitrogen plant status since the degree of leaf greenness is highly correlated to this parameter.
• Chlorophyll content was determined using a Minolta SPAD 502 chlorophyll meter and measurement was performed at time of flowering. SPAD meter readings were done on young fully developed leaf. Three measurements per leaf were taken per plot. Based on this measurement, parameters such as the ratio between seed yield per nitrogen unit [seed yield/N level=seed yield per plant [gr.]/SPAD unit], plant DW per nitrogen unit [DW/N level=plant biomass per plant [gr.]/SPAD unit], and nitrogen level per gram of biomass [N level/DW=SPAD unit/plant biomass per plant (gr.)] were calculated.
• Percent of seed yield reduction—measures the amount of seeds obtained in plants when grown under nitrogen-limiting conditions compared to seed yield produced at normal nitrogen levels expressed in percentages M %.
• Experimental Results
• 10 different Arabidopsis accessions (ecotypes) were grown and characterized for 37 parameters as described above. The average for each of the measured parameters was calculated using the JMP software (Table 7 below). Subsequent correlation analysis between the various transcriptome sets (Table 5) and the average parameters were conducted.

• TABLE 7
  Measured parameters in Arabidopsis accessions

  Ecotype

  Treatment	Line-1	Line-2	Line-3	Line-4	Line-5	Line-6	Line-7	Line-8	Line-9	Line-10

  1	0.12	0.17	0.11	0.08	0.12	0.14	0.11	0.14	0.09	0.07
  2	0.28	0.31	0.28	0.16	0.21	0.28	0.17	0.21	0.17	0.14
  3	0.01	0.02	0.02	0.01	0.02	0.02	0.01	0.02	0.02	0.02
  4	0.08	0.11	0.04	0.03	0.06	0.06	0.06	0.05	0.06	0.03
  5	0.34	0.53	0.21	0.18	0.28	0.28	0.25	0.27	0.24	0.16
  6	0.76	0.71	1.06	1.16	1.00	0.91	0.94	1.12	0.64	1.00
  7	1.43	1.33	1.77	1.97	1.83	1.82	1.64	2.00	1.15	1.75
  8	6.88	7.31	7.31	7.88	7.75	7.63	7.19	8.63	5.93	7.94
  9	0.33	0.27	0.37	0.39	0.37	0.39	0.35	0.38	0.31	0.37
  10	0.63	0.79	0.50	0.49	0.72	0.83	0.65	0.67	0.64	0.61
  11	15.97	20.97	14.84	24.71	23.70	18.06	19.49	23.57	21.89	23.57
  12	0.16	0.12	0.08	0.11	0.12	0.13	0.11	0.15	0.17	0.18
  13	0.03	0.03	0.02	0.01	0.01	0.03	0.02	0.01	0.01	0.01
  14	0.19	0.20	0.29	0.08	0.07	0.24	0.18	0.08	0.08	0.03
  15	0.02	0.02	0.02	0.01	0.02	0.01	0.01	0.02	0.02	0.02
  16	0.02	0.02	0.01	0.01	0.00	0.02	0.01	0.01	0.01	0.00
  17	0.09	0.09	0.06	0.03	0.02	0.08	0.06	0.03	0.04	0.01
  18	72.56	84.70	78.78	88.00	92.62	76.71	81.94	91.30	85.76	91.82
  19	60.75	76.71	78.56	78.14	78.64	73.19	83.07	77.19	70.12	62.97
  20	0.76	0.86	1.48	1.28	1.10	1.24	1.09	1.41	0.89	1.22
  21	1.41	1.57	2.67	2.42	2.14	2.47	1.97	2.72	1.64	2.21
  22	6.25	7.31	8.06	8.75	8.75	8.38	7.13	9.44	6.31	8.06
  23	0.34	0.31	0.52	0.45	0.43	0.50	0.43	0.51	0.41	0.43
  24	0.69	1.02	0.61	0.60	0.65	0.68	0.58	0.61	0.52	0.48
  25	16.37	20.50	14.63	24.00	23.60	15.03	19.75	22.89	18.80	23.38
  26	0.42	0.53	0.38	0.52	0.58	0.50	0.63	0.65	0.57	0.50
  27	22.49			28.27		33.32			39.00	17.64
  28	0.02			0.02		0.02			0.01	0.03
  29	53.71			54.62		66.48			68.05	35.55
  30	0.00			0.00		0.01			0.00	0.00
  31	45.59			42.11		53.11			67.00	28.15
  32	167.30			241.06		194.98			169.34	157.82
  33	0.01			0.00		0.01			0.01	0.01
  34	0.00			0.00		0.00			0.00	0.00
  Table 7. Provided are the measured parameters under various treatments in various ecotypes (Arabidopsis accessions).

• TABLE 8
  Correlation between the expression level of selected genes of some embodiments
  of the invention in various tissues and the phenotypic performance under normal
  or abiotic stress conditions across Arabidopsis accessions

  			Exp.	Corr.				Exp.	Corr.
  Gene Name	R	P value	set	Set ID	Gene Name	R	P value	set	Set ID

  LYD522	0.72	2.88E−02	2	22	LYD522	0.77	1.50E−02	2	21
  LYD522	0.74	2.24E−02	2	7	LYD522	0.70	3.46E−02	2	23
  LYD522	0.77	8.54E−03	3	1	LYD524	0.77	9.08E−03	1	2
  LYD524	0.74	2.21E−02	2	2	LYD524	0.87	1.19E−03	4	2
  LYD524	0.85	2.01E−03	4	1	LYD525	0.80	5.42E−03	1	22
  LYD525	0.73	1.60E−02	1	20	LYD525	0.85	1.68E−03	1	6
  LYD525	0.75	1.28E−02	1	21	LYD525	0.83	3.18E−03	1	7
  LYD525	0.70	3.49E−02	2	3	LYD526	0.75	1.28E−02	1	20
  LYD526	0.73	1.70E−02	1	9	LYD526	0.73	1.58E−02	1	23
  LYD527	0.71	2.24E−02	1	2	LYD527	0.78	8.40E−03	1	14
  LYD527	0.72	1.87E−02	4	14	LYD529	0.72	2.00E−02	3	19
  LYD531	0.72	1.84E−02	1	11	LYD531	0.76	1.16E−02	1	25
  LYD531	0.86	1.51E−03	1	18	LYD533	0.77	8.61E−03	1	11
  LYD533	0.88	8.25E−04	1	25	LYD533	0.80	5.35E−03	1	18
  LYD535	0.72	1.93E−02	3	8	LYD536	0.74	1.46E−02	1	2
  LYD536	0.73	1.75E−02	1	16	LYD536	0.88	7.61E−04	1	4
  LYD536	0.76	1.04E−02	1	17	LYD536	0.86	1.36E−03	1	5
  LYD536	0.82	4.02E−03	1	24
  Table 8. Provided are the correlations (R) between the expression levels of yield improving genes and their homologues in tissues [Leaves or stems; Expression sets (Exp)] and the phenotypic performance in various yield, biomass, growth rate and/or vigor components [Correlation vector (corr.)] under stress conditions or normal conditions across Arabidopsis accessions. P = p value.

Example 4 Production of Tomato Transcriptome and High Throughput Correlation Analysis Using 44K Tomato Oligonucleotide Micro-Array
• In order to produce a high throughput correlation analysis between NUE related phenotypes and gene expression, the present inventors utilized a Tomato oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?lPage=50879]. The array oligonucleotide represents about 44,000 Tomato genes and transcripts. In order to define correlations between the levels of RNA expression with NUE, ABST, yield components or vigor related parameters various plant characteristics of 18 different Tomato varieties were analyzed. Among them, 10 varieties encompassing the observed variance were selected for RNA expression analysis. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test [Hypertext Transfer Protocol://World Wide Web (dot) davidmlane (dot) com/hyperstat/A34739 (dot) html].
• Correlation of Tomato Varieties Across Ecotypes Grown Under Low Nitrogen, Drought and Regular Growth Conditions
• Experimental Procedures:
• 10 Tomato varieties were grown in 3 repetitive blocks, each containing 6 plants per plot were grown at net house. Briefly, the growing protocol was as follows:
• 1. Regular growth conditions: Tomato varieties were grown under normal conditions (4-6 Liters/m² of water per day and fertilized with NPK as recommended in protocols for commercial tomato production).
• 2. Low Nitrogen fertilization conditions: Tomato varieties were grown under normal conditions (4-6 Liters/m² per day and fertilized with NPK as recommended in protocols for commercial tomato production) until flower stage. At this time, Nitrogen fertilization was stopped.
• 3. Drought stress: Tomato variety was grown under normal conditions (4-6 Liters/m² per day) until flower stage. At this time, irrigation was reduced to 50% compared to normal conditions. Plants were phenotyped on a daily basis following the standard descriptor of tomato (Table 10). Harvest was conducted while 50% of the fruits were red (mature). Plants were separated to the vegetative part and fruits, of them, 2 nodes were analyzed for additional inflorescent parameters such as size, number of flowers, and inflorescent weight. Fresh weight of all vegetative material was measured. Fruits were separated to colors (red vs. green) and in accordance with the fruit size (small, medium and large). Next, analyzed data was saved to text files and processed using the JMP statistical analysis software (SAS institute). Data parameters collected are summarized in Tables 11-13, herein below.
• Analyzed Tomato tissues—Two tissues at different developmental stages [flower and leaf], representing different plant characteristics, were sampled and RNA was extracted as described above. For convenience, each micro-array expression information tissue type has received a Set ID as summarized in Table 9 below.

• TABLE 9
  Tomato transcriptome expression sets

  	Expression Set	Set ID
  	Leaf at reproductive stage under Low N conditions	1 + 10
  	Flower under normal conditions	5 + 2
  	Leaf at reproductive stage under normal conditions	8 + 3
  	Flower under drought conditions	9 + 7
  	Leaf at reproductive stage under drought conditions	11 + 4
  	Flower under Low N conditions	12 + 6
  Table 9: Provided are the identification (ID) digits of each of the tomato expression sets.

• Table 10 provides the tomato correlated parameters (Vectors). The average for each of the measured parameter was calculated using the JMP software and values are summarized in Tables 11-13 below. Subsequent correlation analysis was conducted. Results were integrated to the database.

• TABLE 10
  Tomato correlated parameters (vectors)

  Correlated parameter with	Correlation ID

  NUE [yield (gr)/SPAD] (Normal)	1
  NUpE [biomass (gr)/SPAD] (Normal)	2
  HI [yield/yield + biomass] (Normal) (ratio)	3
  NUE2 [total biomass (gr)/SPAD] (Normal)	4
  Total Leaf Area [cm2] (Normal)	5
  Leaflet Length [cm] (Normal)	6
  Leaflet Width (Normal) (cm)	7
  100 weight green fruit (Normal) (gr)	8
  100 weight red fruit (Normal) (gr)	9
  SLA [leaf area/plant biomass] (Normal) (cm2/gr)	10
  Yield/total leaf area (Normal) (gr/cm2)	11
  Yield/SLA (Normal) gr2/cm2	12
  Fruit Yield/Plant (Low N) (gr)	13
  FW/Plant (Low N) (gr)	14
  Average red fruit weight (Low N) (gr)	15
  Fruit yield (Low N)/Fruit yield (Normal) (ratio)	16
  FW (Low N)/FW (Normal) (ratio)	17
  SPAD (Low N) (number)	18
  RWC (Low N) (percentage)	19
  SPAD 100% RWC (NUE) (number)	20
  SPAD (Low N)/SPAD (Normal) (ratio)	21
  SPAD 100% RWC (Low N)/SPAD 100%	22
  RWC (Normal) (ratio)
  RWC (Low N)/RWC (Normal) (ratio)	23
  Number of flowers ((Low N) (number)	24
  Weight clusters (flowers) (Low N) (gr)	25
  Number of Flowers (Low N)/Number of	26
  Flowers (Normal) (ratio)
  Cluster Weight (Low N)/Cluster	27
  Weight (Normal) (ratio)
  RWC Drought (percentage)	28
  RWC Drought/RWC Normal (ratio)	29
  Number of flowers (Drought) (number)	30
  Weight flower clusters (Drought) (gr)	31
  Number of Flower Drought/Normal (number)	32
  Number of Flower Drought/Number of	33
  Flower Drought (Low N) (ratio)
  flower cluster weight (Drought)/flower	34
  cluster weight (Normal) (ratio)
  flower cluster weight Drought/flower	35
  cluster weight (Low N) (ratio)
  Fruit Yield/Plant (Drought) (gr)	36
  FW/Plant (Drought) (gr)	37
  Average red fruit weight Drought (gr)	38
  Fruit Yield (Drought)/Fruit Yield (Normal) (ratio)	39
  Fruit (Drought)/Fruit (Low N) (ratio)	40
  FW (drought)/FW Normal (ratio)	41
  red fruit weight (Drought)/red fruit	42
  weight (Normal) (ratio)
  Fruit yield/Plant (Normal) (gr)	43
  FW/Plant (Normal) (gr)	44
  average red fruit weight (Normal) (gr)	45
  SPAD (Normal) (number)	46
  RWC (Normal) (percentage)	47
  SPAD 100% RWC (Normal) (number)	48
  Number of flowers (Normal) (number)	49
  Weight Flower clusters (Normal) (gr)	50
  Total Leaf Area [cm2]) (Drought)	51
  Leaflet Length [cm]) (Drought)	52
  Leaflet Width [cm] (Drought)	53
  100 weight green fruit (Drought) (gr)	54
  100 weight red fruit (Drought) (gr)	55
  NUE [yield (gr)/SPAD] (Low N)	56
  NUpE [biomass (gr)/SPAD] (Low N)	57
  HI [yield/yield + biomass] (Low N) (ratio)	58
  NUE2 [total biomass (gr)/SPAD] (Low N)	59
  Total Leaf Area [cm2] (Low N)	60
  Leaflet Length [cm] (Low N)	61
  Leaflet Width (Low N) (cm)	62
  100 weight green fruit (Low N) (gr)	63
  SLA [leaf area/plant biomass] (Low N) (cm2/gr)	64
  Yield/total leaf area (Low N) (gr/cm2)	65
  Yield/SLA (Low N) (gr2/cm2)	66
  100 weight red fruit (Low N) (gr)	67
  Table 10. Provided are the tomato correlated parameters, “gr.” = grams; “FW” = fresh weight; “NUE” = nitrogen use efficiency; “RWC” = relative water content; “NUpE” = nitrogen uptake efficiency; “SPAD” = chlorophyll levels (number); “HI” = harvest index (vegetative weight divided on yield); “SLA” = specific leaf area (leaf area divided by leaf dry weight), Treatment in the parenthesis.

• Fruit Weight (grams)—At the end of the experiment [when 50% of the fruits were ripe (red)] all fruits from plots within blocks A-C were collected. The total fruits were counted and weighted. The average fruits weight was calculated by dividing the total fruit weight by the number of fruits.
• Plant vegetative Weight (grams)—At the end of the experiment [when 50% of the fruit were ripe (red)] all plants from plots within blocks A-C were collected. Fresh weight was measured (grams).
• Inflorescence Weight (grans)—At the end of the experiment [when 50% of the fruits were ripe (red)] two Inflorescence from plots within blocks A-C were collected. The Inflorescence weight (gr.) and number of flowers per inflorescence were counted.
• SPAD—Chlorophyll content was determined using a Minolta SPAD 502 chlorophyll meter and measurement was performed at time of flowering. SPAD meter readings were done on young fully developed leaf. Three measurements per leaf were taken per plot.
• Water use efficiency (WUE)—can be determined as the biomass produced per unit transpiration. To analyze WUE, leaf relative water content was measured in control and transgenic plants. Fresh weight (FW) was immediately recorded; then leaves were soaked for 8 hours in distilled water at room temperature in the dark, and the turgid weight (TW) was recorded. Total dry weight (DW) was recorded after drying the leaves at 60° C. to a constant weight. Relative water content (RWC) was calculated according to the following Formula I [(FW−DW/TW−DW)×100] as described above.
• Plants that maintain high relative water content (RWC) compared to control lines were considered more tolerant to drought than those exhibiting reduced relative water content.
• Experimental Results

• TABLE 11
  Measured parameters in Tomato accessions (lines 1-6)

  Ecotype

  Treatment	Line-1	Line-2	Line-3	Line-4	Line-5	Line-6

  1	0.02	0.01	0.01	0.00	0.01	0.01
  2	0.03	0.09	0.05	0.02	0.05	0.05
  3	0.35	0.10	0.14	0.12	0.18	0.19
  4	0.05	0.09	0.06	0.02	0.06	0.06
  5			426.10	582.38	291.40	593.58
  6			6.34	7.99	5.59	7.70
  7			3.69	4.77	3.43	4.56
  8			0.56	3.05	0.24	2.58
  9			0.82	2.46	0.50	2.76
  10			140.99	689.67	130.22	299.12
  11			0.00	0.00	0.00	0.00
  12			0.00	0.00	0.00	0.00
  13	0.41	0.66	0.48	0.46	1.35	0.35
  14	4.04	1.21	2.25	2.54	1.85	3.06
  15	0.02	0.19	0.01	0.01	0.10	0.00
  16	0.49	1.93	0.97	3.80	2.78	0.78
  17	2.65	0.38	0.74	3.01	0.83	1.54
  18	38.40	39.40	47.50	37.00	44.60	41.70
  19	74.07	99.08	69.49	63.24	77.36	77.91
  20	28.47	39.04	33.01	23.42	34.53	32.51
  21	0.77	1.06	0.85	0.80	0.93	0.96
  22	0.79	1.37	0.92	0.75	1.31	0.97
  23	1.02	1.30	1.08	0.94	1.41	1.00
  24	19.00	5.33	9.00	13.00	10.67	16.67
  25	0.53	0.37	0.31	0.35	0.47	0.25
  26	3.35	0.28	1.42	1.70	1.10	2.00
  27	0.46	1.07	0.44	0.01	1.08	0.02
  28	72.12	74.51	65.33	72.22	66.13	68.33
  29	0.99	0.97	1.02	1.08	1.21	0.88
  30	16.67	6.50	15.67	20.33	11.67	25.33
  31	0.37	0.41	0.33	0.29	0.55	0.31
  32	2.94	0.34	2.47	2.65	1.21	3.04
  33	0.88	1.22	1.74	1.56	1.09	1.52
  34	0.32	1.19	0.47	0.01	1.25	0.03
  35	0.69	1.11	1.06	0.82	1.16	1.25
  36	0.47	0.48	0.63	0.35	2.04	0.25
  37	2.62	1.09	1.85	2.22	2.63	2.71
  38	0.01	0.19	0.21	0.00	0.10	0.00
  39	0.57	1.41	1.27	2.88	4.20	0.55
  40	1.15	0.73	1.32	0.76	1.51	0.71
  41	1.72	0.34	0.61	2.63	1.18	1.36
  42	0.19	24.37	25.38	0.02	20.26	0.04
  43	0.83	0.34	0.49	0.12	0.49	0.45
  44	1.53	3.17	3.02	0.84	2.24	1.98
  45	0.05	0.01	0.01	0.29	0.01	0.05
  46	49.70	37.20	55.80	46.40	48.20	43.40
  47	72.83	76.47	64.29	67.07	54.79	77.61
  48	36.17	28.45	35.89	31.09	26.38	33.68
  49	5.67	19.33	6.33	7.67	9.67	8.33
  50	1.17	0.34	0.69	56.35	0.44	11.31
  51	ND	ND	ND	ND	ND	ND
  52	ND	ND	ND	ND	ND	ND
  53	ND	ND	ND	ND	ND	ND
  54	ND	ND	ND	ND	ND	ND
  55	ND	ND	ND	ND	ND	ND
  56	0.01	0.02	0.01	0.02	0.04	0.01
  57	0.14	0.03	0.07	0.11	0.05	0.09
  58	0.09	0.35	0.18	0.15	0.42	0.10
  59	0.16	0.05	0.08	0.13	0.09	0.11
  60	565.93	384.77	294.83	378.00	476.39	197.08
  61	6.40	5.92	3.69	5.43	6.95	3.73
  62	3.47	1.97	1.79	2.55	3.52	1.73
  63	0.87	3.66	0.57	0.37	3.40	0.68
  64	140.04	317.12	131.29	148.82	257.51	64.34
  65	0.00	0.00	0.00	0.00	0.00	0.00
  66	0.00	0.00	0.00	0.00	0.01	0.01
  67	1.06	6.87	0.65	0.53	7.17	0.44
  Table 11. Provided are the values of each of the parameters (as described above) measured in tomato accessions (Seed ID) under all growth conditions. Growth conditions are specified in the experimental procedure section.

• TABLE 12
  Measured parameters in Tomato accessions (lines 7-12)

  Ecotype

  Treatment	Line-7	Line-8	Line-9	Line-10	Line-11	Line-12

  1	0.01	0.01	0.00	0.01	0.02	0.00
  2	0.02	0.04	0.05	0.05	0.05	0.08
  3	0.38	0.17	0.06	0.10	0.27	0.05
  4	0.03	0.05	0.06	0.06	0.06	0.08
  5	947.59	233.35	340.73	339.11	190.14	421.79
  6	7.85	6.22	6.16	5.65	4.39	4.44
  7	4.44	3.15	3.37	3.13	2.40	2.02
  8	6.32	5.75	0.38	0.30	1.95	2.53
  9	5.32	5.24	0.61	0.66	2.70	0.70
  10	1117.74	111.77	106.29	123.14	104.99	111.88
  11	0.00	0.00	0.00	0.00	0.00	0.00
  12	0.00	0.00	0.00	0.00	0.01	0.00
  13	0.01	0.51	0.44	0.47	1.59	0.39
  14	3.13	2.54	1.84	1.52	1.91	1.86
  15	0.01	0.01	0.01	0.01	0.02	0.01
  16	0.02	1.16	2.07	1.51	2.41	2.06
  17	3.70	1.22	0.58	0.55	1.06	0.49
  18	34.40	50.00	44.70	53.70	35.70	58.80
  19	80.49	67.40	67.16	66.07	69.57	69.30
  20	27.66	33.68	30.04	35.50	24.81	40.77
  21	0.80	0.94	0.76	1.05	0.89	1.24
  22	1.11	0.95	0.79	0.92	0.94	1.36
  23	1.38	1.01	1.04	0.88	1.05	1.10
  24	6.00	16.00	15.00	6.00	17.00	13.00
  25	0.29	0.47	0.40	0.30	0.82	0.40
  26	1.20	1.92	1.50	0.86	1.89	1.63
  27	0.37	0.81	0.55	0.36	0.95	0.80
  28	78.13	18.46	73.21	62.50	67.21	75.76
  29	1.34	0.28	1.13	0.83	1.01	1.20
  30	29.73	17.33	14.67	29.67	15.00	10.33
  31	0.45	0.56	0.30	0.31	0.31	0.31
  32	5.95	2.08	1.47	4.24	1.67	1.29
  33	4.96	1.08	0.98	4.94	0.88	0.79
  34	0.56	0.96	0.42	0.38	0.36	0.62
  35	1.52	1.19	0.76	1.04	0.38	0.78
  36	0.05	0.45	0.29	1.02	0.60	0.49
  37	3.41	2.11	1.95	1.76	1.72	1.92
  38	0.03	0.01	0.01	0.00	0.01	0.01
  39	0.09	1.03	1.39	3.28	0.91	2.62
  40	5.06	0.89	0.67	2.17	0.38	1.27
  41	4.02	1.01	0.61	0.64	0.95	0.51
  42	0.15	0.02	0.86	0.74	0.09	1.72
  43	0.53	0.44	0.21	0.31	0.66	0.19
  44	0.85	2.09	3.21	2.75	1.81	3.77
  45	0.23	0.29	0.01	0.01	0.06	0.01
  46	42.90	53.30	58.50	51.10	40.00	47.60
  47	58.18	66.51	64.71	75.25	66.23	63.21
  48	24.98	35.47	37.87	38.43	26.49	30.07
  49	5.00	8.33	10.00	7.00	9.00	8.00
  50	0.79	0.58	0.73	0.83	0.86	0.50
  51	ND	ND	ND	ND	ND	337.63
  52	ND	ND	ND	ND	ND	5.15
  53	ND	ND	ND	ND	ND	2.55
  54	ND	ND	ND	ND	ND	0.80
  55	ND	ND	ND	ND	ND	0.89
  56	0.00	0.02	0.01	0.01	0.06	0.01
  57	0.11	0.08	0.06	0.04	0.08	0.05
  58	0.00	0.17	0.19	0.24	0.45	0.17
  59	0.11	0.09	0.08	0.06	0.14	0.06
  60	453.24	625.51	748.01	453.96	164.85	338.30
  61	4.39	6.72	6.66	4.39	3.90	5.29
  62	1.87	3.54	3.28	2.52	2.61	2.61
  63	0.45	0.47	0.54	0.39	0.97	0.91
  64	144.60	246.05	405.55	299.32	86.19	182.32
  65	0.00	0.00	0.00	0.00	0.01	0.00
  66	0.00	0.00	0.00	0.00	0.02	0.00
  67	1.06	0.55	0.75	0.58	1.27	1.34
  Table 12. Provided are the values of each of the parameters (as described above) measured in tomato accessions (Seed ID) under all growth conditions. Growth conditions are specified in the experimental procedure section.

• TABLE 13
  Measured parameters in Tomato accessions (lines 13-18)

  Ecotype

  Treatment	Line-13	Line-14	Line-15	Line-16	Line-17	Line-18

  1	0.01	0.01	0.01	0.01	0.01	0.00
  2	0.03	0.04	0.05	0.03	0.07	0.04
  3	0.31	0.12	0.14	0.17	0.09	0.11
  4	0.05	0.05	0.06	0.04	0.08	0.04
  5	581.33	807.51	784.06	351.80	255.78	1078.10
  6	6.77	7.42	6.71	5.87	4.16	10.29
  7	3.80	3.74	2.98	3.22	2.09	5.91
  8	1.42	2.03	1.39	2.27	0.45	0.42
  9	2.64	4.67	2.17	0.49	0.34	0.75
  10	307.95	419.37	365.81	212.93	84.94	469.87
  11	0.00	0.00	0.00	0.00	0.00	0.00
  12	0.00	0.00	0.00	0.00	0.00	0.00
  13	0.32	0.45	0.14	0.40	1.44	0.50
  14	2.47	2.62	1.08	1.17	0.92	1.09
  15	0.01	0.05	0.36	0.04	0.63
  16	0.38	1.64	0.41	1.21	4.59	1.70
  17	1.31	1.36	0.51	0.71	0.31	0.47
  18	47.50	45.20	39.00	45.00	65.30	51.90
  19	100.00	57.66	90.79	68.00	59.65	72.17
  20	47.47	26.06	35.38	30.60	38.97	37.46
  21	0.82	0.94	0.89	0.83	1.57	0.88
  22	1.44	1.50	1.05	0.56	1.48	0.84
  23	1.76	1.60	1.17	0.68	0.94	0.96
  24	8.67	9.33	12.67	6.67	9.33	8.00
  25	0.35	0.43	0.35	0.45	0.28	0.47
  26	1.63	1.17	1.65	0.74	0.88	0.89
  27	0.34	0.61	0.94	0.68	0.40	1.44
  28	62.82	70.69	55.75	75.22	63.68	62.31
  29	1.11	1.97	0.72	0.75	1.01	0.83
  30	18.33	12.00	20.33	12.67	12.67	11.33
  31	8.36	0.29	0.34	0.44	0.27	0.43
  32	3.44	1.50	2.65	1.41	1.19	1.26
  33	2.12	1.29	1.61	1.90	1.36	1.42
  34	8.20	0.41	0.91	0.67	0.38	1.31
  35	24.12	0.67	0.97	0.99	0.95	0.91
  36	0.27	0.68	0.14	0.53	0.55	0.41
  37	2.21	3.73	0.75	1.76	0.63	1.11
  38	0.00	0.01	0.30	0.14	0.04	0.09
  39	0.32	2.48	0.41	1.62	1.76	1.42
  40	0.84	1.51	0.98	1.34	0.38	0.84
  41	1.17	1.94	0.35	1.06	0.21	0.48
  42	0.17	0.02	10.50	27.89	11.79	9.98
  43	0.85	0.27	0.35	0.33	0.31	0.29
  44	1.89	1.93	2.14	1.65	3.01	2.29
  45	0.03	0.26	0.03	0.00	0.00	0.01
  46	57.90	48.30	43.60	54.50	41.60	59.10
  47	56.77	35.96	77.62	100.00	63.16	75.13
  48	32.89	17.35	33.82	54.47	26.25	44.43
  49	5.33	8.00	7.67	9.00	10.67	9.00
  50	1.02	0.70	0.38	0.66	0.70	0.33
  51	130.78	557.93	176.67	791.86	517.05	832.27
  52	3.38	7.14	5.48	8.62	6.35	6.77
  53	2.04	4.17	3.09	4.69	3.87	2.91
  54	0.28	0.38	0.63	2.86	1.16	4.40
  55	0.35	0.63	2.27	7.40	2.94	11.60
  56	0.01	0.02	0.00	0.01	0.04	0.01
  57	0.05	0.10	0.03	0.04	0.02	0.03
  58	0.12	0.15	0.12	0.25	0.61	0.31
  59	0.06	0.12	0.03	0.05	0.06	0.04
  60	396.00	236.15	174.58	441.78	489.18	707.80
  61	6.32	5.11	4.72	6.83	7.10	8.21
  62	3.58	2.56	2.48	3.43	3.30	3.69
  63	0.36	0.35	0.57	4.38	2.02	8.13
  64	160.18	90.10	160.99	379.03	531.08	650.68
  65	0.00	0.00	0.00	0.00	0.00	0.00
  66	0.00	0.00	0.00	0.00	0.00	0.00
  67	0.52	0.57	0.94	6.17	3.67	11.33
  Table 13: Provided are the values of each of the parameters (as described above) measured in tomato accessions (Seed ID) under all growth conditions. Growth conditions are specified in the experimental procedure section.

• TABLE 14
  Correlation between the expression level of selected genes of some embodiments
  of the invention in various tissues and the phenotypic performance
  under normal and stress conditions across tomato ecotypes

  			Exp.	Corr.				Exp.	Corr.
  Gene Name	R	P value	set	Set ID	Gene Name	R	P value	set	Set ID

  LYD648	0.71	2.04E−02	1	20	LYD648	0.73	2.70E−02	2	1
  LYD650	0.72	1.95E−02	5	45	LYD650	0.72	1.78E−02	9	37
  LYD650	0.88	8.80E−04	9	41	LYD650	0.79	6.43E−03	11	41
  LYD651	0.72	4.60E−02	2	10	LYD651	0.80	1.69E−02	2	5
  LYD651	0.83	2.96E−03	8	43	LYD651	0.79	6.11E−03	11	35
  LYD651	0.79	6.98E−03	11	31	LYD652	0.71	2.14E−02	1	27
  LYD652	0.80	5.86E−03	10	61	LYD652	0.77	8.52E−03	10	64
  LYD652	0.83	3.29E−03	10	63	LYD652	0.75	1.21E−02	10	67
  LYD653	0.71	3.11E−02	2	2	LYD653	0.72	2.80E−02	3	2
  LYD653	0.74	2.35E−02	3	4	LYD654	0.72	2.74E−02	3	2
  LYD654	0.75	1.89E−02	3	4	LYD655	0.83	1.07E−02	2	9
  LYD655	0.72	1.85E−02	12	19	LYD657	0.78	2.25E−02	2	12
  LYD657	0.76	2.92E−02	2	11	LYD657	0.77	8.89E−03	5	47
  LYD657	0.90	3.73E−04	5	48	LYD657	0.76	1.10E−02	11	30
  LYD657	0.77	9.90E−03	11	32	LYD658	0.79	1.94E−02	2	8
  LYD658	0.73	1.62E−02	6	58	LYD658	0.75	1.27E−02	11	39
  LYD658	0.82	3.75E−03	11	36	LYD659	0.85	1.72E−03	1	21
  LYD659	0.80	8.96E−03	1	15	LYD659	0.88	4.08E−03	2	6
  LYD659	0.89	3.26E−03	2	10	LYD659	0.95	2.50E−04	2	5
  LYD659	0.85	7.44E−03	2	7	LYD659	0.75	1.18E−02	8	50
  LYD659	0.77	9.47E−03	10	65	LYD659	0.73	1.67E−02	12	20
  LYD659	0.73	1.63E−02	12	19	LYD660	0.81	8.70E−03	2	3
  LYD660	0.74	2.21E−02	2	1	LYD660	0.80	5.64E−03	11	33
  LYD660	0.72	2.01E−02	11	40	LYD662	0.93	9.15E−05	6	59
  LYD662	0.86	1.49E−03	6	57	LYD662	0.74	1.45E−02	9	37
  LYD662	0.81	4.76E−03	9	41	LYD662	0.86	1.51E−03	12	24
  LYD662	0.75	1.31E−02	12	14	LYD662	0.75	1.30E−02	12	17
  LYD662	0.82	3.37E−03	12	26	LYD663	0.72	1.82E−02	6	58
  LYD663	0.75	1.22E−02	12	16	LYD663	0.82	3.57E−03	12	21
  LYD663	0.88	1.57E−03	12	15	LYD663	0.86	1.37E−03	12	18
  LYD664	0.71	4.97E−02	2	5	LYD664	0.88	7.76E−04	5	50
  LYD664	0.80	5.82E−03	5	45	LYD664	0.89	4.84E−04	11	33
  LYD664	0.89	4.73E−04	11	30	LYD664	0.83	2.93E−03	11	32
  LYD665	0.71	2.24E−02	1	21	LYD665	0.91	2.59E−04	8	50
  LYD666	0.89	6.17E−04	6	56	LYD666	0.87	1.00E−03	6	65
  LYD666	0.75	1.31E−02	10	60	LYD666	0.83	2.68E−03	10	64
  LYD666	0.84	2.39E−03	12	13	LYD666	0.73	2.69E−02	12	15
  LYD667	0.78	7.42E−03	12	20	LYD667	0.71	2.13E−02	12	23
  LYD667	0.77	9.13E−03	12	19	LYD668	0.79	1.12E−02	2	3
  LYD668	0.75	1.95E−02	2	1	LYD669	0.89	5.38E−04	6	59
  LYD669	0.86	1.55E−03	6	57	LYD669	0.93	7.72E−05	12	24
  LYD669	0.82	3.72E−03	12	14	LYD669	0.81	4.92E−03	12	17
  LYD669	0.94	5.22E−05	12	26	LYD669	0.77	9.06E−03	12	18
  LYD670	0.79	6.65E−03	1	20	LYD670	0.77	8.66E−03	1	22
  LYD670	0.88	4.33E−03	2	12	LYD670	0.76	1.79E−02	2	3
  LYD670	0.88	1.57E−03	2	1	LYD670	0.78	2.37E−02	2	11
  LYD670	0.73	2.59E−02	3	3	LYD670	0.88	1.58E−03	3	1
  LYD672	0.71	2.05E−02	8	43	LYD672	0.83	3.24E−03	11	35
  LYD672	0.74	1.36E−02	11	34	LYD672	0.82	3.71E−03	11	31
  LYD673	0.94	4.23E−04	2	6	LYD673	0.90	2.12E−03	2	10
  LYD673	0.95	3.89E−04	2	5	LYD673	0.95	3.25E−04	2	7
  LYD673	0.73	1.70E−02	10	63	LYD673	0.70	2.34E−02	12	19
  LYD674	0.72	4.59E−02	2	5	LYD674	0.73	1.68E−02	11	36
  LYD675	0.79	2.00E−02	2	6	LYD675	0.84	9.67E−03	2	10
  LYD675	0.88	4.05E−03	2	5	LYD675	0.72	4.37E−02	2	7
  LYD675	0.91	2.96E−04	11	35	LYD675	0.84	2.25E−03	11	34
  LYD675	0.90	4.48E−04	11	31	LYD676	0.73	1.55E−02	8	43
  LYD676	0.78	8.05E−03	11	35	LYD676	0.77	9.17E−03	11	31
  LYD677	0.75	1.91E−02	2	3	LYD677	0.77	2.50E−02	2	10
  LYD677	0.73	4.09E−02	2	5	LYD678	0.78	8.42E−03	8	49
  LYD678	0.72	1.99E−02	11	42	LYD678	0.87	1.12E−03	11	38
  LYD679	0.77	8.47E−03	1	19	LYD679	0.78	2.22E−02	2	6
  LYD679	0.83	1.17E−02	2	10	LYD679	0.85	7.58E−03	2	5
  LYD679	0.75	3.29E−02	2	7	LYD679	0.84	4.95E−03	3	3
  LYD679	0.72	2.97E−02	3	1	LYD679	0.72	1.99E−02	5	43
  LYD679	0.81	4.78E−03	9	35	LYD679	0.81	4.89E−03	9	34
  LYD679	0.81	4.67E−03	9	31	LYD679	0.71	3.31E−02	12	15
  LYD679	0.84	2.28E−03	12	22	LYD680	0.73	1.71E−02	1	27
  LYD680	0.72	4.47E−02	2	7	LYD680	0.71	2.19E−02	8	46
  LYD680	0.80	5.67E−03	10	63	LYD680	0.74	1.48E−02	10	67
  LYD681	0.82	1.26E−02	2	9	LYD681	0.83	5.53E−03	3	1
  LYD681	0.71	2.17E−02	8	48	LYD681	0.73	1.71E−02	9	37
  LYD682	0.75	1.96E−02	2	4	LYD682	0.73	2.54E−02	3	3
  LYD682	0.70	2.29E−02	6	58	LYD682	0.72	2.00E−02	12	16
  LYD682	0.76	1.07E−02	12	21	LYD682	0.80	8.91E−03	12	15
  LYD682	0.72	1.94E−02	11	42	LYD683	0.71	2.22E−02	10	59
  LYD684	0.70	2.33E−02	9	32	LYD685	0.71	2.10E−02	5	43
  LYD685	0.93	1.00E−04	5	45	LYD685	0.75	1.20E−02	8	43
  LYD685	0.74	1.52E−02	9	41	LYD685	0.89	6.58E−04	11	35
  LYD685	0.83	3.23E−03	11	34	LYD685	0.88	6.67E−04	11	31
  LYD686	0.79	6.31E−03	9	35	LYD686	0.72	1.86E−02	9	34
  LYD686	0.78	8.07E−03	9	31	LYD690	0.85	7.24E−03	2	12
  LYD690	0.77	2.66E−02	2	11	LYD690	0.75	1.25E−02	11	35
  LYD690	0.75	1.20E−02	11	34	LYD690	0.75	1.31E−02	11	31
  Table 14. Provided are the correlations (R) between the expression levels yield improving genes and their homologs in various tissues [Expression (Exp) sets] and the phenotypic performance [yield, biomass, growth rate and/or vigor components (Correlation vector (Corr))] under normal conditions across tomato ecotypes. P = p value.

Example 5 Production of Tomato Transcriptome and High Throughput Correlation Analysis Using 44K Tomato Oligonucleotide Micro-Array
• In order to produce a high throughput correlation analysis, the present inventors utilized a Tomato oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?lPage=50879]. The array oligonucleotide represents about 44,000 Tomato genes and transcripts. In order to define correlations between the levels of RNA expression with ABST, yield components or vigor related parameters various plant characteristics of 18 different Tomato varieties were analyzed. Among them, 10 varieties encompassing the observed variance were selected for RNA expression analysis. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test.
• I. Correlation of Tomato Varieties Across Ecotype Grown Under 50% Irrigation Conditions
• Experimental Procedures
• Growth procedure—Tomato variety was grown under normal conditions (4-6 Liters/m² per day) until flower stage. At this time, irrigation was reduced to 50% compared to normal conditions.
• RNA extraction—Two tissues at different developmental stages [flower and leaf], representing different plant characteristics, were sampled and RNA was extracted as described above.
• Fruit Yield (grams)—At the end of the experiment [when 50% of the fruit were ripe (red)] all fruits from plots within blocks A-C were collected. The total fruits were counted and weighted. The average fruits weight was calculated by dividing the total fruit weight by the number of fruits.
• Yield/SLA and Yield/total leaf area—Fruit yield divided by the specific leaf area or the total leaf area gives a measurement of the balance between reproductive and vegetative processes.
• Plant Fresh Weight (grams)—At the end of the experiment [when 50% of the fruit were ripe (red)] all plants from plots within blocks A-C were collected. Fresh weight was measured (grams).
• Inflorescence Weight (grams)—At the end of the experiment [when 50% of the fruits were ripe (red)] two inflorescence from plots within blocks A-C were collected. The inflorescence weight (gr.) and number of flowers per inflorescence were counted.
• SPAD—Chlorophyll content was determined using a Minolta SPAD 502 chlorophyll meter and measurement was performed at time of flowering. SPAD meter readings were done on young fully developed leaf. Three measurements per leaf were taken per plot.
• Water use efficiency (WUE)—can be determined as the biomass produced per unit transpiration. To analyze WUE, leaf relative water content was measured in control and transgenic plants. Fresh weight (FW) was immediately recorded: then leaves were soaked for 8 hours in distilled water at room temperature in the dark, and the turgid weight (TW) was recorded. Total dry weight (DW) was recorded after drying the leaves at 60° C. to a constant weight. Relative water content (RWC) was calculated according to the following Formula I [(FW−DW/TW−DW)×100] as described above.
• Plants that maintain high relative water content (RWC) compared to control lines were considered more tolerant to drought than those exhibiting reduced relative water content.

• TABLE 15
  Tissues used for tomato transcriptome expression sets

  	Expression Set	Set ID
  	Root grown under normal growth conditions	1 + 7
  	Root grown under NUE growth conditions	2 + 4
  	Leaf grown under normal growth conditions	3 + 5
  	Leaf grown under NUE growth conditions	6 + 8
  Table 15: Provided are the identification (ID) digits of each of the tomato expression sets.

• Tomato yield components and vigor related parameters under 50% water irrigation assessment—10 Tomato varieties in 3 repetitive blocks (named A, B, and C), each containing 6 plants per plot were grown at net house. Plants were phenotyped on a daily basis following the standard descriptor of tomato (Table 16, below). Harvest was conducted while 50% of the fruits were red (mature). Plants were separated to the vegetative part and fruits, of them, 2 nodes were analyzed for additional inflorescent parameters such as size, number of flowers, and inflorescent weight. Fresh weight of all vegetative material was measured. Fruits were separated to colors (red vs. green) and in accordance with the fruit size (small, medium and large). Next, analyzed data was saved to text files and processed using the JMP statistical analysis software (SAS institute).
• Data parameters collected are summarized in Table 16, herein below.

• TABLE 16
  Tomato correlated parameters (vectors)

  Correlated parameter with	Correlation ID

  Shoot Biomass [DW]/SPAD (gr/SPAD)	1
  Root Biomass [DW]/SPAD (gr/SPAD)	2
  Total Biomass [Root + Shoot DW]/SPAD (gr/SPAD)	3
  N level/Leaf [SPAD unit/leaf] (SPAD/gr)	4
  Shoot/Root (ratio)	5
  Percent Shoot Biomass reduction	6
  compared to normal (%)
  Percent Root Biomass reduction	7
  compared to normal (%)
  Shoots NUE (gr)	8
  Roots NUE (gr)	9
  Total biomass NUE (gr)	10
  Plant Height NUE (cm)	11
  Plant Height Normal (cm)	12
  SPAD NUE (number)	13
  Leaf number NUE/Normal (ratio)	14
  Plant Height NUE/Normal (ratio)	15
  SPAD NUE/Normal (ratio)	16
  leaf No. NUE (number)	17
  leaf No. Normal (number)	18
  Plant height Normal (cm)	19
  SPAD Normal	20
  Table 16: Provided are the tomato correlated parameters. “NUE” = nitrogen use efficiency; “DW” = dry weight; “cm” = centimeter.

• Experimental Results
• RNA extraction—All 10 selected Tomato varieties were sampled per each treatment. Two tissues [leaves and flowers] growing at 50% irrigation or under normal conditions were sampled and RNA was extracted using TRIzol Reagent from Invitrogen [Hypertext Transfer Protocol://World Wide Web (dot) invitrogen (dot) com/content (dot)cfm?pageid=469]. Extraction of RNA from tissues was performed as described under “General Experimental And Bioinformatics Methods” above.
• 10 different Tomato varieties (accessions) were grown and characterized for 20 parameters as described above. The average for each of the measured parameter was calculated using the JMP software and values are summarized in Tables 17-18 below. Subsequent correlation analysis between expression of selected genes in various transcriptome expression sets and the measured parameters in tomato accessions (Tables 17-18) was conducted, and results were integrated to the database.

• TABLE 17
  Measured parameters in Tomato accessions (line 1-6)

  Ecotype

  Treatment	Line-1	Line-2	Line-3	Line-4	Line-5	Line-6

  1	0.00	0.00	0.00	0.01	0.00	0.01
  2	0.00	0.00	0.00	0.00	0.00	0.00
  3	0.00	0.01	0.00	0.01	0.01	0.01
  4	10.85	11.53	11.41	10.44	11.17	8.93
  5	5.01	6.41	11.39	9.49	11.60	8.20
  6	75.38	62.15	55.11	49.73	63.19	82.67
  7	62.59	143.71	54.16	70.55	59.69	96.13
  8	35.35	38.35	24.09	65.02	46.71	46.67
  9	6.99	7.73	2.54	7.04	5.04	8.01
  10	58.47	69.70	63.75	69.29	71.10	60.54
  11	36.78		39.89	47.00	46.44	45.44
  12	45.33		47.78	55.33	56.22	48.67
  13	34.57		24.87	31.58	29.72	31.83
  14	0.85		0.90	1.09	0.88	1.02
  15	0.81		0.83	0.85	0.83	0.93
  16	1.01		0.98	1.00	0.98	0.98
  17	5.56		6.22	6.78	5.56	6.56
  1	0.01	0.01	0.01	0.01	0.01	0.01
  2	0.00	0.00	0.00	0.00	0.00	0.00
  3	0.01	0.01	0.01	0.02	0.01	0.01
  4	9.29	10.18	8.87	8.43	9.83	8.57
  5	5.40	12.65	10.02	15.42	8.83	7.52
  8	4.69	6.17	4.37	13.08	7.39	5.65
  9	1.12	0.54	0.47	1.00	0.84	0.83
  10	7.47	9.10	8.63	8.85	7.22	7.87
  18	6.56		6.89	6.22	6.33	6.44
  19	45.33		47.78	55.33	56.22	48.67
  20	34.30		25.31	31.43	30.24	32.43
  Table 17. Provided are the measured yield components and vigor related parameters under normal or Nitrogen use efficiency parameters for the tomato accessions (Varieties) according to the Correlation ID numbers (described in Table 16 above)

• TABLE 18
  Measured parameters in Tomato accessions (line 7-12)

  Ecotype

  Treatment	Line-7	Line-8	Line-9	Line-10	Line-11	Line-12

  1	0.01	0.01	0.01	0.01	0.0056
  2	0.00	0.00	0.00	0.00	0.0015
  3	0.01	0.01	0.01	0.01	0.007
  4	7.93	7.99	10.30	8.59	14.491
  5	10.38	10.52	8.24	7.97	3.9092
  6	66.92	107.98	55.40	54.43	59.746
  7	106.50	111.90	81.64	32.21	87.471
  8	120.07	60.09	66.27	56.46	60.32
  9	15.09	9.02	8.78	7.25	15.94
  10	73.90	68.81	66.74	70.82	49.72
  11	47.67	39.33	41.78	41.00		34.44
  12	55.78	37.44	49.56	46.33		40.78
  13	30.33	30.29	31.32	28.77		28.58
  14	0.87	1.06	0.91	1.12		0.98
  15	0.85	1.05	0.84	0.88		0.84
  16	0.93	1.05	1.01	0.99		1.02
  17	5.11	5.89	5.56	6.33		7.22
  1	0.02	0.01	0.01	0.01	0.0094
  2	0.00	0.00	0.00	0.00	0.0017
  3	0.02	0.01	0.01	0.01	0.011
  4	6.57	6.97	8.71	7.35	9.3699
  5	12.61	7.99	14.31	4.80	6.2937
  8	17.94	5.56	11.96	10.37	10.1
  9	0.94	0.81	1.08	2.25	1.82
  10	9.09	7.91	8.55	8.68	6.24
  18	5.89	5.56	6.11	5.67		7.33
  19	55.78	37.44	49.56	46.33		40.78
  20	32.58	28.77	30.92	28.99		28.12
  Table 18: Provided are the measured yield components and vigor related parameters under normal or Nitrogen use efficiency parameters for the tomato accessions (Varieties) according to the Correlation ID numbers (described in Table 16 above)

• TABLE 19
  Correlation between the expression level of selected genes of some embodiments
  of the invention in various tissues and the phenotypic performance under
  normal or low nitrogen use conditions across tomato accessions

  			Exp.	Corr.				Exp.	Corr.
  Gene Name	R	P value	set	Set ID	Gene Name	R	P value	set	Set ID

  LYD648	0.73	2.42E−02	1	2	LYD648	0.72	2.90E−02	2	9
  LYD648	0.71	3.18E−02	2	2	LYD648	0.73	2.66E−02	4	9
  LYD648	0.71	3.26E−02	4	3	LYD648	0.72	2.88E−02	4	2
  LYD648	0.73	2.69E−02	7	2	LYD651	0.76	1.77E−02	6	7
  LYD651	0.76	1.72E−02	8	7	LYD652	0.73	4.09E−02	3	18
  LYD652	0.72	2.84E−02	7	4	LYD653	0.76	2.70E−02	4	15
  LYD653	0.79	1.22E−02	4	6	LYD654	0.81	8.61E−03	2	4
  LYD654	0.78	1.31E−02	4	4	LYD654	0.78	1.38E−02	6	7
  LYD654	0.81	1.42E−02	7	18	LYD655	0.79	1.16E−02	2	8
  LYD655	0.83	5.65E−03	2	9	LYD655	0.76	1.65E−02	2	3
  LYD655	0.75	1.94E−02	2	1	LYD655	0.77	1.53E−02	2	2
  LYD655	0.79	1.14E−02	4	8	LYD655	0.83	5.95E−03	4	9
  LYD655	0.76	1.68E−02	4	3	LYD655	0.75	1.96E−02	4	1
  LYD655	0.76	1.66E−02	4	2	LYD657	0.91	1.90E−03	6	15
  LYD657	0.88	1.67E−03	6	6	LYD658	0.73	2.67E−02	3	9
  LYD658	0.73	2.48E−02	3	2	LYD659	0.89	1.15E−03	6	7
  LYD660	0.81	1.44E−02	4	17	LYD660	0.71	3.19E−02	6	2
  LYD660	0.78	1.35E−02	6	7	LYD660	0.85	4.02E−03	7	4
  LYD660	0.76	2.84E−02	7	18	LYD660	0.78	1.24E−02	8	7
  LYD664	0.74	2.21E−02	6	7	LYD664	0.73	2.43E−02	8	7
  LYD667	0.94	5.35E−04	4	15	LYD667	0.88	1.75E−03	4	6
  LYD667	0.73	2.49E−02	4	7	LYD667	0.81	1.41E−02	6	15
  LYD667	0.89	1.39E−03	6	6	LYD668	0.74	2.32E−02	6	7
  LYD669	0.92	I.38E−03	4	15	LYD669	0.89	3.23E−03	6	15
  LYD669	0.94	1.50E−04	6	6	LYD670	0.75	3.38E−02	6	15
  LYD670	0.74	2.35E−02	6	6	LYD672	0.74	2.26E−02	6	9
  LYD672	0.71	3.33E−02	6	2	LYD672	0.79	1.17E−02	6	7
  LYD673	0.74	3.51E−02	4	12	LYD673	0.74	3.51E−02	7	19
  LYD674	0.72	4.42E−02	6	17	LYD675	0.73	2.60E−02	6	9
  LYD675	0.81	7.67E−03	6	7	LYD675	0.72	2.79E−02	8	9
  LYD675	0.81	8.09E−03	8	7	LYD676	0.75	2.12E−02	6	7
  LYD676	0.81	1.57E−02	7	18	LYD676	0.76	1.84E−02	8	7
  LYD677	0.77	2.57E−02	3	19	LYD677	0.77	2.57E−02	6	12
  LYD678	0.72	4.30E−02	4	16	LYD678	0.72	2.81E−02	4	6
  LYD678	0.79	1.98E−02	6	15	LYD678	0.90	9.54E−04	6	6
  LYD680	0.71	5.02E−02	4	17	LYD682	0.74	3.43E−02	3	20
  LYD683	0.70	3.48E−02	6	7	LYD684	0.85	3.56E−03	6	7
  LYD690	0.70	3.56E−02	4	6	LYD690	0.83	1.16E−02	6	15
  LYD690	0.93	3.18E−04	6	6
  Table 19. Provided are the correlations (R) between the expression levels of yield improving genes and their homologues in tissues [Leaves or roots; Expression sets (Exp)] and the phenotypic performance in various yield, biomass, growth rate and/or vigor components [Correlation vector (corr.)] under stress conditions or normal conditions across tomato accessions. P = p value.

Example 6 Production of B. juncea Transcriptome and High Throughput Correlation Analysis with Yield Parameters Using 60K B. juncea Oligonucleotide Micro-Arrays
• In order to produce a high throughput correlation analysis, the present inventors utilized a B. juncea oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?lPage=50879]. The array oligonucleotide represents about 60,000 B. juncea genes and transcripts. In order to define correlations between the levels of RNA expression with yield components or vigor related parameters, various plant characteristics of 11 different B. juncea varieties were analyzed and used for RNA expression analysis. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test.
• Correlation of B. juncea Genes' Expression Levels with Phenotypic Characteristics Across Ecotype
• Experimental Procedures
• Eleven B. juncea varieties were grown in three repetitive plots, in field. Briefly, the growing protocol was as follows: B. juncea seeds were sown in soil and grown under normal condition till harvest. In order to define correlations between the levels of RNA expression with yield components or vigor related parameters, the eleven different B. juncea varieties were analyzed and used for gene expression analyses.

• TABLE 20
  Tissues used for B, juncea transcriptome expression sets

  Expression Set	Set ID

  Meristem at vegetative stage under normal growth conditions	1
  Flower at flowering stage under normal growth conditions	2
  Leaf at vegetative stage under normal growth conditions	3
  Pod (R1-R3) under normal growth conditions	4
  Pod (R4-R5) under normal growth conditions	5
  Table 20: Provided are the identification (ID) digits of each of the B, juncea expression sets.

• RNA extraction—All 11 selected B. juncea varieties were sample per each treatment. Plant tissues [leaf, Pod, Lateral meristem and flower] growing under normal conditions were sampled and RNA was extracted as described above.
• The collected data parameters were as follows:
• Fresh weight (plot-harvest) [gr/plant]—total fresh weight per plot at harvest time normalized to the number of plants per plot.
• Seed Weight [milligrams/plant]—total seeds from each plot was extracted, weighted and normalized for plant number in each plot.
• Harvest index—The harvest index was calculated: seed weight/fresh weight.
• Days till bolting/flowering—number of days till 50% bolting/flowering for each plot.
• SPAD—Chlorophyll content was determined using a Minolta SPAD 502 chlorophyll meter and measurement was performed at time of flowering. SPAD meter readings were done on young fully developed leaf Three measurements per leaf were taken for each plot.
• Main branch—average node length—total length/total number of nods on main branch.
• Lateral branch—average node length—total length/total number of nods on lateral branch.
• Main branch—20th length—the length of the pod on the 20^th node from the apex of main branch.
• Lateral branch—20th length—the length of the pod on the 20^th node from the apex of lateral branch.
• Main branch—20th seed No.—number of seeds in the pod on the 20^th node from the apex of main branch.
• Lateral branch—20th seed number—number of seeds in the pod on the 20^th node from the apex of lateral branch.
• Number of lateral branches—total number of lateral branches, average of three plants per plot.
• Main branch height [cm]—total length of main branch.
• Min-lateral branch position—lowest node on the main branch that has developed lateral branch.
• Max-lateral branch position [#node of main branch]—highest node on the main branch that has developed lateral branch.
• Max-number of nodes in lateral branch—the highest number of node that a lateral branch had per plant.
• Max length of lateral branch [cm]—the highest length of lateral branch per plant.
• Max diameter of lateral branch [mm]—the highest base diameter that a lateral branch had per plant.
• Oil Content—Indirect oil content analysis was carried out using Nuclear Magnetic Resonance (NMR) Spectroscopy, which measures the resonance energy absorbed by hydrogen atoms in the liquid state of the sample [See for example, Conway T F. and Earle F R., 1963, Journal of the American Oil Chemists' Society: Springer Berlin/Heidelberg, ISSN: 0003-021X (Print) 1558-9331 (Online)].
• Fresh weight (single plant) (gr/plant)—average fresh weight of three plants per plot taken at the middle of the season.
• Main branch base diameter [mm]—the based diameter of main branch, average of three plants per plot.
• 1000 Seeds [gr]—weight of 1000 seeds per plot.
• Experiment Results
• Eleven different B. juncea varieties (i.e., seed ID 646, 648, 650, 657, 661, 662, 663, 664, 669, 670, 671) were grown and characterized for 23 parameters as specified above. The average for each of the measured parameters was calculated using the JMP software and values are summarized in Tables 22-23 below. Subsequent correlation analysis between the various transcriptome expression sets and the average parameters, was conducted. Results ere then integrated to the database.

• TABLE 21
  Correlated parameters in B. juncea accessions

  Correlated parameter with	Correlation ID

  Days till bolting (days)	1
  Fresh weight (plot-harvest) [gr/plant]	2
  Seed weight per plant (gr)	3
  Harvest index (ratio)	4
  Days till flowering (days)	5
  SPAD	6
  Main branch - average node length (cm)	7
  Lateral branch - average node length (cm)	8
  Main branch - 20th length (cm)	9
  Lateral branch - 20th length (cm)	10
  Main branch - 20th seed number (number)	11
  Lateral branch - 20th seed number (number)	12
  Number of lateral branches (number)	13
  Main branch height [cm]	14
  Min-Lateral branch position ([#node of main branch)	15
  Max-Lateral branch position [#node of main branch]	16
  Max-Number of nodes in lateral branch (number)	17
  Max-Length of lateral branch [cm]	18
  Max-Diameter of lateral branch [mm]	19
  Oil content (mg)	20
  Fresh weight (single plant) [gr/plant]	21
  Main branch base diameter [mm]	22
  1000 Seeds [gr]	23
  Table 21. Provided are the B. juncea correlated parameters, “gr.” = grams; mm = millimeters; “cm” = centimeters; “mg” = milligrams; “SPAD” = chlorophyll levels;

• TABLE 22
  Measured parameters in B. juncea accessions (lines 1-6)

  Ecotype

  Treatment	Line-1	Line-2	Line-3	Line-4	Line-5	Line-6

  1	57.33	60.33	59.67	56.33	55.00	46.67
  2	69.24	45.22	39.27	49.11	43.95	46.42
  3	0.00	0.01	0.01	0.01	0.01	0.01
  4	0.00	0.00	0.00	0.00	0.00	0.00
  5	66.00	69.67	69.33	66.00	61.33	53.00
  6	33.02	30.01	32.83	37.53	41.44	35.41
  7	0.48	0.41	0.63	0.43	0.38	0.68
  8	0.65	0.43	0.74	0.57	0.56	0.79
  9	4.28	3.72	3.62	3.50	2.74	5.20
  10	4.32	3.69	4.14	3.37	3.06	3.96
  11	13.22	13.67	10.44	14.11	9.78	15.22
  12	13.00	14.00	13.22	13.44	11.00	13.11
  13	15.22	14.89	13.56	14.89	14.00	9.78
  14	140.72	125.22	112.44	133.39	142.00	101.50
  15	6.78	6.33	5.56	3.67	3.00	3.11
  16	15.22	14.89	13.56	14.89	14.00	10.89
  17	5.22	7.00	5.22	7.00	6.56	9.44
  18	40.44	47.22	41.61	60.50	59.78	59.44
  19	4.20	4.85	4.34	5.74	5.87	5.68
  20	40.19	40.71	40.91	38.57	40.14	42.63
  21	197.78	142.22	147.22	243.33	192.33	163.78
  22	14.53	11.99	19.91	14.32	12.59	12.30
  23	3.76	2.21	3.26	2.36	2.00	3.12
  Table 22. Provided are the values of each of the parameters (as described above) measured in B. juncea accessions (Seed ID) under normal conditions.

• TABLE 23
  Measured parameters in B. juncea accessions (lines 7-11)

  Ecotype

  Treatment	Line-7	Line-8	Line-9	Line- 10	Line-11

  1	59.00	54.33	59.67	57.33	53.00
  2	36.14	32.58	33.16	63.23	60.94
  3	0.00	0.00	0.00	0.01	0.01
  4	0.00	0.00	0.00	0.00	0.00
  5	69.67	63.67	69.67	71.00	58.33
  6	33.17	32.87	34.80	31.82	41.49
  7	0.40	0.63	0.57	0.59	1.55
  8	0.57	0.76	0.96	0.78	0.90
  9	3.91	3.98	3.46	3.73	4.04
  10	4.33	4.21	4.14	4.04	3.88
  11	12.00	12.67	9.89	11.56	15.56
  12	11.89	13.44	11.22	13.22	14.00
  13	16.44	14.33	14.56	14.11	16.78
  14	145.39	131.56	129.89	131.56	116.44
  15	7.78	6.22	5.56	4.89	5.33
  16	16.44	14.33	14.56	14.11	16.78
  17	6.11	5.22	5.67	6.56	6.00
  18	47.28	47.33	44.67	58.67	47.17
  19	4.52	4.89	4.68	5.56	5.49
  20	41.34	40.82	40.82	38.14	37.21
  21	164.44	181.11	176.22	217.89	261.11
  22	12.60	12.91	12.56	13.77	13.56
  23	3.34	3.09	3.39	3.40	2.39
  Table 23: Provided are the values of each of the parameters (as described above) measured in B. juncea accessions (Seed ID) under normal conditions.

• TABLE 24
  Correlation between the expression level of selected genes of some embodiments
  of the invention in various tissues and the phenotypic performance under
  normal or normal conditions across B. Juncea accessions

  			Exp.	Corr.				Exp.	Corr.
  Gene Name	R	P value	set	Set ID	Gene Name	R	P value	set	Set ID

  LYD537	0.76	7.70E−02	2	19	LYD537	0.84	3.50E−02	2	18
  LYD537	0.73	9.84E−02	2	17	LYD537	0.73	9.68E−02	2	2
  LYD537	0.72	1.95E−02	3	4	LYD538	0.77	7.11E−02	2	21
  LYD538	0.90	1.59E−02	2	2	LYD538	0.72	1.09E−01	2	12
  LYD538	0.70	2.40E−02	3	19	LYD538	0.82	4.06E−03	3	11
  LYD538	0.72	2.00E−02	3	3	LYD538	0.76	6.83E−03	5	7
  LYD539	0.75	1.24E−02	3	4	LYD540	0.80	5.79E−02	2	21
  LYD540	0.85	3.24E−02	2	3	LYD540	0.80	5.64E−02	2	7
  LYD540	0.90	1.36E−02	2	2	LYD540	0.86	2.80E−02	2	12
  LYD540	0.76	1.15E−02	3	4	LYD540	0.74	9.59E−03	5	17
  Table 24. Provided are the correlations (R) between the expression levels of yield improving genes and their homologues in tissues [Leaves, meristem, flower and pods; Expression sets (Exp)] and the phenotypic performance in various yield, biomass, growth rate and/or vigor components [Correlation vector (corr.)] under stress conditions or normal conditions across B, juncea accessions. P = p value.

Example 7 Production of B. juncea Transcriptome and High Throughput Correlation Analysis with Yield Parameters of juncea Grown Under Various Population Densities Using 60K B. juncea Oligonucleotide Micro-Arrays
• In order to produce a high throughput correlation analysis, the present inventors utilized a B. juncea oligonucleotide micro-army, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?lPage=50879]. The array oligonucleotide represents about 60,000 B. juncea genes and transcripts. In order to define correlations between the levels of RNA expression with yield components or vigor related parameters, various plant characteristics of two different B. juncea varieties grown under seven different population densities were analyzed and used for RNA expression analysis. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test.
• Correlation of B. juncea Genes' Expression Levels with Phenotypic Characteristics Across Seven Population Densities for Two Ecotypes
• Experimental Procedures
• Two B. juncea varieties were grown in a field under seven population densities (10, 60, 120, 160, 200, 250 and 300 plants per m²) in two repetitive plots. Briefly, the growing protocol was as follows: B. juncea seeds were sown in soil and grown under normal condition till harvest. In order to define correlations between the levels of RNA expression with yield components or vigor related parameters, the two different B. juncea varieties grown under various population densities were analyzed and used for gene expression analyses. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test for each ecotype independently.

• TABLE 25
  Tissues used for B. juncea transcriptome expression sets

  Expression Set	Set ID
  Meristem under normal growth conditions various population	1 + 2
  densities
  Flower under normal growth conditions various population	3
  densities
  Table 25: Provided are the identification (ID) digits of each of the B, juncea expression sets.

• RNA extraction—the two B. juncea varieties grown under seven population densities were sample per each treatment. Plant tissues [Flower and Lateral meristem] growing under Normal conditions were sampled and RNA was extracted as described above. For convenience, each micro-array expression information tissue type has received a Set ID.
• The collected data parameters were as follows:
• Fresh weight (plot-harvest) [gr/plant]—total fresh weight per plot at harvest time normalized to the number of plants per plot.
• Seed weight [gr/plant]—total seeds from each plot was extracted, weighted and normalized for plant number in each plot.
• Harvest index—The harvest index was calculated: seed weight/fresh weight.
• Days till bolting/flowering—number of days till 50% bolting/flowering for each plot.
• SPAD—Chlorophyll content was determined using a Minolta SPAD 502 chlorophyll meter and measurement was performed at time of flowering. SPAD meter readings were done on young fully developed leaf Three measurements per leaf were taken for each plot.
• Main branch—average node length—total length/total number of nods on main branch.
• Lateral branch—average node length—total length/total number of nods on lateral branch.
• Main branch—20th length—the length of the pod on the 20^th node from the apex of main branch.
• Lateral branch—20th length—the length of the pod on the 20^th node from the apex of lateral branch.
• Main branch—20th seed No.—number of seeds in the pod on the 20^th node from the apex of main branch.
• Lateral branch—20th seed number—number of seeds in the pod on the 20^th node from the apex of lateral branch.
• Number of lateral branches—total number of lateral branches, average of three plants per plot.
• Main branch height [cm]—total length of main branch.
• Min-Lateral branch position—lowest node on the main branch that has developed lateral branch.
• Max-Lateral branch position [#node of main branch]—highest node on the main branch that has developed lateral branch.
• Max-number of nodes in lateral branch—the highest number of node that a lateral branch had per plant.
• Max-length of lateral branch [cm]—the highest length of lateral branch per plant.
• Max diameter of lateral branch [mm]—the highest base diameter that a lateral branch had per plant.
• Oil content—Indirect oil content analysis was carried out using Nuclear Magnetic Resonance (NMR) Spectroscopy, which measures the resonance energy absorbed by hydrogen atoms in the liquid state of the sample [See for example, Conway T F. and Earle F R., 1963, Journal of the American Oil Chemists' Society. Springer Berlin/Heidelberg, ISSN: 0003-021X (Print) 1558-9331 (Online)].
• Fresh weight (single plant) (gr/plant)—average fresh weight of three plants per plot taken at the middle of the season.
• Main branch base diameter [mm]—the based diameter of main branch, average of three plants per plot.
• 1000 Seeds [gr]—weight of 1000 seeds per plot.
• Main branch-total number of pods—total number of pods on the main branch, average of three plants per plot.
• Main branch-dist. 1-20—the length between the youngest pod and pod number 20 on the main branch, average of three plants per plot.
• Lateral branch-total number of pods—total number of pods on the lowest lateral branch, average of three plants per plot.
• Lateral branch-dis. 1-20—the length between the youngest pod and pod number 20 on the lowest lateral branch, average of three plants per plot.
• Dry weight/plant—weight of total plants per plot at harvest after three days at oven at 60° C. normalized for the number of plants per plot.
• Total leaf area—Total leaf area per plot was calculated based on random three plants and normalized for number of plants per plot.
• Total Perim.—total perimeter of leaves, was calculated based on random three plants and normalized for number of plants per plot.
• Experimental Results
• Two B. juncea varieties were grown under seven different population densities and characterized for 30. The average for each of the measured parameter was calculated using the JMP software and values are summarized in Tables 27-29 below. Subsequent correlation analysis between the expression of selected genes in various transcriptome expression sets and the average parameters was conducted. Results were then integrated to the database.

• TABLE 26
  Correlation parameters in B. juncea accessions

  Correlated parameter with	Correlation ID

  Main branch base diameter [mm]	1
  Fresh Weight (single plant) [gr/plant]	2
  Main branch height [cm]	3
  Number of lateral branches (number)	4
  Min-Lateral branch position	5
  (number of node on the main stem)
  Max-Lateral branch position	6
  (number of node on the main stem)
  Max-Number of nodes in lateral branch (number)	7
  Max-Length of lateral branch [cm]	8
  Max-Diameter of lateral branch [mm]	9
  Main branch-total number of pods (number)	10
  Main branch-dist. 1-20	11
  Main branch-20th length (cm)	12
  Main branch-20th seed number (number)	13
  Lateral branch-total number of pods (number)	14
  Lateral branch-dist. 1-20	15
  Lateral branch-20th length (cm)	16
  Lateral branch-20th seed number (number)	17
  Oil content (mg)	18
  SPAD	19
  days till bolting (days)	20
  days till flowering (days)	21
  Fresh weight (at harvest)/plant (gr/plant)	22
  Dry weight/plant (gr/plant)	23
  Seed weight/plant (gr/plant)	24
  Fresh weight (harvest)/hectare (Kg/hectare)	25
  Dry weight/hectare (Kg/hectare)	26
  Seed weight/hectare	27
  1000Seeds [gr]	28
  Total leaf area (cm)	29
  Total perim.	30
  Table 26. Provided are the B. juncea correlated parameters. “gr.” = grams; mm = millimeters; “cm” = centimeters; “mg” = milligrams; “SPAD” = chlorophyll levels; “Kg.” = kilograms;

• TABLE 27
  Measured parameters in B. juncea accessions
  at various population densities (line 1-6)

  Ecotype

  Treatment	Line-1	Line-2	Line-3	Line-4	Line-5	Line-6

  1	14.77	6.90	5.62	4.99	6.45	3.95
  2	0.37	0.04	0.03	0.02	0.04	0.02
  3	118.67	115.50	111.33	106.00	117.50	108.00
  4	17.17	19.17	15.83	19.33	18.33	17.83
  5	1.00	11.00	7.00	11.00	9.00	9.00
  6	20.00	23.00	19.00	24.00	22.00	20.00
  7	10.00	4.00	4.00	4.00	6.00	4.00
  8	122.00	41.00	43.00	36.00	40.00	42.00
  9	7.70	2.90	2.50	2.00	3.40	2.50
  10	20.00	15.33	17.67	16.50	23.17	16.83
  11	42.35	27.90	31.22	26.05	27.72	31.85
  12	5.12	4.63	4.60	4.67	4.73	4.68
  13	20.00	17.67	18.00	18.50	17.67	17.50
  14	17.33	11.67	10.67	10.17	12.50	9.83
  15	40.73	17.53	19.08	15.65	15.23	17.73
  16	5.12	4.48	4.37	4.33	4.35	4.40
  17	21.67	19.33	17.00	18.83	15.67	17.17
  18	28.86	29.62	29.57	30.59	29.87	25.22
  19	43.49	41.95	40.48	37.93	39.50	45.57
  20	53.00	50.50	48.00	53.00	50.00	51.50
  21	67.00	64.00	64.00	64.00	64.00	62.50
  22	0.26	0.02	0.01	0.01	0.01	0.01
  23	0.07	0.01	0.00	0.00	0.00	0.00
  24	0.02	0.00	0.00	0.00	0.00	0.00
  25	22434.19	22067.24	32929.29	18596.04	20654.32	24019.71
  26	6109.02	9857.37	8940.70	4363.21	6702.22	6009.09
  27	1797.45	2307.34	2552.84	1466.27	2100.38	1901.67
  28	1.80	1.75	1.62	1.99	1.92	1.54
  29	508.27	37.49	25.00	14.33	50.79	29.13
  30	862.83	100.50	67.98	37.91	97.51	61.17
  Table 27

• TABLE 28
  Measured parameters in B. juncea accessions
  at various population densities (line 7-12)

  Ecotype

  Treatment	Line-7	Line-8	Line-9	Line-10	Line-11	Line-12

  1	7.37	18.90	7.81	6.79	6.95	7.53333
  2	0.07	0.34	0.04	0.03	0.025	0.02833
  3	116.00	133.17	144.58	144.92	138.5	144.167
  4	16.17	12.50	15.33	16.83	16.6667	16.6667
  5	5.00	1.00	8.00	9.00	8	10
  6	20.00	14.00	17.00	21.00	18	19
  7	6.00	11.00	6.00	5.00	4	6
  8	78.00	127.00	42.00	34.00	23	38
  9	4.40	8.40	3.00	2.60	2.1	2.8
  10	15.17	30.67	35.17	29.83	30.8333	29.3333
  11	37.58	38.72	32.85	28.77	25.3	26.3833
  12	5.10	4.67	3.85	4.43	4.11667	4.11667
  13	17.67	14.33	10.33	13.83	10.3333	11
  14	14.00	29.83	17.33	12.83	11.1667	13
  15	28.25	33.42	14.27	9.83	8.6	10.9833
  16	4.95	4.48	3.67	3.98	4.03333	3.96667
  17	14.55	12.83	10.17	12.33	10.6667	9.83333
  18	26.78	34.39	38.65	39.66	36.795	37.1
  19	40.89	43.83	41.31	40.86	39.31	40.46
  20	53.00	55.00	50.50	47.00	48	49
  21	62.50	64.00	61.00	61.00	61	61
  22	0.05	0.19	0.02	0.01	0.0098	0.00884
  23	0.01	0.05	0.00	0.00	0.00377	0.00296
  24	0.00	0.01	0.00	0.00	0.00084	0.00082
  25	33376.44	16427.35	15747.62	18531.77	17182.5	16833.3
  26	7906.66	3979.78	4609.25	5801.02	6581.38	5656.27
  27	2247.01	1270.04	1560.53	1732.85	1472.18	1560.8
  28	1.56	2.82	3.20	2.88	3.25697	3.27691
  29	76.39	1338.58	76.82	34.46	28.2774	41.3294
  30	219.14	1518.31	162.79	82.77	75.366	83.49
  Table 28.

• TABLE 29
  Measured parameters in B. juncea accessions
  at various population densities (line 13-14)

  Ecotype

  Treatment	Line-13	Line-14

  1	5.44167	8.76667
  2	0.02417	0.06583
  3	135.75	157.333
  4	15.5	12.8333
  5	8	3
  6	18	16
  7	4	11
  8	25	109
  9	2.35	8
  10	25.3333	33.8333
  11	25.0667	45.25
  12	4.23333	4.43333
  13	10.6667	13.1667
  14	9	18.5
  15	6.35	21.5833
  16	3.7	4.71667
  17	9	11.1667
  18	37.61	37.545
  19	47.48	39.21
  20	49	51.5
  21	61	61
  22	0.00839	0.03974
  23	0.00253	0.01152
  24	0.00073	0.0034
  25	23055.7	20833.3
  26	6882.52	6039.66
  27	2005.71	1780.97
  28	3.43024	2.77362
  29	92.8963	218.155
  30	143.902	328.97
  Table 29: Provided are the values of each of the parameters (as described above) measured in B. juncea (grown in seven population densities (Populat. Density) under normal conditions. Param. = parameter.

• TABLE 30
  Correlation between the expression level of selected genes of some embodiments
  of the invention in various tissues and the phenotypic performance under normal
  conditions at different densities across B. Juncea accessions

  			Exp.	Corr.				Exp.	Corr.
  Gene Name	R	P value	set	Set ID	Gene Name	R	P value	set	Set ID

  LYD537	0.90	6.06E−03	2	9	LYD537	0.89	6.54E−03	2	8
  LYD537	0.94	1.69E−03	2	1	LYD537	0.88	9.11E−03	2	7
  LYD537	0.89	7.83E−03	2	15	LYD537	0.76	4.62E−02	2	16
  LYD537	0.99	4.02E−05	2	24	LYD537	0.97	2.88E−04	2	13
  LYD537	0.98	1.22E−04	2	29	LYD537	0.75	5.44E−02	2	11
  LYD537	0.98	8.94E−05	2	2	LYD537	0.83	2.18E−02	2	14
  LYD537	0.99	4.94E−05	2	23	LYD537	0.97	2.91E−04	2	30
  LYD537	0.88	8.8OE−O3	2	21	LYD537	0.98	5.98E−05	2	22
  LYD537	0.82	2.42E−02	2	17	LYD538	0.82	2.28E−02	2	9
  LYD538	0.81	2.80E−02	2	8	LYD538	0.89	7.67E−03	2	1
  LYD538	0.82	2.47E−02	2	7	LYD538	0.81	2.78E−02	2	15
  LYD538	0.94	1.52E−03	2	24	LYD538	0.95	1.10E−03	2	13
  LYD538	0.94	1.59E−03	2	29	LYD538	0.94	1.59E−03	2	2
  LYD538	0.73	6.00E−02	2	14	LYD538	0.94	1.71E−03	2	23
  LYD538	0.92	3.68E−03	2	30	LYD538	0.93	2.62E−03	2	21
  LYD538	0.94	1.94E−03	2	22	LYD538	0.75	5.03E−02	2	17
  LYD539	0.70	7.93E−02	2	9	LYD539	0.80	3.23E−02	2	8
  LYD539	0.80	3.12E−02	2	15	LYD539	0.92	3.61E−03	2	16
  LYD539	0.93	2.08E−03	2	12	LYD539	0.85	1.43E−02	2	11
  LYD539	0.76	4.93E−02	2	14	LYD540	0.78	3.84E−02	2	6
  LYD540	0.88	9.11E−03	2	5
  Table 30. Provided are the correlations (R) between the expression levels of yield improving genes and their homologues in tissues [meristem and flower; Expression sets (Exp)] and the phenotypic performance in various yield, biomass, growth rate and/or vigor components [Correlation vector (corr.)] under stress conditions or normal conditions across B, juncea accessions. P = p value.

Example 8 Production of Sorghum Transcriptome and High Throughput Correlation Analysis with ABST Related Parameters Using 44K Sorghum Oligonucleotide Micro-Arrays
• In order to produce a high throughput correlation analysis between plant phenotype and gene expression level, the present inventors utilized a sorghum oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?lPage=50879]. The array oligonucleotide represents about 44,000 sorghum genes and transcripts. In order to define correlations between the levels of RNA expression with ABST, yield and NUE components or vigor related parameters, various plant characteristics of 17 different sorghum hybrids were analyzed. Among them, 10 hybrids encompassing the observed variance were selected for RNA expression analysis. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test [Hypertext Transfer Protocol://World Wide Web (dot) davidmlane (dot) com/hyperstat/A34739 (dot) html].
• Correlation of Sorghum Varieties Across Ecotypes Grown Under Regular Growth Conditions, Severe Drought Conditions and Low Nitrogen Conditions
• Experimental Procedures
• 17 Sorghum varieties were grown in 3 repetitive plots, in field. Briefly, the growing protocol was as follows:
• 1. Regular growth conditions: sorghum plants were grown in the field using commercial fertilization and irrigation protocols (370 liter per meter², fertilization of 14 units of 21% urea per entire growth period).
• 2. Drought conditions: sorghum seeds were sown in soil and grown under normal condition until around 35 days from sowing, around stage V8 (eight green leaves are fully expanded, booting not started yet). At this point, irrigation was stopped, and severe drought stress was developed.
• 3. Low Nitrogen fertilization conditions: sorghum plants were fertilized with 50% less amount of nitrogen in the field than the amount of nitrogen applied in the regular growth treatment. All the fertilizer was applied before flowering.
• Analyzed Sorghum tissues—All 10 selected Sorghum hybrids were sample per each treatment. Tissues [Flag leaf, Flower meristem and Flower] from plants growing under normal conditions, severe drought stress and low nitrogen conditions were sampled and RNA was extracted as described above. Each micro-array expression information tissue type has received a Set ID as summarized in Table 31 below.

• TABLE 31
  Sorghum transcriptome expression sets

  	Expression Set	Set ID

  	Flag leaf Normal	1
  	Flower meristem Normal	2
  	Flower Normal	3
  	Flag leaf Low Nitrogen	4
  	Flower meristem Low Nitrogen	5
  	Flower Low Nitrogen	6
  	Flag leaf Drought	7
  	Flower meristem Drought	8
  	Flower Drought	9
  Table 31: Provided are the sorghum transcriptome expression sets 1, 2, 3 and 4. Flag leaf = the leaf below the flower; Flower meristem = Apical meristem following panicle initiation; Flower = the flower at the anthesis day. Expression sets 1, 2 and 3 are from plants grown under normal conditions. Expression sets 4-6 derived from plants grown under low Nitrogen conditions. Expression sets 7-9 are from plants grown under drought conditions.

• The following parameters were collected using digital imaging system:
• At the end of the growing period the grains were separated from the Plant ‘Head’ and the following parameters were measured and collected:
• Average Grain Area (cm²)—A sample of ˜200 grains were weighted, photographed and images were processed using the below described image processing system. The grain area was measured from those images and was divided by the number of grains.
• (I) Upper and Lower Ratio Average of Grain Area, width, diameter and perimeter—Grain projection of area, width, diameter and perimeter were extracted from the digital images using open source package imagej (nih). Seed data was analyzed in plot average levels as follows:
• Average of all seeds;
• Average of upper 20% fraction—contained upper 20% fraction of seeds;
• Average of lower 20% fraction—contained lower 20% fraction of seeds;
• Further on, ratio between each fraction and the plot average was calculated for each of the data parameters.
• At the end of the growing period 5 ‘Heads’ were, photographed and images were processed using the below described image processing system.
• (II) Head Average Area (cm)—At the end of the growing period 5 ‘Heads’ were, photographed and images were processed using the below described image processing system. The ‘Head’ area was measured from those images and was divided by the number of ‘Heads’.
• (III) Head Average Length (on)—At the end of the growing period 5 ‘Heads’ were, photographed and images were processed using the below described image processing system. The ‘Head’ length (longest axis) was measured from those images and was divided by the number of ‘Heads’.
• (IV) Head Average width (cm)—At the end of the growing period 5 ‘Heads’ were, photographed and images were processed using the below described image processing system. The ‘Head’ width was measured from those images and was divided by the number of ‘Heads’.
• (V) Head Average width (cm)—At the end of the growing period 5 ‘Heads’ were, photographed and images were processed using the below described image processing system. The ‘Head’ perimeter was measured from those images and was divided by the number of ‘Heads’.
• The image processing system was used, which consists of a personal desktop computer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ 1.37, Java based image processing software, which was developed at the U.S. National Institutes of Health and is freely available on the internet at Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/. Images were captured in resolution of 10 Mega Pixels (3888×2592 pixels) and stored in a low compression JPEG (Joint Photographic Experts Group standard) format. Next, image processing output data for seed area and seed length was saved to text files and analyzed using the JMP statistical analysis software (SAS institute).
• Additional parameters were collected either by sampling 5 plants per plot or by measuring the parameter across all the plants within the plot.
• Total Grain Weight/Head (gr.) (grain yield)—At the end of the experiment (plant ‘Heads’) heads from plots within blocks A-C were collected. 5 heads were separately threshed and grains were weighted, all additional heads were threshed together and weighted as well. The average grain weight per head was calculated by dividing the total grain weight by number of total heads per plot (based on plot). In case of 5 heads, the total grains weight of 5 heads was divided by 5.
• FW Head/Plant gram—At the end of the experiment (when heads were harvested) total and 5 selected heads per plots within blocks A-C were collected separately. The heads (total and 5) were weighted (gr.) separately and the average fresh weight per plant was calculated for total (FW Head/Plant gr. based on plot) and for 5 (FW Head/Plant gr. based on 5 plants).
• Plant height—Plants were characterized for height during growing period at 5 time points. In each measure, plants were measured for their height using a measuring tape. Height was measured from ground level to top of the longest leaf.
• SPAD—Chlorophyll content was determined using a Minolta SPAD 502 chlorophyll meter and measurement was performed 64 days post sowing. SPAD meter readings were done on young fully developed leaf. Three measurements per leaf were taken per plot.
• Vegetative fresh weight and Heads—At the end of the experiment (when Inflorescence were dry) all Inflorescence and vegetative material from plots within blocks A-C were collected. The biomass and Heads eight of each plot was separated, measured and divided by the number of Heads.
• Plant biomass (Fresh weight)—At the end of the experiment (when Inflorescence were dry) the vegetative material from plots within blocks A-C were collected. The plants biomass without the Inflorescence were measured and divided by the number of Plants.
• FW Heads/(FW Heads+FW Plants)—The total fresh weight of heads and their respective plant biomass were measured at the harvest day. The heads weight was divided by the sum of weights of heads and plants.
• Experimental Results
• 17 different sorghum varieties were grown and characterized for different parameters: The average for each of the measured parameter was calculated using the JMP software (Tables 33-34) and a subsequent correlation analysis between the various transcriptome expression sets (Table 31) and the average parameters (Tables 33-34), was conducted (Table 35). Results were then integrated to the database.

• TABLE 32
  Sorghum correlated parameters (vectors)

  Correlated parameter with	Correlation ID

  Total grain weight/Head gr (based on plot), Normal	1
  Total grain weight/Head gr (based on 5 heads), Normal	2
  Head Average Area (cm2), Normal	3
  Head Average Perimeter (cm), Normal	4
  Head Average Length (cm), Normal	5
  Head Average Width (cm), Normal	6
  Average Grain Area (cm2), Normal	7
  Upper Ratio Average Grain Area, Normal	8
  Lower Ratio Average Grain Area, Normal	9
  Lower Ratio Average Grain Perimeter, Normal	10
  Lower Ratio Average Grain Length, Normal	11
  Lower Ratio Average Grain Width, Normal	12
  Final Plant Height (cm), Normal	13
  FW - Head/Plant gr (based on 5 plants), Normal	14
  FW - Head/Plant gr (based on plot), Normal	15
  FW/Plant gr (based on plot), Normal	16
  Leaf SPAD 64 DPS (Days Post Sowing), Normal	17
  FW Heads/(FW Heads + FW Plants) (all plot), Normal	18
  [Plant biomass (FW)/SPAD 64 DPS], Normal	19
  [Grain Yield + plant biomass/SPAD 64 DPS], Normal	20
  [Grain yield/SPAD 64 DPS], Normal	21
  Total grain weight/Head (based on plot) gr, Low N	22
  Total grain weight/Head gr (based on 5 beads), Low N	23
  Head Average Area (cm2), Low N	24
  Head Average Perimeter (cm), Low N	25
  Head Average Length (cm), Low N	26
  Head Average Width (cm), Low N	27
  Average Grain Area (cm2), Low N	28
  Upper Ratio Average Grain Area, Low N	29
  Lower Ratio Average Grain Area, Low N	30
  Lower Ratio Average Grain Perimeter, Low N	31
  Lower Ratio Average Grain Length, Low N	32
  Lower Ratio Average Grain Width, Low N	33
  Final Plant Height (cm), Low N	34
  FW - Head/Plant gr (based on 5 plants), Low N	35
  FW - Head/Plant gr (based on plot), Low N	36
  FW/Plant gr (based on plot), Low N	37
  Leaf SPAD 64 DPS (Days Post Sowing), Low N	38
  FW Heads/(FW Heads + FW Plants)(all plot), Low N	39
  [Plant biomass (FW)/SPAD 64 DPS], Low N	40
  [Grain Yield + plant biomass/SPAD 64 DPS], Low N	41
  [Grain yield/SPAD 64 DPS], Low N	42
  Total grain weight/Head gr (based on plot) Drought	43
  Head Average Area (cm2), Drought	44
  Head Average Perimeter (cm), Drought	45
  Head Average Length (cm), Drought	46
  Head Average Width (cm), Drought	47
  Average Grain Area (cm2), Drought	48
  Upper Ratio Average Grain Area, Drought	49
  Final Plant Height (cm), Drought	50
  FW - Head/Plant gr (based on plot), Drought	51
  FW/Plant gr (based on plot), Drought	52
  Leaf SPAD 64 DPS (Days Post Sowing), Drought	53
  FW Heads/(FW Heads + FW Plants)(all plot), Drought	54
  [Plant biomass (FW)/SPAD 64 DPS], Drought	55
  Table 32. Provided are the Sorghum correlated parameters (vectors), “gr.” = grams; “SPAD” = chlorophyll levels; “FW” = Plant Fresh weight; “normal” = standard growth conditions.

• TABLE 33
  Measured parameters in Sorghum accessions

  Ecotype

  Treatment	Line-1	Line-2	Line-3	Line-4	Line-5	Line-6	Line-7	Line-8	Line-9

  1	31.12	26.35	18.72	38.38	26.67	28.84	47.67	31.00	39.99
  2	47.40	46.30	28.37	70.40	32.15	49.23	63.45	44.45	56.65
  3	120.14	167.60	85.14	157.26	104.00	102.48	168.54	109.32	135.13
  4	61.22	67.90	56.26	65.38	67.46	67.46	74.35	56.16	61.64
  5	25.58	26.84	21.02	26.84	23.14	21.82	31.33	23.18	25.70
  6	5.97	7.92	4.87	7.43	5.58	5.88	6.78	5.99	6.62
  7	0.10	0.11	0.13	0.13	0.14	0.14	0.11	0.11	0.10
  8	1.22	1.30	1.13	1.14	1.16	1.15	1.19	1.23	1.25
  9	0.83	0.74	0.78	0.80	0.70	0.70	0.83	0.81	0.84
  10	0.91	0.87	0.91	0.95	0.90	0.91	0.91	0.91	0.92
  11	0.91	0.88	0.92	0.91	0.89	0.88	0.91	0.90	0.92
  12	0.91	0.83	0.85	0.87	0.79	0.80	0.90	0.89	0.91
  13	95.25	79.20	197.85	234.20	189.40	194.67	117.25	92.80	112.65
  14	406.50	518.00	148.00	423.00	92.00	101.33	423.50	386.50	409.50
  15	175.15	223.49	56.40	111.62	67.34	66.90	126.18	107.74	123.86
  16	162.56	212.59	334.83	313.46	462.28	318.26	151.13	137.60	167.98
  17	43.01	.	43.26	44.74	45.76	41.61	45.21	45.14	43.03
  18	0.51	0.51	0.12	0.26	0.12	0.18	0.46	0.43	0.42
  19	0.72	0.43	0.86	0.58	0.69	1.05	0.69	0.93	0.84
  20	4.50	8.17	7.87	10.68	8.34	4.40	3.74	4.83	3.67
  21	3.78	7.74	7.01	10.10	7.65	3.34	3.05	3.90	2.83
  22	25.95	30.57	19.37	35.62	25.18	22.18	49.96	27.48	51.12
  23	50.27	50.93	36.13	73.10	37.87	36.40	71.67	35.00	76.73
  24	96.24	214.72	98.59	182.83	119.64	110.19	172.36	84.81	156.25
  25	56.32	79.20	53.25	76.21	67.27	59.49	79.28	51.52	69.88
  26	23.22	25.58	20.93	28.43	24.32	22.63	32.11	20.38	26.69
  27	5.26	10.41	5.93	8.25	6.19	6.12	6.80	5.25	7.52
  28	0.11	0.11	0.14	0.12	0.14	0.13	0.12	0.12	0.12
  29	1.18	1.31	1.11	1.21	1.19	1.18	1.16	1.23	1.17
  30	0.82	0.77	0.81	0.79	0.78	0.80	0.83	0.79	0.81
  31	0.90	0.88	0.92	0.90	0.92	0.92	0.92	0.89	0.90
  32	0.91	0.90	0.92	0.90	0.91	0.93	0.92	0.89	0.90
  33	0.90	0.85	0.89	0.88	0.86	0.87	0.91	0.89	0.90
  34	104.00	80.93	204.73	125.40	225.40	208.07	121.40	100.27	121.13
  35	388.00	428.67	297.67	280.00	208.33	303.67	436.00	376.33	474.67
  36	214.78	205.05	73.49	122.96	153.07	93.23	134.11	77.43	129.63
  37	204.78	199.64	340.51	240.60	537.78	359.40	149.20	129.06	178.71
  38	38.33	38.98	42.33	40.90	43.15	39.85	42.68	43.31	39.01
  39	0.51	0.51	0.17	0.39	0.21	0.19	0.48	0.37	0.42
  40	5.34	5.12	8.05	5.88	12.46	9.02	3.50	2.98	4.58
  41	6.02	5.91	8.50	6.75	13.05	9.58	4.67	3.61	5.89
  42	0.68	0.78	0.46	0.87	0.58	0.56	1.17	0.63	1.31
  43	22.11	16.77	9.19	104.44	3.24	22.00	9.97	18.58	29.27
  44	83.14	107.79	88.68	135.91	90.76	123.95	86.06	85.20	113.10
  45	52.78	64.49	56.59	64.37	53.21	71.66	55.61	52.96	69.83
  46	21.63	21.94	21.57	22.01	20.99	28.60	21.35	20.81	24.68
  47	4.83	6.31	5.16	7.78	5.28	5.49	5.04	5.07	5.77
  48	0.10	0.11	0.11	0.09	0.09	0.11
  49	1.31	1.19	1.29	1.46	1.21	1.21
  50	89.40	75.73	92.10	94.30	150.80	110.73	99.20	84.00	99.00
  51	154.90	122.02	130.51	241.11	69.03	186.41	62.11	39.02	58.94
  52	207.99	138.02	255.41	402.22	233.55	391.75	89.31	50.61	87.02
  53	40.58	40.88	45.01	42.30	45.24	40.56	44.80	45.07	40.65
  54	0.42	0.47	0.42	0.37	0.23	0.31	0.41	0.44	0.40
  55	5.13	3.38	5.67	9.51	5.16	9.66	1.99	1.12	2.14
  Table 33: Provided are the values of each of the parameters (as described above) measured in Sorghum accessions (ecotype) under normal, low nitrogen and drought conditions. Growth conditions are specified in the experimental procedure section.

• TABLE 34
  Additional measured parameters in Sorghum accessions

  Treatment

  Ecotype	Line-10	Line-11	Line-12	Line-13	Line-14	Line-15	Line-16	Line-17

  1	38.36	32.10	32.69	32.79	51.53	35.71	38.31	42.44
  2	60.00	45.45	58.19	70.60	70.10	53.95	59.87	52.65
  3	169.03	156.10	112.14	154.74	171.70	168.51	162.51	170.46
  4	71.40	68.56	56.44	67.79	71.54	78.94	67.03	74.11
  5	28.82	28.13	22.97	28.09	30.00	30.54	27.17	29.26
  6	7.42	6.98	6.19	7.02	7.18	7.00	7.39	7.35
  7	0.12	0.12	0.11	0.12	0.11	0.10	0.11	0.11
  8	1.24	1.32	1.22	1.18	1.18	1.22	1.25	1.22
  9	0.79	0.77	0.80	0.81	0.82	0.81	0.82	0.82
  10	0.93	0.91	0.92	0.90	0.91	0.90	0.91	0.91
  11	0.92	0.89	0.91	0.91	0.91	0.90	0.90	0.91
  12	0.85	0.86	0.88	0.90	0.90	0.91	0.90	0.90
  13	97.50	98.00	100.00	105.60	151.15	117.10	124.45	126.50
  14	328.95	391.00	435.75	429.50	441.00	415.75	429.50	428.50
  15	102.75	82.33	77.59	91.17	150.44	109.10	107.58	130.88
  16	128.97	97.62	99.32	112.24	157.42	130.55	135.66	209.21
  17	45.59	44.83	45.33	46.54	43.99	45.09	45.14	43.13
  18	0.44	0.46	0.45	0.45	0.51	0.46	0.44	0.39
  19	0.72	0.72	0.70	1.17	0.79	0.85	0.98
  20	2.89	2.91	3.12	4.75	3.69	3.85	5.84
  21	2.18	2.19	2.41	3.58	2.90	3.01	4.85
  22	36.84	29.45	26.70	29.42	51.12	37.04	39.85	41.78
  23	57.58	42.93	36.47	68.60	71.80	49.27	43.87	52.07
  24	136.71	137.70	96.54	158.19	163.95	138.39	135.46	165.64
  25	66.17	67.37	57.90	70.61	73.76	66.87	65.40	75.97
  26	26.31	25.43	23.11	27.87	28.88	27.64	25.52	30.33
  27	6.59	6.85	5.32	7.25	7.19	6.27	6.57	6.82
  28	0.13	0.13	0.12	0.12	0.11	0.11	0.12	0.11
  29	1.22	1.24	1.19	1.23	1.16	1.34	1.21	1.21
  30	0.77	0.74	0.80	0.79	0.82	0.80	0.81	0.81
  31	0.91	0.89	0.90	0.90	0.91	0.89	0.90	0.90
  32	0.91	0.89	0.90	0.89	0.91	0.89	0.89	0.90
  33	0.86	0.84	0.90	0.89	0.91	0.90	0.90	0.90
  34	94.53	110.00	115.07	104.73	173.67	115.60	138.80	144.40
  35	437.67	383.00	375.00	425.00	434.00	408.67	378.50	432.00
  36	99.83	76.95	84.25	92.24	138.83	113.32	95.50	129.49
  37	124.27	101.33	132.12	117.90	176.99	143.67	126.98	180.45
  38	42.71	40.08	43.98	45.44	44.75	42.58	43.81	46.73
  39	0.44	0.43	0.39	0.44	0.44	0.44	0.43	0.42
  40	2.91	2.53	3.00	2.60	3.96	3.38	2.90	3.86
  41	3.77	3.26	3.61	3.24	5.10	4.25	3.81	4.76
  42	0.86	0.73	0.61	0.65	1.14	0.87	0.91	0.89
  43	10.45	14.77	12.86	18.24	11.60	18.65	16.36
  44	100.79	80.41	126.89	86.41	92.29	77.89	76.93
  45	65.14	55.27	69.06	53.32	56.29	49.12	51.88
  46	24.28	21.95	24.98	19.49	20.42	16.81	18.88
  47	5.37	4.66	6.35	5.58	5.76	5.86	5.10
  48
  49
  50	92.20	81.93	98.80	86.47	99.60	83.00	83.53	92.30
  51	76.37	33.47	42.20	41.53	131.67	60.84	44.33	185.44
  52	120.43	37.21	48.18	44.20	231.60	116.01	123.08	342.50
  53	45.43	42.58	44.18	44.60	42.41	43.25	40.30	40.75
  54	0.44	0.47	0.47	0.48	0.35	0.35	0.23	0.33
  55	2.65	0.87	1.09	0.99	5.46	2.68	3.05	8.40
  Table 34: Provided are the values of each of the parameters (as described above) measured in Sorghum accessions (ecotype) under normal, low nitrogen and drought conditions. Growth conditions are specified in the experimental procedure section.

• TABLE 35
  Correlation between the expression level of selected genes of some embodiments
  of the invention in various tissues and the phenotypic performance under normal
  or abiotic stress conditions across Sorghum accessions

  Gene			Exp.	Corr.	Gene			Exp.	Corr.
  Name	R	P value	set	Set ID	Name	R	P value	set	Set ID

  LYD604	0.71	3.28E−02	1	20	LYD605	0.72	2.91E−02	1	21
  LYD605	0.73	2.49E−02	1	20	LYD606	0.73	1.60E−02	3	13
  LYD606	0.90	4.05E−04	3	1	LYD606	0.70	2.31E−02	3	9
  LYD606	0.90	4.24E−04	8	53	LYD606	0.76	1.04E−02	6	30
  LYD606	0.70	2.29E−02	6	33	LYD606	0.78	8.33E−03	6	32
  LYD606	0.82	3.87E−03	6	31	LYD606	0.81	7.55E−03	1	21
  LYD606	0.84	4.28E−03	1	20	LYD606	0.92	1.57E−04	9	50
  LYD606	0.72	1.90E−02	7	51	LYD607	0.71	2.11E−02	2	13
  LYD607	0.71	2.10E−02	2	1	LYD607	0.82	3.42E−03	4	29
  LYD607	0.86	1.33E−03	5	22	LYD607	0.85	1.86E−03	5	42
  LYD607	0.80	5.95E−03	5	34	LYD608	0.88	9.15E−04	2	8
  LYD608	0.82	4.05E−03	2	7	LYD608	0.86	1.29E−03	4	29
  LYD608	0.71	2.22E−02	4	27	LYD608	0.77	8.57E−03	6	39
  LYD608	0.75	1.30E−02	6	32	LYD608	0.72	1.77E−02	5	28
  LYD608	0.80	9.74E−03	1	21	LYD608	0.83	5.67E−03	1	20
  LYD609	0.76	1.04E−02	2	1	LYD609	0.79	6.60E−03	8	55
  LYD609	0.71	2.15E−02	8	51	LYD609	0.80	5.47E−03	8	52
  LYD609	0.74	1.46E−02	5	36	LYD609	0.74	1.38E−02	5	41
  LYD609	0.76	1.04E−02	5	37	LYD610	0.89	6.35E−04	4	22
  LYD610	0.78	7.43E−03	4	26	LYD610	0.83	2.67E−03	4	42
  LYD610	0.71	2.21E−02	4	31	LYD610	0.81	4.83E−03	4	34
  LYD610	0.78	1.41E−02	8	43	LYD610	0.77	1.61E−02	1	21
  LYD610	0.78	7.89E−03	1	15	LYD610	0.77	1.48E−02	1	20
  Table 35. Provided are the correlations (R) between the expression levels of yield improving genes and their homologues in tissues [Flag leaf, Flower meristem, stem and Flower; Expression sets (Exp)] and the phenotypic performance in various yield, biomass, growth rate and/or vigor components [Correlation vector (corr.)] under stress conditions (e.g., drought and low nitrogen) or normal conditions across Sorghum accessions. P = p value.

Example 9
• Production of Soybean (Glycine max) Transcriptome and High Throughput Correlation Analysis with Yield Parameters Using 44K B. Soybean Oligonucleotide Micro-Arrays
• In order to produce a high throughput correlation analysis, the present inventors utilized a Soybean oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?lPage=50879]. The array oligonucleotide represents about 42,000 Soybean genes and transcripts. In order to define correlations between the levels of RNA expression with yield components or plant architecture related parameters or plant vigor related parameters, various plant characteristics of 29 different Glycine max varieties were analyzed and 12 varieties were further used for RNA expression analysis. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test.
• Correlation of Glycine max Genes' Expression Levels with Phenotypic Characteristics Across Ecotype
• Experimental Procedures
• 29 Soybean varieties were grown in three repetitive plots, in field. Briefly, the growing protocol was as follows: Soybean seeds were sown in soil and grown under normal conditions until harvest. In order to define correlations between the levels of RNA expression with yield components or plant architecture related parameters or vigor related parameters, 12 different Soybean varieties (out of 29 varieties) were analyzed and used for gene expression analyses. Analysis was performed at two pre-determined time periods: at pod set (when the soybean pods are formed) and at harvest time (when the soybean pods are ready for harvest, with mature seeds).

• TABLE 36
  Soybean transcriptome expression sets

  Expression Set	Set ID

  Apical meristem at vegetative stage under normal growth	1
  condition
  Leaf at vegetative stage under normal growth condition	2
  Leaf at flowering stage under normal growth condition	3
  Leaf at pod setting stage under normal growth condition	4
  Root at vegetative stage under normal growth condition	5
  Root at flowering stage under normal growth condition	6
  Root at pod setting stage under normal growth condition	7
  Stem at vegetative stage under normal growth condition	8
  Stem at pod setting stage under normal growth condition	9
  Flower bud at flowering stage under normal growth condition	10
  Pod (R3-R4) at pod setting stage under normal growth condition	11
  Table 36.

• RNA extraction—All 12 selected Soybean varieties were sample per treatment. Plant tissues [leaf, root. Stem. Pod, apical meristem. Flower buds] growing under normal conditions were sampled and RNA was extracted as described above.
• The collected data parameters were as follows:
• Main branch base diameter [mm] at pod set—the diameter of the base of the main branch (based diameter) average of three plants per plot.
• Fresh weight [gr/plant] at pod set—total weight of the vegetative portion above ground (excluding roots) before drying at pod set, average of three plants per plot.
• Dry weight [gr/plant] at pod set—total weight of the vegetative portion above ground (excluding roots) after drying at 70° C. in oven for 48 hours at pod set, average of three plants per plot.
• Total number of nodes with pods on lateral branches [value/plant]—counting of nodes which contain pods in lateral branches at pod set, average of three plants per plot.
• Number of lateral branches at pod set [value/plant]—counting number of lateral branches at pod set, average of three plants per plot.
• Total weight of lateral branches at pod set [gr/plant]—weight all lateral branches at pod set, average of three plants per plot.
• Total weight of pods on main stem at pod set [gr/plant]—weight all pods on main stem at pod set, average of three plants per plot.
• Total number of nodes on main stem [value/plant]—count of number of nodes on main stem starting from first node above ground, average of three plants per plot.
• Total number of pods with 1 seed on lateral branches at pod set [value/plant]-count the number of pods containing 1 seed in all lateral branches at pod set, average of three plants per plot.
• Total number of pods with 2 seeds on lateral branches at pod set [slue/plant]—count the number of pods containing 2 seeds in all lateral branches at pod set, average of three plants per plot.
• Total number of pods with 3 seeds on lateral branches at pod set [value/plant]—count the number of pods containing 3 seeds in all lateral branches at pod set, average of three plants per plot.
• Total number of pods with 4 seeds on lateral branches at pod set [value/plant]—count the number of pods containing 4 seeds in all lateral branches at pod set, average of three plants per plot.
• Total number of pods with 1 seed on main stem at pod set [value/plant]—count the number of pods containing 1 seed in main stem at pod set, average of three plants per plot.
• Total number of pods with 2 seeds on main stem at pod set [value/plant]—count the number of pods containing 2 seeds in main stem at pod set, average of three plants per plot.
• Total number of pods with 3 seeds on main stem at pod set [value/plant]—count the number of pods containing 3 seeds in main stem at pod set, average of three plants per plot.
• Total number of pods with 4 seeds on main stem at pod set [value/plant]—count the number of pods containing 4 seeds in main stem at pod set, average of three plants per plot.
• Total number of seeds per plant at pod set [value/plant]—count number of seeds in lateral branches and main stem at pod set, average of three plants per plot.
• Total number of seeds on lateral branches at pod set [value/plant]—count total number of seeds on lateral branches at pod set, average of three plants per plot.
• Total number of seeds on main stem at pod set [value/plant]—count total number of seeds on main stem at pod set, average of three plants per plot.
• Plant height at pod set [cm/plant]—total length from above ground till the tip of the main stem at pod set, average of three plants per plot.
• Plant height at harvest [cm/plant]—total length from above ground till the tip of the main stem at harvest, average of three plants per plot.
• Total weight of pods on lateral branches at pod set [gr/plant]—weight of all pods on lateral branches at pod set, average of three plants per plot.
• Ratio of the number of pods per node on main stem at pod set—calculated in Formula X, average of three plants per plot.
• Formula X: Total number of pods on main stem/Total number of nodes on main stem, average of three plants per plot.
• Ratio of total number of seeds in main stem to number of seeds on lateral branches—calculated in formula XI, average of three plants per plot.
• Formula XI: Total number of seeds on main stem at pod set/Total number of seeds on lateral branches at pod set.
• Total weight of pods per plant at pod set [gr/plant]—weight all pods on lateral branches and main stem at pod set, average of three plants per plot.
• Days till 50% flowering [days]—number of days till 50% flowering for each plot.
• Days till 100% flowering [days]—number of days till 100% flowering for each plot.
• Maturity [days]—measure as 95% of the pods in a plot have ripened (turned 100% brown). Delayed leaf drop and green stems are not considered in assigning maturity. Tests are observed 3 days per week, every other day, for maturity. The maturity date is the date that 95% of the pods have reached final color. Maturity is expressed in days after August 31 [according to the accepted definition of maturity in USA, Descriptor list for SOYBEAN, Hypertext Transfer Protocol://World Wide Web (dot) ars-grin (dot) gov/cgi-bin/npgs/html/desclist (dot) pl?51].
• Seed quality [ranked 1-5]—measure at harvest, a visual estimate based on several hundred seeds. Parameter is rated according to the following scores considering the amount and degree of wrinkling, defective coat (cracks), greenishness, and moldy or other pigment. Rating is 1—very good, 2—good, 3—fair, 4—poor, 5—very poor.
• Lodging [ranked 1-5]—is rated at maturity per plot according to the following scores: 1—most plants in a plot are erected, 2—All plants leaning slightly or a few plants down, 3—all plants leaning moderately, or 25%-50% down, 4—all plants leaning considerably, or 50%-80% down, 5—most plants down. Note: intermediate score such as 1.5 are acceptable.
• Seed size [gr]—weight of 1000 seeds per plot normalized to 13% moisture, measure at harvest.
• Total weight of seeds per plant [gr/plant]—calculated at harvest (per 2 inner rows of a trimmed plot) as weight in grams of cleaned seeds adjusted to 13% moisture and divided by the total number of plants in two inner rows of a trimmed plot.
• Yield at harvest [bushels/hectare]—calculated at harvest (per 2 inner rows of a trimmed plot) as weight in grams of cleaned seeds, adjusted to 13% moisture, and then expressed as bushels per acre.
• Average lateral branch seeds per pod [number]—Calculate Number of Seeds on lateral branches-at pod set and divide by the Number of Total number of pods with seeds on lateral branches-at pod set.
• Average main stem seeds per pod [number]—Calculate Total Number of Seeds on main stem at pod set and divide by the Number of Total number of pods with seeds on main stem at pod setting.
• Main stem average internode length [cm]—Calculate Plant height at pod set and divide by the Total number of nodes on main stem at pod setting.
• Total Number of pods with seeds on main stem [number]—count all pods containing seeds on the main stem at pod setting.
• Total Number of pods with seeds on lateral branches [number]—count all pods containing seeds on the lateral branches at pod setting.
• Total number of pods per plant at pod set [number]—count pods on main stem and lateral branches at pod setting.
• Experimental Results
• Twelve different Soybean varieties were grown and characterized for 40 parameters as specified above. The average for each of the measured parameters was calculated using the JMP software and values are summarized in Tables 38-39 below. Subsequent correlation analysis between the various transcriptome expression sets and the average parameters was conducted. Results were then integrated to the database (Table 40).

• TABLE 37
  Soybean correlated parameters (vectors)

  Correlated parameter with	Correlation ID

  Base diameter at pod set (mm)	1
  DW at pod set (gr)	2
  fresh weight at pod set (gr)	3
  Total number of nodes with pods on lateral branches	4
  (number)
  Number of lateral branches (number)	5
  Total weight of lateral branches at pod set (gr)	6
  Total weight of pods on main stem at pod set (gr)	7
  Total number of nodes on main stem (number)	8
  Total no of pods with 1 seed on lateral branch	9
  (number)
  Number of pods with 1 seed on main stem at pod set	10
  (number)
  Total no of pods with 2 seed on lateral branch	11
  (number)
  Number of pods with 2 seed on main stem (number )	12
  Total no of pods with 3 seed on lateral branch	13
  (number)
  Number of pods with 3 seed on main stem (number)	14
  Total no of pods with 4 seed on lateral branch	15
  (number)
  Number of pods with 4 seed on main stem (number)	16
  Total number of seeds per plant	17
  Total Number of Seeds on lateral branches	18
  Total Number of Seeds on main stem at pod set	19
  Plant height at pod set (cm)	20
  Total weight of pods on lateral branches (gr)	21
  Ratio number of pods per node on main stem (ratio)	22
  Ratio number of seeds per main stem to seeds	23
  per lateral branch (ratio)
  Total weight of pods per plant (gr)	24
  50 percent flowering (days)	25
  Maturity (days)	26
  100 percent flowering (days)	27
  Plant height at harvest (cm)	28
  Seed quality (score 1-5)	29
  Total weight of seeds per plant (gr/plant)	30
  Seed size (gr)	31
  Lodging (score 1-5)	32
  yield at harvest (bushel/hectare)	33
  Average lateral branch seeds per pod (number)	34
  Average main stem seeds per pod (number)	35
  Total number of pods with seeds on main stem	36
  at pod set (number)
  Number pods with seeds on lateral branches-at	37
  pod set (number)
  Total number of pods per plant at pod set (number)	38
  Main stem average internode length (cm/number)	39
  Corrected Seed size (gr)	40
  Table 37.

• TABLE 38
  Measured parameters in Soybean varieties (lines 1-6)

  Treatment

  Ecotype	Line-1	Line-2	Line-3	Line-4	Line-5	Line-6

  1	8.33	9.54	9.68	8.11	8.82	10.12
  2	53.67	50.33	38.00	46.17	60.83	55.67
  3	170.89	198.22	152.56	163.89	224.67	265.00
  4	23.00	16.00	23.11	33.00	15.22	45.25
  5	9.00	8.67	9.11	9.89	7.67	17.56
  6	67.78	63.78	64.89	74.89	54.00	167.22
  7	22.11	14.33	16.00	15.00	33.78	9.00
  8	16.56	16.78	16.11	18.11	16.78	17.11
  9	1.56	3.00	1.78	1.78	5.67	5.63
  10	1.11	4.38	1.44	1.44	4.56	1.67
  11	17.00	18.75	26.44	32.33	21.56	33.50
  12	16.89	16.25	13.22	16.89	27.00	8.11
  13	38.44	2.00	26.44	31.33	8.89	82.00
  14	29.56	1.75	19.78	22.33	11.67	22.78
  15	0.00	0.00	0.00	0.00	0.00	1.50
  16	0.00	0.00	0.11	0.11	0.00	0.44
  17	274.44	99.78	221.67	263.11	169.00	412.50
  18	150.89	55.89	134.00	160.44	75.44	324.63
  19	123.56	43.89	87.67	102.67	93.56	88.00
  20	86.78	69.56	62.44	70.89	69.44	63.89
  21	26.00	14.89	20.11	20.11	21.11	30.25
  22	2.87	1.38	2.13	2.26	2.60	1.87
  23	0.89	0.90	0.87	0.89	2.32	0.37
  24	48.11	29.22	36.11	35.11	54.89	38.88
  25	61.00	65.33	60.67	61.00	54.67	68.33
  26	24.00	43.67	30.33	30.33	38.33	40.00
  27	67.33	71.67	67.67	67.33	60.00	74.00
  28	96.67	76.67	67.50	75.83	74.17	76.67
  29	2.33	3.50	3.00	2.17	2.83	2.00
  30	15.09	10.50	17.23	16.51	12.06	10.25
  31	89.00	219.33	93.00	86.00	191.33	71.33
  32	1.67	1.83	1.17	1.67	2.67	2.83
  33	47.57	43.77	50.37	56.30	44.00	40.33
  34	2.67	1.95	2.43	2.53	2.13	2.68
  35	2.60	1.89	2.52	2.53	2.17	2.59
  36	47.56	23.11	34.56	40.78	43.22	33.00
  37	57.00	28.56	54.67	65.44	36.11	122.63
  38	104.56	51.67	89.22	106.22	79.33	155.63
  39	5.24	4.15	3.91	3.92	4.15	3.74
  40	89.00	*	93.00	86.00	*	71.33
  Table 38.

• TABLE 39
  Measured parameters in Soybean varieties (lines 7-12)

  Treatment

  Ecotype	Line-7	Line-8	Line-9	Line-10	Line-11	Line-12

  1	8.46	8.09	8.26	7.73	8.16	7.89
  2	48.00	52.00	44.17	52.67	56.00	47.50
  3	160.67	196.33	155.33	178.11	204.44	164.22
  4	8.25	25.44	21.88	16.33	22.56	24.22
  5	11.67	12.11	8.00	9.11	6.78	10.00
  6	45.44	83.22	64.33	52.00	76.89	67.00
  7	9.03	16.00	15.89	14.56	30.44	18.00
  8	18.78	18.89	16.78	21.11	19.33	20.78
  9	2.88	3.00	1.25	2.67	1.78	3.00
  10	4.00	4.33	2.11	1.89	3.44	1.22
  11	8.50	22.78	21.75	10.67	23.78	25.67
  12	21.33	17.67	20.33	16.11	28.11	16.56
  13	9.00	42.11	32.75	25.67	45.00	44.33
  14	11.11	28.22	24.11	36.44	39.67	32.33
  15	0.00	0.33	0.00	1.11	0.00	0.00
  16	0.00	0.56	0.00	3.89	0.00	0.00
  17	136.00	302.78	260.50	264.44	363.00	318.67
  18	46.88	176.22	143.00	105.44	184.33	187.33
  19	80.00	126.56	115.11	159.00	178.67	131.33
  20	89.78	82.11	70.56	101.67	79.56	67.22
  21	4.13	20.11	17.00	9.22	28.11	22.56
  22	1.98	2.71	2.78	2.75	3.70	2.84
  23	3.90	0.78	1.18	1.98	1.03	0.83
  24	14.25	36.11	32.75	23.78	58.56	40.56
  25	66.50	65.67	62.33	67.67	61.67	64.33
  26	41.00	38.33	31.00	39.00	27.33	32.67
  27	73.00	72.33	68.67	73.67	68.00	70.67
  28	101.67	98.33	75.83	116.67	76.67	71.67
  29	3.50	2.50	2.17	2.33	2.17	2.17
  30	7.30	11.38	15.68	10.83	12.98	15.16
  31	88.00	75.00	80.67	75.67	76.33	77.33
  32	2.67	2.50	1.83	3.50	3.33	1.50
  33	34.23	44.27	53.67	42.47	43.60	52.20
  34	2.12	2.58	2.58	2.67	2.62	2.58
  35	2.22	2.49	2.47	2.71	2.51	2.61
  36	36.44	50.78	43.63	58.33	71.22	50.11
  37	20.38	68.22	55.75	40.11	70.56	73.00
  38	61.00	119.00	103.25	98.44	141.78	123.11
  39	4.80	4.36	4.20	4.82	4.12	3.83
  40	88.00	75.00	80.67	75.67	76.33	77.33
  Table 39.

• TABLE 40
  Correlation between the expression level of selected genes of some
  embodiments of the invention in various tissues and the phenotypic
  performance under normal conditions across soybean varieties

  Gene			Exp.	Corr.	Gene			Exp.	Corr.
  Name	R	P value	set	Set ID	Name	R	P value	set	Set ID

  LYD611	0.79	6.52E−03	7	3	LYD611	0.73	1.59E−02	7	1
  LYD611	0.79	6.87E−03	5	3	LYD611	0.71	2.08E−02	5	2
  LYD611	0.79	6.22E−03	5	32	LYD611	0.74	1.46E−02	5	15
  LYD611	0.88	3.55E−03	9	16	LYD611	0.75	4.74E−03	1	3
  LYD612	0.74	3.62E−02	9	30	LYD612	0.80	1.83E−02	9	33
  LYD613	0.78	7.35E−03	8	13	LYD613	0.76	1.15E−02	8	18
  LYD613	0.79	6.10E−03	8	5	LYD613	0.70	2.28E−02	8	17
  LYD613	0.75	3.20E−02	9	8	LYD613	0.75	4.90E−03	10	23
  LYD613	0.78	2.59E−03	10	9	LYD614	0.79	6.27E−03	7	30
  LYD614	0.75	1.33E−02	7	33	LYD614	0.75	1.22E−02	5	8
  LYD614	0.75	1.33E−02	8	13	LYD614	0.74	1.37E−02	8	18
  LYD614	0.76	1.13E−02	8	5	LYD614	0.74	3.49E−02	9	30
  LYD614	0.79	2.02E−02	9	33	LYD614	0.75	4.87E−03	1	20
  LYD614	0.73	6.88E−03	10	6	LYD614	0.75	4.90E−03	10	4
  LYD615	0.76	1.10E−02	7	20	LYD615	0.81	4.14E−03	7	28
  LYD615	0.72	8.42E−03	11	29	LYD615	0.89	5.76E−04	5	14
  LYD615	0.88	6.96E−04	5	19	LYD615	0.75	1.22E−02	5	22
  LYD615	0.77	2.49E−02	9	5	LYD616	0.78	7.41E−03	8	3
  LYD616	0.86	1.37E−03	8	15	LYD616	0.72	1.88E−02	8	6
  LYD616	0.80	5.71E−03	8	9	LYD616	0.71	4.69E−02	9	30
  LYD616	0.76	2.71E−02	9	33	LYD616	0.72	8.76E−03	4	7
  LYD616	0.75	4.86E−03	10	13	LYD616	0.72	8.10E−03	10	18
  LYD616	0.77	3.73E−03	10	17	LYD617	0.70	2.31E−02	7	30
  LYD617	0.71	1.01E−02	11	30	LYD617	0.75	5.35E−03	11	33
  LYD617	0.71	2.21E−02	5	18	LYD617	0.81	4.31E−03	5	6
  LYD617	0.80	5.72E−03	5	5	LYD617	0.79	6.36E−03	5	4
  LYD617	0.80	5.60E−03	5	1	LYD617	0.72	4.53E−02	9	30
  LYD617	0.73	3.94E−02	9	24	LYD617	0.72	4.48E−02	9	19
  LYD617	0.78	2.12E−02	9	22	LYD617	0.76	2.82E−02	9	7
  LYD617	0.72	7.75E−03	1	12	LYD617	0.79	2.14E−03	1	24
  LYD617	0.79	2.28E−03	1	7	LYD617	0.72	8.95E−03	10	33
  LYD618	0.82	3.46E−03	7	13	LYD618	0.87	1.13E−03	7	18
  LYD618	0.83	2.69E−03	7	11	LYD618	0.87	1.23E−03	7	6
  LYD618	0.88	8.01E−04	7	4	LYD618	0.88	1.76E−04	11	30
  LYD618	0.84	6.36E−04	11	33	LYD618	0.77	8.80E−03	5	13
  LYD618	0.76	1.12E−02	5	18	LYD618	0.74	1.50E−02	5	4
  LYD618	0.73	1.75E−02	5	17	LYD618	0.71	2.16E−02	8	12
  LYD618	0.78	7.21E−03	8	7	LYD618	0.72	4.22E−02	9	14
  LYD618	0.71	4.93E−02	9	16	LYD618	0.91	1.47E−03	9	13
  LYD618	0.88	4.13E−03	9	18	LYD618	0.73	3.99E−02	9	11
  LYD618	0.80	1.61E−02	9	3	LYD618	0.98	3.10E−05	9	15
  LYD618	0.95	3.66E−04	9	6	LYD618	0.92	1.24E−03	9	5
  LYD618	0.88	3.76E−03	9	4	LYD618	0.92	1.31E−03	9	17
  LYD618	0.89	2.69E−03	9	9	LYD618	0.75	7.41E−03	2	13
  LYD619	0.75	1.28E−02	7	23	LYD619	0.72	1.83E−02	5	12
  LYD619	0.71	2.13E−02	5	19	LYD619	0.76	1.01E−02	5	22
  LYD619	0.82	3.43E−03	8	15	LYD619	0.83	1.02E−02	9	7
  LYD619	0.73	7.05E−03	4	14	LYD619	0.73	7.48E−03	4	13
  LYD619	0.78	2.88E−03	4	17	LYD620	0.72	1.93E−02	7	8
  LYD620	0.71	2.11E−02	7	20	LYD620	0.76	4.11E−03	11	8
  LYD620	0.82	3.33E−03	5	29	LYD620	0.71	2.03E−02	5	19
  LYD620	0.71	2.11E−02	8	18	LYD620	0.84	2.51E−03	8	3
  LYD620	0.85	1.75E−03	8	15	LYD620	0.80	5.24E−03	8	6
  LYD620	0.85	1.73E−03	8	5	LYD620	0.72	1.86E−02	8	4
  LYD620	0.73	1.67E−02	8	1	LYD620	0.76	1.10E−02	8	9
  LYD620	0.72	4.38E−02	9	8	LYD620	0.81	1.57E−02	9	10
  LYD620	0.79	2.23E−03	1	3	LYD620	0.76	4.05E−03	1	9
  LYD620	0.71	1.04E−02	10	33	LYD621	0.78	7.26E−03	5	14
  LYD621	0.84	2.44E−03	5	19	LYD621	0.79	6.70E−03	5	22
  LYD621	0.70	2.30E−02	8	13	LYD621	0.74	1.42E−02	8	18
  LYD621	0.73	1.72E−02	8	3	LYD621	0.71	2.09E−02	8	15
  LYD621	0.72	1.86E−02	8	6	LYD621	0.78	7.80E−03	8	4
  LYD621	0.75	1.25E−02	8	9	LYD621	0.74	8.99E−03	2	22
  LYD621	0.70	1.11E−02	4	14	LYD621	0.74	5.81E−03	4	33
  LYD621	0.71	9.73E−03	4	22	LYD621	0.76	3.82E−03	1	22
  LYD622	0.75	1.18E−02	7	33	LYD622	0.83	8.52E−04	11	30
  LYD622	0.72	8.59E−03	11	33	LYD622	0.81	4.94E−03	5	23
  LYD622	0.70	2.28E−02	8	14	LYD622	0.84	8.41E−03	9	12
  LYD622	0.82	1.29E−02	9	3	LYD622	0.73	3.92E−02	9	7
  LYD622	0.90	2.38E−03	9	15	LYD622	0.90	2.49E−03	9	6
  LYD622	0.77	2.48E−02	9	5	LYD622	0.81	1.58E−02	9	4
  LYD622	0.85	8.19E−03	9	1	LYD622	0.81	1.38E−02	9	9
  LYD623	0.72	8.09E−03	11	19	LYD623	0.74	5.57E−03	11	22
  LYD623	0.79	7.12E−03	8	30	LYD623	0.80	5.75E−03	8	33
  LYD623	0.81	1.39E−02	9	30	LYD623	0.74	3.69E−02	9	22
  LYD624	0.84	2.21E−03	7	13	LYD624	0.86	1.25E−03	7	18
  LYD624	0.74	1.47E−02	7	11	LYD624	0.85	1.85E−03	7	6
  LYD624	0.85	1.98E−03	7	4	LYD624	0.83	2.84E−03	7	21
  LYD624	0.80	5.49E−03	7	17	LYD624	0.75	1.18E−02	5	20
  LYD624	0.72	1.80E−02	5	28	LYD624	0.73	1.59E−02	8	18
  LYD624	0.76	1.05E−02	8	15	LYD624	0.86	1.55E−03	8	6
  LYD624	0.84	2.38E−03	8	4	LYD624	0.81	1.40E−02	9	33
  LYD625	0.72	1.82E−02	5	23	LYD625	0.78	2.12E−02	9	8
  LYD625	0.72	4.46E−02	9	19	LYD625	0.85	7.44E−03	9	15
  LYD625	0.77	2.61E−02	9	6	LYD625	0.80	1.81E−02	9	5
  LYD625	0.81	1.52E−02	9	1	LYD625	0.73	4.02E−02	9	9
  LYD625	0.74	5.84E−03	4	14	LYD625	0.71	9.18E−03	4	7
  LYD626	0.75	3.26E−02	9	30	LYD626	0.73	7.55E−03	4	6
  LYD626	0.72	7.75E−03	4	5	LYD627	0.74	3.61E−02	9	30
  LYD627	0.72	8.06E−03	1	11	LYD627	0.74	5.63E−03	10	2
  LYD627	0.82	9.94E−04	10	32	LYD629	0.74	1.51E−02	5	16
  LYD629	0.73	1.62E−02	5	26	LYD629	0.73	1.74E−02	5	32
  LYD629	0.77	9.29E−03	8	15	LYD629	0.71	2.17E−02	8	9
  LYD629	0.76	2.78E−02	9	7	LYD629	0.70	1.11E−02	4	15
  LYD629	0.73	6.53E−03	4	17	LYD630	0.72	1.99E−02	7	5
  LYD630	0.83	2.92E−03	8	13	LYD630	0.84	2.26E−03	8	18
  LYD630	0.82	3.48E−03	8	4	LYD630	0.72	1.81E−02	8	21
  LYD630	0.84	2.26E−03	8	17	LYD631	0.76	1.01E−02	5	30
  LYD631	0.75	1.22E−02	5	19	LYD631	0.85	1.81E−03	5	22
  LYD631	0.71	2.16E−02	8	9	LYD631	0.90	3.81E−04	8	31
  LYD631	0.76	2.75E−02	9	23	LYD631	0.78	2.35E−02	9	31
  LYD631	0.72	8.88E−03	4	15	LYD631	0.71	9.33E−03	1	7
  LYD632	0.73	1.59E−02	7	30	LYD632	0.78	7.29E−03	7	33
  LYD632	0.84	2.22E−03	5	15	LYD632	0.74	3.60E−02	9	33
  LYD632	0.70	1.10E−02	1	16	LYD632	0.78	2.77E−03	1	20
  LYD632	0.78	3.03E−03	1	28	LYD633	0.73	1.71E−02	5	11
  LYD633	0.79	6.63E−03	5	3	LYD633	0.88	7.77E−04	5	9
  LYD633	0.70	2.42E−02	8	3	LYD633	0.91	2.53E−04	8	15
  LYD633	0.82	3.86E−03	8	6	LYD633	0.75	1.31E−02	8	5
  LYD633	0.76	1.05E−02	8	4	LYD633	0.70	1.06E−02	1	16
  LYD633	0.72	8.59E−03	1	15	LYD634	0.75	3.11E−02	9	8
  LYD634	0.81	1.55E−03	1	8	LYD634	0.78	2.51E−03	1	20
  LYD634	0.77	3.16E−03	10	14	LYD634	0.71	9.38E−03	10	19
  LYD634	0.73	7.50E−03	10	17	LYD635	0.79	1.85E−02	9	14
  LYD635	0.77	2.64E−02	9	8	LYD635	0.83	1.03E−02	9	19
  LYD635	0.83	1.01E−02	9	22	LYD635	0.76	4.03E−03	1	8
  LYD635	0.73	6.59E−03	10	19	LYD635	0.77	3.53E−03	10	22
  LYD636	0.80	4.97E−03	8	14	LYD636	0.71	2.03E−02	8	13
  LYD636	0.77	9.05E−03	8	17	LYD636	0.75	3.20E−02	9	14
  LYD636	0.74	3.74E−02	9	22	LYD636	0.73	6.87E−03	1	14
  LYD636	0.78	2.66E−03	10	14	LYD637	0.82	3.54E−03	8	1
  LYD637	0.73	7.02E−03	10	31	LYD638	0.79	6.71E−03	7	11
  LYD638	0.77	3.48E−03	11	30	LYD638	0.81	1.45E−03	11	33
  LYD638	0.77	9.73E−03	8	13	LYD638	0.79	7.05E−03	8	18
  LYD638	0.90	3.21E−04	8	15	LYD638	0.80	5.26E−03	8	6
  LYD638	0.71	2.05E−02	8	5	LYD638	0.82	4.00E−03	8	4
  LYD638	0.73	1.63E−02	8	17	LYD639	0.70	5.11E−02	9	12
  LYD639	0.78	2.37E−02	9	24	LYD639	0.96	2.19E−04	9	7
  LYD639	0.87	2.55E−04	10	8	LYD641	0.82	3.64E−03	5	13
  LYD641	0.78	7.22E−03	5	18	LYD641	0.75	1.19E−02	5	15
  LYD641	0.75	1.32E−02	5	6	LYD641	0.73	1.76E−02	5	4
  LYD641	0.75	1.21E−02	5	17	LYD641	0.77	2.46E−02	9	16
  LYD641	0.84	8.62E−03	9	13	LYD641	0.82	1.27E−02	9	18
  LYD641	0.71	4.90E−02	9	15	LYD641	0.77	2.67E−02	9	5
  LYD641	0.76	2.91E−02	9	4	LYD641	0.78	2.19E−02	9	17
  LYD641	0.79	3.48E−03	2	13	LYD641	0.70	1.56E−02	2	17
  LYD642	0.77	9.07E−03	7	32	LYD642	0.84	2.18E−03	5	8
  LYD642	0.71	2.22E−02	5	19	LYD642	0.72	8.83E−03	1	31
  LYD643	0.85	1.79E−03	8	3	LYD643	0.85	2.02E−03	8	15
  LYD643	0.80	5.19E−03	8	6	LYD643	0.72	1.94E−02	8	5
  LYD643	0.71	2.06E−02	8	4	LYD643	0.76	9.96E−03	8	9
  LYD643	0.78	2.77E−03	1	3	LYD643	0.77	3.63E−03	1	9
  LYD643	0.75	4.85E−03	10	3	LYD643	0.74	6.03E−03	10	2
  LYD644	0.76	1.07E−02	7	3	LYD644	0.85	1.83E−03	7	9
  LYD644	0.80	5.37E−03	8	16	LYD644	0.72	1.79E−02	8	20
  LYD644	0.84	2.37E−03	8	15	LYD644	0.75	1.31E−02	8	28
  LYD644	0.74	3.71E−02	9	30	LYD644	0.84	9.39E−03	9	33
  LYD644	0.74	6.07E−03	10	26	LYD644	0.72	8.41E−03	10	25
  LYD645	0.85	7.94E−03	9	14	LYD645	0.80	1.60E−02	9	30
  LYD645	0.84	9.84E−03	9	19	LYD645	0.89	3.41E−03	9	22
  LYD645	0.70	1.54E−02	2	20	LYD646	0.84	5.76E−04	11	8
  LYD646	0.76	3.03E−02	9	30	LYD646	0.76	2.86E−02	9	33
  LYD646	0.70	1.05E−02	10	13	LYD646	0.73	7.14E−03	10	18
  LYD646	0.71	1.02E−02	10	4	LYD646	0.74	6.41E−03	10	17
  LYD647	0.73	3.98E−02	9	14	LYD647	0.81	1.50E−02	9	19
  LYD647	0.83	1.06E−02	9	22	LYD647	0.76	2.93E−02	9	7
  LYD647	0.73	7.06E−03	10	13	LYD647	0.74	6.23E−03	10	18
  LYD647	0.70	1.07E−02	10	15	LYD647	0.80	1.69E−03	10	6
  LYD623	0.77	9.13E−03	3	40	LYD627	0.70	2.28E−02	1	40
  LYD637	0.85	7.18E−03	5	40	LYD637	0.78	1.39E−02	2	40
  LYD637	0.76	1.02E−02	8	40	LYD639	0.76	2.80E−02	4	40
  LYD646	0.72	4.52E−02	4	40
  Table 40. Provided are the correlations (R) between the expression levels yield improving genes and their homologs in various tissues [Expression (Exp) sets] and the phenotypic performance [yield, biomass, and plant architecture (Correlation vector (Corr))] under normal conditions across soybean varieties. P = p value.

Example 10 Production of Brachypodium Transcriptome and High Throughput Correlation Analysis Using 60K Brachypodium Oligonucleotide Micro-Array
• In order to produce a high throughput correlation analysis comparing between plant phenotype and gene expression level, the present inventors utilized a brachypodium oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?lPage=50879]. The array oligonucleotide represents about 60K brachypodium genes and transcripts. In order to define correlations between the levels of RNA expression and yield or vigor related parameters, various plant characteristics of 24 different brachypodium accessions were analyzed. Among them, 22 accessions encompassing the observed variance were selected for RNA expression analysis and comparative genomic hybridization (CGH) analysis.
• The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test [Hypertext Transfer Protocol://World Wide Web (dot) davidmlane (dot) com/hyperstat/A34739 (dot) html].
• Additional correlation analysis was done by comparing plant phenotype and gene copy number. The correlation between the normalized copy number hybridization signal and the characterized parameters was analyzed using Pearson correlation test [Hypertext Transfer Protocol://World Wide Web (dot) davidmlane (dot) com/hyperstat/A34739 (dot) html].
• Experimental Procedures
• Analyzed Brachypodium tissues—two tissues [leaf and spike] were sampled and RNA was extracted as described above. Each micro-array expression information tissue type has received a Set ID as summarized in Table 41 below.

• TABLE 41
  Brachypodium transcriptome expression sets

  Expression Set	Set ID
  Leaf at flowering stage under normal growth conditions	1 + 2
  spike at flowering stage under normal growth conditions	3
  Table 41.

• Brachypodium yield components and vigor related parameters assessment—24 brachypodium accessions were grown in 4-6 repetitive plots (8 plant per plot), in a green house. The growing protocol was as follows: brachypodium seeds were sown in plots and grown under normal conditions. Plants were continuously phenotyped during the growth period and at harvest (Table 43-48, below). The image analysis system included a personal desktop computer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ 1.37 (Java based image processing program, which was developed at the U.S. National Institutes of Health and freely available on the internet [Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/]. Next, analyzed data was saved to text files and processed using the JMP statistical analysis software (SAS institute).
• At the end of the growing period the grains were separated from the spikes and the following parameters were measured using digital imaging system and collected:
• No. of tillering—all tillers were counted per plant at harvest (mean per plot).
• Head number—At the end of the experiment, heads were harvested from each plot and were counted.
• Total Grains weight per plot (gr.)—At the end of the experiment (plant ‘Heads’) heads from plots were collected, the heads were threshed and grains were weighted. In addition, the average grain weight per head was calculated by dividing the total grain weight by number of total heads per plot (based on plot).
• Highest number of spikelets—The highest spikelet number per head was calculated per plant (mean per plot).
• Mean number of spikelets—The mean spikelet number per head was calculated per plot.
• Plant height—Each of the plants was measured for its height using measuring tape. Height was measured from ground level to spike base of the longest spike at harvest.
• Spikelets weight (gr.)—The biomass and spikes weight of each plot was separated, measured per plot.
• Average head weight—calculated by dividing spikelets weight with head number (gr.).
• Harvest Index—The harvest index was calculated using Formula XII.
• Spikelets Index—The Spikelets index is calculated using Formula XIII.
• 
  Spikelets Index=Average Spikelets weight per plant/(Average vegetative dry weight per plant plus Average Spikelets weight per plant).  Formula XIII:
• Percent Number of heads with spikelets—The number of heads with more than one spikelet per plant were counted and the percent from all heads per plant was calculated.
• Total dry mater per plot—Calculated as Vegetative portion above ground plus all the spikelet dry weight per plot.
• 10000 grain weight—At the end of the experiment all grains from all plots were collected and weighted and the weight of 1000 were calculated.
• The following parameters were collected using digital imaging system:
• At the end of the growing period the grains were separated from the spikes and the following parameters were measured and collected:
• (i) Average Grain Area (cm²)—A sample of ˜200 grains was weighted, photographed and images were processed using the below described image processing system. The grain area was measured from those images and was divided by the number of grains.
• (ii) Average Grain Length, perimeter and width (cm)—A sample of ˜200 grains was weighted, photographed and images were processed using the below described image processing system. The sum of grain lengths and width (longest axis) was measured from those images and was divided by the number of grains.
• The image processing system was used, which consists of a personal desktop computer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ 1.37, Java based image processing software, which was developed at the U.S. National Institutes of Health and is freely available on the internet at Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/. Images were captured in resolution of 10 Mega Pixels (3888×2592 pixels) and stored in a low compression JPEG (Joint Photographic Experts Group standard) format. Next, image processing output data for seed area and seed length was saved to text files and analyzed using the JMP statistical analysis software (SAS institute).

• TABLE 42
  Brachypodium correlated parameters (vectors)

  Correlated parameter with	Correlation ID
  % Number of heads with spikelets (number)	1 + 26
  1000 grain weight (gr)	2 + 27
  Average head weight (gr)	3 + 28
  Grain area (cm2)	4 + 29
  Grain length (cm)	5 + 30
  Grain Perimeter (cm2)	6 + 31
  Grain width (cm)	7 + 32
  Grains weight per plant (gr)	8 + 33
  Grains weight per plot (gr)	9 + 34
  Harvest index	10 + 35
  Heads per plant (number)	11 + 36
  Heads per plot (number)	12 + 37
  Highest Number of spikelets per plot (number)	13 + 38
  Mean Number of spikelets per plot (number)	14 + 39
  Number of heads with spikelets per plant (number)	15 + 40
  Plant height (cm)	16 + 41
  Plant Vegetative DW (gr)	17 + 42
  Plants number (number)	18 + 43
  Spikelets DW per plant (gr)	19 + 44
  Spikelets weight (gr)	20 + 45
  Spikes index	21 + 46
  Tillering (number)	22
  Total dry mater per plant (gr)	23 + 47
  Total dry mater per plot (gr)	24 + 48
  Vegetative DW (gr)	25 + 49
  Table 42. Provided are the Brachypodium correlated parameters.

• Experimental Results
• 24 different Brachypodium accessions were grown and characterized for different parameters as described above. The average for each of the measured parameters was calculated using the JMP software and values are summarized in Tables 43-48 below. Subsequent correlation analysis between the various transcriptome sets and the average parameters (Tables 43-48) was conducted. Follow, results were integrated to the database.

• TABLE 43
  Measured parameters of correlation IDs in Brachypodium
  accessions under normal conditions (lines 1-9)

  Treatment Correlation ID

  Ecotype	Line-1	Line-2	Line-3	Line-4	Line-5	Line-6	Line-7	Line-8	Line-9

  1	27.61	35.33	21.67	52.40	20.84	47.73	17.55	16.51	5.42
  2	3.75	3.78	3.35	3.70	3.90	4.87	4.82	4.76	5.54
  3	0.06	0.04	0.05	0.09	0.04	0.09	0.06	0.06	0.04
  4	0.10	0.10	0.09	0.09	0.09	0.11	0.10	0.11	0.11
  5	0.73	0.72	0.72	0.75	0.72	0.87	0.79	0.79	0.83
  6	1.67	1.62	1.62	1.65	1.60	1.90	1.80	1.82	1.82
  7	0.18	0.17	0.17	0.15	0.15	0.16	0.17	0.18	0.16
  8	0.14	0.06	0.08	0.35	0.27	0.44	0.32	0.07	0.14
  9	1.05	0.44	0.61	2.58	2.03	3.40	2.58	0.39	1.11
  10	0.13	0.14	0.15	0.21	0.17	0.18	0.15	0.11	0.20
  11	16.29	7.08	6.59	16.11	21.40	17.05	25.88	8.02	10.48
  12	121.75	56.60	52.75	123.50	156.83	135.0	207.00	48.60	82.40
  13	3.00	2.60	3.00	2.83	2.33	4.50	2.60	2.00	2.00
  14	2.10	2.10	1.72	2.17	1.85	2.85	1.93	1.56	1.38
  15	5.27	2.50	2.06	9.44	5.02	7.72	4.90	1.87	0.71
  16	31.65	23.44	22.75	45.35	29.41	46.74	38.39	29.15	34.36
  17	0.42	0.12	0.13	0.82	0.67	1.05	0.87	0.31	0.32
  18	7.50	8.00	8.00	7.50	7.33	7.88	8.00	6.40	7.80
  19	0.96	0.31	0.33	1.46	0.96	1.42	1.56	0.45	0.44
  20	7.18	2.50	2.68	11.31	7.16	11.05	12.44	2.66	3.45
  21	0.71	0.72	0.73	0.68	0.60	0.57	0.65	0.60	0.58
  22	16.84	7.20	7.00	16.99	23.61	18.25	27.20	8.60	10.67
  23	1.38	0.43	0.47	2.28	1.63	2.47	2.43	0.76	0.76
  24	10.26	3.45	3.74	17.78	12.29	19.27	19.40	4.47	6.00
  25	3.08	0.95	1.06	6.47	5.13	8.23	6.96	1.81	2.55
  Table 43. Correlation IDs refer to those described in Table 42 above [Brachypodium correlated parameters (vectors)].

• TABLE 44
  Measured parameters of correlation IDs in Brachypodium
  accessions under normal conditions (lines 10-18)

  Treatment

  Ecotype	Line-10	Line-11	Line-12	Line-13	Line-14	Line-15	Line-16	Line-17	Line-18

  1	15.42	14.00	6.40	4.51	15.52	20.34	8.11	53.21	55.41
  2	4.98	4.88	4.83	5.54	4.73	5.24	4.96	4.00	3.84
  3	0.06	0.07	0.05	0.04	0.05	0.05	0.06	0.10	0.08
  4	0.11	0.09	0.10	0.11	0.10	0.12	0.10	0.10	0.10
  5	0.82	0.74	0.78	0.90	0.75	0.86	0.74	0.84	0.75
  6	1.83	1.69	1.74	1.93	1.69	1.91	1.71	1.81	1.68
  7	0.17	0.16	0.17	0.16	0.17	0.19	0.17	0.15	0.17
  8	0.14	0.26	0.14	0.11	0.39	0.14	0.13	0.37	0.08
  9	1.07	1.96	1.09	0.84	3.07	1.09	1.07	2.99	0.50
  10	0.16	0.20	0.14	0.26	0.22	0.09	0.18	0.09	0.07
  11	9.09	11.63	14.13	5.88	23.75	16.06	9.74	22.19	11.89
  12	70.13	83.40	110.33	47.00	185.50	125.	80.75	177.50	81.50
  13	2.25	2.20	1.83	2.00	2.50	2.40	2.00	3.50	3.50
  14	1.65	1.69	1.43	1.25	1.76	1.83	1.42	2.71	2.41
  15	1.94	2.08	1.08	0.35	4.98	3.70	0.89	12.58	7.59
  16	28.65	31.95	28.88	24.74	37.30	45.09	22.39	55.04	31.40
  17	0.32	0.38	0.39	0.13	0.87	0.69	0.34	1.72	0.44
  18	7.75	7.20	7.83	8.00	7.75	8.00	8.25	8.00	6.50
  19	0.56	0.88	0.67	0.26	1.14	0.83	0.59	2.27	0.92
  20	4.29	6.42	5.29	2.04	8.89	6.65	4.92	18.15	6.25
  21	0.66	0.71	0.64	0.66	0.59	0.54	0.68	0.56	0.69
  22	9.38	11.97	14.58	6.35	25.50	16.56	10.53	27.15	12.38
  23	0.88	1.25	1.06	0.38	2.01	1.53	0.93	3.99	1.36
  24	6.78	9.12	8.34	3.04	15.79	12.20	7.76	31.94	9.21
  25	2.48	2.69	3.05	1.00	6.89	5.55	2.84	13.80	2.96
  Table 44. Correlation IDs refer to those described in Table 42 above [Brachypodium correlated parameters (vectors)].

• TABLE 45
  Measured parameters of correlation IDs in Brachypodium
  accessions under normal conditions (lines 19-22)

  Ecotype/Treatment	Line-19	Line-20	Line-21	Line-22

  1	47.81	42.81	59.01	34.92
  2	4.26	5.99	3.76	4.34
  3	0.08	0.08	0.09	0.06
  4	0.09	0.12	0.09	0.09
  5	0.80	0.84	0.76	0.74
  6	1.75	1.87	1.68	1.66
  7	0.14	0.18	0.15	0.16
  8	0.49	0.31	0.30	0.20
  9	3.52	2.41	1.92	1.47
  10	0.16	0.18	0.09	0.11
  11	24.32	13.25	25.54	19.22
  12	172.80	98.60	177.00	143.17
  13	3.80	2.80	3.17	2.83
  14	2.61	2.12	2.79	2.15
  15	12.13	6.35	15.36	7.15
  16	45.34	40.20	58.82	39.18
  17	1.32	0.48	1.73	0.63
  18	7.00	7.60	6.83	7.33
  19	1.91	1.09	2.25	1.26
  20	13.49	8.35	15.55	9.42
  21	0.59	0.70	0.57	0.66
  22	26.30	13.56	29.09	20.79
  23	3.23	1.57	3.98	1.89
  24	22.78	12.04	27.67	14.14
  25	9.28	3.70	12.12	4.72
  Table 45. Correlation IDs refer to those described in Table 51 above [Brachypodium correlated parameters (vectors)].

• TABLE 46
  Measured parameters of correlation IDs in Brachypodium
  accessions under normal conditions (lines 23-30)

  Treatment

  Ecotype	Line-23	Line-24	Line-25	Line-26	Line-27	Line-28	Line-29	Line-30

  26	27.61	35.33	21.67	14.00	5.42	15.42	6.40	4.51
  27	3.75	3.78	3.35	4.88	5.54	4.98	4.83	5.54
  28	0.06	0.04	0.05	0.07	0.04	0.06	0.05	0.04
  29	0.10	0.10	0.09	0.09	0.11	0.11	0.10	0.11
  30	0.73	0.72	0.72	0.74	0.83	0.82	0.78	0.90
  31	1.67	1.62	1.62	1.69	1.82	1.83	1.74	1.93
  32	0.18	0.17	0.17	0.16	0.16	0.17	0.17	0.16
  33	0.14	0.06	0.08	0.26	0.14	0.14	0.14	0.11
  34	1.05	0.44	0.61	1.96	1.11	1.07	1.09	0.84
  35	0.13	0.14	0.15	0.20	0.20	0.16	0.14	0.26
  36	16.29	7.08	6.59	11.63	10.48	9.09	14.13	5.88
  37	121.75	56.60	52.75	83.40	82.40	70.13	110.33	47.00
  38	3.00	2.60	3.00	2.20	2.00	2.25	1.83	2.00
  39	2.10	2.10	1.72	1.69	1.38	1.65	1.43	1.25
  40	5.27	2.50	2.06	2.08	0.71	1.94	1.08	0.35
  41	31.65	23.44	22.75	31.95	34.36	28.65	28.88	24.74
  42	0.42	0.12	0.13	0.38	0.32	0.32	0.39	0.13
  43	7.50	8.00	8.00	7.20	7.80	7.75	7.83	8.00
  44	0.96	0.31	0.33	0.88	0.44	0.56	0.67	0.26
  45	7.18	2.50	2.68	6.42	3.45	4.29	5.29	2.04
  46	0.71	0.72	0.73	0.71	0.58	0.66	0.64	0.66
  22	16.84	7.20	7.00	11.97	10.67	9.38	14.58	6.35
  47	1.38	0.43	0.47	1.25	0.76	0.88	1.06	0.38
  48	10.26	3.45	3.74	9.12	6.00	6.78	8.34	3.04
  49	3.08	0.95	1.06	2.69	2.55	2.48	3.05	1.00
  Table 46. Correlation IDs refer to those described in Table 42 above [Brachypodium correlated parameters (vectors)].

• TABLE 47
  Measured parameters of correlation IDs in Brachypodium
  accessions under normal conditions (lines 31-40)

  Treatment

  Ecotype	Line-31	Line-32	Line-33	Line-34	Line-35	Line-36	Line-37	Line-38	Line-39	Line-40

  26	55.41	16.51	15.52	20.34	8.11	53.21	47.81	42.81	34.92	52.40
  27	3.84	4.76	4.73	5.24	4.96	4.00	4.26	5.99	4.34	3.70
  28	0.08	0.06	0.05	0.05	0.06	0.10	0.08	0.08	0.06	0.09
  29	0.10	0.11	0.10	0.12	0.10	0.10	0.09	0.12	0.09	0.09
  30	0.75	0.79	0.75	0.86	0.74	0.84	0.80	0.84	0.74	0.75
  31	1.68	1.82	1.69	1.91	1.71	1.81	1.75	1.87	1.66	1.65
  32	0.17	0.18	0.17	0.19	0.17	0.15	0.14	0.18	0.16	0.15
  33	0.08	0.07	0.39	0.14	0.13	0.37	0.49	0.31	0.20	0.35
  34	0.50	0.39	3.07	1.09	1.07	2.99	3.52	2.41	1.47	2.58
  35	0.07	0.11	0.22	0.09	0.18	0.09	0.16	0.18	0.11	0.21
  36	11.89	8.02	23.75	16.06	9.74	22.19	24.32	13.25	19.22	16.11
  37	81.50	48.60	185.50	125.00	80.75	177.50	172.80	98.6	143.17	123.5
  38	3.50	2.00	2.50	2.40	2.00	3.50	3.80	2.80	2.83	2.83
  39	2.41	1.56	1.76	1.83	1.42	2.71	2.61	2.12	2.15	2.17
  40	7.59	1.87	4.98	3.70	0.89	12.58	12.13	6.35	7.15	9.44
  41	31.40	29.15	37.30	45.09	22.39	55.04	45.34	40.20	39.18	45.35
  42	0.44	0.31	0.87	0.69	0.34	1.72	1.32	0.48	0.63	0.82
  43	6.50	6.40	7.75	8.00	8.25	8.00	7.00	7.60	7.33	7.50
  44	0.92	0.45	1.14	0.83	0.59	2.27	1.91	1.09	1.26	1.46
  45	6.25	2.66	8.89	6.65	4.92	18.15	13.49	8.35	9.42	11.31
  46	0.69	0.60	0.59	0.54	0.68	0.56	0.59	0.70	0.66	0.68
  22	12.38	8.60	25.50	16.56	10.53	27.15	26.30	13.56	20.79	16.99
  47	1.36	0.76	2.01	1.53	0.93	3.99	3.23	1.57	1.89	2.28
  48	9.21	4.47	15.79	12.20	7.76	31.94	22.78	12.04	14.14	17.78
  49	2.96	1.81	6.89	5.55	2.84	13.8	9.28	3.70	4.72	6.47
  Table 47. Correlation IDs refer to those described in Table 42 above [Brachypodium correlated parameters (vectors)].

• TABLE 48
  Measured parameters of correlation IDs in Brachypodium
  accessions under normal conditions (lines 41-44)

  Ecotype/Treatment	Line-41	Line-42	Line-43	Line-44

  26	20.84	17.55	47.73	59.01
  27	3.90	4.82	4.87	3.76
  28	0.04	0.06	0.09	0.09
  29	0.09	0.10	0.11	0.09
  30	0.72	0.79	0.87	0.76
  31	1.60	1.80	1.90	1.68
  32	0.15	0.17	0.16	0.15
  33	0.27	0.32	0.44	0.30
  34	2.03	2.58	3.40	1.92
  35	0.17	0.15	0.18	0.09
  36	21.40	25.88	17.05	25.54
  37	156.83	207.00	135.00	177.00
  38	2.33	2.60	4.50	3.17
  39	1.85	1.93	2.85	2.79
  40	5.02	4.90	7.72	15.36
  41	29.41	38.39	46.74	58.82
  42	0.67	0.87	1.05	1.73
  43	7.33	8.00	7.88	6.83
  44	0.96	1.56	1.42	2.25
  45	7.16	12.44	11.05	15.55
  46	0.60	0.65	0.57	0.57
  22	23.61	27.20	18.25	29.09
  47	1.63	2.43	2.47	3.98
  48	12.29	19.40	19.27	27.67
  49	5.13	6.96	8.23	12.12
  Table 48. Correlation IDs refer to those described in Table 42 above [Brachypodium correlated parameters (vectors)].

• TABLE 49
  Correlation between the expression level of selected genes of some
  embodiments of the invention in various tissues and the phenotypic performance
  under normal conditions across brachypodium varieties

  Gene			Exp.	Corr.	Gene			Exp.	Corr.
  Name	R	P value	set	Set ID	Name	R	P value	set	Set ID

  LYD542	0.80	3.32E−03	2	46	LYD543	0.75	1.17E−02	3	30
  LYD543	0.75	1.22E−02	3	31	LYD544	0.72	8.85E−03	1	8
  LYD544	0.73	7.10E−03	1	9	LYD544	0.71	1.39E−02	2	29
  LYD545	0.82	1.84E−03	2	37	LYD545	0.86	7.41E−04	2	22
  LYD545	0.79	3.49E−03	2	48	LYD545	0.80	3.10E−03	2	44
  LYD545	0.80	3.05E−03	2	49	LYD545	0.82	1.88E−03	2	42
  LYD545	0.79	4.13E−03	2	40	LYD545	0.78	4.87E−03	2	45
  LYD545	0.83	1.68E−03	2	36	LYD545	0.82	2.17E−03	2	47
  LYD546	0.70	1.06E−02	1	8	LYD546	0.78	2.93E−03	1	9
  Table 49. Provided are the correlations (R) between the expression levels yield improving genes and their homologs in various tissues [Expression (Exp) sets] and the phenotypic performance [yield, biomass, growth rate and/or vigor components (Correlation vector (Corr))] under normal conditions across brachypodium varieties. P = p value.

Example 11 Plant Fiber Development in Cotton Production of Cotton Transcriptome and High Throughput Correlation Analysis Using Cotton Oligonucleotide Microarray
• In order to conduct high throughput gene expression correlation analysis, the present inventors used cotton oligonucleotide microarray, designed and produced by “Comparative Evolutionary Genomics of Cotton” [Hypertext Transfer Protocol cottonevolution (dot) info/). This Cotton Oligonucleotide Microarray is composed of 12,006 Integrated DNA Technologies (IDT) oligonucleotides derived from an assembly of more than 180,000 Gossypium ESTs sequenced from 30 cDNA libraries. For additional details see PCT/IL2005/000627 and PCT/IL2007/001590 which are fully incorporated herein by reference.

• TABLE 50
  Cotton transcriptome experimental sets

  Expression Set	Set ID

  Fiber

  15 days after anthesis under normal growth conditions	1
  Fiber 5 days after anthesis under normal growth conditions	2
  Fiber 10 days after anthesis under normal growth conditions	3
  Table 50. Provided are the cotton transcriptome expression sets.

• In order to define correlations between the levels of RNA expression and fiber length, fibers from 8 different cotton lines were analyzed. These fibers were selected showing very good fiber quality and high lint index (Pima types, originating from other cotton species, namely G. barbadense), different levels of quality and lint indexes from various G. hirsutum lines: good quality and high lint index (Acala type), and poor quality and short lint index (Tamcot type, and old varieties). A summary of the fiber length of the different lines is provided in Table 51.
• Experimental Procedures
• RNA extraction—Fiber development stages, representing different fiber characteristics, at 5, 10 and 15 DPA were sampled and RNA was extracted as described above.
• Fiber length assessment—Fiber length of the selected cotton lines was measured using fibrograph. The fibrograph system was used to compute length in terms of “Upper Half Mean” length. The upper half mean (UHM) is the average length of longer half of the fiber distribution. The fibrograph measures length in span lengths at a given percentage point World Wide Web (dot) cottoninc (dot) com/ClassificationofCotton/?Pg=4#Length].
Experimental Results
• Eight different cotton lines were grown, and their fiber length was measured. The fibers UHM values are summarized in Table 51 herein below. The R square was calculated for each of the genes.

• TABLE 51
  Summary of the fiber length of the 8 different cotton lines

  Treatment

  Ecotype	Line-1	Line-2	Line-3	Line-4	Line-5	Line-6	Line-7	Line-8
  1	1.21	1.1	1.36	1.26	0.89	1.01	1.06	1.15
  Table 51: Presented are the means 8 different cotton lines.

• TABLE 52
  Correlation between the expression level of selected genes of some
  embodiments of the invention in various tissues and the phenotypic
  performance under normal conditions across cotton ecotypes

  Gene			Exp.	Corr.	Gene			Exp.	Corr.
  Name	R	P value	set	Set ID	Name	R	P value	set	Set ID
  LYD554	0.90	2.19E−03	1	1	LYD555	0.73	3.82E−02	1	1
  LYD555	0.85	1.50E−02	3	1
  Table 52. Provided are the correlations (R) between the expression levels yield improving genes and their homologs in various tissues [Expression (Exp) sets] and the phenotypic performance [yield, biomass, growth rate and/or vigor components (Correlation vector (Corr))] under normal conditions across cotton ecotypes. P = p value.

Example 12 Identification of Genes which Increase Yield, Biomass, Growth Rate, Vigor, Oil Content, Abiotic Stress Tolerance of Plants and Nitrogen Use Efficiency
• Based on the above described bioinformatics and experimental tools, the present inventors have identified 164 genes which have a major impact on yield, seed yield, oil yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency when expression thereof is increased in plants. The identified genes (including genes identified by bioinformatics tools and curated sequences thereof), and polypeptide sequences encoded thereby are summarized in Table 53, hereinbelow.

• TABLE 53
  Identified polynucleotides which affect plant yield, seed yield, oil yield,
  oil content, biomass, growth rate, vigor, fiber yield, fiber quality
  abiotic stress tolerance and/or nitrogen use efficiency of a plant

  		Polyn.	Polyp
  		SEQ	SEQ
  Gene Name	Organism/Cluster tag	ID NO:	ID NO:

  LYD521	arabidopsis|10v1|AT1G08410	1	362
  LYD522	arabidopsis|10v1|AT1G19110	2	363
  LYD524	arabidopsis|10v1|AT2G20340	3	364
  LYD525	arabidopsis|10v1|AT2G45030	4	365
  LYD526	arabidopsis|10v1|AT2G45730	5	366
  LYD527	arabidopsis|10v1|AT2G47920	6	367
  LYD528	arabidopsis|10v1|AT3G15650	7	368
  LYD529	arabidopsis|10v1|AT4G00500	8	369
  LYD530	arabidopsis|10v1|AT4G13110	9	370
  LYD531	arabidopsis|10v1|AT4G16146	10	371
  LYD532	arabidopsis|10v1|AT5G02830	11	372
  LYD533	arabidopsis|10v1|AT5G06700	12	373
  LYD534	arabidopsis|10v1|AT5G43150	13	374
  LYD535	arabidopsis|10v1|AT5G46790	14	375
  LYD536	arabidopsis|10v1|AT5G65280	15	376
  LYD537	b_juncea|10v2|E6ANDIZ01AI14E	16	377
  LYD538	b_juncea|10v2|E6ANDIZ01AWH6F	17	378
  LYD539	b_juncea|10v2|E6ANDIZ01B0PVK	18	379
  LYD540	b_juncea|10v2|E6ANDIZ01CQ2ZQ	19	380
  LYD541	b_rapa|11v1|BQ704427	20	381
  LYD542	brachypodium|09v1|DV480497	21	382
  LYD543	brachypodium|09v1|GT759735	22	383
  LYD544	brachypodium|09v1|GT835824	23	384
  LYD545	brachypodium|09v1|GT841411	24	385
  LYD546	brachypodium|09v1|SRR031797S0017542	25	386
  LYD547	canola|10v1|CD822163	26	387
  LYD548	canola|10v1|CX192172	27	388
  LYD549	canola|10v1|EE556201	28	389
  LYD550	canola|11v1|DY020414	29	390
  LYD551	canola|11v1|EE429972	30	391
  LYD552	canola|11v1|EE440823	31	392
  LYD553	canola|11v1|EE481252	32	393
  LYD554	cotton|10v2|DN804535	33	394
  LYD555	cotton|11v1|CO098912	34	395
  LYD556	lotus|09v1|AW719664	35	396
  LYD558	medicago|09v1|LLAW329230	36	397
  LYD559	medicago|11v1|AI083094	37	398
  LYD560	medicago|11v1|AI974457	38	399
  LYD561	medicago|11v1|AJ388759	39	400
  LYD562	medicago|11v1|AL368425	40	401
  LYD563	medicago|11v1|AL370319	41	402
  LYD564	medicago|11v1|AL372358	42	403
  LYD565	medicago|11v1|AL383170	43	404
  LYD566	medicago|11v1|AL384827	44	405
  LYD567	medicago|11v1|AW125911	45	406
  LYD568	medicago|11v1|AW126198	46	407
  LYD570	medicago|11v1|AW299069	47	408
  LYD571	medicago|11v1|AW299099	48	409
  LYD572	medicago|11v1|AW683620	49	410
  LYD573	medicago|11v1|AW684312	50	411
  LYD574	medicago|11v1|AW686798	51	412
  LYD575	medicago|11v1|AW688064	52	413
  LYD576	medicago|11v1|AW688428	53	414
  LYD577	medicago|11v1|AW690765	54	415
  LYD578	medicago|11v1|AW691134	55	416
  LYD579	medicago|11v1|AW695894	56	417
  LYD580	medicago|11v1|AW775280	57	418
  LYD581	medicago|11v1|AW980738	58	419
  LYD583	medicago|11v1|BE204527	59	420
  LYD584	medicago|11v1|BE325825	60	421
  LYD585	medicago|11v1|BE942833	61	422
  LYD586	medicago|11v1|BE998813	62	423
  LYD587	medicago|11v1|BF005808	63	424
  LYD588	medicago|11v1|BF640823	64	425
  LYD589	medicago|11v1|BG644974	65	426
  LYD590	medicago|11v1|BQ139188	66	427
  LYD591	medicago|11v1|EV259134	67	428
  LYD592	medicago|11v1|XM_003625686	68	429
  LYD593	medicago|12v1|AL366306	69	430
  LYD594	medicago|12v1|BF633538	70	431
  LYD595	rice|gb170|OS01G51360	71	432
  LYD596	rice|gb170|OS01G70930	72	433
  LYD597	rice|gb170|OS02G22020	73	434
  LYD598	rice|gb170|OS03G12840	74	435
  LYD599	rice|gb170|OS04G40100	75	436
  LYD600	rice|gb170|OS06G01200	76	437
  LYD601	rice|gb170|OS06G04250	77	438
  LYD602	rice|gb170|OS06G33810	78	439
  LYD603	rice|gb170|OS08G29170	79	440
  LYD604	sorghum|09v1|SB01G049980	80	441
  LYD605	sorghum|09v1|SB02G037340	81	442
  LYD606	sorghum|09v1|SB03G025590	82	443
  LYD607	sorghum|09v1|SB03G037600	83	444
  LYD608	sorghum|09v1|SB06G006920	84	445
  LYD609	sorghum|09v1|SB09G025850	85	446
  LYD610	sorghum|11v1|SB01G036260	86	447
  LYD611	soybean|11v1|GLYMA01G02290	87	448
  LYD612	soybean|11v1|GLYMA02G02070	88	449
  LYD613	soybean|11v1|GLYMA02G04840	89	450
  LYD614	soybean|11v1|GLYMA02G42250	90	451
  LYD615	soybean|11v1|GLYMA03G27800	91	452
  LYD616	soybean|11v1|GLYMA03G36910	92	453
  LYD617	soybean|11v1|GLYMA03G37120	93	454
  LYD618	soybean|11v1|GLYMA03G41760	94	455
  LYD619	soybean|11v1|GLYMA04G38690	95	456
  LYD620	soybean|11v1|GLYMA05G00370	96	457
  LYD621	soybean|11v1|GLYMA05G34620	97	458
  LYD622	soybean|11v1|GLYMA06G03760	98	459
  LYD623	soybean|11v1|GLYMA06G05880	99	460
  LYD624	soybean|11v1|GLYMA06G11430	100	461
  LYD625	soybean|11v1|GLYMA07G27370	101	462
  LYD626	soybean|11v1|GLYMA08G14740	102	463
  LYD627	soybean|11v1|GLYMA08G39520	103	464
  LYD628	soybean|11v1|GLYMA09G27600	104	465
  LYD629	soybean|11v1|GLYMA09G30190	105	466
  LYD630	soybean|11v1|GLYMA09G35750	106	467
  LYD631	soybean|11v1|GLYMA09G36720	107	468
  LYD632	soybean|11v1|GLYMA10G40890	108	469
  LYD633	soybean|11v1|GLYMA12G02590	109	470
  LYD633	soybean|11v1|GLYMA12G02590	109	543
  LYD634	soybean|11v1|GLYMA12G09830	110	471
  LYD635	soybean|11v1|GLYMA13G04780	111	472
  LYD636	soybean|11v1|GLYMA13G18990	112	473
  LYD637	soybean|11v1|GLYMA13G22160	113	474
  LYD638	soybean|11v1|GLYMA13G41580	114	475
  LYD639	soybean|11v1|GLYMA14G32430	115	476
  LYD640	soybean|11v1|GLYMA14G35690	116	477
  LYD641	soybean|11v1|GLYMA15G02690	117	478
  LYD642	soybean|11v1|GLYMA15G15380	118	479
  LYD643	soybean|11v1|GLYMA16G03140	119	480
  LYD644	soybean|11v1|GLYMA17G01400	120	481
  LYD645	soybean|11v1|GLYMA17G02420	121	482
  LYD646	soybean|11v1|GLYMA17G10240	122	483
  LYD647	soybean|11v1|GLYMA18G15530	123	484
  LYD648	tomato|10v1|AI780847	124	485
  LYD650	tomato|11v1|AF204783	125	486
  LYD651	tomato|11v1|AF211784	126	487
  LYD652	tomato|11v1|AI771255	127	488
  LYD653	tomato|11v1|AI778101	128	489
  LYD654	tomato|11v1|AI782247	129	490
  LYD655	tomato|11v1|AI896168	130	491
  LYD657	tomato|11v1|AW030194	131	492
  LYD658	tomato|11v1|AW094631	132	493
  LYD659	tomato|11v1|AW217526	133	494
  LYD660	tomato|11v1|AW616260	134	495
  LYD661	tomato|11v1|AW616620	135	496
  LYD662	tomato|11v1|AW618546	136	497
  LYD663	tomato|11v1|AY376851	137	498
  LYD664	tomato|11v1|BE460507	138	499
  LYD665	tomato|11v1|BF097728	139	500
  LYD666	tomato|11v1|BG123259	140	501
  LYD667	tomato|11v1|BG123287	141	502
  LYD668	tomato|11v1|BG125390	142	503
  LYD669	tomato|11v1|BG125858	143	504
  LYD670	tomato|11v1|BG126384	144	505
  LYD671	tomato|11v1|BG129734	145	506
  LYD672	tomato|11v1|BG131939	146	507
  LYD673	tomato|11v1|BG132287	147	508
  LYD674	tomato|11v1|BG133722	148	509
  LYD675	tomato|11v1|BG134175	149	510
  LYD676	tomato|11v1|BG135207	150	511
  LYD677	tomato|11v1|BG592613	151	512
  LYD678	tomato|11v1|BG626546	152	513
  LYD679	tomato|11v1|BG628242	153	514
  LYD680	tomato|11v1|BG628985	154	515
  LYD681	tomato|11v1|BG630045	155	516
  LYD682	tomato|11v1|BG630298	156	517
  LYD683	tomato|11v1|BG643762	157	518
  LYD684	tomato|11v1|BG734982	158	519
  LYD685	tomato|11v1|BI210592	159	520
  LYD686	tomato|11v1|BI405665	160	521
  LYD687	tomato|11v1|BM066565	161	522
  LYD688	tomato|11v1|BM067954	162	523
  LYD689	tomato|11v1|BQ512926	163	524
  LYD690	tomato|11v1|DV623174	164	525
  LYD539_H11	arabidopsis|10v1|AT2G35260	165	526
  LYD532	arabidopsis|10v1|AT5G02830	166	527
  LYD535	arabidopsis|10v1|AT5G46790	167	375
  LYD538	b_juncea|10v2|E6ANDIZ01AWH6F	168	528
  LYD539	b_juncea|10v2|E6ANDIZ01B0PVK	169	529
  LYD540	b_juncea|10v2|E6ANDIZ01CQ2ZQ	170	530
  LYD541	b_rapa|11v1|BQ704427	171	381
  LYD544	brachypodium|09v1|GT835824	172	531
  LYD546	brachypodium|09v1|SRR031797S0017542	173	532
  LYD548	canola|10v1|CX192172	174	533
  LYD549	canola|10v1|EE556201	175	534
  LYD550	canola|11v1|DY020414	176	535
  LYD552	canola|11v1|EE440823	177	392
  LYD553	canola|11v1|EE481252	178	536
  LYD567	medicago|11v1|AW125911	179	406
  LYD581	medicago|11v1|AW980738	180	419
  LYD584	medicago|11v1|BE325825	181	537
  LYD587	medicago|11v1|BF005808	182	538
  LYD589	medicago|11v1|BG644974	183	426
  LYD591	medicago|11v1|EV259134	184	428
  LYD592	medicago|11v1|XM_003625686	185	539
  LYD595	rice|gb170|OS01G51360	186	432
  LYD597	rice|gb170|OS02G22020	187	434
  LYD600	rice|gb170|OS06G01200	188	437
  LYD604	sorghum|09v1|SB01G049980	189	441
  LYD606	sorghum|09v1|SB03G025590	190	443
  LYD616	soybean|11v1|GLYMA03G36910	191	453
  LYD619	soybean|11v1|GLYMA04G38690	192	540
  LYD628	soybean|11v1|GLYMA09G27600	193	541
  LYD632	soybean|11v1|GLYMA10G40890	194	542
  LYD654	tomato|11v1|AI782247	195	544
  LYD663	tomato|11v1|AY376851	196	498
  LYD676	tomato|11v1|BG135207	197	545
  LYD681	tomato|11v1|BG630045	198	516
  LYD685	tomato|11v1|BI210592	199	520
  LYD687	tomato|11v1|BM066565	200	522
  LYD690	tomato|11v1|DV623174	201	546
  LYD521	arabidopsis|10v1|AT1G08410	202	362
  LYD522	arabidopsis|10v1|AT1G19110	203	363
  LYD524	arabidopsis|10v1|AT2G20340	204	364
  LYD525	arabidopsis|10v1|AT2G45030	205	365
  LYD526	arabidopsis|10v1|AT2G45730	206	366
  LYD527	arabidopsis|10v1|AT2G47920	207	547
  LYD528	arabidopsis|10v1|AT3G15650	208	368
  LYD529	arabidopsis|10v1|AT4G00500	209	369
  LYD530	arabidopsis|10v1|AT4G13110	210	548
  LYD531	arabidopsis|10v1|AT4G16146	211	371
  LYD532	arabidopsis|10v1|AT5G02830	212	549
  LYD533	arabidopsis|10v1|AT5G06700	213	373
  LYD534	arabidopsis|10v1|AT5G43150	214	374
  LYD535	arabidopsis|10v1|AT5G46790	215	375
  LYD536	arabidopsis|10v1|AT5G65280	216	376
  LYD537	b_juncea|10v2|E6ANDIZ01AI14E	217	550
  LYD538	b_juncea|10v2|E6ANDIZ01AWH6F	218	378
  LYD540	b_juncea|10v2|E6ANDIZ01CQ2ZQ	219	551
  LYD541	b_rapa|11v1|BQ704427	220	381
  LYD542	brachypodium|09v1|DV480497	221	382
  LYD543	brachypodium|09v1|GT759735	222	552
  LYD545	brachypodium|09v1|GT841411	223	385
  LYD546	brachypodium|09v1|SRR031797S0017542	224	386
  LYD547	canola|10v1|CD822163	225	387
  LYD548	canola|10v1|CX192172	226	553
  LYD549	canola|10v1|EE556201	227	554
  LYD550	canola|11v1|DY020414	228	555
  LYD551	canola|11v1|EE429972	229	391
  LYD552	canola|11v1|EE440823	230	392
  LYD553	canola|11v1|EE481252	231	556
  LYD554	cotton|10v2|DN804535	232	557
  LYD555	cotton|11v1|CO098912	233	558
  LYD556	lotus|09v1|AW719664	234	396
  LYD558	medicago|09v1|LLAW329230	235	397
  LYD559	medicago|11v1|AI083094	236	559
  LYD560	medicago|11v1|AI974457	237	560
  LYD561	medicago|11v1|AJ388759	238	400
  LYD562	medicago|11v1|AL368425	239	401
  LYD563	medicago|11v1|AL370319	240	402
  LYD564	medicago|11v1|AL372358	241	403
  LYD565	medicago|11v1|AL383170	242	404
  LYD566	medicago|11v1|AL384827	243	561
  LYD567	medicago|11v1|AW125911	244	406
  LYD568	medicago|11v1|AW126198	245	407
  LYD570	medicago|11v1|AW299069	246	562
  LYD571	medicago|11v1|AW299099	247	563
  LYD572	medicago|11v1|AW683620	248	564
  LYD573	medicago|11v1|AW684312	249	411
  LYD574	medicago|11v1|AW686798	250	412
  LYD575	medicago|11v1|AW688064	251	565
  LYD576	medicago|11v1|AW688428	252	414
  LYD577	medicago|11v1|AW690765	253	566
  LYD578	medicago|11v1|AW691134	254	567
  LYD579	medicago|11v1|AW695894	255	568
  LYD580	medicago|11v1|AW775280	256	569
  LYD581	medicago|11v1|AW980738	257	419
  LYD583	medicago|11v1|BE204527	258	570
  LYD584	medicago|11v1|BE325825	259	421
  LYD585	medicago|11v1|BE942833	260	422
  LYD586	medicago|11v1|BE998813	261	423
  LYD587	medicago|11v1|BF005808	262	571
  LYD588	medicago|11v1|BF640823	263	572
  LYD589	medicago|11v1|BG644974	264	573
  LYD591	medicago|11v1|EV259134	265	574
  LYD592	medicago|11v1|XM_003625686	266	575
  LYD593	medicago|12v1|AL366306	267	576
  LYD594	medicago|12v1|BF633538	268	577
  LYD595	rice|gb170|OS01G51360	269	432
  LYD596	rice|gb170|OS01G70930	270	433
  LYD597	rice|gb170|OS02G22020	271	434
  LYD598	rice|gb170|OS03G12840	272	435
  LYD599	rice|gb170|OS04G40100	273	436
  LYD600	rice|gb170|OS06G01200	274	437
  LYD601	rice|gb170|OS06G04250	275	438
  LYD602	rice|gb170|OS06G33810	276	439
  LYD603	rice|gb170|OS08G29170	277	440
  LYD604	sorghum|09v1|SB01G049980	278	441
  LYD605	sorghum|09v1|SB02G037340	279	578
  LYD606	sorghum|09v1|SB03G025590	280	443
  LYD607	sorghum|09v1|SB03G037600	281	444
  LYD608	sorghum|09v1|SB06G006920	282	445
  LYD609	sorghum|09v1|SB09G025850	283	446
  LYD610	sorghum|11v1|SB01G036260	284	447
  LYD611	soybean|11v1|GLYMA01G02290	285	448
  LYD612	soybean|11v1|GLYMA02G02070	286	449
  LYD613	soybean|11v1|GLYMA02G04840	287	450
  LYD614	soybean|11v1|GLYMA02G42250	288	451
  LYD615	soybean|11v1|GLYMA03G27800	289	452
  LYD616	soybean|11v1|GLYMA03G36910	290	453
  LYD617	soybean|11v1|GLYMA03G37120	291	454
  LYD618	soybean|11v1|GLYMA03G41760	292	579
  LYD619	soybean|11v1|GLYMA04G38690	293	580
  LYD620	soybean|11v1|GLYMA05G00370	294	457
  LYD621	soybean|11v1|GLYMA05G34620	295	458
  LYD622	soybean|11v1|GLYMA06G03760	296	459
  LYD623	soybean|11v1|GLYMA06G05880	297	460
  LYD624	soybean|11v1|GLYMA06G11430	298	461
  LYD625	soybean|11v1|GLYMA07G27370	299	462
  LYD626	soybean|11v1|GLYMA08G14740	300	463
  LYD627	soybean|11v1|GLYMA08G39520	301	464
  LYD628	soybean|11v1|GLYMA09G27600	302	465
  LYD629	soybean|11v1|GLYMA09G30190	303	466
  LYD630	soybean|11v1|GLYMA09G35750	304	467
  LYD631	soybean|11v1|GLYMA09G36720	305	468
  LYD632	soybean|11v1|GLYMA10G40890	306	581
  LYD633	soybean|11v1|GLYMA12G02590	307	470
  LYD634	soybean|11v1|GLYMA12G09830	308	471
  LYD635	soybean|11v1|GLYMA13G04780	309	472
  LYD636	soybean|11v1|GLYMA13G18990	310	473
  LYD637	soybean|11v1|GLYMA13G22160	311	582
  LYD638	soybean|11v1|GLYMA13G41580	312	475
  LYD639	soybean|11v1|GLYMA14G32430	313	476
  LYD640	soybean|11v1|GLYMA14G35690	314	477
  LYD641	soybean|11v1|GLYMA15G02690	315	583
  LYD642	soybean|11v1|GLYMA15G15380	316	479
  LYD643	soybean|11v1|GLYMA16G03140	317	480
  LYD644	soybean|11v1|GLYMA17G01400	318	481
  LYD645	soybean|11v1|GLYMA17G02420	319	482
  LYD646	soybean|11v1|GLYMA17G10240	320	584
  LYD647	soybean|11v1|GLYMA18G15530	321	484
  LYD648	tomato|10v1|AI780847	322	485
  LYD650	tomato|11v1|AF204783	323	585
  LYD651	tomato|11v1|AF211784	324	586
  LYD652	tomato|11v1|AI771255	325	587
  LYD654	tomato|11v1|AI782247	326	490
  LYD655	tomato|11v1|AI896168	327	491
  LYD657	tomato|11v1|AW030194	328	492
  LYD658	tomato|11v1|AW094631	329	493
  LYD659	tomato|11v1|AW217526	330	494
  LYD660	tomato|11v1|AW616260	331	588
  LYD661	tomato|11v1|AW616620	332	496
  LYD662	tomato|11v1|AW618546	333	497
  LYD663	tomato|11v1|AY376851	334	498
  LYD664	tomato|11v1|BE460507	335	499
  LYD665	tomato|11v1|BF097728	336	589
  LYD666	tomato|11v1|BG123259	337	590
  LYD667	tomato|11v1|BG123287	338	591
  LYD668	tomato|11v1|BG125390	339	592
  LYD669	tomato|11v1|BG125858	340	504
  LYD670	tomato|11v1|BG126384	341	505
  LYD671	tomato|11v1|BG129734	342	593
  LYD672	tomato|11v1|BG131939	343	507
  LYD673	tomato|11v1|BG132287	344	594
  LYD674	tomato|11v1|BG133722	345	509
  LYD675	tomato|11v1|BG134175	346	595
  LYD676	tomato|11v1|BG135207	347	596
  LYD677	tomato|11v1|BG592613	348	512
  LYD678	tomato|11v1|BG626546	349	513
  LYD679	tomato|11v1|BG628242	350	597
  LYD680	tomato|11v1|BG628985	351	598
  LYD681	tomato|11v1|BG630045	352	516
  LYD682	tomato|11v1|BG630298	353	517
  LYD683	tomato|11v1|BG643762	354	599
  LYD684	tomato|11v1|BG734982	355	519
  LYD685	tomato|11v1|BI210592	356	600
  LYD686	tomato|11v1|BI405665	357	521
  LYD688	tomato|11v1|BM067954	358	601
  LYD689	tomato|11v1|BQ512926	359	524
  LYD690	tomato|11v1|DV623174	360	525
  LYD539_H11	arabidopsis|10v1|AT2G35260	361	526
  Table 53: Provided are the identified genes, their annotation (cluster tag), organism and polynucleotide and polypeptide sequence identifiers. “polyn.” = polynucleotide; “polyp.” = polypeptide.

Example 13 Identification of Homologous Sequences that Increase Seed Yield, Oil Yield, Growth Rate, Oil Content, Fiber Yield, Fiber Quality, Biomass, Vigor, ABST and/or NUE of a Plant
• The concepts of orthology and paralogy have recently been applied to functional characterizations and classifications on the scale of whole-genome comparisons.
• Orthologs and paralogs constitute two major types of homologs: The first evolved from a common ancestor by specialization, and the latter are related by duplication events. It is assumed that paralogs arising from ancient duplication events are likely to have diverged in function while true orthologs are more likely to retain identical function over evolutionary time.
• To identify putative orthologs of the genes affecting plant yield, oil yield, oil content, seed yield, growth rate, vigor, biomass, abiotic stress tolerance and/or nitrogen use efficiency, all sequences were aligned using the BLAST (Basic Local Alignment Search Tool). Sequences sufficiently similar were tentatively grouped. These putative orthologs were further organized under a Phylogram—a branching diagram (tree) assumed to be a representation of the evolutionary relationships among the biological taxa. Putative ortholog groups were analyzed as to their agreement with the phylogram and in cases of disagreements these ortholog groups were broken accordingly.
• Expression data was analyzed and the EST libraries were classified using a fixed vocabulary of custom terms such as developmental stages (e.g., genes showing similar expression profile through development with up regulation at specific stage, such as at the seed filling stage) and/or plant organ (e.g., genes showing similar expression profile across their organs with up regulation at specific organs such as seed). The annotations from all the ESTs clustered to a gene were analyzed statistically by comparing their frequency in the cluster versus their abundance in the database, allowing the construction of a numeric and graphic expression profile of that gene, which is termed “digital expression”. The rationale of using these two complementary methods with methods of phenotypic association studies of QTLs. SNPs and phenotype expression correlation is based on the assumption that true orthologs are likely to retain identical function over evolutionary time. These methods provide different sets of indications on function similarities between two homologous genes, similarities in the sequence level—identical amino acids in the protein domains and similarity in expression profiles.
• The search and identification of homologous genes involves the screening of sequence information available, for example, in public databases such as the DNA Database of Japan (DDBJ), Genbank, and the European Molecular Biology Laboratory Nucleic Acid Sequence Database (EMBL) or versions thereof or the MIPS database. A number of different search algorithms have been developed, including but not limited to the suite of programs referred to as BLAST programs. There are five implementations of BLAST, three designed for nucleotide sequence queries (BLASTN. BLASTX, and TBLASTX) and two designed for protein sequence queries (BLASTP and TBLASTN) (Coulson, Trends in Biotechnology: 76-80, 1994; Birren et al., Genome Analysis, I: 543, 1997). Such methods involve alignment and comparison of sequences. The BLAST algorithm calculates percent sequence identity and performs a statistical analysis of the similarity between the two sequences. The software for performing BLAST analysis is publicly available through the National Centre for Biotechnology Information. Other such software or algorithms are GAP. BESTFIT. FASTA and TFASTA. GAP uses the algorithm of Needleman and Wunsch (J. Mol. Biol. 48: 443-453, 1970) to find the alignment of two complete sequences that maximizes the number of matches and minimizes the number of gaps.
• The homologous genes may belong to the same gene family. The analysis of a gene family may be carried out using sequence similarity analysis. To perform this analysis one may use standard programs for multiple alignments e.g. Clustal W. A neighbour-joining tree of the proteins homologous to the genes in this invention may be used to provide an overview of structural and ancestral relationships. Sequence identity may be calculated using an alignment program as described above. It is expected that other plants will carry a similar functional gene (ortholog) or a family of similar genes and those genes will provide the same preferred phenotype as the genes presented here. Advantageously, these family members may be useful in the methods of the invention. Example of other plants are included here but not limited to, barley (Hordeum vulgare), Arabidopsis (Arabidopsis thaliana), maize (Zea mays), cotton (Gossypium), Oilseed rape (Brassica napus), Rice (Oryza sativa), Sugar cane (Saccharum officinarum), Sorghum (Sorghum bicolor), Soybean (Glycine max), Sunflower (Helianthus annuus), Tomato (Lycopersicon esculentum), Wheat (Triticum aestivum).
• The above-mentioned analyses for sequence homology can be carried out on a full-length sequence, but may also be based on a comparison of certain regions such as conserved domains. The identification of such domains, would also be well within the realm of the person skilled in the art and would involve, for example, a computer readable format of the nucleic acids of the present invention, the use of alignment software programs and the use of publicly available information on protein domains, conserved motifs and boxes. This information is available in the PRODOM (Hypertext Transfer Protocol://World Wide Web (dot) biochem (dot) ucl (dot) ac (dot) ukLbsm/dbbrowser/protocol/prodomqry (dot) html), PIR (Hypertext Transfer Protocol://pir (dot) Georgetown (dot) edu/) or Pfam (Hypertext Transfer Protocol://World Wide Web (dot) sanger (dot) ac (dot) uk/Software/Pfam/) database.
• Sequence analysis programs designed for motif searching may be used for identification of fragments, regions and conserved domains as mentioned above. Preferred computer programs include, but are not limited to, MEME, SIGNALSCAN, and GENESCAN.
• A person skilled in the art may use the homologous sequences provided herein to find similar sequences in other species and other organisms. Homologues of a protein encompass, peptides, oligopeptides, polypeptides, proteins and enzymes having amino acid substitutions, deletions and/or insertions relative to the unmodified protein in question and having similar biological and functional activity as the unmodified protein from which they are derived. To produce such homologues, amino acids of the protein may be replaced by other amino acids having similar properties (conservative changes, such as similar hydrophobicity, hydrophilicity, antigenicity, propensity to form or break a-helical structures or 3-sheet structures). Conservative substitution tables are well known in the art (see for example Creighton (1984) Proteins. W.H. Freeman and Company). Homologues of a nucleic acid encompass nucleic acids having nucleotide substitutions, deletions and/or insertions relative to the unmodified nucleic acid in question and having similar biological and functional activity as the unmodified nucleic acid from which they are derived.
• Polynucleotides and polypeptides with significant homology to the identified genes described in Table 53 (Example 12 above) were identified from the databases using BLAST software with the Blastp and tBlastn algorithms as filters for the first stage, and the needle (EMBOSS package) or Frame+ algorithm alignment for the second stage. Local identity (Blast alignments) was defined with a very permissive cutoff—60% Identity on a span of 60% of the sequences lengths because it is used only as a filter for the global alignment stage. The default filtering of the Blast package was not utilized (by setting the parameter “-F F”).
• In the second stage, homologs were defined based on a global identity of at least 80% to the core gene polypeptide sequence. Two distinct forms for finding the optimal global alignment for protein or nucleotide sequences were used in this application:
• 1. Between two proteins (following the blastp filter):
• EMBOSS-6.0.1 Needleman-Wunsch algorithm with the following modified parameters: gapopen=8 gapextend=2. The rest of the parameters were unchanged from the default options described hereinabove.
• 2. Between a protein sequence and a nucleotide sequence (following the tblastn filter):
• GenCore 6.0 OneModel application utilizing the Frame+ algorithm with the following parameters: model=frame+_p2n.model mode=qglobal -q=protein.sequence -db=nucleotide.sequence. The rest of the parameters are unchanged from the default options described hereinabove.
• The query polypeptide sequences were SEQ ID NOs: 362-601 (which are encoded by the polynucleotides SEQ ID NOs:1-361, shown in Table 53 above) and the identified orthologous and homologous sequences having at least 80% global sequence identity are provided in Table 54, below. These homologous genes are expected to increase plant yield, seed yield, oil yield, oil content, growth rate, fiber yield, fiber quality, biomass, vigor, ABST and/or NUE of a plant.

• TABLE 54
  Homologous polynucleotides and polypeptides which can increase plant yield, seed yield, oil yield,
  oil content, growth rate, fiber yield, fiber quality, biomass, vigor, ABST and/or NUE of a plant

  				Hom. To	%
  Gene				SEQ ID	global
  Name	Organism/Cluster tag	P.N.	P.P.	NO:	identity	Algor.

  LYD521_H1	arabidopsis_lyrata|09v1|JGIAL000805_P1	602	2429	362	95.9	globlastp
  LYD521_H2	thellungiella_parvulum|11v1|BY806918	603	2430	362	89.2	globlastp
  LYD521_H3	thellungiella_halophilum|11v1|BY806918	604	2431	362	88.3	globlastp
  LYD521_H6	b_rapa|11v1|CD813110_P1	605	2432	362	85.6	globlastp
  LYD521_H4	canola|11v1|EE468045_P1	606	2433	362	85.2	globlastp
  LYD521_H5	canola|11v1|ES952287_T1	607	2434	362	82.37	glotblastn
  LYD522_H1	arabidopsis_lyrata|09v1|JGIAL002005_P1	608	2435	363	96.9	globlastp
  LYD522_H2	thellungiella_halophilum|11v1|BQ079260	609	2436	363	92.1	globlastp
  LYD522_H3	thellungiella_parvulum|11v1|BQ079260	610	2437	363	90.8	globlastp
  LYD522_H4	canola|11v1|FG573664_T1	611	2438	363	89.27	glotblastn
  LYD522_H7	b_rapa|11v1|DY013296_P1	612	2439	363	89	globlastp
  LYD522_H8	b_rapa|11v1|EE443767_P1	613	2440	363	88.4	globlastp
  LYD522_H5	canola|11v1|ES902667_T1	614	2441	363	88.39	glotblastn
  LYD522_H6	canola|11v1|EE443767_P1	615	2442	363	87.6	globlastp
  LYD522_H9	b_rapa|11v1|ES270429_P1	616	2443	363	87.2	globlastp
  LYD524_H1	arabidopsis_lyrata|09v1|JGIAL012501_P1	617	2444	364	97.1	globlastp
  LYD524_H6	b_rapa|11v1|E6ANDIZ01A63NK_P1	618	2445	364	89.8	globlastp
  LYD524_H2	thellungiella_halophilum|11v1|EHJGI11021169	619	2446	364	89.6	globlastp
  LYD524_H3	thellungiella_halophilum|11v1|EHJGI11027144	620	2447	364	87.8	globlastp
  LYD524_H7	b_rapa|11v1|CD822356_P1	621	2448	364	86.8	globlastp
  LYD524_H8	b_rapa|11v1|ES908014_P1	622	2449	364	85.7	globlastp
  LYD524_H4	radish|gb164|EV536118	623	2450	364	84.8	globlastp
  LYD524_H5	thellungiella_parvulum|11v1|EPCRP013365	624	2451	364	82.3	globlastp
  LYD524_H9	b_rapa|11v1|SRR001111.64443_P1	625	2452	364	81.8	globlastp
  LYD525_H1	arabidopsis_lyrata|09v1|JGIAL015890_P1	626	2453	365	98.7	globlastp
  LYD525_H2	arabidopsis|10v1|AT1G45332_P1	627	2454	365	98.7	globlastp
  LYD525_H3	thellungiella_halophilum|11v1|BY819164	628	2455	365	95.5	globlastp
  LYD525_H4	thellungiella_parvulum|11v1|BY819164	629	2456	365	94.2	globlastp
  LYD525_H38	b_rapa|11v1|AT000510_P1	630	2457	365	92.7	globlastp
  LYD525_H5	cacao|10v1|CU478363_P1	631	2458	365	87.3	globlastp
  LYD525_H39	cotton|11v1|DT462624_P1	632	2459	365	86.3	globlastp
  LYD525_H6	cotton|10v2|SRR032367S0023872	633	2460	365	86.3	globlastp
  LYD525_H40	gossypium_raimondii|12v1|DT462624_P1	634	2461	365	86.1	globlastp
  LYD525_H41	cotton|11v1|DT047985_P1	635	2462	365	86	globlastp
  LYD525_H42	gossypium_raimondii|12v1|ES825881_P1	636	2463	365	86	globlastp
  LYD525_H43	bean|12v1|CB539945_P1	637	2464	365	85.3	globlastp
  LYD525_H44	chickpea|11v1|GR393166_P1	638	2465	365	84.8	globlastp
  LYD525_H7	grape|11v1|GSVIVT01018186001_P1	639	2466	365	84.5	globlastp
  LYD525_H45	beech|11v1|SRR006294.21324_P1	640	2467	365	84.4	globlastp
  LYD525_H8	cotton|10v2|SRR032367S0009321	641	2468	365	84.2	globlastp
  LYD525_H9	apple|11v1|CN899815_P1	642	2469	365	84.1	globlastp
  LYD525_H10	clementine|11v1|DY261585_P1	643	2470	365	84	globlastp
  LYD525_H11	orange|11v1|DY261585_P1	644	2470	365	84	globlastp
  LYD525_H12	cucumber|09v1|DV631607_P1	645	2471	365	83.9	globlastp
  LYD525_H13	amsonia|11v1|SRR098688X113063_T1	646	2472	365	83.66	glotblastn
  LYD525_H14	poplar|10v1|BI136702_P1	647	2473	365	83.6	globlastp
  LYD525_H15	aquilegia|10v2|DT749020_P1	648	2474	365	83.4	globlastp
  LYD525_H16	eucalyptus|11v2|SRR001659X12134_P1	649	2475	365	83.3	globlastp
  LYD525_H17	watermelon|11v1|AM716765	650	2476	365	83.2	globlastp
  LYD525_H18	prunus|10v1|CN899815	651	2477	365	83.1	globlastp
  LYD525_H19	euphorbia|11v1|DV149525_P1	652	2478	365	82.9	globlastp
  LYD525_H20	cassava|09v1|JGICASSAVA2572VALIDM1_P1	653	2479	365	82.5	globlastp
  LYD525_H21	strawberry|11v1|DV439076	654	2480	365	82.3	globlastp
  LYD525_H22	tomato|11v1|AW032413	655	2481	365	82.3	globlastp
  LYD525_H46	poppy|11v1|SRR030259.126125_T1	656	2482	365	82.26	glotblastn
  LYD525_H47	banana|12v1|MAGEN2012034630_P1	657	2483	365	82	globlastp
  LYD525_H23	vinca|11v1|SRR098690X120383	658	2484	365	82	globlastp
  LYD525_H24	valeriana|11v1|SRR099039X102865	659	2485	365	81.87	glotblastn
  LYD525_H25	potato|10v1|BG591483_P1	660	2486	365	81.8	globlastp
  LYD525_H26	solanum_phureja|09v1|SPHAW032413	661	2486	365	81.8	globlastp
  LYD525_H48	medicago|12v1|BF634704_P1	662	2487	365	81.7	globlastp
  LYD525_H27	poplar|10v1|CX282997_T1	663	2488	365	81.44	glotblastn
  LYD525_H28	lettuce|10v1|DW064105	664	2489	365	81.2	globlastp
  LYD525_H49	beet|12v1|BI096237_P1	665	2490	365	81.1	globlastp
  LYD525_H29	phalaenopsis|11v1|SRR125771.1000581_P1	666	2491	365	81	globlastp
  LYD525_H30	trigonella|11v1|SRR066195X105848	667	2492	365	80.9	glotblastn
  LYD525_H50	oil_palm|11v1|EY403951_P1	668	2493	365	80.8	globlastp
  LYD525_H51	brachypodium|12v1|BRADI1G41990_P1	669	2494	365	80.7	globlastp
  LYD525_H31	brachypodium|09v1|DV479885	670	2494	365	80.7	globlastp
  LYD525_H32	flaveria|11v1|SRR149229.134858_P1	671	2495	365	80.7	globlastp
  LYD525_H33	flaveria|11v1|SRR149229.104091_P1	672	2496	365	80.6	globlastp
  LYD525_H34	monkeyflower|10v1|CV521415_T1	673	2497	365	80.5	glotblastn
  LYD525_H35	arnica|11v1|SRR099034X126312_T1	674	2498	365	80.39	glotblastn
  LYD525_H52	sorghum|12v1|SB01G001500_T1	675	2499	365	80.26	glotblastn
  LYD525_H36	sorghum|11v1|SB01G001500	676	2499	365	80.26	glotblastn
  LYD525_H37	rice|11v1|AA749912_P1	677	2500	365	80.1	globlastp
  LYD525_H37	rice|gb170|OS03G36780	678	2500	365	80.1	globlastp
  LYD526_H1	arabidopsis_lyrata|09v1|JGIAL015968_T1	679	2501	366	94.87	glotblastn
  LYD526_H2	thellungiella_halophilum|11v1|EHJGI11009328	680	2502	366	88.3	globlastp
  LYD526_H3	thellungiella_parvulum|11v1|BY818477	681	2503	366	87.7	globlastp
  LYD526_H4	canola|11v1|EE446150_T1	682	2504	366	85.27	glotblastn
  LYD526_H5	radish|gb164|EV543432	683	2505	366	84.73	glotblastn
  LYD526_H8	b_rapa|11v1|EE446150_P1	684	2506	366	84	globlastp
  LYD526_H9	b_juncea|12v1|E6ANDIZ02HAY46_P1	685	2507	366	82.7	globlastp
  LYD526_H6	canola|11v1|SRR019557.37442_T1	686	2508	366	82.55	glotblastn
  LYD526_H10	b_rapa|11v1|CN829199_P1	687	2509	366	82.4	globlastp
  LYD526_H7	canola|11v1|EV120639_P1	688	2510	366	81.8	globlastp
  LYD527_H1	arabidopsis_lyrata|09v1|JGIAL016215_P1	689	2511	367	86.3	globlastp
  LYD527_H2	arabidopsis_lyrata|09v1|CRPALE018554_P1	690	2512	367	85.9	globlastp
  LYD528_H1	arabidopsis_lyrata|09v1|JGIAL010051_P1	691	2513	368	98.4	globlastp
  LYD528_H2	thellungiella_parvulum|11v1|EPCRP009845	692	2514	368	94.9	globlastp
  LYD528_H17	b_rapa|11v1|DN964807_P1	693	2515	368	94.5	globlastp
  LYD528_H3	canola|11v1|SRR329661.233011_P1	694	2516	368	94.1	globlastp
  LYD528_H4	thellungiella_halophilum|11v1|EHJGI11003890	695	2517	368	93.3	globlastp
  LYD528_H5	canola|11v1|SRR341923.1074360_T1	696	2518	368	92.94	glotblastn
  LYD528_H6	canola|11v1|SRR329661.212936_T1	697	2519	368	92.55	glotblastn
  LYD528_H7	canola|11v1|SRR329661.203365_T1	698	2520	368	92.16	glotblastn
  LYD528_H18	b_rapa|11v1|EX109671_P1	699	2521	368	89.6	globlastp
  LYD528_H19	b_rapa|11v1|E6ANDIZ01EED7M_P1	700	2522	368	89.2	globlastp
  LYD528_H8	thellungiella_parvulum|11v1|EPCRP002185	701	2523	368	87.1	globlastp
  LYD528_H9	arabidopsis_lyrata|09v1|JGIAL004771_T1	702	2524	368	86.77	glotblastn
  LYD528_H10	arabidopsis|10v1|AT1G52700_P1	703	2525	368	86.3	globlastp
  LYD528_H11	thellungiella_halophilum|11v1|EHJGI11004658	704	2526	368	85.5	globlastp
  LYD528_H12	canola|11v1|SRR341920.125536_P1	705	2527	368	85.1	globlastp
  LYD528_H13	radish|gb164|EW717735	706	2528	368	85.1	globlastp
  LYD528_H20	b_rapa|11v1|BRA030973_P1	707	2529	368	84.7	globlastp
  LYD528_H14	b_rapa|gb162|DN964807	708	2530	368	83.9	globlastp
  LYD528_H21	b_rapa|11v1|E6ANDIZ01EBPM4_T1	709	2531	368	81.96	glotblastn
  LYD528_H15	castorbean|11v1|EG661187_P1	710	2532	368	81.8	globlastp
  LYD528_H16	poplar|10v1|BU891181_P1	711	2533	368	80.6	globlastp
  LYD529_H1	arabidopsis_lyrata|09v1|JGIAL023826_P1	712	2534	369	96.1	globlastp
  LYD529_H2	thellungiella_halophilum|11v1|EHJGI11017680	713	2535	369	90	globlastp
  LYD529_H3	thellungiella_parvulum|11v1|EPCRP024486	714	2536	369	89.3	globlastp
  LYD529_H4	canola|11v1|EV182687_T1	715	2537	369	87.04	glotblastn
  LYD529_H5	b_rapa|11v1|EV182687_P1	716	2538	369	86.8	globlastp
  LYD531_H1	arabidopsis_lyrata|09v1|JGIAL026618_P1	717	2539	371	90.2	globlastp
  LYD531_H2	canola|11v1|EE458414_P1	718	2540	371	83.3	globlastp
  LYD531_H3	b_oleracea|gb161|EH427989_P1	719	2541	371	80.4	globlastp
  LYD532_H1	arabidopsis_lyrata|09v1|CRPALE021692_P1	720	2542	372	93	globlastp
  LYD532_H2	thellungiella_halophilum|11v1|EHJGI11026551	721	2543	372	88.7	globlastp
  LYD532_H3	thellungiella_parvulum|11v1|EPCRP024311	722	2544	372	88.5	globlastp
  LYD532_H4	b_rapa|11v1|H07430_P1	723	2545	372	85.5	globlastp
  LYD533_H1	arabidopsis_lyrata109v1|JGIAL020349_P1	724	2546	373	95.3	globlastp
  LYD533_H2	thellungiella_halophilum|11v1|DN772696	725	2547	373	85	globlastp
  LYD533_H3	thellungiella_parvulum|11v1|DN772696	726	2548	373	85	globlastp
  LYD533_H4	b_rapa|11v1|DY006448_P1	727	2549	373	80.6	globlastp
  LYD534_H1	arabidopsis_lyrata|09v1|JGIAL028732_P1	728	2550	374	94.6	globlastp
  LYD534_H2	thellungiella_halophilum|11v1|EHJGI11028247	729	2551	374	83.5	globlastp
  LYD534_H3	b_juncea|10v2|E6ANDIZ01AURFX_P1	730	2552	374	83	globlastp
  LYD534_H3	b_juncea|10v2|E6ANDIZ01AURFX	731	—	374	83	globlastp
  LYD534_H4	b_oleracea|gb161|AM062082_T1	732	2553	374	82.61	glotblastn
  LYD534_H5	thellungiella_halophilum|11v1|EHPRD125218	733	2554	374	82.47	glotblastn
  LYD534_H6	b_rapa|gb162|CV546549	734	2555	374	81.91	glotblastn
  LYD534_H7	radish|gb164|EW725622	735	2556	374	81.91	glotblastn
  LYD534_H12	b_rapa|11v1|CV546549_P1	736	2557	374	81.9	globlastp
  LYD534_H8	b_juncea|10v2|E6ANDIZ01BUSA3	737	2558	374	81.9	globlastp
  LYD534_H9	canola|11v1|EV089507_P1	738	2557	374	81.9	globlastp
  LYD534_H10	canola|11v1|EE446184_P1	739	2559	374	81.5	globlastp
  LYD534_H13	b_juncea|12v1|E6ANDIZ01BUSA3_P1	740	2560	374	80.9	globlastp
  LYD534_H11	b_juncea|10v2|E6ANDIZ01A0W7T	741	2561	374	80.9	globlastp
  LYD534_H14	b_rapa|11v1|CD829151_P1	742	2562	374	80.2	globlastp
  LYD534_H15	b_rapa|11v1|EE505776_P1	743	2562	374	80.2	globlastp
  LYD535_H1	arabidopsis_lyrata|09v1|JGIAL028142_P1	744	2563	375	89.1	globlastp
  LYD536_H1	arabidopsis_lyrata|09v1|JGIAL031214_P1	745	2564	376	92.6	globlastp
  LYD536_H2	thellungiella_halophilum|11v1|EHJGI11019132	746	2565	376	88.8	globlastp
  LYD536_H3	thellungiella_parvulum|11v1|EPCRP006079	747	2566	376	87.56	glotblastn
  LYD536_H4	canola|11v1|DW999348_P1	748	2567	376	87.2	globlastp
  LYD536_H6	b_rapa|11v1|CD815782_P1	749	2568	376	87	globlastp
  LYD536_H7	b_juncea|12v1|E6ANDIZ01CHJGT_P1	750	2569	376	86.3	globlastp
  LYD536_H5	radish|gb164|EW715863	751	2570	376	86.3	globlastp
  LYD537_H10	b_rapa|11v1|EH416474_P1	752	2571	377	97.5	globlastp
  LYD537_H1	b_rapa|gb162|EX039662	753	2571	377	97.5	globlastp
  LYD537_H3	b_oleracea|gb161|AM387255_T1	754	2572	377	96.45	glotblastn
  LYD537_H4	canola|11v1|EV093336_T1	755	2573	377	95.43	glotblastn
  LYD537_H6	thellungiella_halophilum|11v1|DN774047	756	2574	377	89.4	globlastp
  LYD537_H7	thellungiella|gb167|DN774047	757	2574	377	89.4	globlastp
  LYD537_H9	arabidopsis_lyrata|09v1|JGIAL011355_P1	758	2575	377	86	globlastp
  LYD538_H22	b_rapa|11v1|D78493_P1	759	378	378	100	globlastp
  LYD538_H2	b_rapa|gb162|D78493	760	378	378	100	globlastp
  LYD538_H23	b_juncea|12v1|E6ANDIZ01A102H_P1	761	2576	378	98.3	globlastp
  LYD538_H3	b_oleracea|gb161|AM388274_P1	762	2577	378	98.3	globlastp
  LYD538_H4	canola|11v1|CN829815_P1	763	2578	378	97.9	globlastp
  LYD538_H24	b_juncea|12v1|E6ANDIZ01A6UK3_P1	764	2579	378	97.4	globlastp
  LYD538_H25	b_juncea|12v1|E6ANDIZ01D1DA8_P1	765	2580	378	97.4	globlastp
  LYD538_H5	b_juncea|10v2|E6ANDIZ01A102H	766	2581	378	97	globlastp
  LYD538_H6	b_juncea|10v2|E6ANDIZ01D1DA8	767	2582	378	97	globlastp
  LYD538_H1	canola|11v1|DY025281_P1	768	2583	378	96.2	globlastp
  LYD538_H8	b_rapa|gb162|CA992498	769	2584	378	94.9	globlastp
  LYD538_H9	canola|11v1|CN732901_P1	770	2585	378	94.9	globlastp
  LYD538_H26	b_juncea|12v1|E6ANDIZ01A8ZZF_P1	771	2586	378	94.4	globlastp
  LYD538_H27	wheat|12v3|ERR125558X206533D1_P1	772	2587	378	94.4	globlastp
  LYD538_H7	b_juncea|10v2|E6ANDIZ01AFTUB	773	2586	378	94.4	globlastp
  LYD538_H11	b_juncea|10v2|E6ANDIZ01A8ZZF	774	2588	378	94.4	globlastp
  LYD538_H28	b_rapa|11v1|CD830505_P1	775	2589	378	94	globlastp
  LYD538_H12	radish|gb164|EX762568	776	2590	378	94	globlastp
  LYD538_H15	radish|gb164|EY906991	777	2591	378	93.6	globlastp
  LYD538_H14	radish|gb164|EV543577	778	2592	378	93.2	globlastp
  LYD538_H16	thellungiella_halophilum|11v1|DN773489	779	2593	378	92.7	globlastp
  LYD538_H17	thellungiella_parvulum|11v1|DN773489	780	2594	378	92.7	globlastp
  LYD538_H18	thellungiella_parvulum|11v1|EPPRD115512	781	2594	378	92.7	globlastp
  LYD538_H19	thellungiella|gb167|DN773489	782	2593	378	92.7	globlastp
  LYD538_H20	radish|gb164|EV536694	783	2595	378	91.9	globlastp
  LYD538_H10	arabidopsis_lyrata|09v1|JGIAL022891_P1	784	2596	378	85.9	globlastp
  LYD538_H13	arabidopsis|10v1|AT4G09650_P1	785	2597	378	85.1	globlastp
  LYD538_H21	cleome_spinosa|10v1|SRR015531S0004048_P1	786	2598	378	80.1	globlastp
  LYD539_H14	b_rapa|11v1|ES922502_P1	787	2599	379	95.7	globlastp
  LYD539_H7	canola|11v1|EV186519_P1	788	2600	379	95.7	globlastp
  LYD539_H10	b_rapa|gb162|EX024134	789	2601	379	95.21	glotblastn
  LYD539_H8	canola|11v1|EV204662_P1	790	2602	379	93.4	globlastp
  LYD539_H15	b_juncea|12v1|E6ANDIZ01B2FLS_P1	791	2603	379	92.8	globlastp
  LYD539_H16	b_rapa|11v1|EH415044_P1	792	2604	379	92.8	globlastp
  LYD539_H1	canola|11v1|EE473969_P1	793	2605	379	92.3	globlastp
  LYD539_H2	canola|11v1|EE431340_P1	794	2606	379	92.3	globlastp
  LYD539_H4	thellungiella_parvulum|11v1|DN772747	795	2607	379	91.1	globlastp
  LYD539_H3	radish|gb164|EV546508	796	2608	379	90.2	globlastp
  LYD539_H6	arabidopsis_lyrata|09v1|JGIAL014664_P1	797	2609	379	90.2	globlastp
  LYD539_H9	thellungiella_halophilum|11v1|DN772747	798	2610	379	89.5	globlastp
  LYD540_H5	b_rapa|11v1|CN830957_P1	799	2611	380	89.5	globlastp
  LYD540_H1	canola|11v1|CN830957_P1	800	2612	380	88.7	globlastp
  LYD541_H1	canola|11v1|ES977027_T1	801	2613	381	99.23	glotblastn
  LYD541_H7	wheat|12v3|TA12V3PRD011584_T1	802	2614	381	92.81	glotblastn
  LYD541_H2	thellungiella_parvulum|11v1|EPCRP002741	803	2615	381	88.7	globlastp
  LYD541_H3	canola|11v1|ES976757_T1	804	2616	381	88.55	glotblastn
  LYD541_H8	b_rapa|11v1|AM395348_P1	805	2617	381	86.8	globlastp
  LYD541_H4	thellungiella_halophilum|11v1|EHJGI11022196	806	2618	381	86.42	glotblastn
  LYD541_H5	canola|11v1|EE503031XX1_P1	807	2619	381	84.1	globlastp
  LYD541_H6	arabidopsis_lyrata|09v1|JGIAL017560_P1	808	2620	381	80.9	globlastp
  LYD542_H1	barley|10v2|BF622260	809	2621	382	92.3	globlastp
  LYD542_H2	wheat|10v2|BE428760	810	2622	382	92.1	globlastp
  LYD542_H2	wheat|12v3|BQ579180_P1	811	2622	382	92.1	globlastp
  LYD542_H3	foxtail_millet|11v3|PHY7SI017408M_P1	812	2623	382	87.2	globlastp
  LYD542_H7	sorghum|12v1|SB04G028030_P1	813	2624	382	87	globlastp
  LYD542_H4	sorghum|11v1|SB04G028030	814	2624	382	87	globlastp
  LYD542_H5	maize|10v1|AI600679_P1	815	2625	382	85.6	globlastp
  LYD542_H6	rice|11v1|CA753844_P1	816	2626	382	84.4	globlastp
  LYD542_H6	rice|gb170|OS02G51100	817	2627	382	81.8	globlastp
  LYD542_H8	rye|12v1|DRR001012.114491_P1	818	2628	382	80.4	globlastp
  LYD544_H1	brachypodium|12v1|BRADI2G59740_T1	819	2629	384	86.63	glotblastn
  LYD545_H14	brachypodium|12v1|BRADI1G39260_P1	820	2630	385	95.6	globlastp
  LYD545_H1	rice|11v1|BI808593_P1	821	2631	385	89.3	globlastp
  LYD545_H1	rice|gb170|OS06G31100	822	2631	385	89.3	globlastp
  LYD545_H15	sorghum|12v1|SB10G020060_P1	823	2632	385	89.1	globlastp
  LYD545_H2	sorghum|11v1|SB10G020060	824	2632	385	89.1	globlastp
  LYD545_H3	foxtail_millet|11v3|PHY7SI006167M_P1	825	2633	385	88.6	globlastp
  LYD545_H16	rye|12v1|BE587152_P1	826	2634	385	88.4	globlastp
  LYD545_H17	rye|12v1|DRR001012.114248_P1	827	2635	385	88.4	globlastp
  LYD545_H18	rye|12v1|DRR001012.135473_P1	828	2636	385	88.3	globlastp
  LYD545_H4	sugarcane|10v1|CA093342	829	2637	385	88.3	globlastp
  LYD545_H5	wheat|12v3|BE404680_P1	830	2638	385	88.3	globlastp
  LYD545_H5	wheat|10v2|BE403258	831	2639	385	87.9	globlastp
  LYD545_H6	wheat|10v2|BG906212	832	2640	385	87.6	globlastp
  LYD545_H7	wheat|10v2|BE586039	833	2641	385	87.4	globlastp
  LYD545_H8	leymus|gb166|EG379479_P1	834	2642	385	87.3	globlastp
  LYD545_H9	maize|10v1|BG458966_P1	835	2643	385	87.2	globlastp
  LYD545_H19	wheat|12v3|BE586039_P1	836	2644	385	84.7	globlastp
  LYD545_H10	switchgrass|gb167|FE609538	837	2645	385	80.64	glotblastn
  LYD545_H11	maize|10v1|BG517650_T1	838	2646	385	80.28	glotblastn
  LYD545_H20	sorghum|12v1|SB04G009720_T1	839	2647	385	80.11	glotblastn
  LYD545_H12	sorghum|11v1|SB04G009720	840	2647	385	80.11	glotblastn
  LYD545_H13	foxtail_millet|11v3|EC613481_P1	841	2648	385	80	globlastp
  LYD547_H11	b_rapa|11v1|CD822163_P1	842	387	387	100	globlastp
  LYD547_H1	b_rapa|gb162|CV545936	843	387	387	100	globlastp
  LYD547_H12	b_juncea|12v1|E6ANDIZ01BB4X5_P1	844	2649	387	96.7	globlastp
  LYD547_H2	b_oleracea|gb161|EE535189_P1	845	2650	387	95	globlastp
  LYD547_H3	radish|gb164|EX749320	846	2651	387	89	globlastp
  LYD547_H4	radish|gb164|EX772827	847	2652	387	88.4	glotblastn
  LYD547_H5	radish|gb164|EV524435	848	2653	387	87.8	globlastp
  LYD547_H6	b_juncea|10v2|E6ANDIZ01BB4X5	849	2654	387	86.74	glotblastn
  LYD547_H7,	arabidopsis|10v1|AT1G10522_P1	850	2655	387	83.5	globlastp
  LYD547_H8
  LYD547_H7,	arabidopsis|10v1|AT1G10522	851	—	387	83.5	globlastp
  LYD547_H8
  LYD547_H9	thellungiella_halophilum|11v1|BY811044	852	2656	387	82.6	globlastp
  LYD547_H10	thellungiella|gb167|BY811044	853	2656	387	82.6	globlastp
  LYD548_H15	b_rapa|11v1|CV433382_P1	854	2657	388	99.4	globlastp
  LYD548_H1	canola|11v1|EV096783_P1	855	2658	388	99.1	globlastp
  LYD548_H2	b_rapa|gb162|CV433382	856	2659	388	99.1	globlastp
  LYD548_H16	b_juncea|12v1|E6ANDIZ01BQSST_P1	857	2660	388	97.8	globlastp
  LYD548_H4	radish|gb164|EV524991	858	2661	388	97.5	globlastp
  LYD548_H5	thellungiella_parvulum|11v1|BI698654	859	2662	388	96	globlastp
  LYD548_H7	thellungiella_halophilum|11v1|DN772727	860	2663	388	93.8	globlastp
  LYD548_H8	thellungiella|gb167|BI698654	861	2663	388	93.8	globlastp
  LYD548_H6	arabidopsis|10v1|AT4G09750_P1	862	2664	388	92.9	globlastp
  LYD548_H9	arabidopsis_lyrata|09v1|JGIAL022899_P1	863	2665	388	92.9	globlastp
  LYD548_H10	cleome_spinosa|10v1|SRR015531S0001848_P1	864	2666	388	85.1	globlastp
  LYD548_H17	nasturtium|11v1|SRR032558.125769_P1	865	2667	388	82	globlastp
  LYD548_H18	heritiera|10v1|SRR005794S0003093_P1	866	2668	388	80	globlastp
  LYD549_H2	thellungiella_parvulum|11v1|BY806948	867	2669	389	85	globlastp
  LYD549_H3	thellungiella_halophilum|11v1|BY806948	868	2670	389	80.7	globlastp
  LYD549_H4	arabidopsis_lyrata|09v1|JGIAL014484_P1	869	2671	389	80.7	globlastp
  LYD549_H5	arabidopsis|10v1|AT2G33580_P1	870	2672	389	80.7	globlastp
  LYD550_H46	b_rapa|11v1|CX270458_P1	871	2673	390	95.7	globlastp
  LYD550_H2	thellungiella_halophilum|11v1|DN774121	872	2674	390	89.2	globlastp
  LYD550_H3	thellungiella_parvulum|11v1|DN774121	873	2675	390	87.8	globlastp
  LYD550_H5	arabidopsis_lyrata|09v1|JGIAL010121_P1	874	2676	390	87.6	globlastp
  LYD551_H9	b_rapa|11v1|BQ791522_P1	875	391	391	100	globlastp
  LYD551_H1	b_rapa|gb162|BQ791522	876	391	391	100	globlastp
  LYD551_H2	canola|11v1|DY024382_P1	877	2677	391	98.4	globlastp
  LYD551_H3	radish|gb164|EV524465	878	2678	391	94	globlastp
  LYD551_H4	thellungiella_parvulum|11v1|EPCRP002902	879	2679	391	92.8	globlastp
  LYD551_H5	thellungiella_halophilum|11v1|EHJGI11006208	880	2680	391	88.8	globlastp
  LYD551_H6	arabidopsis_lyrata|09v1|JGIAL000319_P1	881	2681	391	86.4	globlastp
  LYD551_H7	arabidopsis|10v1|AT1G03870_P1	882	2682	391	84.4	globlastp
  LYD551_H8	thellungiella_parvulum|11v1|EPCRP008913	883	2683	391	80.08	glotblastn
  LYD552_H4	b_rapa|11v1|EE440823_P1	884	2684	392	94.9	globlastp
  LYD552_H1	radish|gb164|EV537053	885	2685	392	88.5	globlastp
  LYD552_H5	b_rapa|11v1|CD839492_T1	886	2686	392	86.64	glotblastn
  LYD552_H2	b_rapa|gb162|EX018471	887	2687	392	86.4	globlastp
  LYD552_H3	thellungiella_parvulum|11v1|BY800613	888	2688	392	81.35	glotblastn
  LYD553_H5	thellungiella_halophilum|11v1|EHJGI11004320	889	2689	393	94.2	globlastp
  LYD554_H3	cotton|11v1|AI728201_P1	890	2690	394	99.2	globlastp
  LYD555_H1	cotton|10v2|ES850546	891	2691	395	96.68	glotblastn
  LYD555_H2	gossypium_raimondii|12v1|DT457613_P1	892	2692	395	92.8	globlastp
  LYD556_H2	pigeonpea|11v1|SRR054580X111609_T1	893	2693	396	80.73	glotblastn
  LYD556_H1	pigeonpea|10v1|SRR054580S0002555	894	2693	396	80.73	glotblastn
  LYD558_H1	trigonella|11v1|SRR066194X122160	895	2694	397	91.08	glotblastn
  LYD558_H2	chickpea|11v1|SRR133517.102289_P1	896	2695	397	85.1	globlastp
  LYD559_H22	chickpea|11v1|DY475242_P1	897	2696	398	85.8	globlastp
  LYD559_H2	chickpea|09v2|DY475242	898	2696	398	85.8	globlastp
  LYD559_H23	pigeonpea|11v1|SRR054580X120956_P1	899	2697	398	84.1	globlastp
  LYD559_H4	soybean|11v1|GLYMA12G16380	900	2698	398	83.7	globlastp
  LYD559_H5	spurge|gb161|DV117048	901	2699	398	83	globlastp
  LYD559_H6	lotus|09v1|AI967656_P1	902	2700	398	82.7	globlastp
  LYD559_H24	cotton|11v1|AW186999_P1	903	2701	398	82	globlastp
  LYD559_H25	gossypium_raimondii|12v1|AW186999_P1	904	2701	398	82	globlastp
  LYD559_H8	cotton|10v2|CO071682	905	2701	398	82	globlastp
  LYD559_H9	eucalyptus|11v2|CD668373_P1	906	2702	398	81.7	globlastp
  LYD559_H26	cotton|11v1|CO069437_P1	907	2703	398	81.4	globlastp
  LYD559_H27	cotton|11v1|DT543683_P1	908	2704	398	81.4	globlastp
  LYD559_H10	euphorbia|11v1|DV117048_P1	909	2705	398	81.2	globlastp
  LYD559_H11	peanut|10v1|CD038760_P1	910	2706	398	81.2	globlastp
  LYD559_H12	valeriana|11v1|SRR099039X101600	911	2707	398	81.1	globlastp
  LYD559_H13	pigeonpea|10v1|SRR054580S0006801	912	2708	398	80.9	globlastp
  LYD559_H14	poplar|10v1|AI166111_P1	913	2709	398	80.8	globlastp
  LYD559_H15	kiwi|gb166|FG427674_P1	914	2710	398	80.6	globlastp
  LYD559_H16	chestnut|gb170|SRR006295S0023483_P1	915	2711	398	80.4	globlastp
  LYD559_H17	primula|11v1|SRR098679X101226XX1_T1	916	2712	398	80.33	glotblastn
  LYD559_H18	platanus|11v1|AM260510_P1	917	2713	398	80.2	globlastp
  LYD559_H28	b_juncea|12v1|E6ANDIZ01A1HSY_T1	918	2714	398	80.11	glotblastn
  LYD559_H20	fraxinus|11v1|SRR058827.103366_P1	919	2715	398	80.1	globlastp
  LYD559_H21	scabiosa|11v1|SRR063723X100713	920	2716	398	80.1	globlastp
  LYD560_H1	trigonella|11v1|SRR066194X100341	921	2717	399	97.6	globlastp
  LYD560_H3	pea|11v1|Y17796_P1	922	2718	399	92.6	globlastp
  LYD560_H158	pigeonpea|11v1|SRR054580X104938_P1	923	2719	399	86.7	globlastp
  LYD560_H15	strawberry|11v1|CO378466	924	2720	399	85.4	globlastp
  LYD560_H29	phyla|11v2|SRR099035X102776_P1	925	2721	399	84.1	globlastp
  LYD560_H34	euonymus|11v1|SRR070038X101097_T1	926	2722	399	83.87	glotblastn
  LYD560_H38	euonymus|11v1|SRR070038X127843_P1	927	2723	399	83.7	globlastp
  LYD560_H43	tripterygium|11v1|SRR098677X102820	928	2724	399	83.6	globlastp
  LYD560_H48	orobanche|10v1|SRR023189S0012604_P1	929	2725	399	83.4	globlastp
  LYD560_H58	clementine|11v1|BQ623022_P1	930	2726	399	83.2	globlastp
  LYD560_H71	citrus|gb166|BQ623022	931	2727	399	83	globlastp
  LYD560_H94	rice|11v1|AA750598_P1	932	2728	399	82.5	globlastp
  LYD560_H94	rice|gb170|OS05G49800	933	2728	399	82.5	globlastp
  LYD560_H99	clementine|11v1|CB293579_P1	934	2729	399	82.4	globlastp
  LYD560_H100	orange|11v1|BQ623022_P1	935	2729	399	82.4	globlastp
  LYD560_H159	blueberry|12v1|SRR353282X18635D1_T1	936	2730	399	82.31	glotblastn
  LYD560_H106	antirrhinum|gb166|AJ558721_T1	937	2731	399	82.03	glotblastn
  LYD560_H107	cassava|09v1|CK646362_P1	938	2732	399	82	globlastp
  LYD560_H123	tripterygium|11v1|SRR098677X101139	939	2733	399	81.5	globlastp
  LYD560_H131	cotton|10v2|BE053665	940	2734	399	80.8	globlastp
  LYD560_H160	poppy|11v1|SRR030259.11437_T1	941	2735	399	80.72	glotblastn
  LYD560_H161	gossypium_raimondii|12v1|BE053665_P1	942	2736	399	80.6	globlastp
  LYD560_H162	cotton|11v1|BE053665_P1	943	2737	399	80.3	globlastp
  LYD560_H149	tobacco|gb162|DW004467	944	2738	399	80.23	glotblastn
  LYD560_H163	blueberry|12v1|SRR353282X40527D1_P1	945	2739	399	80	globlastp
  LYD561_H1	trigonella|11v1|SRR066194X416969	946	2740	400	91.6	globlastp
  LYD561_H2	clover|gb162|BB903437_P1	947	2741	400	83.6	globlastp
  LYD562_H1	soybean|11v1|GLYMA16G01070	948	2742	401	83.4	globlastp
  LYD562_H2	soybean|11v1|GLYMA07G04480	949	2743	401	83.1	globlastp
  LYD562_H4	bean|12v1|FG228272_P1	950	2744	401	83	globlastp
  LYD562_H5	pigeonpea|11v1|GR464005_P1	951	2745	401	83	globlastp
  LYD562_H3	pigeonpea|10v1|GR464005	952	2746	401	82.5	globlastp
  LYD563_H1	trigonella|11v1|SRR066194X190527	953	2747	402	92.3	globlastp
  LYD563_H4	chickpea|11v1|GR392227_P1	954	2748	402	87	globlastp
  LYD563_H2	pea|11v1|FG534485_P1	955	2749	402	86.7	globlastp
  LYD563_H3	lotus|09v1|AV413185_P1	956	2750	402	80	globlastp
  LYD564_H1	trigonella|11v1|SRR066194X144531	957	2751	403	99.5	globlastp
  LYD564_H130	chickpea|11v1|GR396842_P1	958	2752	403	95.2	globlastp
  LYD564_H2	pea|11v1|FG530295XX1_P1	959	2753	403	94.1	globlastp
  LYD564_H3	chickpea|09v2|GR396842	960	2754	403	93.4	globlastp
  LYD564_H4	cowpea|12v1|FF538026_P1	961	2755	403	92.5	globlastp
  LYD564_H5	soybean|11v1|GLYMA04G25800	962	2756	403	92.5	globlastp
  LYD564_H6	soybean|11v1|GLYMA11G16210	963	2757	403	90.5	globlastp
  LYD564_H131	bean|12v1|CA896686_P1	964	2758	403	89.5	globlastp
  LYD564_H7	bean|gb167|BQ481858	965	2759	403	89.5	globlastp
  LYD564_H8	cowpea|12v1|FF556286_P1	966	2760	403	89.5	globlastp
  LYD564_H8	cowpea|gb166|FF556286	967	2760	403	89.5	globlastp
  LYD564_H9	cirsium|11v1|SRR346952.16734_T1	968	2761	403	89.07	glotblastn
  LYD564_H132	sunflower|12v1|DY907147_P1	969	2762	403	88.6	globlastp
  LYD564_H10	fagopyrum|11v1|SRR063703X104472_T1	970	2763	403	88.52	glotblastn
  LYD564_H11	orobanche|10v1|SRR023189S0000792_T1	971	2764	403	88.52	glotblastn
  LYD564_H12	ambrosia|11v1|SRR346935.602112_P1	972	2765	403	88.5	globlastp
  LYD564_H13	dandelion|10v1|DY824048_P1	973	2766	403	88.5	globlastp
  LYD564_H14	senecio|gb170|DY663921	974	2767	403	88.5	globlastp
  LYD564_H15	tragopogon|10v1|SRR020205S0016332	975	2768	403	88.5	globlastp
  LYD564_H133	pigeonpea|11v1|GW352750_P1	976	2769	403	88.1	globlastp
  LYD564_H16	fagopyrum|11v1|SRR063689X100418_T1	977	2770	403	88.04	glotblastn
  LYD564_H17	flaveria|11v1|SRR149229.110435_P1	978	2771	403	88	globlastp
  LYD564_H18	safflower|gb162|EL407197	979	2772	403	88	globlastp
  LYD564_H19	phyla|11v2|SRR099036X248170_T1	980	2773	403	87.98	glotblastn
  LYD564_H20	centaurea|gb166|EH717776_P1	981	2774	403	87.6	globlastp
  LYD564_H21	sunflower|10v1|DY907147	982	2775	403	87.6	globlastp
  LYD564_H134	bean|12v1|CA900936_P1	983	2776	403	87.4	globlastp
  LYD564_H22	bean|gb167|CA900936	984	2776	403	87.4	globlastp
  LYD564_H135	sunflower|12v1|DY923354_P1	985	2777	403	87.2	globlastp
  LYD564_H136	sunflower|12v1|DY944220_P1	986	2777	403	87.2	globlastp
  LYD564_H23	cynara|gb167|GE588051_P1	987	2778	403	87.2	globlastp
  LYD564_H24	flaveria|11v1|SRR149229.111588_P1	988	2779	403	87.2	globlastp
  LYD564_H25	grape|11v1|GSVIVT01032214001_P1	989	2780	403	87.2	globlastp
  LYD564_H26	lotus|09v1|LLBG662335_P1	990	2781	403	87.2	globlastp
  LYD564_H27	sunflower|10v1|DY923354	991	2777	403	87.2	globlastp
  LYD564_H28	cleome_gynandra|10v1|SRR015532S0011580_P1	992	2782	403	87.1	globlastp
  LYD564_H29	ambrosia|11v1|SRR346943.287416_T1	993	2783	403	87.03	glotblastn
  LYD564_H137	sesame|12v1|JK047154_P1	994	2784	403	86.9	globlastp
  LYD564_H30	artemisia|10v1|EY062833_P1	995	2785	403	86.9	globlastp
  LYD564_H31	petunia|gb171|FN000395_P1	996	2786	403	86.9	globlastp
  LYD564_H32	flaveria|11v1|SRR149232.13647_P1	997	2787	403	86.7	globlastp
  LYD564_H33	triphysaria|10v1|EY002738	998	2788	403	86.2	globlastp
  LYD564_H34	sarracenia|11v1|SRR192669.103612	999	2789	403	86.1	glotblastn
  LYD564_H35	pepper|12v1|CA520536_P1	1000	2790	403	85.9	globlastp
  LYD564_H35	pepper|gb171|CA520536	1001	2790	403	85.9	globlastp
  LYD564_H36	salvia|10v1|CV170107	1002	2791	403	85.9	globlastp
  LYD564_H37	tobacco|gb162|DV157807	1003	2792	403	85.9	globlastp
  LYD564_H38	coffea|10v1|DV664647_P1	1004	2793	403	85.6	globlastp
  LYD564_H39	catharanthus|11v1|FD660937_P1	1005	2794	403	85.4	globlastp
  LYD564_H40	citrus|gb166|BQ623391	1006	2795	403	85.35	glotblastn
  LYD564_H41	clementine|11v1|BQ623391_T1	1007	2796	403	85.35	glotblastn
  LYD564_H42	orange|11v1|BQ623391_T1	1008	2795	403	85.35	glotblastn
  LYD564_H43	tomato|11v1|BG643022	1009	2797	403	85.3	globlastp
  LYD564_H44	ipomoea_nil|10v1|BJ561525_P1	1010	2798	403	85.2	globlastp
  LYD564_H45	oak|10v1|DB997519_P1	1011	2799	403	85.1	globlastp
  LYD564_H46	oak|10v1|SRR039735S0009498_P1	1012	2799	403	85.1	globlastp
  LYD564_H47	tabernaemontana|11v1|SRR098689X106773	1013	2800	403	85.1	globlastp
  LYD564_H48	lettuce|10v1|DW075465	1014	2801	403	84.9	globlastp
  LYD564_H138	nasturtium|11v1|SRR032558.116424_T1	1015	2802	403	84.82	glotblastn
  LYD564_H49	artemisia|10v1|SRR019254S0026008_P1	1016	2803	403	84.8	globlastp
  LYD564_H50	cichorium|gb171|EH703642_P1	1017	2804	403	84.8	globlastp
  LYD564_H51	eggplant|10v1|FS001669_P1	1018	2805	403	84.8	globlastp
  LYD564_H52	utricularia|11v1|SRR094438.107075	1019	2806	403	84.8	globlastp
  LYD564_H139	blueberry|12v1|SRR353282X27016D1_P1	1020	2807	403	84.7	globlastp
  LYD564_H53	dandelion|10v1|DY802954_P1	1021	2808	403	84.7	globlastp
  LYD564_H54	lettuce|10v1|DW076259	1022	2809	403	84.7	globlastp
  LYD564_H55	castorbean|11v1|XM_002517708_T1	1023	2810	403	84.62	glotblastn
  LYD564_H140	plantago|11v2|SRR066373X110282_P1	1024	2811	403	84.6	globlastp
  LYD564_H56	canola|11v1|EE511611_P1	1025	2812	403	84.6	globlastp
  LYD564_H57	plantago|11v1|SRR066373X110282	1026	2811	403	84.6	globlastp
  LYD564_H141	gossypium_raimondii|12v1|AI727289_T1	1027	2813	403	84.54	glotblastn
  LYD564_H58	cotton|10v2|BQ412972	1028	2813	403	84.54	glotblastn
  LYD564_H59	thellungiella_halophilum|11v1|EHJGI11025782	1029	2814	403	84.46	glotblastn
  LYD564_H60	potato|10v1|BG592695_P1	1030	2815	403	84.3	globlastp
  LYD564_H61	solanum_phureja|09v1|SPHBG643022	1031	2815	403	84.3	globlastp
  LYD564_H62	chestnut|gb170|SRR006295S0014027_P1	1032	2816	403	84.2	globlastp
  LYD564_H63	oak|10v1|FN723381_P1	1033	2816	403	84.2	globlastp
  LYD564_H64	vinca|11v1|SRR098690X111539	1034	2817	403	84.2	globlastp
  LYD564_H65	valeriana|11v1|SRR099039X212264	1035	2818	403	84.15	glotblastn
  LYD564_H142	cotton|11v1|AI727289_T1	1036	2819	403	84.02	glotblastn
  LYD564_H66	lettuce|10v1|DW123070	1037	2820	403	84	globlastp
  LYD564_H67	strawberry|11v1|EX659306	1038	2821	403	84	globlastp
  LYD564_H48,	lettuce|12v1|DW075465_P1	1039	2820	403	84	globlastp
  LYD564_H66
  LYD564_H68	eucalyptus|11v2|CU394869_T1	1040	2822	403	83.92	glotblastn
  LYD564_H143	lettuce|12v1|DW076259_P1	1041	2823	403	83.6	globlastp
  LYD564_H69	bruguiera|gb166|BP939279_P1	1042	2824	403	83.6	globlastp
  LYD564_H70	peanut|10v1|EE124748_P1	1043	2825	403	83.6	globlastp
  LYD564_H71	platanus|11v1|SRR096786X116310_P1	1044	2826	403	83.6	globlastp
  LYD564_H72	radish|gb164|EW715474	1045	2827	403	83.6	globlastp
  LYD564_H73	tripterygium|11v1|SRR098677X11813	1046	2828	403	83.6	globlastp
  LYD564_H74	thellungiella_parvulum|11v1|EPCRP023807	1047	2829	403	83.5	globlastp
  LYD564_H75	humulus|11v1|SRR098683X103967XX1_T1	1048	2830	403	83.42	glotblastn
  LYD564_H76	b_oleracea|gb161|ES943633_P1	1049	2831	403	83.4	globlastp
  LYD564_H77	thellungiella_halophilum|11v1|EHJGI11024070	1050	2832	403	83.4	globlastp
  LYD564_H78	kiwi|gb166|FG439670_P1	1051	2833	403	83.2	globlastp
  LYD564_H79	olea|11v1|SRR014463.26573_P1	1052	2834	403	83.2	globlastp
  LYD564_H80	arabidopsis|10v1|AT5G13780_P1	1053	2835	403	83	globlastp
  LYD564_H81	papaya|gb165|EX281447_P1	1054	2836	403	83	globlastp
  LYD564_H82	arabidopsis_lyrata|09v1|JGIAL021061_P1	1055	2837	403	82.9	globlastp
  LYD564_H144	banana|12v1|FL657740_T1	1056	2838	403	82.89	glotblastn
  LYD564_H83	antirrhinum|gb166|AJ791317_P1	1057	2839	403	82.8	globlastp
  LYD564_H145	oil_palm|11v1|EY408003_T1	1058	2840	403	82.7	glotblastn
  LYD564_H84	ginger|gb164|DY360679_T1	1059	2841	403	82.7	glotblastn
  LYD564_H85	cassava|09v1|DR083932_P1	1060	2842	403	82.6	globlastp
  LYD564_H146	spruce|11v1|ES254811_T1	1061	2843	403	82.51	glotblastn
  LYD564_H147	b_rapa|11v1|CD823802_P1	1062	2844	403	82.5	globlastp
  LYD564_H86	b_rapa|gb162|CV546927	1063	2844	403	82.5	globlastp
  LYD564_H87	tea|10v1|GE650599	1064	2845	403	82.4	globlastp
  LYD564_H88	canola|11v1|DY024886_P1	1065	2846	403	82.3	globlastp
  LYD564_H89	ipomoea_batatas|10v1|BU690124_P1	1066	2847	403	82.3	globlastp
  LYD564_H90	monkeyflower|10v1|GO989362_P1	1067	2848	403	82.3	globlastp
  LYD564_H91	aristolochia|10v1|FD763380_P1	1068	2849	403	82.2	globlastp
  LYD564_H92	euphorbia|11v1|SRR098678X101714_P1	1069	2850	403	82.1	globlastp
  LYD564_H148	spruce|11v1|ES251408_T1	1070	2851	403	81.97	glotblastn
  LYD564_H149	spruce|11v1|EX364957_T1	1071	2851	403	81.97	glotblastn
  LYD564_H93	spruce|gb162|CO483132	1072	2851	403	81.97	glotblastn
  LYD564_H94	amorphophallus|11v2|SRR089351X207625_T1	1073	2852	403	81.91	glotblastn
  LYD564_H95	b_juncea|10v2|E6ANDIZ01A14OT	1074	2853	403	81.9	globlastp
  LYD564_H96	canola|11v1|DY024420_P1	1075	2854	403	81.9	globlastp
  LYD564_H97	curcuma|10v1|DY391831_T1	1076	2855	403	81.82	glotblastn
  LYD564_H98	poplar|10v1|AI162059_P1	1077	2856	403	81.7	globlastp
  LYD564_H99	cassava|09v1|DV445645_P1	1078	2857	403	81.6	globlastp
  LYD564_H150	banana|12v1|FL662727_T1	1079	2858	403	81.54	glotblastn
  LYD564_H151	oil_palm|11v1|ES370541_T1	1080	2859	403	81.52	glotblastn
  LYD564_H100	euphorbia|11v1|AW821927_P1	1081	2860	403	81.5	globlastp
  LYD564_H101	abies|11v2|SRR098676X107677_T1	1082	2861	403	81.42	glotblastn
  LYD564_H102	distylium|11v1|SRR065077X14314_T1	1083	2862	403	81.42	glotblastn
  LYD564_H103	podocarpus|10v1|SRR065014S0008986_T1	1084	2863	403	81.42	glotblastn
  LYD564_H104	pseudotsuga|11v1|SRR065119S0002063	1085	2864	403	81.42	glotblastn
  LYD564_H105	sciadopitys|10v1|SRR065035S0030946	1086	2865	403	81.42	glotblastn
  LYD564_H106	euonymus|11v1|SRR070038X112482_P1	1087	2866	403	81.3	globlastp
  LYD564_H107	poplar|10v1|BU833771_P1	1088	2867	403	81.3	globlastp
  LYD564_H108	tripterygium|11v1|SRR098677X133407	1089	2868	403	81.25	glotblastn
  LYD564_H109	cannabis|12v1|EW701715_P1	1090	2869	403	81.2	globlastp
  LYD564_H110	phalaenopsis|11v1|CB032868_T1	1091	2870	403	81.18	glotblastn
  LYD564_H111	cleome_spinosa|10v1|GR931668_P1	1092	2871	403	81	globlastp
  LYD564_H112	chelidonium|11v1|SRR084752X104265_T1	1093	2872	403	80.83	glotblastn
  LYD564_H113	canola|11v1|EE480839_P1	1094	2873	403	80.8	globlastp
  LYD564_H114	prunus|10v1|CN489292	1095	2874	403	80.77	glotblastn
  LYD564_H115	spurge|gb161|AW821927	1096	2875	403	80.7	globlastp
  LYD564_H152	b_rapa|11v1|CD823960_P1	1097	2876	403	80.6	globlastp
  LYD564_H116	b_rapa|gb162|CV546937	1098	2876	403	80.6	globlastp
  LYD564_H117	cacao|10v1|CA798010_P1	1099	2877	403	80.6	globlastp
  LYD564_H118	flax|11v1|JG027336_P1	1100	2878	403	80.6	globlastp
  LYD564_H119	flax|11v1|JG032028_P1	1101	2879	403	80.6	globlastp
  LYD564_H153	poppy|11v1|SRR030259.103044_P1	1102	2880	403	80.5	globlastp
  LYD564_H154	poppy|11v1|SRR030259.106398XX1_P1	1103	2880	403	80.5	globlastp
  LYD564_H120	euonymus|11v1|SRR070038X116092_P1	1104	2881	403	80.5	globlastp
  LYD564_H121	silene|11v1|GH292679	1105	2882	403	80.5	globlastp
  LYD564_H122	silene|11v1|SRR096785X122338	1106	2882	403	80.5	globlastp
  LYD564_H123	aquilegia|10v2|JGIAC016088_T1	1107	2883	403	80.41	glotblastn
  LYD564_H155	spruce|11v1|SRR065814X412166_T1	1108	2884	403	80.33	glotblastn
  LYD564_H124	cephalotaxus|11v1|SRR064395X117984_T1	1109	2885	403	80.33	glotblastn
  LYD564_H125	distylium|11v1|SRR065077X112028_T1	1110	2886	403	80.33	glotblastn
  LYD564_H126	maritime_pine|10v1|BX254986_T1	1111	2887	403	80.33	glotblastn
  LYD564_H156	rose|12v1|SRR397984.111801_P1	1112	2888	403	80.3	globlastp
  LYD564_H127	canola|11v1|SRR019556.1870_P1	1113	2889	403	80.2	globlastp
  LYD564_H157	poppy|11v1|SRR096789.168678_P1	1114	2890	403	80.1	globlastp
  LYD564_H128	beet|gb162|BI543861	1115	2891	403	80	globlastp
  LYD564_H129	cynodon|10v1|ES293564_T1	1116	2892	403	80	glotblastn
  LYD565_H5	chickpea|11v1|SRR133517.116272_T1	1117	2893	404	86.65	glotblastn
  LYD565_H6	pigeonpea|11v1|SRR054580X109139_P1	1118	2894	404	85.1	globlastp
  LYD565_H1	pigeonpea|10v1|SRR054580S0046177	1119	2894	404	85.1	globlastp
  LYD565_H7	bean|12v1|CA913713_P1	1120	2895	404	83.5	globlastp
  LYD565_H2	soybean|11v1|GLYMA04G01720	1121	2896	404	82.41	glotblastn
  LYD565_H3	soybean|11v1|GLYMA06G01810	1122	2897	404	80.58	glotblastn
  LYD565_H4	peanut|10v1|EG030338_P1	1123	2898	404	80.2	globlastp
  LYD566_H2	medicago|12v1|AW127599_P1	1124	2899	405	97.5	globlastp
  LYD566_H1	medicago|09v1|AW127599	1125	2899	405	97.5	globlastp
  LYD567_H1	medicago|09v1|LLCO511773	1126	2900	406	93.3	globlastp
  LYD567_H2	pea|11v1|AJ308129_P1	1127	2901	406	92	globlastp
  LYD567_H3	pea|11v1|CD860470_P1	1128	2902	406	92	globlastp
  LYD567_H10	chickpea|11v1|FE669744_P1	1129	2903	406	90.8	globlastp
  LYD567_H4	chickpea|09v2|FE669744	1130	2903	406	90.8	globlastp
  LYD567_H5	pea|11v1|AJ308126_P1	1131	2904	406	89.3	globlastp
  LYD567_H6	clover|gb162|BB915852_P1	1132	2905	406	88	globlastp
  LYD567_H7	trigonella|11v1|SRR066194X123223	1133	2906	406	86.7	globlastp
  LYD567_H11	chickpea|11v1|X95708_T1	1134	2907	406	85.53	glotblastn
  LYD567_H12	chickpea|11v1|SRR133522.101553_P1	1135	2908	406	85.5	globlastp
  LYD567_H8	chickpea|09v2|CD051353	1136	2908	406	85.5	globlastp
  LYD567_H9	trigonella|11v1|SRR066194X28674	1137	2909	406	85.3	globlastp
  LYD568_H16	chickpea|11v1|AJ630657_P1	1138	2910	407	91.6	globlastp
  LYD568_H1	chickpea|09v2|AJ630657	1139	2910	407	91.6	globlastp
  LYD568_H17	pigeonpea|11v1|SRR054580X103634_P1	1140	2911	407	90.4	globlastp
  LYD568_H2	pigeonpea|10v1|SRR054580S0000977	1141	2911	407	90.4	globlastp
  LYD568_H3	liquorice|gb171|FS248176_P1	1142	2912	407	89.9	globlastp
  LYD568_H4	lotus|09v1|AW163923_P1	1143	2913	407	89.9	globlastp
  LYD568_H18	peanut|10v1|GO266966_T1	1144	2914	407	86.52	glotblastn
  LYD568_H5	soybean|11v1|GLYMA04G01390	1145	2915	407	86.5	globlastp
  LYD568_H6	cowpea|12v1|FF389144_P1	1146	2916	407	82	globlastp
  LYD568_H6	cowpea|gb166|FF389144	1147	2916	407	82	globlastp
  LYD568_H7	flax|11v1|GW866793_P1	1148	2917	407	81.8	globlastp
  LYD568_H8	cacao|10v1|CU490694_P1	1149	2918	407	81.5	globlastp
  LYD568_H9	flax|11v1|EU830291_T1	1150	2919	407	81.46	glotblastn
  LYD568_H19	cotton|11v1|AI055160_P1	1151	2920	407	80.9	globlastp
  LYD568_H20	cotton|11v1|DT461579_P1	1152	2921	407	80.9	globlastp
  LYD568_H21	gossypium_raimondii|12v1|AI055160_P1	1153	2921	407	80.9	globlastp
  LYD568_H22	nasturtium|11v1|SRR032558.13527_P1	1154	2922	407	80.9	globlastp
  LYD568_H10	bean|gb167|CV538261	1155	2923	407	80.9	glotblastn
  LYD568_H11	castorbean|11v1|EE259809_T1	1156	2924	407	80.9	glotblastn
  LYD568_H12	cotton|10v2|AI055160	1157	2921	407	80.9	globlastp
  LYD568_H13	cassava|09v1|CK645402_P1	1158	2925	407	80.7	globlastp
  LYD568_H23	bean|12v1|SRR001334.136593_T1	1159	2926	407	80.34	glotblastn
  LYD568_H14	poplar|10v1|BU813245_P1	1160	2927	407	80.3	globlastp
  LYD568_H15	tomato|11v1|BG129131	1161	2928	407	80.3	globlastp
  LYD570_H1	trigonella|11v1|SRR066194X239168	1162	2929	408	92.9	globlastp
  LYD570_H2	chickpea|09v2|EH058717	1163	2930	408	83	globlastp
  LYD572_H1	medicago|12v1|EV255012_P1	1164	2931	410	98.2	globlastp
  LYD573_H1	trigonella|11v1|SRR066194X104366	1165	2932	411	94	globlastp
  LYD573_H2	chickpea|11v1|SRR133517.141259_T1	1166	2933	411	88.61	glotblastn
  LYD574_H20	chickpea|11v1|SRR133517.128864_P1	1167	2934	412	94.9	globlastp
  LYD574_H21	pigeonpea|11v1|SRR054580X111703_P1	1168	2935	412	91.5	globlastp
  LYD574_H1	soybean|11v1|GLYMA02G02340	1169	2936	412	90.8	globlastp
  LYD574_H2	lotus|09v1|LLBG662424_P1	1170	2937	412	90	globlastp
  LYD574_H22	bean|12v1|CA908921_P1	1171	2938	412	89.5	globlastp
  LYD574_H3	peanut|10v1|EG029423_P1	1172	2939	412	87.6	globlastp
  LYD574_H4	poplar|10v1|BU869776_P1	1173	2940	412	82.3	globlastp
  LYD574_H5	peanut|10v1|EC366411_P1	1174	2941	412	82.2	globlastp
  LYD574_H6	soybean|11v1|GLYMA01G05160	1175	2942	412	82.02	glotblastn
  LYD574_H7	chestnut|gb170|SRR006295S0025482_P1	1176	2943	412	81.9	globlastp
  LYD574_H23	bean|12v1|SRR001334.279981_T1	1177	2944	412	81.88	glotblastn
  LYD574_H8	bean|gb167|CV542123	1178	2944	412	81.88	glotblastn
  LYD574_H9	soybean|11v1|GLYMA08G40920	1179	2945	412	81.6	globlastp
  LYD574_H24	beech|11v1|SRR006293.10412_P1	1180	2946	412	81.5	globlastp
  LYD574_H10	prunus|10v1|BU039536	1181	2947	412	81.2	globlastp
  LYD574_H11	poplar|10v1|BU820298_P1	1182	2948	412	81.1	globlastp
  LYD574_H25	pigeonpea|11v1|SRR054580X100050_T1	1183	2949	412	80.96	glotblastn
  LYD574_H12	pigeonpea|10v1|SRR054580S0004056	1184	2949	412	80.96	glotblastn
  LYD574_H13	soybean|11v1|GLYMA18G16060	1185	2950	412	80.9	globlastp
  LYD574_H14	oak|10v1|FP041194_T1	1186	2951	412	80.52	glotblastn
  LYD574_H15	apple|11v1|CN864765_P1	1187	2952	412	80.5	globlastp
  LYD574_H16	cacao|10v1|CA794423_P1	1188	2953	412	80.5	globlastp
  LYD574_H17	castorbean|11v1|GE632527_P1	1189	2954	412	80.5	globlastp
  LYD574_H26	gossypium_raimondii|12v1|AI728125_T1	1190	2955	412	80.34	glotblastn
  LYD574_H27	cotton|11v1|AI728125_P1	1191	2956	412	80.3	globlastp
  LYD574_H18	grape|11v1|GSVIVT01020041001_P1	1192	2957	412	80.3	globlastp
  LYD574_H19	strawberry|11v1|CO817255	1193	2958	412	80.1	globlastp
  LYD578_H146	chickpea|11v1|FL512454_P1	1194	2959	416	95.4	globlastp
  LYD578_H2	soybean|11v1|GLYMA16G34500	1195	2960	416	92	globlastp
  LYD578_H147	pigeonpea|11v1|SRR054580X10565_P1	1196	2961	416	91.9	globlastp
  LYD578_H3	prunus|10v1|BU047195	1197	2962	416	91.2	globlastp
  LYD578_H148	bean|12v1|CA910341_P1	1198	2963	416	90.4	globlastp
  LYD578_H4	flax|11v1|CA482751_P1	1199	2964	416	90.2	globlastp
  LYD578_H5	eucalyptus|11v2|CT982512_P1	1200	2965	416	90	globlastp
  LYD578_H6	apple|11v1|CN489546_P1	1201	2966	416	89.8	globlastp
  LYD578_H7	melon|10v1|AM726472_P1	1202	2967	416	89.8	globlastp
  LYD578_H8	watermelon|11v1|AM726472	1203	2968	416	89.7	globlastp
  LYD578_H9	cucumber|09v1|DN910557_P1	1204	2969	416	89.5	globlastp
  LYD578_H10	apple|11v1|CN996236_P1	1205	2970	416	89.4	globlastp
  LYD578_H11	strawberry|11v1|CO380109	1206	2971	416	88.5	globlastp
  LYD578_H12	cacao|10v1|CF974101_P1	1207	2972	416	88.4	globlastp
  LYD578_H13	euonymus|11v1|SRR070038X118639_P1	1208	2973	416	88.3	globlastp
  LYD578_H15	euonymus|11v1|SRR070038X138821_P1	1209	2974	416	88.2	globlastp
  LYD578_H16	chestnut|gb170|SRR006295S0032584_P1	1210	2975	416	88	globlastp
  LYD578_H17	silene|11v1|SRR096785X101977	1211	2976	416	88	globlastp
  LYD578_H18	tripterygium|11v1|SRR098677X118762	1212	2977	416	88	globlastp
  LYD578_H19	oak|10v1|FP033276_P1	1213	2978	416	87.8	globlastp
  LYD578_H21	peanut|10v1|ES712396_T1	1214	2979	416	87.59	glotblastn
  LYD578_H23	grape|11v1|GSVIVT01011574001_P1	1215	2980	416	87.3	globlastp
  LYD578_H26	euphorbia|11v1|DV112988_P1	1216	2981	416	87.1	globlastp
  LYD578_H149	poppy|11v1|SRR030259.373171_P1	1217	2982	416	86.8	globlastp
  LYD578_H29	tomato|11v1|BG131155	1218	2983	416	86.8	globlastp
  LYD578_H150	poppy|11v1|SRR030259.105041_P1	1219	2984	416	86.7	globlastp
  LYD578_H30	canola|11v1|EE564982_T1	1220	2985	416	86.61	glotblastn
  LYD578_H151	oil_palm|11v1|EL687687_P1	1221	2986	416	86.5	globlastp
  LYD578_H31	arabidopsis_lyrata|09v1|JGIAL016352_P1	1222	2987	416	86.5	globlastp
  LYD578_H32	cassava|09v1|DV443394_P1	1223	2988	416	86.5	globlastp
  LYD578_H152	medicago|12v1|AW684124_P1	1224	2989	416	86.3	globlastp
  LYD578_H36	arabidopsis|10v1|AT2G01970_P1	1225	2990	416	86.3	globlastp
  LYD578_H37	medicago|09v1|LLAW684124	1226	2989	416	86.3	globlastp
  LYD578_H39	thellungiella_parvulum|11v1|DN778102	1227	2991	416	86.3	globlastp
  LYD578_H40	canola|11v1|EE549996_P1	1228	2992	416	86.2	globlastp
  LYD578_H42	canola|11v1|EE454097_T1	1229	2993	416	86.13	glotblastn
  LYD578_H43	canola|11v1|DY006061_P1	1230	2994	416	86.1	globlastp
  LYD578_H44	canola|11v1|DY020128_P1	1231	2995	416	86.1	globlastp
  LYD578_H45	humulus|11v1|EX520208_P1	1232	2996	416	86.1	globlastp
  LYD578_H46	thellungiella_halophilum|11v1|DN778102	1233	2997	416	86.1	globlastp
  LYD578_H153	b_rapa|11v1|CD825207_P1	1234	2998	416	86	globlastp
  LYD578_H154	oil_palm|11v1|EL691164_P1	1235	2999	416	85.8	globlastp
  LYD578_H47	lotus|09v1|AI967723_P1	1236	3000	416	85.8	globlastp
  LYD578_H48	watermelon|11v1|AM739846	1237	3001	416	85.8	globlastp
  LYD578_H155	eschscholzia|11v1|CD477858_P1	1238	3002	416	85.7	globlastp
  LYD578_H156	b_rapa|11v1|H74789_P1	1239	3003	416	85.6	globlastp
  LYD578_H49	phyla|11v2|SRR099035X100102_P1	1240	3004	416	85.6	globlastp
  LYD578_H50	thellungiella_parvulum|11v1|BY807072	1241	3005	416	85.6	globlastp
  LYD578_H51	apple|11v1|CX024719_P1	1242	3006	416	85.5	globlastp
  LYD578_H52	arabidopsis|10v1|AT1G14670_P1	1243	3007	416	85.5	globlastp
  LYD578_H54	prunus|10v1|CN492032	1244	3008	416	85.4	globlastp
  LYD578_H55	tabernaemontana|11v1|SRR098689X101380	1245	3009	416	85.4	globlastp
  LYD578_H56	thellungiella_halophilum|11v1|BY809962	1246	3010	416	85.4	globlastp
  LYD578_H58	solanum_phureja|09v1|SPHBG131155	1247	3011	416	85.3	globlastp
  LYD578_H59	triphysaria|10v1|DR175111	1248	3012	416	85.3	globlastp
  LYD578_H60	artemisia|10v1|EY072332_P1	1249	3013	416	85.2	globlastp
  LYD578_H157	sunflower|12v1|DY905094_P1	1250	3014	416	85.1	globlastp
  LYD578_H158	oil_palm|11v1|SRR190698.107991_T1	1251	3015	416	85.06	glotblastn
  LYD578_H63	apple|11v1|CN492032_P1	1252	3016	416	85	globlastp
  LYD578_H65	solanum_phureja|09v1|SPHDB721762	1253	3017	416	85	globlastp
  LYD578_H66	strawberry|11v1|DY674763	1254	3018	416	85	globlastp
  LYD578_H68	solanum_phureja|09v1|SPHBG134887	1255	3019	416	84.9	globlastp
  LYD578_H69	tomato|11v1|BG134887	1256	3020	416	84.9	globlastp
  LYD578_H159	banana|12v1|FF557959_P1	1257	3021	416	84.7	globlastp
  LYD578_H160	banana|12v1|FL660505_P1	1258	3022	416	84.7	globlastp
  LYD578_H74	artemisia|10v1|EY043221_P1	1259	3023	416	84.6	globlastp
  LYD578_H75	vinca|11v1|SRR098690X121789	1260	3024	416	84.6	globlastp
  LYD578_H76	cacao|10v1|CU588720_T1	1261	3025	416	84.55	glotblastn
  LYD578_H77	catharanthus|11v1|EG557449_T1	1262	3026	416	84.55	glotblastn
  LYD578_H78	amsonia|11v1|SRR098688X111096_P1	1263	3027	416	84.5	globlastp
  LYD578_H80	flaveria|11v1|SRR149229.114845_P1	1264	3028	416	84.5	globlastp
  LYD578_H82	sunflower|10v1|DY903830	1265	3029	416	84.5	globlastp
  LYD578_H161	banana|12v1|MAGEN2012035391_P1	1266	3030	416	84.4	globlastp
  LYD578_H162	sunflower|12v1|DY903830_P1	1267	3031	416	84.4	globlastp
  LYD578_H163	sunflower|12v1|DY913973_P1	1268	3032	416	84.4	globlastp
  LYD578_H84	sunflower|10v1|DY907361	1269	3032	416	84.4	globlastp
  LYD578_H85	tobacco|gb162|DW003003	1270	3033	416	84.4	globlastp
  LYD578_H86	vinca|11v1|SRR098690X103710	1271	3034	416	84.4	globlastp
  LYD578_H87	tripterygium|11v1|SRR098677X117684	1272	3035	416	84.38	glotblastn
  LYD578_H88	cucumber|09v1|AM739846_P1	1273	3036	416	84.3	globlastp
  LYD578_H90	ambrosia|11v1|SRR346935.3835_T1	1274	3037	416	84.21	glotblastn
  LYD578_H164	banana|12v1|BBS1314T3_P1	1275	3038	416	84.1	globlastp
  LYD578_H91	chestnut|gb170|SRR006295S0045171_P1	1276	3039	416	84.1	globlastp
  LYD578_H92	euonymus|11v1|SRR070038X113826_P1	1277	3040	416	84.1	globlastp
  LYD578_H93	catharanthus|11v1|SRR098691X104034_T1	1278	3041	416	84.03	glotblastn
  LYD578_H165	sunflower|12v1|DY907361_P1	1279	3042	416	84	globlastp
  LYD578_H94	arnica|11v1|SRR099034X111318_P1	1280	3043	416	84	globlastp
  LYD578_H95	lettuce|10v1|DW111094	1281	3044	416	84	globlastp
  LYD578_H96	poplar|10v1|AI166075_P1	1282	3045	416	84	globlastp
  LYD578_H97	poplar|10v1|BI128092_P1	1283	3046	416	84	globlastp
  LYD578_H166	plantago|11v2|SRR066373X102361_P1	1284	3047	416	83.9	globlastp
  LYD578_H98	plantago|11v1|SRR066373X102361	1285	3047	416	83.9	globlastp
  LYD578_H99	tabernaemontana|11v1|SRR098689X100108	1286	3048	416	83.9	globlastp
  LYD578_H101	vinca|11v1|SRR098690X110217	1287	3049	416	83.9	glotblastn
  LYD578_H103	canola|11v1|EE485698_T1	1288	3050	416	83.87	glotblastn
  LYD578_H167	nasturtium|11v1|SRR032558.117106_P1	1289	3051	416	83.8	globlastp
  LYD578_H104	cassava|09v1|JGICASSAVA18083VALIDM1_P1	1290	3052	416	83.8	globlastp
  LYD578_H105	tomato|11v1|DB721762	1291	3053	416	83.8	globlastp
  LYD578_H168	banana|12v1|ES436693_P1	1292	3054	416	83.6	globlastp
  LYD578_H110	ambrosia|11v1|SRR346935.101384_P1	1293	3055	416	83.4	globlastp
  LYD578_H111	oak|10v1|FN730940_P1	1294	3056	416	83.4	globlastp
  LYD578_H112	ambrosia|11v1|SRR346935.101406_T1	1295	3057	416	83.33	glotblastn
  LYD578_H169	b_juncea|12v1|E6ANDIZ01AHJJJ_T1	1296	3058	416	83.31	glotblastn
  LYD578_H113	centaurea|gb166|EH717543_P1	1297	3059	416	83.3	globlastp
  LYD578_H114	arnica|11v1|SRR099034X103662_T1	1298	3060	416	83.28	glotblastn
  LYD578_H115	rice|11v1|AA751885_P1	1299	3061	416	83.2	globlastp
  LYD578_H115	rice|gb170|OS03G13380	1300	3061	416	83.2	globlastp
  LYD578_H170	brachypodium|12v1|BRADI1G68750_P1	1301	3062	416	82.9	globlastp
  LYD578_H116	phalaenopsis|11v1|SRR125771.1004728_P1	1302	3063	416	82.9	globlastp
  LYD578_H117	silene|11v1|SRR096785X115898	1303	3064	416	82.9	globlastp
  LYD578_H171	sunflower|12v1|DY903937_P1	1304	3065	416	82.7	globlastp
  LYD578_H118	sunflower|10v1|DY903937	1305	3066	416	82.7	globlastp
  LYD578_H119	oat|11v1|AA231831_P1	1306	3067	416	82.5	globlastp
  LYD578_H121	poplar|10v1|AI164784_P1	1307	3068	416	82.4	globlastp
  LYD578_H124	flaveria|11v1|SRR149229.25937_P1	1308	3069	416	82.1	globlastp
  LYD578_H126	arabidopsis_lyrata|09v1|JGIAL027304_P1	1309	3070	416	82	globlastp
  LYD578_H127	ambrosia|11v1|SRR346935.566463_P1	1310	3071	416	81.8	globlastp
  LYD578_H128	arnica|11v1|SRR099034X115318_P1	1311	3072	416	81.8	globlastp
  LYD578_H130,	arabidopsis|10v1|AT5G37310_P1	1312	3073	416	81.6	globlastp
  LGP44
  LYD578_H172	oil_palm|11v1|EL692338_P1	1313	3074	416	81.5	globlastp
  LYD578_H132	phalaenopsis|11v1|SRR125771.1010602_P1	1314	3075	416	81.5	globlastp
  LYD578_H133	flaveria|11v1|SRR149229.122528_T1	1315	3076	416	81.46	glotblastn
  LYD578_H135	canola|11v1|EE543932_P1	1316	3077	416	81.2	globlastp
  LYD578_H137	flaveria|11v1|SRR149229.125055_T1	1317	3078	416	80.95	glotblastn
  LYD578_H173	b_rapa|11v1|CD825294_P1	1318	3079	416	80.9	globlastp
  LYD578_H138	cannabis|12v1|SOLX00055372_P1	1319	3080	416	80.6	globlastp
  LYD578_H174	eschscholzia|11v1|CD480510XX1_P1	1320	3081	416	80.5	globlastp
  LYD578_H139	maritime_pine|10v1|AL750688_P1	1321	3082	416	80.5	globlastp
  LYD578_H140	amorphophallus|11v2|SRR089351X125537_P1	1322	3083	416	80.4	globlastp
  LYD578_H142	vinca|11v1|SRR098690X112534	1323	3084	416	80.3	globlastp
  LYD578_H143	abies|11v2|SRR098676X100567_P1	1324	3085	416	80.1	globlastp
  LYD578_H144	sequoia|10v1|SRR065044S0014146	1325	3086	416	80.1	globlastp
  LYD578_H145	brachypodium|09v1|DV486133	1326	3087	416	80.07	glotblastn
  LYD579_H7	chickpea|11v1|FE670056_P1	1327	3088	417	87.7	globlastp
  LYD579_H8	pigeonpea|11v1|SRR054580X447982_P1	1328	3089	417	84.3	globlastp
  LYD579_H1	lotus|09v1|AV410218_P1	1329	3090	417	84	globlastp
  LYD579_H2	cowpea|12v1|FC461356_P1	1330	3091	417	83.6	globlastp
  LYD579_H2	cowpea|gb166|FC461356	1331	3091	417	83.6	globlastp
  LYD579_H9	bean|12v1|SRR001336.56224_P1	1332	3092	417	83	globlastp
  LYD579_H3	bean|gb167|CV530490	1333	3092	417	83	globlastp
  LYD579_H4	soybean|11v1|GLYMA05G38570	1334	3093	417	82.7	globlastp
  LYD579_H5	soybean|11v1|GLYMA08G01060	1335	3094	417	82.5	globlastp
  LYD579_H6	peanut|10v1|CD037684_P1	1336	3095	417	80.7	globlastp
  LYD580_H3	medicago|12v1|XM_003597757_P1	1337	3096	418	95	globlastp
  LYD580_H4	chickpea|11v1|GR911819_P1	1338	3097	418	86.7	globlastp
  LYD585_H1	medicago|09v1|LLBE942833	1339	3098	422	98.2	globlastp
  LYD585_H2	trigonella|11v1|SRR066194X116540	1340	3099	422	90	globlastp
  LYD585_H3	chickpea|11v1|SRR133517.103317_P1	1341	3100	422	80.3	globlastp
  LYD586_H2	chickpea|11v1|SRR133518.12586_P1	1342	3101	423	81.5	globlastp
  LYD586_H1	lotus|09v1|AW719808_P1	1343	3102	423	80.6	globlastp
  LYD588_H1	medicago|09v1|CRPMT003032	1344	3103	425	87.08	glotblastn
  LYD588_H3	medicago|12v1|XM_003615634_P1	1345	3104	425	80.6	globlastp
  LYD590_H1	chickpea|11v1|SRR133517.134494_T1	1346	3105	427	88.06	glotblastn
  LYD591_H1	chickpea|11v1|SRR133517.166672_P1	1347	3106	428	83.9	globlastp
  LYD592_H2	soybean|11v1|GLYMA19G37270_P1	1348	3107	429	81.6	globlastp
  LYD592_H3	soybean|11v1|GLYMA03G34580_P1	1349	3108	429	80.6	globlastp
  LYD594_H1	medicago|09v1|LLBF633538	1350	3109	431	97	globlastp
  LYD598_H1	wheat|10v2|BE400730XX2	1351	3110	435	85.4	globlastp
  LYD598_H1	wheat|12v3|BT009540_P1	1352	3110	435	85.4	globlastp
  LYD598_H6	rye|12v1|DRR001012.100407_P1	1353	3111	435	85.1	globlastp
  LYD598_H7	sorghum|12v1|SB01G042010_P1	1354	3112	435	84.9	globlastp
  LYD598_H2	sorghum|11v1|SB01G042010	1355	3112	435	84.9	globlastp
  LYD598_H3	maize|10v1|AI586617_T1	1356	3113	435	81.84	glotblastn
  LYD598_H4	foxtail_millet|11v31PHY7SI035780M_P1	1357	3114	435	81.4	globlastp
  LYD598_H5	switchgrass|gb167|FL903075	1358	3115	435	80.7	globlastp
  LYD601	rice|11v1|BI306238_P1	1359	3116	438	98.9	globlastp
  LYD601	rice|11v1|CK007248_P1	1360	3116	438	98.9	globlastp
  LYD601_H1	wheat|10v2|BE400601	1361	3117	438	83.1	globlastp
  LYD601_H8	sorghum|12v1|SB10G002190_P1	1362	3118	438	82.5	globlastp
  LYD601_H2	sorghum|11v1|SB10G002190	1363	3118	438	82.5	globlastp
  LYD601_H1	wheat|12v3|CD931110_P1	1364	3119	438	82.2	globlastp
  LYD601_H3	foxtail_millet|11v3|PHY7SI006804M_P1	1365	3120	438	81.1	globlastp
  LYD601_H4	switchgrass|gb167|FL690669	1366	3121	438	81.1	globlastp
  LYD601_H5	sugarcane|10v1|CA084453	1367	3122	438	80.8	globlastp
  LYD601_H9	brachypodium|12v1|BRADI1G50140_T1	1368	3123	438	80.29	glotblastn
  LYD601_H6	barley|10v2|AW982216	1369	3124	438	80.29	glotblastn
  LYD601_H7	brachypodium|09v1|SRR031798S0051694	1370	3123	438	80.29	glotblastn
  LYD603_H1	wheat|10v2|BG906907	1371	3125	440	80.05	glotblastn
  LYD603_H1	wheat|12v3|BE591745_T1	1372	3125	440	80.05	glotblastn
  LYD604_H1	maize|10v1|BM896111_P1	1373	3126	441	90.4	globlastp
  LYD604_H2	sugarcane|10v1|BQ533093	1374	3127	441	90.34	glotblastn
  LYD604_H3	foxtail_millet|11v3|PHY7SI014187M_P1	1375	3128	441	84.9	globlastp
  LYD604_H4	switchgrass|gb167|FL751571	1376	3129	441	82.61	glotblastn
  LYD604_H5	foxtail_millet|11v3|PHY7SI014332M_P1	1377	3130	441	82.2	globlastp
  LYD605_H1	maize|10v1|AI395969_P1	1378	3131	442	90.2	globlastp
  LYD605_H3	foxtail_millet|11v3|PHY7SI032402M_P1	1379	3132	442	85.4	globlastp
  LYD606_H1	maize|10v1|CD998192_P1	1380	3133	443	88.9	globlastp
  LYD606_H2	foxtail_millet|11v3|PHY7SI003355M_P1	1381	3134	443	85.9	globlastp
  LYD606_H3	switchgrass|gb167|FE620000	1382	3135	443	82	globlastp
  LYD607_H1	sugarcane|10v1|CA090822	1383	3136	444	98.3	globlastp
  LYD607_H2	maize|10v1|AI461578_P1	1384	3137	444	97	globlastp
  LYD607_H3	foxtail_millet|11v3|EC613899_P1	1385	3138	444	88.4	globlastp
  LYD607_H4	millet|10v1|EVO454PM019085_P1	1386	3139	444	87.9	globlastp
  LYD607_H5	switchgrass|gb167|FL736062	1387	3140	444	87.9	globlastp
  LYD607_H6	rice|11v1|CA756435_P1	1388	3141	444	84.5	globlastp
  LYD607_H6	rice|gb170|OS01G59500	1389	3141	444	84.5	globlastp
  LYD607_H10	brachypodium|12v1|BRADI2G52910_P1	1390	3142	444	81.9	globlastp
  LYD607_H7	brachypodium|09v1|DV477071	1391	3142	444	81.9	globlastp
  LYD607_H8	cynodon|10v1|ES293393_T1	1392	3143	444	81.9	glotblastn
  LYD607_H9	oat|11v1|CN815678_P1	1393	3144	444	81	globlastp
  LYD608_H1	foxtail_millet|11v3|PHY7SI009630M_P1	1394	3145	445	91.6	globlastp
  LYD608_H2	maize|10v1|BM498393_P1	1395	3146	445	91.3	globlastp
  LYD608_H3	rice|11v1|CB629440_P1	1396	3147	445	82.1	globlastp
  LYD608_H3	rice|gb170|OS09G32840	1397	3147	445	82.1	globlastp
  LYD608_H4	millet|10v1|EVO454PM008964_P1	1398	3148	445	80.7	globlastp
  LYD609_H1	maize|10v1|AW091479_P1	1399	3149	446	90.8	globlastp
  LYD609_H2	foxtail_millet|11v3|PHY7SI021503M_P1	1400	3150	446	87.8	globlastp
  LYD609_H3	maize|10v1|AW066176_P1	1401	3151	446	84.3	globlastp
  LYD610_H1	maize|10v1|AW313273_P1	1402	3152	447	93.4	globlastp
  LYD610_H2	maize|10v1|CD941624_P1	1403	3153	447	93.2	globlastp
  LYD610_H3	foxtail_millet|11v3|PHY7SI034180M_P1	1404	3154	447	91.2	globlastp
  LYD610_H4	millet|10v1|EVO454PM000391_T1	1405	3155	447	89.61	glotblastn
  LYD610_H8	rice|11v1|OSCRP015914_P1	1406	3156	447	84.8	globlastp
  LYD610_H5	rice|11v1|CA767059_P1	1407	3157	447	84.8	globlastp
  LYD610_H5	rice|gb170|OS01G56330	1408	3157	447	84.8	globlastp
  LYD610_H9	brachypodium|12v1|BRADI1G63320_P1	1409	3158	447	83.8	globlastp
  LYD610_H6	brachypodium|09v1|GT772226	1410	3158	447	83.8	globlastp
  LYD610_H10	rye|12v1|DRR001012.101001_P1	1411	3159	447	82.8	globlastp
  LYD610_H11	rye|12v1|DRR001012.103223_P1	1412	3160	447	82.6	globlastp
  LYD610_H12	rice|11v1|OSCRP079749_P1	1413	3161	447	81.3	globlastp
  LYD610_H7	rice|11v1|C22581_P1	1414	3161	447	81.3	globlastp
  LYD610_H7	rice|gb170|OS03G21540	1415	3161	447	81.3	globlastp
  LYD610_H13	wheat|12v3|BE637867_P1	1416	3162	447	80.4	globlastp
  LYD610_H14	wheat|12v3|BI751671_T1	1417	3163	447	80.36	glotblastn
  LYD611_H1	soybean|11v1|GLYMA09G33700	1418	3164	448	92.8	globlastp
  LYD611_H2	cowpea|12v1|FG852821_P1	1419	3165	448	87.8	globlastp
  LYD611_H2	cowpea|gb166|FG852821	1420	3165	448	87.8	globlastp
  LYD611_H3	bean|12v1|SRR001335.371744_P1	1421	3166	448	87.3	globlastp
  LYD611_H4	pigeonpea|11v1|CCIIPG11007623_P1	1422	3167	448	86.5	globlastp
  LYD612_H1	soybean|11v1|GLYMA10G02210	1423	3168	449	91.9	globlastp
  LYD612_H6	pigeonpea|11v1|GR466527_P1	1424	3169	449	90.8	globlastp
  LYD612_H2	pigeonpea|10v1|GW351945	1425	3169	449	90.8	globlastp
  LYD612_H7	bean|12v1|CA910393_P1	1426	3170	449	84	globlastp
  LYD612_H3	cowpea|12v1|FF384755_P1	1427	3171	449	82.8	globlastp
  LYD612_H3	cowpea|gb166|VIRARG2	1428	3171	449	82.8	globlastp
  LYD612_H4	bean|gb167|CA910393	1429	3172	449	82	globlastp
  LYD612_H5	bean|gb167|CB540659	1430	3173	449	82	glotblastn
  LYD613_H1	pigeonpea|11v1|SRR054580X110249_P1	1431	3174	450	82.9	globlastp
  LYD613_H2	bean|12v1|SRR090491.1230988_P1	1432	3175	450	80.2	globlastp
  LYD614_H1	soybean|11v1|GLYMA14G06640	1433	3176	451	86	globlastp
  LYD615_H1	soybean|11v1|GLYMA19G30660	1434	3177	452	94.4	globlastp
  LYD615_H4	bean|12v1|CB543286_P1	1435	3178	452	88.9	globlastp
  LYD615_H5	pigeonpea|11v1|SRR054580X163954_P1	1436	3179	452	88.5	globlastp
  LYD615_H2	lotus|09v1|BP070765_P1	1437	3180	452	81.5	globlastp
  LYD615_H6	medicago|12v1|AW684979_P1	1438	3181	452	81.4	globlastp
  LYD615_H3	medicago|09v1|AW684979	1439	3181	452	81.4	globlastp
  LYD616_H4	bean|12v1|SRR001334.260126_T1	1440	3182	453	88.4	glotblastn
  LYD616_H5	pigeonpea|11v1|SRR054580X112099_T1	1441	3183	453	87.88	glotblastn
  LYD616_H6	chickpea|11v1|FE671275_T1	1442	3184	453	84.37	glotblastn
  LYD616_H1	lotus|09v1|CRPLJ028046_T1	1443	3185	453	82.69	glotblastn
  LYD616_H7	medicago|12v1|BG450022_P1	1444	3186	453	82.5	globlastp
  LYD616_H2	medicago|09v1|BG450022	1445	3186	453	82.5	globlastp
  LYD616_H3	soybean|11v1|GLYMA19G39560	1446	3187	453	80.8	globlastp
  LYD617_H1	cyamopsis|10v1|EG979147_P1	1447	3188	454	93.3	globlastp
  LYD617_H2	liquorice|gb171|FS251251_P1	1448	3189	454	93.3	globlastp
  LYD617_H3	cowpea|12v1|FF382757_P1	1449	3190	454	91.3	globlastp
  LYD617_H19	chickpea|11v1|SRR133517.118502_P1	1450	3191	454	91	globlastp
  LYD617_H3	cowpea|gb166|FF382757	1451	3192	454	90.2	globlastp
  LYD617_H20	pigeonpea|11v1|GR470046_P1	1452	3193	454	88.8	globlastp
  LYD617_H4	pigeonpea|10v1|GR470046	1453	3193	454	88.8	globlastp
  LYD617_H21	medicago|12v1|AW329294_P1	1454	3194	454	87.6	globlastp
  LYD617_H5	medicago|09v1|AW329294	1455	3194	454	87.6	globlastp
  LYD617_H22	medicago|12v1|BF632685_P1	1456	3195	454	85.4	globlastp
  LYD617_H6	trigonella|11v1|SRR066194X345953	1457	3196	454	85.4	globlastp
  LYD617_H23	medicago|12v1|AL381382_P1	1458	3197	454	84.3	globlastp
  LYD617_H7	lotus|09v1|AW428820_P1	1459	3198	454	84.3	globlastp
  LYD617_H8	medicago|09v1|AL381382	1460	3197	454	84.3	globlastp
  LYD617_H24	chickpea|11v1|GR394427_P1	1461	3199	454	83.1	globlastp
  LYD617_H9	soybean|11v1|GLYMA10G02430	1462	3200	454	83.1	globlastp
  LYD617_H25	bean|12v1|CA898865_P1	1463	3201	454	82	globlastp
  LYD617_H26	pigeonpea|11v1|SRR054580X13373_P1	1464	3202	454	82	globlastp
  LYD617_H10	bean|gb167|CA898865	1465	3201	454	82	globlastp
  LYD617_H11	clover|gb162|BB921888_P1	1466	3203	454	82	globlastp
  LYD617_H12	pigeonpea|10v1|SRR054580S0013374	1467	3202	454	82	globlastp
  LYD617_H13	soybean|11v1|GLYMA02G17370	1468	3204	454	82	globlastp
  LYD617_H14	cassava|09v1|DV442613_P1	1469	3205	454	80.9	globlastp
  LYD617_H15	cowpea|12v1|FF385220_P1	1470	3206	454	80.9	globlastp
  LYD617_H16	cucurbita|11v1|SRR091276X10451_T1	1471	3207	454	80.9	glotblastn
  LYD617_H17	oak|10v1|FP034480_P1	1472	3208	454	80.9	globlastp
  LYD617_H18	trigonella|11v1|SRR066194X186437	1473	3209	454	80.9	globlastp
  LYD620_H1	soybean|11v1|GLYMA17G08660	1474	3210	457	92.9	globlastp
  LYD620_H2	bean|12v1|CA902170_P1	1475	3211	457	84.2	globlastp
  LYD620_H3	pigeonpea|11v1|SRR054580X100276_P1	1476	3212	457	82.4	globlastp
  LYD621_H1	soybean|11v1|GLYMA08G05040	1477	3213	458	96	globlastp
  LYD621_H5	bean|12v1|CB542975_P1	1478	3214	458	92.1	globlastp
  LYD621_H6	pigeonpea|11v1|SRR054580X105242_P1	1479	3215	458	91.4	globlastp
  LYD621_H2	pigeonpea|10v1|SRR054580S0018657	1480	3216	458	91.35	glotblastn
  LYD621_H3	lotus|09v1|GO024264_P1	1481	3217	458	86	globlastp
  LYD621_H7	chickpea|11v1|SRR133517.133212_T1	1482	3218	458	85.77	glotblastn
  LYD621_H8	medicago|12v1|AI974296_P1	1483	3219	458	84.3	globlastp
  LYD621_H4	medicago|09v1|AI974296	1484	3219	458	84.3	globlastp
  LYD622_H1	soybean|11v1|GLYMA04G03680	1485	3220	459	97.8	globlastp
  LYD622_H12	pigeonpea|11v1|SRR054580X103966_P1	1486	3221	459	91.4	globlastp
  LYD622_H2	cowpea|12v1|FF543494_P1	1487	3222	459	90	globlastp
  LYD622_H2	cowpea|gb166|FF543494	1488	3222	459	90	globlastp
  LYD622_H3	pigeonpea|10v1|SRR054580S0037538	1489	3223	459	87.5	globlastp
  LYD622_H13	bean|12v1|FE899993_P1	1490	3224	459	87.1	globlastp
  LYD622_H4	lotus|09v1|CB828440_P1	1491	3225	459	84	globlastp
  LYD622_H14	chickpea|11v1|GR396021_P1	1492	3226	459	83.5	globlastp
  LYD622_H5	peanut|10v1|GO338761_P1	1493	3227	459	82.4	globlastp
  LYD622_H6	liquorice|gb171|FS241834_P1	1494	3228	459	81.9	globlastp
  LYD622_H7	cassava|09v1|DV454935_P1	1495	3229	459	81.4	globlastp
  LYD622_H8	clover|gb162|BB911490_P1	1496	3230	459	81.4	globlastp
  LYD622_H9	bean|gb167|FE899993	1497	3231	459	81.03	glotblastn
  LYD622_H10	medicago|09v1|LLBF646969	1498	3232	459	80.8	globlastp
  LYD622_H15	medicago|12v1|BF646969_T1	1499	3233	459	80.34	glotblastn
  LYD622_H11	trigonella|11v1|SRR066194X120913	1500	3234	459	80.3	globlastp
  LYD623_H1	soybean|11v1|GLYMA04G05890	1501	3235	460	85	globlastp
  LYD624_H3	bean|12v1|GFXX53603X1_P1	1502	3236	461	83.6	globlastp
  LYD624_H1	bean|gb167|GFXX53603X1	1503	3236	461	83.6	globlastp
  LYD624_H2	soybean|11v1|GLYMA13G02510	1504	3237	461	80.4	globlastp
  LYD625_H1	pigeonpea|11v1|SRR054580X387827_P1	1505	3238	462	84.8	globlastp
  LYD625_H2	bean|12v1|FE703801_P1	1506	3239	462	81.5	globlastp
  LYD626_H5	pigeonpea|11v1|SRR054580X120385_P1	1507	3240	463	90	globlastp
  LYD626_H1	pigeonpea|10v1|SRR054580S0079586	1508	3240	463	90	globlastp
  LYD626_H2	cowpea|12v1|FF384015_P1	1509	3241	463	84	globlastp
  LYD626_H2	cowpea|gb166|FF384015	1510	3241	463	84	globlastp
  LYD626_H6	bean|12v1|FE683652_P1	1511	3242	463	82.7	globlastp
  LYD626_H3	bean|gb167|CV530073	1512	3242	463	82.7	globlastp
  LYD626_H7	medicago|12v1|AW776098_P1	1513	3243	463	80.8	globlastp
  LYD626_H4	medicago|09v1|AW776098	1514	3243	463	80.8	globlastp
  LYD627_H1	soybean|11v1|GLYMA18G19050	1515	3244	464	94.46	glotblastn
  LYD627_H8	pigeonpea|11v1|SRR054580X103254_T1	1516	3245	464	88.69	glotblastn
  LYD627_H9	bean|12v1|CK901542_T1	1517	3246	464	88.53	glotblastn
  LYD627_H2	bean|gb167|CK901542	1518	3246	464	88.53	glotblastn
  LYD627_H3	pigeonpea|10v1|SRR054580S0002136	1519	3247	464	87.69	glotblastn
  LYD627_H4	cowpea|12v1|FC461147_T1	1520	3248	464	86.65	glotblastn
  LYD627_H4	cowpea|gb166|FC461147	1521	3248	464	86.65	glotblastn
  LYD627_H5	lotus|09v1|AV775154_T1	1522	3249	464	85.93	glotblastn
  LYD627_H10	chickpea|11v1|SRR133517.106923_T1	1523	3250	464	84.54	glotblastn
  LYD627_H6	peanut|10v1|GO263794_T1	1524	3251	464	83.29	glotblastn
  LYD627_H7	clover|gb162|BB914886_T1	1525	3252	464	81.86	glotblastn
  LYD628_H2	pigeonpea|11v1|CCIIPG11026354_T1	1526	3253	465	88.95	glotblastn
  LYD628_H1	soybean|11v1|GLYMA16G32600	1527	3254	465	88	globlastp
  LYD628_H3	bean|12v1|CV534892_P1	1528	3255	465	86.6	globlastp
  LYD629_H1	soybean|11v1|GLYMA07G12030	1529	3256	466	96.8	globlastp
  LYD629_H12	pigeonpea|11v1|SRR054580X119400_P1	1530	3257	466	90.5	globlastp
  LYD629_H2	pigeonpea|10v1|SRR054580S0000470	1531	3257	466	90.5	globlastp
  LYD629_H3	cowpea|12v1|EG594224_P1	1532	3258	466	89.3	globlastp
  LYD629_H3	cowpea|gb166|EG594224	1533	3258	466	89.3	globlastp
  LYD629_H4	bean|gb167|CV543026	1534	3259	466	88.4	globlastp
  LYD629_H13	bean|12v1|SRR001334.139650_P1	1535	3260	466	88.1	globlastp
  LYD629_H14	chickpea|11v1|GR393168_P1	1536	3261	466	86.4	globlastp
  LYD629_H5	lotus|09v1|BF177689_P1	1537	3262	466	85.2	globlastp
  LYD629_H6	trigonella|11v1|SRR066194X308576	1538	3263	466	84.2	globlastp
  LYD629_H15	medicago|12v1|AW256951_P1	1539	3264	466	83.3	globlastp
  LYD629_H7	medicago|09v1|LLAW256951	1540	3264	466	83.3	globlastp
  LYD629_H16	medicago|12v1|BI311156_P1	1541	3265	466	83	globlastp
  LYD629_H8	medicago|09v1|LLBI311156	1542	3265	466	83	globlastp
  LYD629_H9	trigonella|11v1|SRR066194X184937	1543	3266	466	83	globlastp
  LYD629_H10	peanut|10v1|SRR042413S0011977_P1	1544	3267	466	81.4	globlastp
  LYD629_H11	soybean|11v1|GLYMA08G06100	1545	3268	466	81.4	globlastp
  LYD630_H1	soybean|11v1|GLYMA12G01600	1546	3269	467	96.6	globlastp
  LYD630_H5	pigeonpea|11v1|SRR054580X116473_P1	1547	3270	467	90.2	globlastp
  LYD630_H6	bean|12v1|CB280685_P1	1548	3271	467	87.5	globlastp
  LYD630_H2	bean|gb167|CB280685	1549	3272	467	87.3	globlastp
  LYD630_H3	lotus|09v1|BP040921_P1	1550	3273	467	84.5	globlastp
  LYD630_H7	medicago|12v1|AW256804_T1	1551	3274	467	80.59	glotblastn
  LYD630_H4	medicago|09v1|LLAW776894	1552	3275	467	80.4	glotblastn
  LYD631_H1	soybean|11v1|GLYMA12G00640	1553	3276	468	94	globlastp
  LYD631_H2	cowpea|12v1|FG816078_P1	1554	3277	468	92	globlastp
  LYD631_H8	bean|12v1|EG562963_P1	1555	3278	468	91.1	globlastp
  LYD631_H2	cowpea|gb166|FG816078	1556	3279	468	87.7	globlastp
  LYD631_H9	pigeonpea|11v1|CCIIPG11021826_P1	1557	3280	468	87.4	globlastp
  LYD631_H10	pigeonpea|11v1|SRR054580X555062_P1	1558	3280	468	87.4	globlastp
  LYD631_H3	peanut|10v1|ES712405_P1	1559	3281	468	85.8	globlastp
  LYD631_H4	bean|gb167|CV530804	1560	3282	468	84.2	globlastp
  LYD631_H5	lotus|09v1|LLAW720068_P1	1561	3283	468	83	globlastp
  LYD631_H6	medicago|09v1|BE239557	1562	3284	468	81.9	glotblastn
  LYD631_H11	chickpea|11v1|SRR133517.10769_P1	1563	3285	468	81.8	globlastp
  LYD631_H12	medicago|12v1|BE239557_T1	1564	3286	468	81.61	glotblastn
  LYD631_H7	trigonella|11v1|SRR066194X150691	1565	3287	468	81.38	glotblastn
  LYD632_H3	soybean|11v1|GLYMA03G36100	1566	3288	469	95	globlastp
  LYD632_H6	pigeonpea|11v1|GR464470_P1	1567	3289	469	90.1	globlastp
  LYD632_H7	bean|12v1|FE693882_P1	1568	3290	469	89.1	globlastp
  LYD632_H4	bean|gb167|CV541137	1569	3291	469	88.8	globlastp
  LYD632_H5	cowpea|12v1|FF390940_P1	1570	3292	469	88.4	globlastp
  LYD632_H5	cowpea|gb166|FF390940	1571	3292	469	88.4	globlastp
  LYD634_H1	soybean|11v1|GLYMA11G18460	1572	3293	471	89.9	globlastp
  LYD634_H2	cowpea|12v1|FF384860_P1	1573	3294	471	87.6	globlastp
  LYD634_H2	cowpea|gb166|FF384860	1574	3294	471	87.6	globlastp
  LYD634_H6	bean|12v1|FE899187_P1	1575	3295	471	86.6	globlastp
  LYD634_H3	bean|gb167|CV532868	1576	3295	471	86.6	globlastp
  LYD634_H7	pigeonpea|11v1|EE605085_P1	1577	3296	471	83.7	globlastp
  LYD634_H4	pigeonpea|10v1|EE605085	1578	3296	471	83.7	globlastp
  LYD634_H5	soybean|11v1|GLYMA13G39040	1579	3297	471	80.71	glotblastn
  LYD635_H1	soybean|11v1|GLYMA19G01910	1580	3298	472	95	globlastp
  LYD635_H4	bean|12v1|SRR001334.123668_P1	1581	3299	472	84.1	globlastp
  LYD635_H5	pigeonpea|11v1|SRR054580X104907_P1	1582	3300	472	83.6	globlastp
  LYD635_H2	bean|gb167|FE680073	1583	3301	472	83.55	glotblastn
  LYD635_H3	cowpea|12v1|FF391308_P1	1584	3302	472	81.8	globlastp
  LYD635_H3	cowpea|gb166|FF391308	1585	3303	472	81.2	globlastp
  LYD636_H3	bean|12v1|CA908996_P1	1586	3304	473	92.5	globlastp
  LYD636_H1	soybean|11v1|GLYMA10G04660	1587	3305	473	91.6	globlastp
  LYD636_H4	pigeonpea|11v1|SRR054580X16507_P1	1588	3306	473	89.8	globlastp
  LYD636_H2	pigeonpea|10v1|SRR054580S0016508	1589	3307	473	87	globlastp
  LYD636_H5	chickpea|11v1|SRR133517.131366_P1	1590	3308	473	84.2	globlastp
  LYD636_H6	medicago|12v1|AW256943_P1	1591	3309	473	81.2	globlastp
  LYD638_H1	soybean|11v1|GLYMA15G03820	1592	3310	475	98.9	globlastp
  LYD638_H2	cowpea|12v1|FF394689_P1	1593	3311	475	97.1	globlastp
  LYD638_H2	cowpea|gb166|FF394689	1594	3311	475	97.1	globlastp
  LYD638_H81	pigeonpea|11v1|SRR054580X102130_P1	1595	3312	475	96.4	globlastp
  LYD638_H82	bean|12v1|FG229632_P1	1596	3313	475	95.7	globlastp
  LYD638_H3	bean|gb167|CV530755	1597	3313	475	95.7	globlastp
  LYD638_H83	chickpea|11v1|SRR133517.112219_P1	1598	3314	475	93.8	globlastp
  LYD638_H4	trigonella|11v1|SRR066194X12107	1599	3315	475	91.7	globlastp
  LYD638_H5	medicago|09v1|DY618321	1600	3316	475	91.3	globlastp
  LYD638_H6	castorbean|11v1|GE635823_P1	1601	3317	475	89.9	globlastp
  LYD638_H7	monkeyflower|10v1|GO987981_P1	1602	3318	475	89.9	globlastp
  LYD638_H84	beech|11v1|SRR006293.6452_T1	1603	3319	475	89.13	glotblastn
  LYD638_H8	orobanche|10v1|SRR023189S0002399_P1	1604	3320	475	89.1	globlastp
  LYD638_H9	cacao|10v1|CF974571_P1	1605	3321	475	88.8	globlastp
  LYD638_H10	grape|11v1|GSVIVT01025302001_P1	1606	3322	475	88.8	globlastp
  LYD638_H11	watermelon|11v1|CV004917	1607	3323	475	88.8	globlastp
  LYD638_H12	cotton|10v2|DV849102	1608	3324	475	88.41	glotblastn
  LYD638_H13	cotton|10v2|SRR032878S0082451	1609	3325	475	88.41	glotblastn
  LYD638_H14	fagopyrum|11v1|SRR063689X125403_T1	1610	3326	475	88.41	glotblastn
  LYD638_H15	cotton|10v2|CO088742	1611	3327	475	88.4	globlastp
  LYD638_H16	cotton|10v2|DT053039	1612	3327	475	88.4	globlastp
  LYD638_H17	cotton|10v2|SRR032878S0001106	1613	3328	475	88.4	globlastp
  LYD638_H18	cassava|09v1|JGICASSAVA30684VALIDM1_P1	1614	3329	475	88	globlastp
  LYD638_H19	oak|10v1|FP073589_P1	1615	3330	475	88	globlastp
  LYD638_H20	cucumber|09v1|CV004917_P1	1616	3331	475	87.7	globlastp
  LYD638_H21	flaveria|11v1|SRR149229.153655_P1	1617	3332	475	87.7	globlastp
  LYD638_H22	fagopyrum|11v1|SRR063689X115245_T1	1618	3333	475	87.32	glotblastn
  LYD638_H85	lettuce|12v1|DY981698_P1	1619	3334	475	87.3	globlastp
  LYD638_H23	artemisia|10v1|EY093426_P1	1620	3335	475	87.3	globlastp
  LYD638_H24	citrus|gb166|CB290538	1621	3336	475	87.3	globlastp
  LYD638_H25	orange|11v1|CB290538_P1	1622	3336	475	87.3	globlastp
  LYD638_H26	strawberry|11v1|CO381546	1623	3337	475	87.3	globlastp
  LYD638_H27	valeriana|11v1|SRR099039X104058	1624	3338	475	87.3	globlastp
  LYD638_H86	nasturtium|11v1|SRR032558.128316_P1	1625	3339	475	87	globlastp
  LYD638_H28	aquilegia|10v2|DR946895_P1	1626	3340	475	87	globlastp
  LYD638_H29	cannabis|12v1|JK501697_P1	1627	3341	475	87	globlastp
  LYD638_H30	clementine|11v1|CB290538_P1	1628	3342	475	87	globlastp
  LYD638_H31	flaveria|11v1|SRR149229.229217_P1	1629	3343	475	87	globlastp
  LYD638_H32	poplar|10v1|BU869270_P1	1630	3344	475	87	globlastp
  LYD638_H33	potato|10v1|BQ118035_P1	1631	3345	475	87	globlastp
  LYD638_H34	primula|11v1|SRR098679X102565_P1	1632	3346	475	87	globlastp
  LYD638_H35	solanum_phureja|09v1|SPHBG126806	1633	3345	475	87	globlastp
  LYD638_H36	tragopogon|10v1|SRR020205S0000931	1634	3347	475	87	globlastp
  LYD638_H37	cirsium|11v1|SRR346952.102669_P1	1635	3348	475	86.6	globlastp
  LYD638_H38	sunflower|10v1|EE615497	1636	3349	475	86.6	globlastp
  LYD638_H39	eucalyptus|11v2|ES588617_P1	1637	3350	475	86.2	globlastp
  LYD638_H40	euphorbia|11v1|DV126968_P1	1638	3351	475	86.2	globlastp
  LYD638_H41	tomato|11v1|BG126806	1639	3352	475	86.2	globlastp
  LYD638_H87	sunflower|12v1|EE615497_P1	1640	3353	475	85.9	globlastp
  LYD638_H42	apple|11v1|CV129099_P1	1641	3354	475	85.9	globlastp
  LYD638_H43	centaurea|gb166|EH713237_P1	1642	3355	475	85.9	globlastp
  LYD638_H44	cirsium|11v1|SRR346952.1023775_P1	1643	3355	475	85.9	globlastp
  LYD638_H45	prunus|10v1|BU039771	1644	3356	475	85.9	globlastp
  LYD638_H46	silene|11v1|SRR096785X108818	1645	3357	475	85.9	globlastp
  LYD638_H47	ambrosia|11v1|SRR346935.354746_T1	1646	3358	475	85.87	glotblastn
  LYD638_H48	aristolochia|10v1|SRR039082S0002743_P1	1647	3359	475	85.6	globlastp
  LYD638_H88	oil_palm|11v1|EL687196_P1	1648	3360	475	85.5	globlastp
  LYD638_H49	ambrosia|11v1|SRR346935.108772_T1	1649	3361	475	85.14	glotblastn
  LYD638_H50	flaveria|11v1|SRR149232.113890_T1	1650	3362	475	85.14	glotblastn
  LYD638_H89	poppy|11v1|SRR030259.114169_P1	1651	3363	475	85.1	globlastp
  LYD638_H90	amborella|12v3|SRR038634.23330_P1	1652	3364	475	84.8	globlastp
  LYD638_H51	poplar|10v1|XM002303855_P1	1653	3365	475	84.8	globlastp
  LYD638_H52	rice|11v1|AU031876_P1	1654	3366	475	84.8	globlastp
  LYD638_H52	rice|gb170|OS02G10230	1655	3366	475	84.8	globlastp
  LYD638_H53	thellungiella_parvulum|11v1|BY812134	1656	3367	475	84.8	globlastp
  LYD638_H91	onion|12v1|CF441304_T1	1657	3368	475	84.78	glotblastn
  LYD638_H54	monkeyflower|10v1|SRR037227S0052581_P1	1658	3369	475	84.6	globlastp
  LYD638_H92	beet|12v1|BQ593198_P1	1659	3370	475	84.5	globlastp
  LYD638_H93	poppy|11v1|SRR030259.110127_T1	1660	3371	475	84.42	glotblastn
  LYD638_H55	cirsium|11v1|SRR346952.1012572_T1	1661	3372	475	84.42	glotblastn
  LYD638_H56	tripterygium|11v1|SRR098677X170048	1662	3373	475	84.4	globlastp
  LYD638_H94	bean|12v1|SRR090491.1076536_P1	1663	3374	475	84.1	globlastp
  LYD638_H95	poppy|11v1|SRR033668.365155_P1	1664	3375	475	84.1	globlastp
  LYD638_H57	soybean|11v1|GLYMA11G14090	1665	3376	475	84.1	globlastp
  LYD638_H58	cucurbita|11v1|SRR091276X112061_T1	1666	3377	475	84.06	glotblastn
  LYD638_H96	b_juncea|12v1|E6ANDIZ01A97YX_P1	1667	3378	475	83.7	globlastp
  LYD638_H59	b_juncea|10v2|E6ANDIZ01A97YX	1668	3378	475	83.7	globlastp
  LYD638_H60	canola|11v1|EE439609_P1	1669	3378	475	83.7	globlastp
  LYD638_H61	canola|11v1|EE473348_P1	1670	3378	475	83.7	globlastp
  LYD638_H62	canola|11v1|SRR019557.21478_P1	1671	3378	475	83.7	globlastp
  LYD638_H63	phalaenopsis|11v1|SRR125771.1013801_P1	1672	3379	475	83.7	globlastp
  LYD638_H64	b_rapa|gb162|EE519713	1673	3380	475	83.33	glotblastn
  LYD638_H65	radish|gb164|EV530173	1674	3381	475	83.3	globlastp
  LYD638_H97	b_rapa|11v1|CD813392_P1	1675	3382	475	83.1	globlastp
  LYD638_H98	gossypium_raimondii|12v1|DV849102_P1	1676	3383	475	83	globlastp
  LYD638_H66	thellungiella_halophilum|11v1|BY812134	1677	3384	475	82.7	globlastp
  LYD638_H67	amorphophallus|11v2|SRR089351X167144_T1	1678	3385	475	82.61	glotblastn
  LYD638_H68	phyla|11v2|SRR099037X109540_T1	1679	3386	475	82.61	glotblastn
  LYD638_H99	chickpea|11v1|SRR133517.214658_T1	1680	3387	475	82.25	glotblastn
  LYD638_H69	ambrosia|11v1|SRR346935.23488_P1	1681	3388	475	82.2	globlastp
  LYD638_H70	arabidopsis_lyrata|09v1|JGIAL010678_P1	1682	3389	475	82.2	globlastp
  LYD638_H71	triphysaria|10v1|EY128050	1683	3390	475	82.2	globlastp
  LYD638_H100	b_juncea|12v1|E6ANDIZ01EK3W2_P1	1684	3391	475	81.5	globlastp
  LYD638_H101	medicago|12v1|BE324303_P1	1685	3392	475	81.5	globlastp
  LYD638_H72	arabidopsis|10v1|AT3G20870_P1	1686	3393	475	81.5	globlastp
  LYD638_H73	lotus|09v1|BP048291_P1	1687	3394	475	81.5	globlastp
  LYD638_H74	podocarpus|10v1|SRR065014S0046390_T1	1688	3395	475	80.94	glotblastn
  LYD638_H102	pigeonpea|11v1|CCIIPG11000248_P1	1689	3396	475	80.9	globlastp
  LYD638_H75	dandelion|10v1|DY818839_P1	1690	3397	475	80.9	globlastp
  LYD638_H103	spruce|11v1|EX419926_P1	1691	3398	475	80.8	globlastp
  LYD638_H76	spruce|gb162|CO487657	1692	3398	475	80.8	globlastp
  LYD638_H104	brachypodium|12v1|BRADI3G07080T2_P1	1693	3399	475	80.5	globlastp
  LYD638_H77	brachypodium|09v1|DV486023	1694	3399	475	80.5	globlastp
  LYD638_H78	peanut|10v1|SRR042413S0014432_P1	1695	3400	475	80.4	globlastp
  LYD638_H105	rye|12v1|DRR001012.1356_P1	1696	3401	475	80.1	globlastp
  LYD638_H79	barley|10v2|BG417171	1697	3402	475	80.1	globlastp
  LYD638_H80	wheat|10v2|BE213609	1698	3403	475	80.1	globlastp
  LYD639_H1	soybean|11v1|GLYMA19G11770	1699	3404	476	88.6	globlastp
  LYD639_H3	pigeonpea|11v1|SRR054580X152862_P1	1700	3405	476	81.8	globlastp
  LYD639_H2	cowpea|12v1|FF389274_T1	1701	3406	476	81.38	glotblastn
  LYD639_H2	cowpea|gb166|FF389274	1702	3407	476	80.87	glotblastn
  LYD640_H1	soybean|11v1|GLYMA02G37400	1703	3408	477	93.4	globlastp
  LYD640_H4	pigeonpea|11v1|SRR054580X16367_P1	1704	3409	477	87.1	globlastp
  LYD640_H2	cowpea|12v1|VIRPSAS_T1	1705	3410	477	87.07	glotblastn
  LYD640_H2	cowpea|gb166|VIRPSAS	1706	3410	477	87.07	glotblastn
  LYD640_H5	bean|12v1|SRR001334.200990_P1	1707	3411	477	86.8	globlastp
  LYD640_H3	bean|gb167|CV535087	1708	3412	477	86.34	glotblastn
  LYD642_H9	pigeonpea|11v1|EE604557_P1	1709	3413	479	91.1	globlastp
  LYD642_H1	bean|gb167|FD785160	1710	3414	479	91.1	globlastp
  LYD642_H2	cowpea|12v1|FF540232_P1	1711	3415	479	91.1	globlastp
  LYD642_H2	cowpea|gb166|FF540232	1712	3415	479	91.1	globlastp
  LYD642_H3	pigeonpea|10v1|EE604557	1713	3413	479	91.1	globlastp
  LYD642_H4	soybean|11v1|GLYMA09G04350	1714	3416	479	90.3	globlastp
  LYD642_H10	bean|12v1|SRR001335.120177_P1	1715	3417	479	90	globlastp
  LYD642_H5	lotus|09v1|LLGO008153_P1	1716	3418	479	87.9	globlastp
  LYD642_H6	liquorice|gb171|FS239800_P1	1717	3419	479	87	globlastp
  LYD642_H11	medicago|12v1|AL377555_T1	1718	3420	479	83.52	glotblastn
  LYD642_H7	medicago|09v1|AL377555	1719	3421	479	83.5	globlastp
  LYD642_H12	chickpea|11v1|SRR133517.117851_P1	1720	3422	479	81.3	globlastp
  LYD642_H8	prunus|10v1|CO416682	1721	3423	479	80.43	glotblastn
  LYD643_H1	soybean|11v1|GLYMA07G06550	1722	3424	480	93.1	globlastp
  LYD643_H8	pigeonpea|11v1|GR470036_P1	1723	3425	480	91.6	globlastp
  LYD643_H2	pigeonpea|10v1|GR470036	1724	3425	480	91.6	globlastp
  LYD643_H3	cowpea|gb166|FF540040	1725	3426	480	89.3	globlastp
  LYD643_H9	bean|12v1|CB542964_P1	1726	3427	480	88.4	globlastp
  LYD643_H4	bean|gb167|CB542736	1727	3428	480	88	globlastp
  LYD643_H10	cowpea|12v1|FF540040_P1	1728	3429	480	87.9	globlastp
  LYD643_H11	medicago|12v1|BG452896_P1	1729	3430	480	85.6	globlastp
  LYD643_H5	medicago|09v1|BG452896	1730	3430	480	85.6	globlastp
  LYD643_H6	lotus|09v1|LLGO012566_T1	1731	3431	480	85.05	glotblastn
  LYD643_H12	chickpea|11v1|SRR133517.113264_P1	1732	3432	480	83.2	globlastp
  LYD643_H7	clover|gb162|BB918052_P1	1733	3433	480	82.7	globlastp
  LYD644_H1	soybean|11v1|GLYMA07G39320	1734	3434	481	98.2	globlastp
  LYD644_H6	bean|12v1|SRR001334.118891_P1	1735	3435	481	91.4	globlastp
  LYD644_H2	trigonella|11v1|SRR066194X104241	1736	3436	481	87.4	globlastp
  LYD644_H7	medicago|12v1|BE204178_P1	1737	3437	481	86.6	globlastp
  LYD644_H8	medicago|12v1|BF641611_P1	1738	3437	481	86.6	globlastp
  LYD644_H4	soybean|11v1|GLYMA13G10490	1739	3438	481	85.7	globlastp
  LYD644_H5	soybean|11v1|GLYMA20G16230	1740	3439	481	85.5	globlastp
  LYD644_H9	pigeonpea|11v1|SRR054580X124197_P1	1741	3440	481	84.3	globlastp
  LYD644_H10	bean|12v1|SRR001334.288940_P1	1742	3441	481	83.5	globlastp
  LYD645_H1	soybean|11v1|GLYMA07G38340	1743	3442	482	92.2	globlastp
  LYD645_H6	bean|12v1|CB542096_P1	1744	3443	482	87.4	globlastp
  LYD645_H2	bean|gb167|CB542096	1745	3443	482	87.4	globlastp
  LYD645_H3	cowpea|12v1|FF383417_P1	1746	3444	482	86.6	globlastp
  LYD645_H3	cowpea|gb166|FF383417	1747	3444	482	86.6	globlastp
  LYD645_H7	pigeonpea|11v1|SRR054580X16291_P1	1748	3445	482	86	globlastp
  LYD645_H4	pigeonpea|10v1|SRR054580S0016292	1749	3445	482	86	globlastp
  LYD645_H5	lotus|09v1|CB827458_P1	1750	3446	482	80.5	globlastp
  LYD647_H1	soybean|11v1|GLYMA08G41040	1751	3447	484	83.9	globlastp
  LYD648_H1	potato|10v1|BF153552_P1	1752	3448	485	95.4	globlastp
  LYD648_H2	solanum_phureja|09v1|SPHAI780847	1753	3449	485	95.1	globlastp
  LYD648_H7	pepper|12v1|GD067902_P1	1754	3450	485	92.2	globlastp
  LYD648_H3	eggplant|10v1|FS007304_P1	1755	3451	485	91.9	globlastp
  LYD648_H4	tobacco|gb162|EB443178	1756	3452	485	83.7	globlastp
  LYD648_H5	nicotiana_benthamiana|gb162|CK281577_P1	1757	3453	485	82.9	globlastp
  LYD648_H6	nicotiana_benthamiana|gb162|CK282667_P1	1758	3454	485	82.2	globlastp
  LYD650_H1	solanum_phureja|09v1|SPHAF204783	1759	3455	486	95.5	globlastp
  LYD650_H2	potato|10v1|CV494921_T1	1760	3456	486	93.33	glotblastn
  LYD650_H4	eggplant|10v1|FS037047_P1	1761	3457	486	85.8	globlastp
  LYD650_H5	pepper|12v1|BM066147_P1	1762	3458	486	84.9	globlastp
  LYD650_H5	pepper|gb171|BM066147	1763	3458	486	84.9	globlastp
  LYD651_H2	tobacco|gb162|AF211738	1764	3459	487	80.7	globlastp
  LYD653_H1	tomato|11v1|BG123578	1765	3460	489	85.33	glotblastn
  LYD653_H2	petunia|gb171|CV294459_P1	1766	3461	489	83.1	globlastp
  LYD653_H3	potato|10v1|BQ516821_T1	1767	3462	489	81.33	glotblastn
  LYD653_H4	solanum_phureja|09v1|SPHBG123578	1768	3463	489	81.33	glotblastn
  LYD654_H1	solanum_phureja|09v1|SPHAI782247	1769	3464	490	98	globlastp
  LYD654_H2	pepper|12v1|BM063093_P1	1770	3465	490	95	globlastp
  LYD655_H1	solanum_phureja|09v1|SPHAI896168	1771	3466	491	95.6	globlastp
  LYD655_H2	pepper|12v1|CO909199_P1	1772	3467	491	88.4	globlastp
  LYD655_H2	pepper|gb171|CO909199	1773	3467	491	88.4	globlastp
  LYD655_H3	potato|10v1|BF460284_P1	1774	3468	491	85.9	globlastp
  LYD655_H4	tobacco|gb162|CV019561	1775	3469	491	85.58	glotblastn
  LYD655_H5	petunia|gb171|CV295783_P1	1776	3470	491	81.3	globlastp
  LYD657_H1	solanum_phureja|09v1|SPHAW030194	1777	3471	492	96.9	globlastp
  LYD658_H1	solanum_phureja|09v1|SPHAW094631	1778	3472	493	94.6	globlastp
  LYD658_H2	potato|10v1|BF187607_P1	1779	3473	493	81.7	globlastp
  LYD658_H3	nicotiana_benthamiana|gb162|CK280675_T1	1780	3474	493	80.46	glotblastn
  LYD658_H4	nicotiana_benthamiana|gb162|CK288269_P1	1781	3475	493	80.2	globlastp
  LYD659_H1	solanum_phureja|09v1|SPHAW217526	1782	3476	494	97	globlastp
  LYD659_H2	amsonia|11v1|SRR098688X140968_T1	1783	3477	494	80.71	glotblastn
  LYD660_H1	solanum_phureja|09v1|SPHAW616260	1784	3478	495	97.4	globlastp
  LYD661_H1	solanum_phureja|09v1|SPHAW616620	1785	3479	496	98.3	globlastp
  LYD661_H2	cacao|10v1|CU538010_P1	1786	3480	496	82	globlastp
  LYD661_H3	cassava|09v1|DB937952_P1	1787	3481	496	81.9	globlastp
  LYD661_H4	poplar|10v1|BI069117_P1	1788	3482	496	81.3	globlastp
  LYD661_H5	eucalyptus|11v2|ES591203_P1	1789	3483	496	81	globlastp
  LYD661_H6	grape|11v1|GSVIVT01033168001_P1	1790	3484	496	80.9	globlastp
  LYD661_H10	cotton|11v1|DW488153_P1	1791	3485	496	80.7	globlastp
  LYD661_H11	gossypium_raimondii|12v1|DR454811_P1	1792	3486	496	80.7	globlastp
  LYD661_H7	castorbean|11v1|XM_002515320_P1	1793	3487	496	80.7	globlastp
  LYD661_H8	cotton|10v2|DR454811	1794	3488	496	80.6	globlastp
  LYD661_H12	cotton|11v1|AI727236_T1	1795	3489	496	80.43	glotblastn
  LYD661_H13	cotton|11v1|BE054582_T1	1796	3490	496	80.43	glotblastn
  LYD661_H14	cotton|11v1|DR454811_P1	1797	3491	496	80.4	globlastp
  LYD661_H15	gossypium_raimondii|12v1|AI727236_P1	1798	3492	496	80.4	globlastp
  LYD661_H9	cotton|10v2|AI727236	1799	3493	496	80.3	globlastp
  LYD662_H1	solanum_phureja|09v1|SPHAW618546	1800	3494	497	96.5	globlastp
  LYD662_H2	eggplant|10v1|FS033651_P1	1801	3495	497	89	globlastp
  LYD663_H1	solanum_phureja|09v1|SPHAY376851	1802	3496	498	90.5	globlastp
  LYD663_H2	potato|10v1|CV502621_T1	1803	3497	498	88.51	glotblastn
  LYD664_H1	solanum_phureja|09v1|SPHBE460507	1804	3498	499	90	globlastp
  LYD666_H3	pepper|12v2|BM061649_P1	1805	3499	501	91.6	globlastp
  LYD666_H3	pepper|gb171|BM061649	1806	3499	501	91.6	globlastp
  LYD666_H4	tobacco|gb162|AY639146	1807	3500	501	87.5	globlastp
  LYD667_H1	solanum_phureja|09v1|SPHBG123287	1808	3501	502	98.2	globlastp
  LYD667_H2	pepper|12v1|CA522829_P1	1809	3502	502	86.6	globlastp
  LYD667_H2	pepper|gb171|CA522829	1810	3502	502	86.6	globlastp
  LYD667_H3	potato|10v1|BG350145_P1	1811	3503	502	85.7	globlastp
  LYD667_H4	solanum_phureja|09v1|SPHBG126102	1812	3503	502	85.7	globlastp
  LYD667_H5	tomato|11v1|BG126102	1813	3504	502	85.7	globlastp
  LYD669_H1	solanum_phureja|09v1|SPHBG127852	1814	3505	504	99.1	globlastp
  LYD669_H2	pepper|12v1|BM063343_P1	1815	3506	504	96.2	globlastp
  LYD669_H3	catharanthus|11v1|EG555968_P1	1816	3507	504	86.8	globlastp
  LYD669_H4	vinca|11v1|SRR098690X137330	1817	3508	504	86.55	glotblastn
  LYD669_H5	tabernaemontana|11v1|SRR098689X113952	1818	3509	504	86.5	globlastp
  LYD669_H6	amsonia|11v1|SRR098688X123659_P1	1819	3510	504	86.1	globlastp
  LYD669_H7	vinca|11v1|SRR098690X130330	1820	3511	504	85.23	glotblastn
  LYD669_H8	valeriana|11v1|SRR099039X100383	1821	3512	504	85	globlastp
  LYD669_H9	kiwi|gb166|FG397105_P1	1822	3513	504	84.1	globlastp
  LYD669_H10	potato|10v1|BF459943_P1	1823	3514	504	84.1	globlastp
  LYD669_H33	beech|11v1|SRR006293.14617_T1	1824	3515	504	83.18	glotblastn
  LYD669_H11	chestnut|gb170|SRR006295S0021602_P1	1825	3516	504	83	globlastp
  LYD669_H12	citrus|gb166|BE205717	1826	3517	504	83	globlastp
  LYD669_H13	clementine|11v1|BE205717_P1	1827	3518	504	83	globlastp
  LYD669_H14	orange|11v1|BE205717_P1	1828	3519	504	82.7	globlastp
  LYD669_H15	watermelon|11v1|VMEL00070338543255	1829	3520	504	82.1	globlastp
  LYD669_H34	beech|11v1|FR603623_T1	1830	3521	504	81.84	glotblastn
  LYD669_H16	oak|10v1|DN950840_P1	1831	3522	504	81.8	globlastp
  LYD669_H17	phyla|11v2|SRR099035X111901_P1	1832	3523	504	81.8	globlastp
  LYD669_H35	gossypium_raimondii|12v1|CA993556_P1	1833	3524	504	81.4	globlastp
  LYD669_H18	apple|11v1|CN578861_P1	1834	3525	504	81.4	globlastp
  LYD669_H36	gossypium_raimondii|12v1|DR452577_P1	1835	3526	504	81.2	globlastp
  LYD669_H19	cotton|10v2|CO116252	1836	3527	504	81.2	globlastp
  LYD669_H20	prunus|10v1|BU047497	1837	3528	504	81.2	globlastp
  LYD669_H21	strawberry|11v1|CO380648	1838	3529	504	81.2	globlastp
  LYD669_H37	lettuce|12v1|LS12v1CRP084179_P1	1839	3530	504	81	globlastp
  LYD669_H38	cotton|11v1|CA993556_P1	1840	3531	504	80.9	globlastp
  LYD669_H22	cacao|10v1|CU483136_P1	1841	3532	504	80.9	globlastp
  LYD669_H23	cucumber|09v1|BGI454G0169927_P1	1842	3533	504	80.9	globlastp
  LYD669_H24	poplar|10v1|BU879857_P1	1843	3534	504	80.9	globlastp
  LYD669_H39	cotton|11v1|DR452577XX1_T1	1844	3535	504	80.72	glotblastn
  LYD669_H25	cotton|10v2|CA993556	1845	3536	504	80.7	globlastp
  LYD669_H26	euonymus|11v1|SRR070038X104702_P1	1846	3537	504	80.7	globlastp
  LYD669_H27	melon|10v1|VMEL00070338543255_P1	1847	3538	504	80.7	globlastp
  LYD669_H28	aristolochia|10v1|FD752757_P1	1848	3539	504	80.5	globlastp
  LYD669_H29	euonymus|11v1|SRR070038X151093_P1	1849	3540	504	80.5	globlastp
  LYD669_H30	tripterygium|11v1|SRR098677X123156	1850	3541	504	80.5	globlastp
  LYD669_H31	poplar|10v1|BU820108_P1	1851	3542	504	80.3	globlastp
  LYD669_H32	apple|11v1|CN496454_P1	1852	3543	504	80	globlastp
  LYD670_H1	solanum_phureja|09v1|SPHBG126384	1853	3544	505	93.7	globlastp
  LYD670_H2	potato|10v1|BE922534_T1	1854	3545	505	90.66	glotblastn
  LYD672_H1	solanum_phureja|09v1|SPHBG134039	1855	3546	507	95.3	globlastp
  LYD672_H2	pepper|12v1|CA519411_P1	1856	3547	507	88.3	globlastp
  LYD672_H2	pepper|gb171|CA519411	1857	3547	507	88.3	globlastp
  LYD672_H3	tobacco|gb162|DW004996	1858	3548	507	82.57	glotblastn
  LYD674_H1	potato|10v1|BE921584_P1	1859	3549	509	93	globlastp
  LYD674_H2	solanum_phureja|09v1|SPHBG133722	1860	3550	509	93	globlastp
  LYD674_H3	eggplant|10v1|FS004197_P1	1861	3551	509	87.3	globlastp
  LYD674_H4	nicotiana_benthamiana|gb162|CK293409_P1	1862	3552	509	81.8	globlastp
  LYD677_H1	solanum_phureja|09v1|SPHBG592613	1863	3553	512	96	globlastp
  LYD678_H1	potato|10v1|BG598437_P1	1864	3554	513	97.5	globlastp
  LYD678_H2	solanum_phureja|09v1|SPHBG626546	1865	3555	513	96.8	globlastp
  LYD680_H2	tabernaemontana|11v1|SRR098689X116012	1866	3556	515	80.77	glotblastn
  LYD681_H1	solanum_phureja|09v1|SPHBG630045	1867	3557	516	98.6	globlastp
  LYD681_H2	potato|10v1|BF053994_P1	1868	3558	516	98.4	globlastp
  LYD681_H3	amsonia|11v1|SRR098688X101055_P1	1869	3559	516	89.7	globlastp
  LYD681_H4	catharanthus|11v1|SRR098691X104148_P1	1870	3560	516	89.7	globlastp
  LYD681_H5	tabernaemontana|11v1|SRR098689X106474	1871	3561	516	89.1	globlastp
  LYD681_H6	vinca|11v1|SRR098690X10387	1872	3562	516	87.7	globlastp
  LYD681_H7	phyla|11v2|SRR099035X141015_T1	1873	3563	516	87.3	glotblastn
  LYD681_H8	orobanche|10v1|SRR023189S0004460_P1	1874	3564	516	86.3	globlastp
  LYD681_H9	monkeyflower|10v1|DV211803_P1	1875	3565	516	85.7	globlastp
  LYD681_H10	arnica|11v1|SRR099034X102089_P1	1876	3566	516	85.5	globlastp
  LYD681_H58	sunflower|12v1|DY921230_P1	1877	3567	516	85.1	globlastp
  LYD681_H11	arabidopsis_lyrata|09v1|JGIAL027489_P1	1878	3568	516	85.1	globlastp
  LYD681_H12	sunflower|10v1|DY921230	1879	3567	516	85.1	globlastp
  LYD681_H13	arabidopsis_lyrata|09v1|JGIAL005462_P1	1880	3569	516	84.9	globlastp
  LYD681_H14	arabidopsis|10v1|AT1G64190_P1	1881	3570	516	84.9	globlastp
  LYD681_H15	thellungiella_halophilum|11v1|BY804243	1882	3571	516	84.9	globlastp
  LYD681_H16	canola|11v1|EE413371_T1	1883	3572	516	84.88	glotblastn
  LYD681_H17	canola|11v1|EE415072_T1	1884	3573	516	84.88	glotblastn
  LYD681_H59	b_rapa|11v1|BG543930_P1	1885	3574	516	84.7	globlastp
  LYD681_H60	b_rapa|11v1|CV433796_P1	1886	3575	516	84.7	globlastp
  LYD681_H18	b_rapa|gb162|CV433796	1887	3575	516	84.7	globlastp
  LYD681_H19	canola|11v1|EE417941_P1	1888	3575	516	84.7	globlastp
  LYD681_H20	canola|11v1|ES911843_P1	1889	3575	516	84.7	globlastp
  LYD681_H61	b_rapa|11v1|CD814820_T1	1890	3576	516	84.68	glotblastn
  LYD681_H21	arabidopsis|10v1|AT5G41670_P1	1891	3577	516	84.5	globlastp
  LYD681_H22	lettuce|10v1|DW169046	1892	3578	516	84.5	globlastp
  LYD681_H23	ambrosia|11v1|SRR346935.204066_T1	1893	3579	516	84.48	glotblastn
  LYD681_H24	ambrosia|11v1|SRR346935.404337_T1	1894	3580	516	84.48	glotblastn
  LYD681_H22	lettuce|12v1|DW166137_P1	1895	3581	516	84.1	globlastp
  LYD681_H25	cirsium|11v1|SRR346952.13802_T1	1896	3582	516	84.07	glotblastn
  LYD681_H26	vinca|11v1|SRR098690X113839	1897	3583	516	84.07	glotblastn
  LYD681_H62	nasturtium|11v1|SRR032558.171608_P1	1898	3584	516	83.5	globlastp
  LYD681_H27	cacao|10v1|CU508968_P1	1899	3585	516	83.1	globlastp
  LYD681_H28	citrus|gb166|CN190890	1900	3586	516	83.06	glotblastn
  LYD681_H29	ambrosia|11v1|SRR346935.402152_T1	1901	3587	516	82.9	glotblastn
  LYD681_H30	cucumber|09v1|EB716020_P1	1902	3588	516	82.9	globlastp
  LYD681_H31	cynara|gb167|GE577931_T1	1903	3589	516	82.86	glotblastn
  LYD681_H63	pigeonpea|11v1|GW359493_P1	1904	3590	516	82.8	globlastp
  LYD681_H32	castorbean|11v1|GE634479_P1	1905	3591	516	82.7	globlastp
  LYD681_H33	soybean|11v1|GLYMA08G02410	1906	3592	516	82.7	globlastp
  LYD681_H64	cotton|11v1|BQ410946_P1	1907	3593	516	82.5	globlastp
  LYD681_H34	castorbean|11v1|XM_002509856_P1	1908	3594	516	82.5	globlastp
  LYD681_H35	euonymus|11v1|SRR070038X108968_P1	1909	3595	516	82.5	globlastp
  LYD681_H36	grape|11v1|GSVIVT01019467001_P1	1910	3596	516	82.5	globlastp
  LYD681_H37	tripterygium|11v1|SRR098677X111190	1911	3597	516	82.5	globlastp
  LYD681_H65	gossypium_raimondii|12v1|AI730491_P1	1912	3598	516	82.3	globlastp
  LYD681_H38	cotton|10v2|CO076294	1913	3599	516	82.3	globlastp
  LYD681_H39	watermelon|11v1|AM715537	1914	3600	516	82.3	globlastp
  LYD681_H40	strawberry|11v1|EX672776	1915	3601	516	82.2	globlastp
  LYD681_H41	soybean|11v1|GLYMA05G37170	1916	3602	516	82.1	globlastp
  LYD681_H42	trigonella|11v1|SRR066194X112434	1917	3603	516	82.1	globlastp
  LYD681_H43	medicago|09v1|LLAL384701	1918	3604	516	82.06	glotblastn
  LYD681_H44	clementine|11v1|CN190890_P1	1919	3605	516	81.9	globlastp
  LYD681_H45	prunus|10v1|CN863535	1920	3606	516	81.9	globlastp
  LYD681_H46	thellungiella_halophilum|11v1|EHJGI11021359	1921	3607	516	81.9	globlastp
  LYD681_H47	euonymus|11v1|SRR070038X107038_P1	1922	3608	516	81.8	globlastp
  LYD681_H48	platanus|11v1|SRR096786X140780_P1	1923	3609	516	81.7	globlastp
  LYD681_H49	lotus|09v1|LLAV410725_P1	1924	3610	516	81.5	globlastp
  LYD681_H50	oak|10v1|FP025719_P1	1925	3611	516	81.5	globlastp
  LYD681_H66	beech|11v1|SRR006293.12520_P1	1926	3612	516	81.4	globlastp
  LYD681_H67	chickpea|11v1|GR912701_P1	1927	3613	516	81.3	globlastp
  LYD681_H68	poppy|11v1|SRR030259.136321_P1	1928	3614	516	81.3	globlastp
  LYD681_H51	aquilegia|10v2|DR920343_P1	1929	3615	516	81.3	globlastp
  LYD681_H52	poplar|10v1|BU829466_P1	1930	3616	516	81.3	globlastp
  LYD681_H69	poppy|11v1|FE965679_P1	1931	3617	516	81.1	globlastp
  LYD681_H53	chestnut|gb170|SRR006295S0044488_P1	1932	3618	516	81.1	globlastp
  LYD681_H70	poppy|11v1|SRR096789.181966_T1	1933	3619	516	81.05	glotblastn
  LYD681_H71	poppy|11v1|SRR030259.353240_P1	1934	3620	516	80.9	globlastp
  LYD681_H54	poplar|10v1|AI165699_P1	1935	3621	516	80.8	globlastp
  LYD681_H55	aristolochia|10v1|FD755163_T1	1936	3622	516	80.65	glotblastn
  LYD681_H72	bean|12v1|CA900025_T1	1937	3623	516	80.52	glotblastn
  LYD681_H73	amborella|12v3|SRR038635.70340_P1	1938	3624	516	80.5	globlastp
  LYD681_H56	orange|11v1|CN190890_P1	1939	3625	516	80.5	globlastp
  LYD681_H57	silene|11v1|SRR096785X102909	1940	3626	516	80.24	glotblastn
  LYD682_H1	solanum_phureja|09v1|SPHBG630298	1941	3627	517	95.9	globlastp
  LYD684_H1	solanum_phureja|09v1|SPHBG734982	1942	3628	519	96.2	globlastp
  LYD684_H2	pepper|gb171|CA524110	1943	3629	519	85.5	globlastp
  LYD685_H1	solanum_phureja|09v1|SPHS70186	1944	3630	520	91.05	glotblastn
  LYD685_H2	potato|10v1|S70186_P1	1945	3631	520	89.8	globlastp
  LYD686_H1	solanum_phureja|09v1|SPHBI405665	1946	3632	521	96.4	globlastp
  LYD686_H2	solanum_phureja|09v1|SPHBG130034	1947	3633	521	83.1	globlastp
  LYD686_H3	tomato|11v1|BG130034	1948	3634	521	81.1	globlastp
  LYD686_H4	amsonia|11v1|SRR098688X125511_P1	1949	3635	521	80.2	globlastp
  LYD687_H1	solanum_phureja|09v1|SPHSRR015435S0022465	1950	3636	522	98.5	globlastp
  LYD689_H1	solanum_phureja|09v1|SPHBQ512926	1951	3637	524	91.9	globlastp
  LYD689_H2	potato|10v1|BQ512926_P1	1952	3638	524	91.4	globlastp
  LYD689_H3	eggplant|10v1|FS050105_P1	1953	3639	524	82.7	globlastp
  LYD689_H4	pepper|12v1|GD093486_P1	1954	3640	524	81.8	globlastp
  LYD689_H5	tobacco|gb162|EB425168	1955	3641	524	80.8	globlastp
  LYD690_H1	solanum_phureja|09v1|SPHDN978843	1956	3642	525	81.2	globlastp
  LYD538_H29	b_juncea|12v1|E6ANDIZ01DI5V0_P1	1957	3643	528	85.4	globlastp
  LYD539_H5	arabidopsis_lyrata|09v1|JGIAL032238_T1	1958	3644	529	94.23	glotblastn
  LYD539_H12	b_oleracea|gb161|EH415045_P1	1959	3645	529	87.7	globlastp
  LYD539_H13	cleome_spinosa|10v1|GR933964_T1	1960	3646	529	82.28	glotblastn
  LYD540_H2	thellungiella_parvulum|11v1|BM986015	1961	3647	530	84.57	glotblastn
  LYD540_H3	thellungiella_halophilum|11v1|BY819763	1962	3648	530	81.91	glotblastn
  LYD540_H4	arabidopsis_lyrata|09v1|JGIAL006775_T1	1963	3649	530	81.38	glotblastn
  LYD548_H11	euphorbia|11v1|DV124286_P1	1964	3650	533	82.5	globlastp
  LYD548_H12	spurge|gb161|DV124286	1965	3651	533	82.1	globlastp
  LYD548_H19	beech|11v1|SRR006293.7878_T1	1966	3652	533	80	glotblastn
  LYD548_H13	papaya|gb165|EX247662_T1	1967	3653	533	80	glotblastn
  LYD548_H14	prunus|10v1|BU039510	1968	3654	533	80	glotblastn
  LYD549_H1	b_rapa|gb162|BG544752	1969	3655	534	98.89	glotblastn
  LYD550_H1	canola|11v1|EV151262_T1	1970	3656	535	97.94	glotblastn
  LYD550_H4	arabidopsis|10v1|AT3G16290_T1	1971	3657	535	95.46	glotblastn
  LYD550_H6	radish|gb164|EV569321	1972	3658	535	92.4	globlastp
  LYD550_H7	cacao|10v1|CU477476_T1	1973	3659	535	88.25	glotblastn
  LYD550_H8	poplar|10v1|CA924970_T1	1974	3660	535	87.63	glotblastn
  LYD550_H9	apple|11v1|CN496155_T1	1975	3661	535	86.8	glotblastn
  LYD550_H10	castorbean|11v1|EE255437_T1	1976	3662	535	86.8	glotblastn
  LYD550_H11	prunus|10v1|BU043895	1977	3663	535	86.8	glotblastn
  LYD550_H47	gossypium_raimondii|12v1|AI725752_T1	1978	3664	535	86.39	glotblastn
  LYD550_H12	cassava|09v1|CK643710_T1	1979	3665	535	86.39	glotblastn
  LYD550_H13	eucalyptus|11v2|SRR001659X130634_T1	1980	3666	535	86.39	glotblastn
  LYD550_H14	vinca|11v1|SRR098690X123915	1981	3667	535	86.39	glotblastn
  LYD550_H48	cotton|11v1|AI725752_T1	1982	3668	535	86.19	glotblastn
  LYD550_H15	grape|11v1|GSVIVT01017029001_T1	1983	3669	535	86.19	glotblastn
  LYD550_H16	cotton|10v2|SRR032367S0109017	1984	3670	535	86.01	glotblastn
  LYD550_H49	pigeonpea|11v1|SRR054580X104890_T1	1985	3671	535	85.77	glotblastn
  LYD550_H17	clementine|11v1|CD574164_T1	1986	3672	535	85.77	glotblastn
  LYD550_H18	orange|11v1|CD574164_T1	1987	3673	535	85.77	glotblastn
  LYD550_H19	pigeonpea|10v1|SRR054580S0015969	1988	3674	535	85.77	glotblastn
  LYD550_H20	prunus|10v1|CN934625	1989	3675	535	85.77	glotblastn
  LYD550_H21	tripterygium|11v1|SRR098677X101640	1990	3676	535	85.77	glotblastn
  LYD550_H22	oak|10v1|FP027246_T1	1991	3677	535	85.57	glotblastn
  LYD550_H23	watermelon|11v1|AM733953	1992	3678	535	85.36	glotblastn
  LYD550_H50	sesame|12v1|SESI12V1405091_T1	1993	3679	535	85.15	glotblastn
  LYD550_H24	strawberry|11v1|DV439362	1994	3680	535	85.15	glotblastn
  LYD550_H25	amsonia|11v1|SRR098688X115480_T1	1995	3681	535	84.95	glotblastn
  LYD550_H26	monkeyflower|10v1|DV209912_T1	1996	3682	535	84.95	glotblastn
  LYD550_H27	tabernaemontana|11v1|SRR098689X108650	1997	3683	535	84.95	glotblastn
  LYD550_H28	artemisia|10v1|EY090642_T1	1998	3684	535	84.74	glotblastn
  LYD550_H51	bean|12v1|CA902012_T1	1999	3685	535	84.33	glotblastn
  LYD550_H29	soybean|11v1|GLYMA15G02170	2000	3686	535	84.33	glotblastn
  LYD550_H30	soybean|11v1|GLYMA13G43180	2001	3687	535	83.92	glotblastn
  LYD550_H31	cotton|10v2|SRR032367S1095891	2002	3688	535	83.8	globlastp
  LYD550_H32	solanum_phureja|09v1|SPHAI781891	2003	3689	535	83.78	glotblastn
  LYD550_H33	flaveria|11v1|SRR149229.156308_T1	2004	3690	535	83.71	glotblastn
  LYD550_H34	cucumber|09v1|AM733953_T1	2005	3691	535	83.51	glotblastn
  LYD550_H35	flaveria|11v1|SRR149229.187611_T1	2006	3692	535	83.51	glotblastn
  LYD550_H36	tomato|11v1|AI781891	2007	3693	535	83.16	glotblastn
  LYD550_H37	melon|10v1|AM733953_T1	2008	3694	535	82.79	glotblastn
  LYD550_H52	beech|11v1|SRR006293.13266_P1	2009	3695	535	82.7	globlastp
  LYD550_H38	sunflower|10v1|DY912854	2010	3696	535	82.68	glotblastn
  LYD550_H53	oil_palm|11v1|EL930445_T1	2011	3697	535	82.47	glotblastn
  LYD550_H39	ambrosia|11v1|SRR346935.130719_T1	2012	3698	535	82.47	glotblastn
  LYD550_H54	banana|12v1|MAGEN2012034046_T1	2013	3699	535	82.27	glotblastn
  LYD550_H40	ambrosia|11v1|SRR346935.123018_T1	2014	3700	535	82.27	glotblastn
  LYD550_H41	silene|11v1|SRR096785X132229	2015	3701	535	81.44	glotblastn
  LYD550_H42	aristolochia|10v1|FD762492_T1	2016	3702	535	81.03	glotblastn
  LYD550_H43	cirsium|11v1|SRR346952.1061150_P1	2017	3703	535	81	globlastp
  LYD550_H44	aquilegia|10v2|DR915316_T1	2018	3704	535	80.82	glotblastn
  LYD550_H55	poppy|11v1|SRR030259.168193_T1	2019	3705	535	80.41	glotblastn
  LYD550_H45	cirsium|11v1|SRR346952.1049224_T1	2020	3706	535	80.41	glotblastn
  LYD553_H3	canola|11v1|SRR341920.517375_T1	2021	3707	536	92.8	glotblastn
  LYD553_H6	canola|11v1|EE475615_P1	2022	3708	536	90.5	globlastp
  LYD584_H1	trigonella|11v1|SRR066194X103417	2023	3709	537	92.46	glotblastn
  LYD584_H2	soybean|11v1|GLYMA08G44490	2024	3710	537	81.26	glotblastn
  LYD584_H3	pigeonpea|11v1|SRR054580X106211_T1	2025	3711	537	80.67	glotblastn
  LYD592_H1	medicago|09v1|CRPMT037344	2026	3712	539	94.1	globlastp
  LYD619_H1	soybean|11v1|GLYMA06G16290	2027	3713	540	80.6	globlastp
  LYD633_H1	soybean|11v1|GLYMA11G10300	2028	3714	543	89	globlastp
  LYD633_H2	bean|12v1|SRR001334.148755_P1	2029	3715	543	86	globlastp
  LYD633_H3	pigeonpea|11v1|SRR054580X352353_P1	2030	3716	543	83.8	globlastp
  LYD537_H2	radish|gb164|EV525517	2031	3717	550	98	globlastp
  LYD537_H5	thellungiella_parvulum|11v1|DN774047	2032	3718	550	93.1	globlastp
  LYD537_H8	arabidopsis|10v1|AT2G04039_P1	2033	3719	550	86.6	globlastp
  LYD548_H20	pigeonpea|11v1|SRR054580X121566_P1	2034	3720	553	80.7	globlastp
  LYD549_H6	b_rapa|11v1|BG544752_P1	2035	3721	554	99.1	globlastp
  LYD553_H9	b_rapa|11v1|BQ704191_P1	2036	556	556	100	globlastp
  LYD553_H1	b_rapa|gb162|EX029238	2037	3722	556	98.9	glotblastn
  LYD553_H2	radish|gb164|EW723928	2038	3723	556	97.8	globlastp
  LYD553_H4	thellungiella_parvulum|11v1|EPCRP010138	2039	3724	556	95.3	globlastp
  LYD553_H10	b_rapa|11v1|E6ANDIZ01AZWQB_P1	2040	3725	556	93.1	globlastp
  LYD553_H7	arabidopsis_lyrata|09v1|JGIAL010738_P1	2041	3726	556	92.3	globlastp
  LYD553_H8	arabidopsis|10v1|AT3G21420_P1	2042	3727	556	92.3	globlastp
  LYD554_H4	gossypium_raimondii|12v1|CO087573_P1	2043	3728	557	99.6	globlastp
  LYD554_H1	cacao|10v1|CU507663_P1	2044	3729	557	88.3	globlastp
  LYD554_H2	pteridium|11v1|SRR043594X132113	2045	3730	557	85.48	glotblastn
  LYD559_H1	trigonella|11v1|SRR066194X140992	2046	3731	559	97.4	globlastp
  LYD559_H29	chickpea|11v1|SRR133517.115958_P1	2047	3732	559	87.7	globlastp
  LYD559_H3	soybean|11v1|GLYMA06G42080	2048	3733	559	84.2	globlastp
  LYD559_H30	bean|12v1|CA896695_P1	2049	3734	559	82.8	globlastp
  LYD559_H7	cacao|10v1|CA794256_P1	2050	3735	559	82.5	globlastp
  LYD559_H19	kiwi|gb166|FG404235_T1	2051	3736	559	80.45	glotblastn
  LYD559_H31	kiwi|gb166|FG396783_P1	2052	3737	559	80.2	globlastp
  LYD559_H32	orange|11v1|Z82983_P1	2053	3738	559	80	globlastp
  LYD560_H164	chickpea|11v1|FL518933_P1	2054	3739	560	93.3	globlastp
  LYD560_H2	liquorice|gb171|FS249643_P1	2055	3740	560	93.3	globlastp
  LYD560_H4	soybean|11v1|GLYMA13G36730	2056	3741	560	87.5	globlastp
  LYD560_H5	trigonella|11v1|SRR066194X108453	2057	3742	560	87.4	globlastp
  LYD560_H165	chickpea|11v1|GR395239_P1	2058	3743	560	87.2	globlastp
  LYD560_H6	cowpea|12v1|FC458592_P1	2059	3744	560	87.2	globlastp
  LYD560_H6	cowpea|gb166|CK151399	2060	3744	560	87.2	globlastp
  LYD560_H7	soybean|11v1|GLYMA12G33760	2061	3745	560	87.2	globlastp
  LYD560_H166	bean|12v1|CA896625_P1	2062	3746	560	86.3	globlastp
  LYD560_H8	apple|11v1|CN491810_P1	2063	3747	560	86.2	globlastp
  LYD560_H9	bean|gb167|CA896625	2064	3748	560	86.13	glotblastn
  LYD560_H11	peanut|10v1|CD037768_P1	2065	3749	560	86.1	globlastp
  LYD560_H167	pigeonpea|11v1|SRR054580X101487_P1	2066	3750	560	86	globlastp
  LYD560_H10	humulus|11v1|CD527124_P1	2067	3751	560	86	globlastp
  LYD560_H168	beech|11v1|DT317640_P1	2068	3752	560	85.9	globlastp
  LYD560_H12	cannabis|12v1|GR220771_P1	2069	3753	560	85.9	globlastp
  LYD560_H13	humulus|11v1|SRR098683X104055_T1	2070	3754	560	85.67	glotblastn
  LYD560_H169	rose|12v1|BQ105339_P1	2071	3755	560	85.6	globlastp
  LYD560_H14	grape|11v1|GSVIVT01020689001_P1	2072	3756	560	85.6	globlastp
  LYD560_H170	cowpea|12v1|FC461925_P1	2073	3757	560	85.4	globlastp
  LYD560_H171	sesame|12v1|JK065449_P1	2074	3758	560	85.4	globlastp
  LYD560_H16	soybean|11v1|GLYMA12G14420	2075	3759	560	85.4	globlastp
  LYD560_H17	prunus|10v1|BU039550	2076	3760	560	85.4	globlastp
  LYD560_H172	bean|12v1|CB539455_P1	2077	3761	560	85.3	globlastp
  LYD560_H18	platanus|11v1|AM260502_P1	2078	3762	560	85.3	globlastp
  LYD560_H19	triphysaria|10v1|BE574775	2079	3763	560	85.2	globlastp
  LYD560_H20	catharanthus|11v1|HM006896_P1	2080	3764	560	85.1	globlastp
  LYD560_H22	eucalyptus|11v2|CD669407_P1	2081	3765	560	85	globlastp
  LYD560_H21	amsonia|11v1|SRR098688X10135_P1	2082	3766	560	84.9	globlastp
  LYD560_H25	flaveria|11v1|SRR149229.116025_T1	2083	3767	560	84.66	glotblastn
  LYD560_H23	cichorium|gb171|DT211113_P1	2084	3768	560	84.6	globlastp
  LYD560_H24	poplar|10v1|BI068438_P1	2085	3769	560	84.6	globlastp
  LYD560_H26	watermelon|11v1|AI563215	2086	3770	560	84.4	globlastp
  LYD560_H27	triphysaria|10v1|BM356564	2087	3771	560	84.4	globlastp
  LYD560_H173	b_juncea|12v1|E6ANDIZ01A2814_P1	2088	3772	560	84.3	globlastp
  LYD560_H30	platanus|11v1|SRR096786X109671_P1	2089	3773	560	84.3	globlastp
  LYD560_H174	sunflower|12v1|DY904533_P1	2090	3774	560	84.2	globlastp
  LYD560_H28	euphorbia|11v1|BI946379_P1	2091	3775	560	84.2	globlastp
  LYD560_H32	sunflower|10v1|DY905884	2092	3774	560	84.2	globlastp
  LYD560_H146	lettuce|12v1|DW056546_P1	2093	3776	560	84.2	globlastp
  LYD560_H31	monkeyflower|10v1|DV206354_P1	2094	3777	560	84.1	globlastp
  LYD560_H33	oak|10v1|CN725669_P1	2095	3778	560	84.1	globlastp
  LYD560_H35	melon|10v1|DV632098_P1	2096	3779	560	84	globlastp
  LYD560_H36	sunflower|10v1|DY904533	2097	3780	560	84	globlastp
  LYD560_H39	radish|gb164|EV525375	2098	3781	560	83.9	globlastp
  LYD560_H37	chestnut|gb170|SRR006295S0002507_P1	2099	3782	560	83.8	globlastp
  LYD560_H40	arnica|11v1|SRR099034X101317_P1	2100	3783	560	83.8	globlastp
  LYD560_H41	flaveria|11v1|SRR149229.17385_P1	2101	3784	560	83.8	globlastp
  LYD560_H42	tabernaemontana|11v1|SRR098689X103361	2102	3785	560	83.8	globlastp
  LYD560_H44	aquilegia|10v2|DR912607_P1	2103	3786	560	83.7	globlastp
  LYD560_H45	vinca|11v1|SRR098690X101887	2104	3787	560	83.6	globlastp
  LYD560_H46	canola|11v1|CN831246_P1	2105	3788	560	83.6	globlastp
  LYD560_H49	poplar|10v1|CA923778_P1	2106	3789	560	83.6	globlastp
  LYD560_H47	chelidonium|11v1|SRR084752X101401_P1	2107	3790	560	83.5	globlastp
  LYD560_H50	potato|10v1|BF153344_P1	2108	3791	560	83.5	globlastp
  LYD560_H51	cleome_gynandra|10v1|SRR015532S0001111_T1	2109	3792	560	83.5	glotblastn
  LYD560_H52	ambrosia|11v1|SRR346935.128656_T1	2110	3793	560	83.48	glotblastn
  LYD560_H53	ambrosia|11v1|SRR346943.17478_T1	2111	3794	560	83.48	glotblastn
  LYD560_H55	flaveria|11v1|SRR149232.78867_T1	2112	3795	560	83.45	glotblastn
  LYD560_H175	gossypium_raimondii|12v1|AI728816_P1	2113	3796	560	83.4	globlastp
  LYD560_H54	castorbean|11v1|EG661185_P1	2114	3797	560	83.4	globlastp
  LYD560_H56	arabidopsis|10v1|AT3G58610_P1	2115	3798	560	83.4	globlastp
  LYD560_H57	canola|11v1|CN829948_P1	2116	3799	560	83.4	globlastp
  LYD560_H59	cucumber|09v1|AI563215_P1	2117	3800	560	83.4	globlastp
  LYD560_H60	plantago|11v1|SRR066373X112712	2118	3801	560	83.4	globlastp
  LYD560_H61	potato|10v1|BF153566_P1	2119	3802	560	83.4	globlastp
  LYD560_H62	switchgrass|gb167|FE598038	2120	3803	560	83.4	globlastp
  LYD560_H66	foxtail_millet|11v3|PHY7SI021528M_P1	2121	3804	560	83.3	globlastp
  LYD560_H67	switchgrass|gb167|DN146770	2122	3805	560	83.3	globlastp
  LYD560_H68	flaveria|11v1|SRR149232.196243_T1	2123	3806	560	83.22	glotblastn
  LYD560_H176	b_rapa|11v1|BG732247_P1	2124	3807	560	83.2	globlastp
  LYD560_H63	cacao|10v1|CA796626_P1	2125	3808	560	83.2	globlastp
  LYD560_H64	canola|11v1|CN726713_P1	2126	3809	560	83.2	globlastp
  LYD560_H65	flaveria|11v1|SRR149229.101043_P1	2127	3810	560	83.2	globlastp
  LYD560_H69	b_rapa|gb162|CA992458	2128	3807	560	83.2	globlastp
  LYD560_H72	tragopogon|10v1|SRR020205S0020857	2129	3811	560	83.2	globlastp
  LYD560_H177	cotton|11v1|AI728816_P1	2130	3812	560	83.1	globlastp
  LYD560_H178	cotton|11v1|BE054370_P1	2131	3813	560	83.1	globlastp
  LYD560_H70	canola|11v1|DY006367_P1	2132	3814	560	83.1	globlastp
  LYD560_H73	canola|11v1|CX278693_T1	2133	3815	560	83.1	glotblastn
  LYD560_H74	cotton|10v2|SRR032367S0201653	2134	3812	560	83.1	globlastp
  LYD560_H75	flaveria|11v1|SRR149229.154246_P1	2135	3816	560	83.1	globlastp
  LYD560_H76	b_rapa|gb162|L33635	2136	3817	560	83.05	glotblastn
  LYD560_H77	switchgrass|gb167|DN140714	2137	3818	560	83.05	glotblastn
  LYD560_H179	sunflower|12v1|CD852201_P1	2138	3819	560	83	globlastp
  LYD560_H180	sunflower|12v1|CD858388_P1	2139	3820	560	83	globlastp
  LYD560_H78	arabidopsis_lyrata|09v1|JGIAL019161_P1	2140	3821	560	83	globlastp
  LYD560_H79	oil_palm|gb166|CN599790	2141	3822	560	83	globlastp
  LYD560_H80	sunflower|10v1|CD852201	2142	3823	560	83	globlastp
  LYD560_H81	tabernaemontana|11v1|SRR098689X102834	2143	3824	560	82.91	glotblastn
  LYD560_H82	tabernaemontana|11v1|SRR098689X103761	2144	3825	560	82.91	glotblastn
  LYD560_H181	b_rapa|11v1|L33635_P1	2145	3826	560	82.9	globlastp
  LYD560_H83	aristolochia|10v1|FD748169_P1	2146	3827	560	82.9	globlastp
  LYD560_H84	euphorbia|11v1|SRR098678X100620_P1	2147	3828	560	82.8	globlastp
  LYD560_H85	maize|10v1|AI391790_P1	2148	3829	560	82.8	globlastp
  LYD560_H86	wheat|10v2|CA605463	2149	3829	560	82.8	globlastp
  LYD560_H88	aquilegia|10v2|DR937512_P1	2150	3830	560	82.7	globlastp
  LYD560_H89	cirsium|11v1|SRR346952.104841_P1	2151	3831	560	82.7	globlastp
  LYD560_H90	fescue|gb161|DT685772_P1	2152	3832	560	82.7	globlastp
  LYD560_H91	peanut|10v1|EL966584_P1	2153	3833	560	82.7	globlastp
  LYD560_H97	vinca|11v1|SRR098690X104754	2154	3834	560	82.7	globlastp
  LYD560_H87	arnica|11v1|SRR099034X101454XX1_T1	2155	3835	560	82.69	glotblastn
  LYD560_H182	oil_palm|11v1|SRR190698.12262_T1	2156	3836	560	82.68	glotblastn
  LYD560_H183	b_rapa|11v1|BQ791335_P1	2157	3837	560	82.6	globlastp
  LYD560_H184	sorghum|12v1|SB03G029720_P1	2158	3838	560	82.6	globlastp
  LYD560_H92	pepper|gb171|BM063882	2159	3839	560	82.6	globlastp
  LYD560_H93	rice|11v1|BE228654_P1	2160	3840	560	82.6	globlastp
  LYD560_H93	rice|gb170|OS01G46380	2161	3840	560	82.6	globlastp
  LYD560_H95	sorghum|11v1|SB03G029720	2162	3838	560	82.6	globlastp
  LYD560_H96	thellungiella_parvulum|11v1|BM985551	2163	3841	560	82.6	globlastp
  LYD560_H185	oil_palm|11v1|SRR190698.100020_T1	2164	3842	560	82.5	glotblastn
  LYD560_H186	rye|12v1|DRR001012.115524_P1	2165	3843	560	82.5	globlastp
  LYD560_H98	canola|11v1|SRR023610.26048_P1	2166	3844	560	82.5	globlastp
  LYD560_H102	brachypodium|09v1|DV469933	2167	3845	560	82.5	globlastp
  LYD560_H187	poppy|11v1|SRR030259.10325_P1	2168	3846	560	82.4	globlastp
  LYD560_H101	b_rapa|gb162|BQ791335	2169	3847	560	82.4	globlastp
  LYD560_H103	barley|10v2|BE413220	2170	3848	560	82.4	globlastp
  LYD560_H188	eschscholzia|11v1|CD478497_P1	2171	3849	560	82.3	globlastp
  LYD560_H189	onion|12v1|BI095623_P1	2172	3850	560	82.3	globlastp
  LYD560_H190	rye|12v1|DRR001012.11842_P1	2173	3851	560	82.3	globlastp
  LYD560_H105	sugarcane|10v1|CA069523	2174	3852	560	82.3	globlastp
  LYD560_H104	flaveria|11v1|SRR149241.124510_T1	2175	3853	560	82.29	glotblastn
  LYD560_H191	oil_palm|11v1|CN600787_P1	2176	3854	560	82.2	globlastp
  LYD560_H108	thellungiella_halophilum|11v1|BM985551	2177	3855	560	82.2	globlastp
  LYD560_H109	tomato|11v1|BG124037	2178	3856	560	82.2	globlastp
  LYD560_H110	wheat|10v2|BE399048	2179	3857	560	82.2	globlastp
  LYD560_H110	wheat|12v3|BE399048_P1	2180	3857	560	82.2	globlastp
  LYD560_H111	foxtail_millet|11v3|EC612034_P1	2181	3858	560	82.1	globlastp
  LYD560_H112	leymus|gb166|EG374815_P1	2182	3859	560	82.1	globlastp
  LYD560_H113	wheat|10v2|BE413925	2183	3860	560	82.1	globlastp
  LYD560_H113	wheat|12v3|BE413925_P1	2184	3860	560	82.1	globlastp
  LYD560_H192	poppy|11v1|SRR030259.155979_T1	2185	3861	560	82.03	glotblastn
  LYD560_H193	banana|12v1|FF557878_P1	2186	3862	560	82	globlastp
  LYD560_H114	cassava|09v1|DV446011_P1	2187	3863	560	82	globlastp
  LYD560_H115	artemisia|10v1|EY032298_P1	2188	3864	560	82	globlastp
  LYD560_H194	banana|12v1|FL659215_P1	2189	3865	560	81.9	globlastp
  LYD560_H195	plantago|11v2|SRR066373X112712_P1	2190	3866	560	81.9	globlastp
  LYD560_H196	poppy|11v1|SRR030259.101863_P1	2191	3867	560	81.8	globlastp
  LYD560_H197	sorghum|12v1|SB09G029170_P1	2192	3868	560	81.8	globlastp
  LYD560_H117	flaveria|11v1|SRR149229.264618_P1	2193	3869	560	81.8	globlastp
  LYD560_H118	solanum_phureja|09v1|SPHBG124037	2194	3870	560	81.8	globlastp
  LYD560_H119	sugarcane|10v1|CA069008	2195	3871	560	81.8	globlastp
  LYD560_H120	wheat|10v2|BE402709	2196	3872	560	81.8	globlastp
  LYD560_H120	wheat|12v3|BE402709_P1	2197	3872	560	81.8	globlastp
  LYD560_H153	sorghum|11v1|SB09G029170	2198	3868	560	81.8	globlastp
  LYD560_H116	ambrosia|11v1|SRR346935.124709_T1	2199	3873	560	81.79	glotblastn
  LYD560_H121	flaveria|11v1|SRR149232.69233_T1	2200	3874	560	81.76	glotblastn
  LYD560_H122	millet|10v1|EVO454PM006129_P1	2201	3875	560	81.7	globlastp
  LYD560_H198	hornbeam|12v1|SRR364455.102657_P1	2202	3876	560	81.6	globlastp
  LYD560_H124	onion|gb162|BI095623	2203	3877	560	81.57	glotblastn
  LYD560_H125	cassava|09v1|CK643930_T1	2204	3878	560	81.55	glotblastn
  LYD560_H199	oil_palm|11v1|EY407536_P1	2205	3879	560	81.5	globlastp
  LYD560_H126	castorbean|11v1|EE257398_P1	2206	3880	560	81.5	globlastp
  LYD560_H127	cirsium|11v1|SRR346952.101419_P1	2207	3881	560	81.5	globlastp
  LYD560_H128	oat|11v1|GO589350_P1	2208	3882	560	81.5	globlastp
  LYD560_H200	brachypodium|12v1|BRADI2G15790_T1	2209	—	560	81.48	glotblastn
  LYD560_H130	flaveria|11v1|SRR149229.44395_P1	2210	3883	560	81.4	globlastp
  LYD560_H129	artemisia|10v1|EY057322_P1	2211	3884	560	81.3	globlastp
  LYD560_H201	oil_palm|11v1|CN599858_P1	2212	3885	560	81.2	globlastp
  LYD560_H202	gossypium_raimondii|12v1|DW233183_P1	2213	3886	560	81.1	globlastp
  LYD560_H203	oil_palm|11v1|EL683104_T1	2214	3887	560	81.07	glotblastn
  LYD560_H204	cotton|11v1|CO494385_T1	2215	3888	560	81.03	glotblastn
  LYD560_H205	amborella|12v3|CK756678_P1	2216	3889	560	81	globlastp
  LYD560_H132	potato|10v1|BF153113_P1	2217	3890	560	81	globlastp
  LYD560_H133	solanum_phureja|09v1|SPHAA824938	2218	3890	560	81	globlastp
  LYD560_H206	banana|12v1|ES435770_P1	2219	3891	560	80.9	globlastp
  LYD560_H134	valeriana|11v1|SRR099039X100132	2220	3892	560	80.9	globlastp
  LYD560_H135	cacao|10v1|CA794506_T1	2221	3893	560	80.88	glotblastn
  LYD560_H207	brachypodium|12v1|BRADI2G45330_P1	2222	3894	560	80.8	globlastp
  LYD560_H137	brachypodium|09v1|DV472499	2223	3894	560	80.8	globlastp
  LYD560_H138	flaveria|11v1|SRR149229.115395_P1	2224	3895	560	80.8	globlastp
  LYD560_H140	silene|11v1|SRR096785X101730	2225	3896	560	80.8	globlastp
  LYD560_H136	tomato|11v1|AA824938	2226	3897	560	80.78	glotblastn
  LYD560_H141	ambrosia|11v1|SRR346935.63652_T1	2227	3898	560	80.76	glotblastn
  LYD560_H139	flaveria|11v1|SRR149229.1150942_P1	2228	3899	560	80.7	globlastp
  LYD560_H142	cotton|10v2|BF268414	2229	3900	560	80.7	globlastp
  LYD560_H208	beet|12v1|BE590351_T1	2230	3901	560	80.61	glotblastn
  LYD560_H209	cotton|11v1|CO107572_P1	2231	3902	560	80.6	globlastp
  LYD560_H143	ambrosia|11v1|SRR346935.109161_P1	2232	3903	560	80.6	globlastp
  LYD560_H144	ambrosia|11v1|SRR346935.395723XX2_P1	2233	3904	560	80.6	globlastp
  LYD560_H145	flaveria|11v1|SRR149232.112827_P1	2234	3905	560	80.6	globlastp
  LYD560_H146	lettuce|10v1|DW056546	2235	3906	560	80.6	globlastp
  LYD560_H147	millet|10v1|EVO454PM014502_T1	2236	3907	560	80.52	glotblastn
  LYD560_H148	canola|11v1|CN725975_P1	2237	3908	560	80.5	globlastp
  LYD560_H151	chelidonium|11v1|SRR084752X100065_P1	2238	3909	560	80.4	globlastp
  LYD560_H152	momordica|10v1|SRR071315S0002438_P1	2239	3910	560	80.4	globlastp
  LYD560_H150	fagopyrum|11v1|SRR063689X104708_T1	2240	3911	560	80.38	glotblastn
  LYD560_H154	flaveria|11v1|SRR149241.109217_T1	2241	3912	560	80.3	glotblastn
  LYD560_H210	b_juncea|12v1|E6ANDIZ01A9Y9Z_P1	2242	3913	560	80.2	globlastp
  LYD560_H211	nasturtium|11v1|GH167255_T1	2243	3914	560	80.2	glotblastn
  LYD560_H155	amorphophallus|11v2|SRR089351X10005_P1	2244	3915	560	80.2	globlastp
  LYD560_H156	fagopyrum|11v1|GO496319_T1	2245	3916	560	80.17	glotblastn
  LYD560_H157	pseudoroegneria|gb167|FF349256	2246	3917	560	80.17	glotblastn
  LYD560_H212	grape|11v1|GSVIVT01021204001_T1	2247	3918	560	80.03	glotblastn
  LYD560_H213	humulus|11v1|SRR098683X109313_T1	2248	3919	560	80.03	glotblastn
  LYD560_H214	flaveria|11v1|SRR149229.139497_P1	2249	3920	560	80	globlastp
  LYD571_H1	trigonella|11v1|SRR066194X103623	2250	3921	563	97.04	glotblastn
  LYD571_H8	chickpea|11v1|GR915346_P1	2251	3922	563	94.4	globlastp
  LYD571_H9	pigeonpea|11v1|SRR054580X102540_P1	2252	3923	563	88.5	globlastp
  LYD571_H2	lotus|09v1|AW720127_P1	2253	3924	563	87.2	globlastp
  LYD571_H3	cowpea|12v1|FF390005_P1	2254	3925	563	86.8	globlastp
  LYD571_H3	cowpea|gb166|FF390005	2255	3925	563	86.8	globlastp
  LYD571_H4	soybean|11v1|GLYMA09G08190	2256	3926	563	86.33	glotblastn
  LYD571_H10	bean|12v1|SRR001334.141366_P1	2257	3927	563	86.1	globlastp
  LYD571_H5	citrus|gb166|CB250284	2258	3928	563	81	globlastp
  LYD571_H6	clementine|11v1|CB250284_P1	2259	3928	563	81	globlastp
  LYD571_H7	orange|11v1|CB250284_P1	2260	3928	563	81	globlastp
  LYD572_H2	clover|gb162|BB915599_T1	2261	3929	564	80.35	glotblastn
  LYD575_H1	trigonella|11v1|SRR066194X189015	2262	3930	565	81.2	globlastp
  LYD575_H2	lotus|09v1|AV416874_P1	2263	3931	565	80.1	globlastp
  LYD577_H19	chickpea|11v1|SRR133517.111644_P1	2264	3932	566	92.6	globlastp
  LYD577_H20	pigeonpea|11v1|SRR054580X103980_P1	2265	3933	566	89.6	globlastp
  LYD577_H1	soybean|11v1|GLYMA04G39980	2266	3934	566	89.3	globlastp
  LYD577_H2	soybean|11v1|GLYMA06G14870	2267	3935	566	88.7	globlastp
  LYD577_H21	bean|12v1|CA898729_P1	2268	3936	566	87.9	globlastp
  LYD577_H3	oak|10v1|FP043216_P1	2269	3937	566	85.6	globlastp
  LYD577_H4	grape|11v1|GSVIVT01022300001_P1	2270	3938	566	83.5	globlastp
  LYD577_H6	prunus|10v1|CN862404	2271	3939	566	83.2	globlastp
  LYD577_H5	apple|11v1|CN911043_P1	2272	3940	566	83.1	globlastp
  LYD577_H7	eucalyptus|11v2|CD668107_P1	2273	3941	566	82.5	globlastp
  LYD577_H8	castorbean|11v1|XM_002521692_P1	2274	3942	566	82.4	globlastp
  LAB627_H19	beet|12v1|BQ584887_T1	2275	3943	566	82.12	glotblastn
  LYD577_H9	watermelon|11v1|AM720533	2276	3944	566	82.1	globlastp
  LYD577_H10	cassava|09v1|CK645412_P1	2277	3945	566	82	globlastp
  LYD577_H11	aquilegia|10v2|DR932473_P1	2278	3946	566	81.6	globlastp
  LYD577_H13	clementine|11v1|CK701542_T1	2279	3947	566	81.56	glotblastn
  LYD577_H12	cucumber|09v1|DV737259_P1	2280	3948	566	81.5	globlastp
  LYD577_H14	valeriana|11v1|SRR099039X110137	2281	3949	566	81.48	glotblastn
  LAB627_H26	sunflower|12v1|DY906340_P1	2282	3950	566	81.2	globlastp
  LYD577_H15	sunflower|10v1|DY906340	2283	3951	566	81	globlastp
  LYD577_H16	thellungiella_halophilum|11v1|BY808300	2284	3952	566	80.7	globlastp
  LAB627_H11	oil_palm|11v1|EY396859_P1	2285	3953	566	80.4	globlastp
  LYD577_H17	arabidopsis_lyrata|09v1|JGIAL012212_P1	2286	3954	566	80.4	globlastp
  LYD577_H22	b_rapa|11v1|DY009615_P1	2287	3955	566	80.3	globlastp
  LYD577_H18	poplar|10v1|BI129795_P1	2288	3956	566	80.3	globlastp
  LYD577_H23	monkeyflower|10v1|GR046028_P1	2289	3957	566	80.2	globlastp
  LYD577_H24	canola|11v1|ES905120_T1	2290	3958	566	80.13	glotblastn
  LYD578_H1	trigonella|11v1|SRR066194X120334	2291	3959	567	98.6	globlastp
  LYD578_H14	aquilegia|10v2|DR913123_P1	2292	3960	567	88.6	globlastp
  LYD578_H175	cotton|11v1|AI055621_P1	2293	3961	567	88.3	globlastp
  LYD578_H22	cotton|10v2|AI055621	2294	3961	567	88.3	globlastp
  LYD578_H176	gossypium_raimondii|12v11AI055621_P1	2295	3962	567	88.1	globlastp
  LYD578_H177	cotton|11v1|AI727988_P1	2296	3963	567	87.9	globlastp
  LYD578_H20	cassava|09v1|DV444573_P1	2297	3964	567	87.9	globlastp
  LYD578_H25	cotton|10v2|CO119212	2298	3963	567	87.9	globlastp
  LYD578_H24	chelidonium|11v1|SRR084752X102130_T1	2299	3965	567	87.69	glotblastn
  LYD578_H178	cotton|11v1|AI055263_P1	2300	3966	567	87.4	globlastp
  LYD578_H179	gossypium_raimondii|12v1|AI055263_P1	2301	3967	567	87.2	globlastp
  LYD578_H27	cassava|09v1|DV449138_P1	2302	3968	567	87.2	globlastp
  LYD578_H28	cotton|10v2|BG444918	2303	3969	567	87.2	globlastp
  LYD578_H35	soybean|11v1|GLYMA08G09740	2304	3970	567	86.7	globlastp
  LYD578_H33	citrus|gb166|CB250290	2305	3971	567	86.6	globlastp
  LYD578_H34	clementine|11v1|CD574218_P1	2306	3972	567	86.6	globlastp
  LYD578_H38	soybean|11v1|GLYMA05G26750	2307	3973	567	86.5	globlastp
  LYD578_H41	clementine|11v1|CB250290_P1	2308	3974	567	86.5	globlastp
  LYD578_H67	trigonella|11v1|SRR066194X119293	2309	3975	567	85.8	globlastp
  LYD578_H180	pigeonpea|11v1|SRR054580X105689_P1	2310	3976	567	85.7	globlastp
  LYD578_H53	canola|11v1|EG021317_P1	2311	3977	567	85.7	globlastp
  LYD578_H57	monkeyflower|10v1|DV207594_P1	2312	3978	567	85.7	globlastp
  LYD578_H61	monkeyflower|10v1|DV208027_P1	2313	3979	567	85.5	globlastp
  LYD578_H70	castorbean|11v1|T23277_P1	2314	3980	567	85.5	globlastp
  LYD578_H62	orobanche|10v1|SRR023189S0000345_P1	2315	3981	567	85.2	globlastp
  LYD578_H64	euonymus|11v1|SRR070038X10094_P1	2316	3982	567	85.2	globlastp
  LYD578_H81	oak|10v1|FP030675_P1	2317	3983	567	85.2	globlastp
  LYD578_H79	eucalyptus|11v2|CT987127_P1	2318	3984	567	85.1	globlastp
  LYD578_H89	eucalyptus|11v2|CT984993_P1	2319	3985	567	85.1	globlastp
  LYD578_H71	valeriana|11v1|SRR099039X102744	2320	3986	567	85	globlastp
  LYD578_H72	amsonia|11v1|SRR098688X103450_P1	2321	3987	567	84.9	globlastp
  LYD578_H73	zostera|10v1|AM767776	2322	3988	567	84.8	globlastp
  LYD578_H181	gossypium_raimondii|12v1|AI054718_P1	2323	3989	567	84.5	globlastp
  LYD578_H83	euonymus|11v1|SRR070038X166372_T1	2324	3990	567	84.49	glotblastn
  LYD578_H182	oil_palm|11v1|EL695363_P1	2325	3991	567	84.4	globlastp
  LYD578_H183	nasturtium|11v1|SRR032558.101620_T1	2326	3992	567	84.15	glotblastn
  LYD578_H184	cotton|11v1|AI054718_P1	2327	3993	567	84.1	globlastp
  LYD578_H102	zostera|10v1|SRR057351S0005912	2328	3994	567	84.1	globlastp
  LYD578_H185	barley|12v1|BI946608_P1	2329	3995	567	84	globlastp
  LYD578_H186	rye|12v1|DRR001012.100198_P1	2330	3995	567	84	globlastp
  LYD578_H100	valeriana|11v1|SRR099039X113494	2331	3996	567	84	globlastp
  LYD578_H107	foxtail_millet|11v3|PHY7SI034806M_P1	2332	3997	567	84	globlastp
  LYD578_H108	barley|10v2|BI946608	2333	3995	567	84	globlastp
  LYD578_H109	wheat|10v2|BF291626	2334	3995	567	84	globlastp
  LYD578_H109	wheat|12v3|BE444286_P1	2335	3995	567	84	globlastp
  LYD578_H187	oil_palm|11v1|EL684249_P1	2336	3998	567	83.8	globlastp
  LYD578_H106	centaurea|gb166|EH713185_P1	2337	3999	567	83.8	globlastp
  LYD578_H188	lettuce|12v1|DW052763_P1	2338	4000	567	83.4	globlastp
  LYD578_H123	maize|10v1|AI987493_P1	2339	4001	567	82.7	globlastp
  LYD578_H189	amborella|12v3|FD429782_P1	2340	4002	567	82.6	globlastp
  LYD578_H120	aristolochia|10v1|SRR039083S0092867_P1	2341	4003	567	82.6	globlastp
  LYD578_H122	maize|10v1|AI601039_P1	2342	4004	567	82.5	globlastp
  LYD578_H125	sugarcane|10v1|BQ533651	2343	4005	567	82.5	globlastp
  LYD578_H190	sorghum|12v1|SB01G041650_P1	2344	4006	567	82.2	globlastp
  LYD578_H129	sorghum|11v1|SB01G041650	2345	4006	567	82.2	globlastp
  LYD578_H131	amorphophallus|11v2|SRR089351X155622_P1	2346	4007	567	81.7	globlastp
  LYD578_H134	ambrosia|11v1|SRR346935.11798_P1	2347	4008	567	81.7	globlastp
  LYD578_H191	amborella|12v3|CK743344_P1	2348	4009	567	81.4	globlastp
  LYD578_H136	thellungiella_halophilum|11v1|BY807071	2349	4010	567	81.1	globlastp
  LYD578_H141	pine|10v2|AI725121_P1	2350	4011	567	80.8	globlastp
  LYD578_H192	podocarpus|10v1|SRR065014S0003582_P1	2351	4012	567	80.1	globlastp
  LYD580_H1	clover|gb162|BB906292_P1	2352	4013	569	84.7	globlastp
  LYD580_H5	pigeonpea|11v1|SRR054580X133160_P1	2353	4014	569	80.1	globlastp
  LYD580_H2	pigeonpea|10v1|SRR054580S0027058	2354	4014	569	80.1	globlastp
  LYD583_H1	pigeonpea|11v1|SRR054581X208104_P1	2355	4015	570	80.4	globlastp
  LYD587_H1	chickpea|11v1|SRR133517.128822_P1	2356	4016	571	83.4	globlastp
  LYD588_H4	medicago|12v1|BE322031_P1	2357	4017	572	86.3	globlastp
  LYD588_H2	medicago|09v1|BE322031	2358	4018	572	84.7	globlastp
  LYD588_H5	medicago|12v1|BI272020_P1	2359	4019	572	80.9	globlastp
  LYD589_H1	soybean|11v1|GLYMA09G32750	2360	4020	573	83.7	globlastp
  LYD589_H2	bean|gb167|EC911408	2361	4021	573	83	globlastp
  LYD589_H4	pigeonpea|11v1|SRR054580X14159_P1	2362	4022	573	81.9	globlastp
  LYD589_H3	soybean|11v1|GLYMA16G21310	2363	4023	573	81.5	globlastp
  LYD589_H5	bean|12v1|EC911765_P1	2364	4024	573	81.2	globlastp
  LYD593_H1	trigonella|11v1|SRR066194X116418	2365	4025	576	96.3	globlastp
  LYD593_H5	chickpea|11v1|SRR133517.177493_P1	2366	4026	576	87.3	globlastp
  LYD593_H6	pigeonpea|11v1|SRR054580X103481_P1	2367	4027	576	85.8	globlastp
  LYD593_H2	soybean|11v1|GLYMA17G18500	2368	4028	576	85.2	globlastp
  LYD593_H7	bean|12v1|SRR001334.191933_T1	2369	4029	576	83.08	glotblastn
  LYD593_H3	peanut|10v1|GO330608_P1	2370	4030	576	82.2	globlastp
  LYD593_H4	cowpea|12v1|FG826472_P1	2371	4031	576	80.4	globlastp
  LYD593_H4	cowpea|gb166|FG826472	2372	4031	576	80.4	globlastp
  LYD605_H2	foxtail_millet|11v3|PHY7SI029408M_P1	2373	4032	578	86.2	globlastp
  LYD618_H3	bean|12v1|CB542893_P1	2374	4033	579	88.5	globlastp
  LYD618_H4	pigeonpea|11v1|SRR054580X169953_P1	2375	4034	579	88	globlastp
  LYD618_H1	cowpea|gb166|FF547523	2376	4035	579	87.12	glotblastn
  LYD618_H2	lotus|09v1|BW622754_P1	2377	4036	579	81.9	globlastp
  LYD632_H2	soybean|11v1|GLYMA19G38740	2378	4037	581	99.8	globlastp
  LYD637_H1	soybean|11v1|GLYMA0084S00210	2379	4038	582	96.2	globlastp
  LYD637_H4	pigeonpea|11v1|SRR054580X528923_P1	2380	4039	582	88.2	globlastp
  LYD637_H2	bean|gb167|CV530100	2381	4040	582	87.2	globlastp
  LYD637_H3	cowpea|12v1|FF546955_T1	2382	4041	582	84.66	glotblastn
  LYD637_H3	cowpea|gb166|FF546955	2383	4042	582	84.4	globlastp
  LYD637_H5	bean|12v1|SRR001334.120242_P1	2384	4043	582	81.1	globlastp
  LYD641_H1	soybean|11v1|GLYMA13G42740	2385	4044	583	95.2	globlastp
  LNU337_H33	pigeonpea|11v1|SRR054580X108382_P1	2386	4045	583	86.1	globlastp
  LYD641_H2	bean|12v1|CA902313_P1	2387	4046	583	85.5	globlastp
  LYD646_H1	soybean|11v1|GLYMA05G01650	2388	4047	584	90.6	globlastp
  LYD646_H2	pigeonpea|11v1|SRR054580X108829_P1	2389	4048	584	89.2	globlastp
  LYD646_H3	bean|12v1|SRR001334.187433_P1	2390	4049	584	88.1	globlastp
  LYD650_H3	tobacco|gb162|DV157531	2391	4050	585	87	globlastp
  LYD651_H1	solanum_phureja|09v1|SPHAI485479	2392	4051	586	94	globlastp
  LYD652_H1	solanum_phureja|09v1|SPHAI771255	2393	4052	587	98	globlastp
  LYD652_H2	eggplant|10v1|FS071038_P1	2394	4053	587	81.6	globlastp
  LYD652_H3	solanum_phureja|09v1|SPHBG130927_P1	2395	4054	587	80.1	globlastp
  LYD660_H2	solanum_phureja|09v1|SPHCRPSP010629	2396	4055	588	82	globlastp
  LYD660_H3	tomato|11v1|AW223948	2397	4056	588	81.65	glotblastn
  LYD665_H1	solanum_phureja|09v1|SPHBF097728	2398	4057	589	91.27	glotblastn
  LYD665_H2	solanum_phureja|09v1|SPHDN589048	2399	4058	589	85.28	glotblastn
  LYD665_H3	eggplant|10v1|FS008366_T1	2400	4059	589	82.48	glotblastn
  LYD666_H1	solanum_phureja|09v1|SPHBG123259	2401	4060	590	96	globlastp
  LYD666_H2	potato|10v1|BF153474_P1	2402	4061	590	95.8	globlastp
  LYD668_H1	solanum_phureja|09v1|SPHBG125390	2403	4062	592	97.4	globlastp
  LYD668_H2	ipomoea_nil|10v1|BJ560832_P1	2404	4063	592	86.5	globlastp
  LYD668_H3	amsonia|11v1|SRR098688X1058_P1	2405	4064	592	85.9	globlastp
  LYD668_H4	tabernaemontana|11v1|SRR098689X118673	2406	4065	592	85.1	globlastp
  LYD668_H5	phyla|11v2|SRR099035X102114_P1	2407	4066	592	84.7	globlastp
  LYD668_H11	blueberry|12v1|SRR353282X100511D1_P1	2408	4067	592	83	globlastp
  LYD668_H6	monkeyflower|10v1|GO963338_P1	2409	4068	592	83	globlastp
  LYD668_H7	triphysaria|10v1|EY170500	2410	4069	592	81.8	globlastp
  LYD668_H8	cacao|10v1|CU484627_P1	2411	4070	592	81	globlastp
  LYD668_H9	cirsium|11v1|SRR346952.105209_P1	2412	4071	592	80.4	globlastp
  LYD668_H10	phyla|11v2|SRR099035X106776_P1	2413	4072	592	80.4	globlastp
  LYD668_H12	valeriana|11v1|SRR099039X108687_P1	2414	4073	592	80.2	globlastp
  LYD668_H13	prunus|10v1|CN947564_T1	2415	4074	592	80.12	glotblastn
  LYD668_H14	sarracenia|11v1|SRR192669.14959_T1	2416	4075	592	80.12	glotblastn
  LYD671_H1	solanum_phureja|09v1|SPHBG129734	2417	4076	593	90.8	globlastp
  LYD671_H2	potato|10v1|BG350219_P1	2418	4077	593	90	globlastp
  LYD673_H1	solanum_phureja|09v1|SPHBG132287	2419	4078	594	94.7	globlastp
  LYD675_H1	potato|10v1|BQ515816_P1	2420	4079	595	92.5	globlastp
  LYD675_H2	solanum_phureja|09v1|SPHBG134175	2421	4080	595	91.9	globlastp
  LYD676_H1	solanum_phureja|09v1|SPHBG135207	2422	4081	596	92.5	globlastp
  LYD679_H1	solanum_phureja|09v1|SPHBG628242	2423	4082	597	92.4	globlastp
  LYD680_H1	solanum_phureja|09v1|SPHBG628985	2424	4083	598	97.1	globlastp
  LYD680_H3	ipomoea_nil|10v1|BJ560522_P1	2425	4084	598	80.7	globlastp
  LYD683_H1	potato|10v1|CK248027_P1	2426	4085	599	92.3	globlastp
  LYD683_H2	solanum_phureja|09v1|SPHBG643762	2427	4085	599	92.3	globlastp
  LYD688_H1	solanum_phureja|09v1|SPHBG593254	2428	4086	601	98.2	globlastp
  Table 54: Provided are polynucleotides (P.N.) and polypeptides (P.P.) which are homologous to the identified polynucleotides or polypeptides of Table 53. Hom. = homologue; Algor. = Algorithm;

Example 14 Gene Cloning and Generation of Binary Vectors for Plant Expression
• To validate their role in improving plant yield, oil content, seed yield, biomass, growth rate, fiber yield, fiber quality, ABST, NUE and/or vigor, selected genes were over-expressed in plants, as follows.
• Cloning Strategy
• Selected genes from those listed in Examples 1-13 hereinabove were cloned into binary vectors for the generation of transgenic plants. For cloning, the full-length open reading frame (ORF) was first identified. In case of ORF-EST clusters and in some cases already published mRNA sequences were analyzed to identify the entire open reading frame by comparing the results of several translation algorithms to known proteins from other plant species. To clone the full-length cDNAs, reverse transcription (RT) followed by polymerase chain reaction (PCR; RT-PCR) was performed on total RNA extracted from leaves, flowers, siliques or other plant tissues, growing under normal and different treated conditions. Total RNA was extracted as described in “GENERAL EXPERIMENTAL AND BIOINFORMATICS METHODS” above. Production of cDNA and PCR amplification was performed using standard protocols described elsewhere (Sambrook J., E. F. Fritsch, and T. Maniatis. 1989. Molecular Cloning. A Laboratory Manual., 2nd Ed. Cold Spring Harbor Laboratory Press, New York), which are well known to those skilled in the art. PCR products were purified using PCR purification kit (Qiagen). In case where the entire coding sequence was not found, RACE kit from Invitrogen (RACE=Rapid Amplification of cDNA Ends) was used to access the full cDNA transcript of the gene from the RNA samples described above. RACE products were cloned into high copy vector followed by sequencing or directly sequenced.
• The information from the RACE procedure was used for cloning of the full length ORF of the corresponding genes.
• In case genomic DNA was cloned, the genes are amplified by direct PCR on genomic DNA extracted from leaf tissue using the DNAeasy kit (Qiagen Cat. No. 69104).
• Usually, 2 sets of primers were synthesized for the amplification of each gene from a cDNA or a genomic sequence; an external set of primers and an internal set (nested PCR primers). When needed (e.g., when the first PCR reaction does not result in a satisfactory product for sequencing), an additional primer (or two) of the nested PCR primers is used.
• To facilitate cloning of the cDNAs/genomic sequences, an 8-12 bp extension was added to the 5′ of each primer. The primer extension includes an endonuclease restriction site. The restriction sites were selected using two parameters: (a). The site does not exist in the cDNA sequence; and (b). The restriction sites in the forward and reverse primers were designed such that the digested cDNA was inserted in the sense formation into the binary vector utilized for transformation.
• PCR products were digested with the restriction endonucleases (New England BioLabs Inc) according to the sites designed in the primers. Each digested PCR product was inserted into a high copy vector pUC19 (New England BioLabs Inc], or into plasmids originating from this vector or into CloneJet (Thermo Scientific). In some cases the undigested PCR product was inserted into pCR-Blunt II-TOPO (Invitrogen) or directly into the binary vector.
• Sequencing of the amplified PCR products was performed, using ABI 377 sequencer (Amersham Biosciences Inc). In some cases, after confirming the sequences of the cloned genes, the cloned cDNA was introduced into a modified pGI binary vector containing the At6669 promoter via digestion with appropriate restriction endonucleases. The digested products and the linearized plasmid vector were ligated using T4 DNA ligase enzyme (Roche, Switzerland).
• High copy plasmids containing the cloned genes were digested with the restriction endonucleases (New England BioLabs Inc) according to the sites designed in the primers and cloned into binary vectors.
• Several DNA sequences of the selected genes were synthesized by a commercial supplier GeneArt (Life Technologies) [Hypertext Transfer Protocol://World Wide Web (dot) geneart (dot) com]. Synthetic DNA was designed in silico. Suitable restriction enzymes sites were added to the cloned sequences at the 5′ end and at the 3′ end to enable later cloning into the pQFNc or other required binary vector downstream of the At6669 promoter (SEQ ID NO: 4111).
• Binary vectors used for cloning: The plasmid pPI was constructed by inserting a synthetic poly-(A) signal sequence, originating from pGL3 basic plasmid vector (Promega. Acc No U47295; bp 4658-4811) into the HindIII restriction site of the binary vector pBI101.3 (Clontech, Acc. No. U12640). pGI (pBXYN) was similar to pPI, but the original gene in the backbone, the GUS gene, was replaced by the GUS-Intron gene followed by the NOS terminator (SEQ ID NO: 4122) (Vancanneyt. G, et al MGG 220, 245-50, 1990). pGI was used in the past to clone the polynucleotide sequences, initially under the control of 35S promoter [Odell, J T, et al. Nature 313, 810-812 (28 Feb. 1985); SEQ ID NO:4109].
• The modified pGI vectors [pQXNc (FIG. 8): or pQFN (FIG. 2), pQFNc (FIG. 2) or pQYN_6669 (FIG. 1)] were modified versions of the pGI vector in which the cassette was inverted between the left and right borders so the gene and its corresponding promoter were close to the right border and the NPTII gene was close to the left border.
• At6669, the Arabidopsis thaliana promoter sequence (SEQ ID NO: 4111) was inserted in the modified pGI binary vector, upstream to the cloned genes, followed by DNA ligation and binary plasmid extraction from positive E. coli colonies, as described above.
• Colonies were analyzed by PCR using the primers covering the insert which are designed to span the introduced promoter and gene. Positive plasmids were identified, isolated and sequenced.
• Selected genes cloned by the present inventors are provided in Table 55 below.

• TABLE 55
  Genes cloned in high copy number plasmids

  				Polyn.	Polyp.
  				SEQ	SEQ
  Gene Name	High copy plasmid	Organism	Primers used SEQ ID NOs:	ID NO:	ID NO:

  LYD521	pUC19c_LYD521	Arabidopsis thaliana	4123, 4267, 4411, 4508	202	362
  LYD522	pUC19c_LYD522	Arabidopsis thaliana	4124, 4268, 4412, 4509	203	363
  LYD524	pUC19c_LYD524	Arabidopsis thaliana	4125, 4269, 4413, 4510	204	364
  LYD525_GA	pMA-RQ_LYD525_GA	GENEART ®		205	365
  LYD526	pUC19c_LYD526	Arabidopsis thaliana	4126, 4270, 4414, 4511	206	366
  LYD527	pUC19c_LYD527	Arabidopsis thaliana	4127, 4271, 4127, 4271	207	547
  LYD528	pUC19c_LYD528	Arabidopsis thaliana	4128, 4272, 4415, 4512	208	368
  LYD529	TopoB_LYD529	Arabidopsis thaliana	4129, 4273, 4416, 4513	209	369
  LYD530	TopoB_LYD530	Arabidopsis thaliana	4130, 4274, 4417, 4514	210	548
  LYD531	pUC19c_LYD531	Arabidopsis thaliana	4131, 4275, 4418, 4515	211	371
  LYD532	pUC19c_LYD532	Arabidopsis thaliana	4132, 4276, 4132, 4276	212	549
  LYD533	pUC19c_LYD533	Arabidopsis thaliana	4133, 4277, 4419, 4516	213	373
  LYD534	pQFNc_LYD534	Arabidopsis thaliana	4134, 4278, 4134, 4278	214	374
  LYD535	pQFNc_LYD535	Arabidopsis thaliana	4135, 4279, 4420, 4517	215	375
  LYD536	pUC19c_LYD536	Arabidopsis thaliana	4136, 4280, 4136, 4280	216	376
  LYD537	pUC19c_LYD537	Brassica juncea	4137, 4281, 4137, 4281	217	550
  LYD538	pQFNc_LYD538	Brassica juncea	4138, 4282, 4138, 4518	218	378
  LYD539_H11_GA	pMA_LYD539_H11_GA	GENEART ®		361	526
  LYD540	pJET_LYD540	Brassica juncea	4139, 4283, 4421, 4519	219	551
  LYD541_GA	pMA_LYD541_GA	GENEART ®		220	381
  LYD542	pUC19c_LYD542	Brachypodium distachyon	4140, 4284, 4422, 4520	221	382
  LYD543	pQFNc_LYD543	Brachypodium distachyon	4141, 4285, 4423, 4521	222	552
  LYD545	pQFNc_LYD545	Brachypodium distachyon	4142, 4286, 4424, 4522	223	385
  LYD546	TopoB_LYD546	Brachypodium distachyon	4143, 4287, 4143, 4287	224	386
  LYD547	pQFNc_LYD547	CANOLA Brassica napus	4144, 4288, 4425, 4523	225	387
  LYD548	pQFNc_LYD548	CANOLA Brassica napus	4145, 4289, 4426, 4524	226	553
  LYD549	pQFNc_LYD549	CANOLA Brassica napus	4146, 4290, 4146, 4290	227	554
  LYD550	pUC19c_LYD550	CANOLA Brassica napus	4147, 4291, 4427, 4525	228	555
  LYD551	pQFNc_LYD551	CANOLA Brassica napus	4148, 4292, 4428, 4526	229	391
  LYD552	pQFNc_LYD552	CANOLA Brassica napus	4149, 4293, 4149, 4293	230	392
  LYD553	pUC19c_LYD553	CANOLA Brassica napus	4150, 4294, 4429, 4527	231	556
  LYD554	pUC19c_LYD554	Gossypium barbadense	4151, 4295, 4430, 4528	232	557
  LYD555	pJET_LYD555	Gossypium barbadense	4152, 4296	233	558
  LYD556_GA	pMA-T_LYD556_GA	GENEART ®		234	396
  LYD558_GA	pMA_LYD558_GA	GENEART ®		235	397
  LYD559	pQFNc_LYD559	Medicago trancatula	4153, 4297, 4153, 4297	236	559
  LYD560	pUC19c_LYD560	Medicago trancatula	4154, 4298, 4431, 4529	237	560
  LYD561	pUC19c_LYD561	Medicago trancatula	4155, 4299, 4432, 4530	238	400
  LYD562_GA	pMA-RQ_LYD562_GA	GENEART ®		239	401
  LYD563	pUC19c_LYD563	Medicago trancatula	4156, 4300, 4433, 4531	240	402
  LYD564	pUC19c_LYD564	Medicago trancatula	4157, 4301, 4157, 4301	241	403
  LYD565_GA	pMA_LYD565_GA	GENEART ®		242	404
  LYD566	pQFNc_LYD566	Medicago trancatula	4158, 4302, 4158, 4302	243	561
  LYD567	pQFNc_LYD567	Medicago trancatula	4159, 4303, 4159, 4303	244	406
  LYD568	pUC19c_LYD568	Medicago trancatula	4160, 4304, 4434, 4532	245	407
  LYD570	pUC19c_LYD570	Medicago trancatula	4161, 4305, 4435, 4533	246	562
  LYD571	pUC19c_LYD571	Medicago trancatula	4162, 4306, 4162, 4306	247	563
  LYD572	pQFNc_LYD572	Medicago trancatula	4163, 4307, 4436, 4534	248	564
  LYD573_GA	pMA-T_LYD573_GA	GENEART ®		249	411
  LYD574_GA	pMA-RQ_LYD574_GA	GENEART ®		250	412
  LYD575	TopoB_LYD575	Medicago trancatula	4164, 4308, 4437, 4535	251	565
  LYD576_GA	pMA-T_LYD576_GA	GENEART ®		252	414
  LYD577	pUC19c_LYD577	Medicago trancatula	4165, 4309, 4438, 4536	253	566
  LYD578	pUC19c_LYD578	Medicago trancatula	4166, 4310, 4439, 4537	254	567
  LYD579	pUC19c_LYD579	Medicago trancatula	4167, 4311, 4167, 4311	255	568
  LYD580	pUC19c_LYD580	Medicago trancatula	4168, 4312, 4440, 4538	256	569
  LYD581_GA	pMA_LYD581_GA	GENEART ®		257	419
  LYD583	pUC19c_LYD583	Medicago trancatula	4169, 4313, 4441, 4539	258	570
  LYD584	pUC19c_LYD584	Medicago trancatula	4170, 4314, 4170, 4314	259	421
  LYD585_GA	pMA-T_LYD585_GA	GENEART ®		260	422
  LYD586	pUC19c_LYD586	Medicago trancatula	4171, 4315, 4171, 4315	261	423
  LYD587	pUC19c_LYD587	Medicago trancatula	4172, 4316, 4172, 4316	262	571
  LYD588	pQFNc_LYD588	Medicago trancatula	4173, 4317, 4173, 4317	263	572
  LYD589	pQFNc_LYD589	Medicago trancatula	4174, 4318, 4174, 4318	264	573
  LYD591	pQFNc_LYD591	Medicago trancatula	4175, 4319, 4175, 4319	265	574
  LYD592	TopoB_LYD592	Medicago trancatula	4176, 4320, 4176, 4320	266	575
  LYD593	pUC19c_LYD593	Medicago trancatula	4177, 4321, 4442, 4540	267	576
  LYD594	pQFNc_LYD594	Medicago trancatula	4178, 4322, 4178, 4322	268	577
  LYD595	pUC19c_LYD595	Oryza sativa L.	4179, 4323, 4443, 4541	269	432
  LYD596	pJET_LYD596	Oryza sativa L.	4180, 4324, 4444, 4542	270	433
  LYD597	pQFNc_LYD597	Oryza sativa L.	4181, 4325, 4445, 4543	271	434
  LYD598	pQFNc_LYD598	Oryza sativa L.	4182, 4326, 4446, 4544	272	435
  LYD599	pQFNc_LYD599	Oryza sativa L.	4183, 4327, 4447, 4545	273	436
  LYD600_GA	pMA-RQ_LYD600_GA	GENEART ®		274	437
  LYD601	pUC19c_LYD601	Oryza sativa L.	4184, 4328, 4448, 4546	275	438
  LYD602	pUC19c_LYD602	Oryza sativa L.	4185, 4329, 4449, 4547	276	439
  LYD603	pUC19c_LYD603	Oryza sativa L.	4186, 4330, 4186, 4330	277	440
  LYD604	pQFNc_LYD604	Sorghum bicolor	4187, 4331, 4187, 4331	278	441
  LYD605	pUC19c_LYD605	Sorghum bicolor	4188, 4332, 4188, 4332	279	578
  LYD606	pQFNc_LYD606	Sorghum bicolor	4189, 4333, 4189, 4333	280	443
  LYD607	pUC19c_LYD607	Sorghum bicolor	4190, 4334, 4450, 4548	281	444
  LYD608	pUC19c_LYD608	Sorghum bicolor	4191, 4335, 4451, 4549	282	445
  LYD609	pUC19c_LYD609	Sorghum bicolor	4192, 4336, 4192, 4336	283	446
  LYD610	TopoB_LYD610	Sorghum bicolor	4193, 4337, 4193, 4337	284	447
  LYD611	pQFNc_LYD611	Glycine max	4194, 4338, 4194, 4550	285	448
  LYD612	pQFNc_LYD612	Glycine max	4195, 4339, 4452, 4551	286	449
  LYD613	pQFNc_LYD613	Glycine max	4196, 4340, 4453, 4552	287	450
  LYD614_GA	pMA-RQ_LYD614_GA	GENEART ®		288	451
  LYD615	pUC19c_LYD615	Glycine max	4197, 4341, 4454, 4553	289	452
  LYD616	pUC19c_LYD616	Glycine max	4198, 4342, 4198, 4342	290	453
  LYD617	pUC19c_LYD617	Glycine max	4199, 4343, 4455, 4554	291	454
  LYD618	pUC19c_LYD618	Glycine max	4200, 4344, 4456, 4555	292	579
  LYD619	pUC19c_LYD619	Glycine max	4201, 4345, 4457, 4556	293	580
  LYD620	pUC19c_LYD620	Glycine max	4202, 4346, 4202, 4346	294	457
  LYD621	pUC19c_LYD621	Glycine max	4203, 4347, 4458, 4557	295	458
  LYD622	pUC19c_LYD622	Glycine max	4204, 4348, 4459, 4558	296	459
  LYD623	pUC19c_LYD623	Glycine max	4205, 4349, 4205, 4349	297	460
  LYD624	pQFNc_LYD624	Glycine max	4206, 4350, 4460, 4559	298	461
  LYD625	pUC19c_LYD625	Glycine max	4207, 4351, 4461, 4560	299	462
  LYD626	pUC19c_LYD626	Glycine max	4208, 4352, 4462, 4561	300	463
  LYD627	pUC19c_LYD627	Glycine max	4209, 4353, 4463, 4562	301	464
  LYD628	pQFNc_LYD628	Glycine max	4210, 4354, 4210, 4354	302	465
  LYD629	pUC19c_LYD629	Glycine max	4211, 4355, 4464, 4563	303	466
  LYD630	pUC19c_LYD630	Glycine max	4212, 4356, 4465, 4564	304	467
  LYD631	pUC19c_LYD631	Glycine max	4213, 4357, 4213, 4357	305	468
  LYD632	pUC19c_LYD632	Glycine max	4214, 4358, 4466, 4565	306	581
  LYD633p	pQFNc_LYD633p	Glycine max	4215, 4359, 4215, 4359	307	470
  LYD634	pQFNc_LYD634	Glycine max	4216, 4360, 4467, 4566	308	471
  LYD635	pUC19c_LYD635	Glycine max	4217, 4361, 4468, 4567	309	472
  LYD636	pUC19c_LYD636	Glycine max	4218, 4362, 4469, 4568	310	473
  LYD637	pQFNc_LYD637	Glycine max	4219, 4363, 4219, 4363	311	582
  LYD638	pQFNc_LYD638	Glycine max	4220, 4364, 4220, 4364	312	475
  LYD639	pUC19c_LYD639	Glycine max	4221, 4365, 4470, 4569	313	476
  LYD640	pUC19c_LYD640	Glycine max	4222, 4366, 4471, 4570	314	477
  LYD641	pUC19c_LYD641	Glycine max	4223, 4367, 4472, 4571	315	583
  LYD642	pQFNc_LYD642	Glycine max	4224, 4368, 4473, 4572	316	479
  LYD643	pUC19c_LYD643	Glycine max	4225, 4369, 4474, 4573	317	480
  LYD644	pUC19c_LYD644	Glycine max	4226, 4370, 4226, 4370	318	481
  LYD645	pUC19c_LYD645	Glycine max	4227, 4371, 4475, 4574	319	482
  LYD646	pUC19c_LYD646	Glycine max	4228, 4372, 4228, 4372	320	584
  LYD647	pUC19c_LYD647	Glycine max	4229, 4373, 4476, 4575	321	484
  LYD648	pQFNc_LYD648	Lycopersicum ND	4230, 4374, 4477, 4576	322	485
  LYD650	pUC19c_LYD650	Lycopersicum ND	4231, 4375, 4478, 4577	323	585
  LYD651	pQFNc_LYD651	Lycopersicum ND	4232, 4376, 4232, 4376	324	586
  LYD652	pUC19c_LYD652	Lycopersicum ND	4233, 4377, 4479, 4578	325	587
  LYD654_GA	pMA-RQ_LYD654_GA	GeneArt ®		326	490
  LYD655	pUC19c_LYD655	Lycopersicum ND	4234, 4378, 4480, 4579	327	491
  LYD657	pUC19c_LYD657	Lycopersicum ND	4235, 4379, 4481, 4580	328	492
  LYD658	pUC19c_LYD658	Lycopersicum ND	4236, 4380, 4482, 4581	329	493
  LYD659_GA	pMA_LYD659_GA	GeneArt ®		330	494
  LYD660	pUC19c_LYD660	Lycopersicum ND	4237, 4381, 4237, 4381	331	588
  LYD661	pUC19c_LYD661	Lycopersicum ND	4238, 4382, 4483, 4582	332	496
  LYD662	pUC19c_LYD662	Lycopersicum ND	4239, 4383, 4484, 4583	333	497
  LYD663	pQFNc_LYD663	Lycopersicum ND	4240, 4384, 4485, 4584	334	498
  LYD664	pUC19c_LYD664	Lycopersicum ND	4241, 4385, 4486, 4585	335	499
  LYD665	pUC19c_LYD665	Lycopersicum ND	4242, 4386, 4487, 4586	336	589
  LYD666	pUC19c_LYD666	Lycopersicum ND	4243, 4387, 4243, 4587	337	590
  LYD667	pUC19c_LYD667	Lycopersicum ND	4244, 4388, 4488, 4588	338	591
  LYD668	pUC19c_LYD668	Lycopersicum ND	4245, 4389, 4489, 4589	339	592
  LYD669	pUC19c_LYD669	Lycopersicum ND	4246, 4390, 4490, 4590	340	504
  LYD670	pQFNc_LYD670	Lycopersicum ND	4247, 4391, 4491, 4591	341	505
  LYD671	pQFNc_LYD671	Lycopersicum ND	4248, 4392, 4248, 4392	342	593
  LYD672	pUC19c_LYD672	Lycopersicum ND	4249, 4393, 4492, 4592	343	507
  LYD673	pQFNc_LYD673	Lycopersicum ND	4250, 4394, 4493, 4593	344	594
  LYD674	pQFNc_LYD674	Lycopersicum ND	4251, 4395, 4494, 4594	345	509
  LYD675	pUC19c_LYD675	Lycopersicum ND	4252, 4396, 4495, 4595	346	595
  LYD676	pQFNc_LYD676	Lycopersicum ND	4253, 4397, 4496, 4596	347	596
  LYD677	pUC19c_LYD677	Lycopersicum ND	4254, 4398, 4497, 4597	348	512
  LYD678	pUC19c_LYD678	Lycopersicum ND	4255, 4399, 4498, 4598	349	513
  LYD679	pUC19c_LYD679	Lycopersicum ND	4256, 4400, 4499, 4599	350	597
  LYD680	pUC19c_LYD680	Lycopersicum ND	4257, 4401, 4257, 4600	351	598
  LYD681	pQFNc_LYD681	Lycopersicum ND	4258, 4402, 4500, 4601	352	516
  LYD682	pUC19c_LYD682	Lycopersicum ND	4259, 4403, 4501, 4602	353	517
  LYD683	pUC19c_LYD683	Lycopersicum ND	4260, 4404, 4502, 4603	354	599
  LYD684	pQFNc_LYD684	Lycopersicum ND	4261, 4405, 4503, 4604	355	519
  LYD685	pQFNc_LYD685	Lycopersicum ND	4262, 4406, 4504, 4605	356	600
  LYD686	pUC19c_LYD686	Lycopersicum ND	4263, 4407, 4505, 4606	357	521
  LYD688	pQFNc_LYD688	Lycopersicum ND	4264, 4408, 4264, 4408	358	601
  LYD689	pQFNc_LYD689	Lycopersicum ND	4265, 4409, 4506, 4607	359	524
  LYD690	TopoB_LYD690	Lycopersicum ND	4266, 4410, 4507, 4608	360	525
  Table 55. “Polyn.”—Polynucleotide; “Polyp.”—polypeptide. For cloning of each gene at least 2 primers were used: Forward (Fwd) or Reverse (Rev). In some cases, 4 primers were used: External forward (EF), External reverse (ER), nested forward (NF) or nested reverse (NR). The sequences of the primers used for cloning the genes are provided in the sequence listing. The genes were cloned from the same organism as identified in the list of genes provided in Table 62 above, except for the genes that were synthetically produced by GENEART (Life Technologies Corporation).

Example 15 Evaluation of Transgenic Arabidopsis for Seed Yield and Plant Growth Rate Under Normal Conditions in Greenhouse Assays (GH-SM Assays)
• Assay 1: Seed yield plant biomass and plant growth rate under normal greenhouse conditions—This assay follows seed yield production, the biomass formation and the rosette area growth of plants grown in the greenhouse at non-limiting nitrogen growth conditions. Transgenic Arabidopsis seeds were sown in agar media supplemented with ½ MS medium and a selection agent (Kanamycin). The T₂ transgenic seedlings were then transplanted to 1.7 trays filled with peat and perlite in a 1:1 ratio. The trays were irrigated with a solution containing 6 mM inorganic nitrogen in the form of KNO₃ with 1 mM KH₂PO₄, 1 mM MgSO₄, 2 mM CaCl₂ and microelements. All plants were grown in the greenhouse until mature seeds. Seeds were harvested, extracted and weight. The remaining plant biomass (the above ground tissue) was also harvested, and weighted immediately or following drying in oven at 50° C. for 24 hours.
• Each construct was validated at its T₂ generation. Transgenic plants transformed with a construct conformed by an empty vector carrying the At6669 promoter and the selectable marker was used as control.
• The plants were analyzed for their overall size, growth rate, flowering, seed yield, 1,000-seed weight, dry matter and harvest index (HI-seed yield/dry matter). Transgenic plants performance was compared to control plants grown in parallel under the same conditions. Mock-transgenic plants expressing the uidA reporter gene (GUS-Intron) or with no gene at all, under the same promoter were used as control.
• The experiment was planned in nested randomized plot distribution. For each gene of the invention three to five independent transformation events were analyzed from each construct.
• Digital imaging—A laboratory image acquisition system, which consists of a digital reflex camera (Canon EOS 300D) attached with a 55 mm focal length lens (Canon EF-S series), mounted on a reproduction device (Kaiser RS), which includes 4 light units (4×150 Watts light bulb) was used for capturing images of plant samples.
• The image capturing process was repeated every 2 days starting from day 1 after transplanting till day 15. Same camera, placed in a custom made iron mount, was used for capturing images of larger plants sawn in white tubs in an environmental controlled greenhouse. The tubs are square shape include 1.7 liter trays. During the capture process, the tubs were placed beneath the iron mount, while avoiding direct sun light and casting of shadows.
• An image analysis system was used, which consists of a personal desktop computer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ 1.39 [Java based image processing program which was developed at the U.S. National Institutes of Health and freely available on the internet at Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/]. Images were captured in resolution of 10 Mega Pixels (3888×2592 pixels) and stored in a low compression JPEG (Joint Photographic Experts Group standard) format. Next, analyzed data was saved to text files and processed using the JMP statistical analysis software (SAS institute).
• Leaf analysis—Using the digital analysis leaves data was calculated, including leaf number, rosette area, rosette diameter, and leaf blade area.
• Vegetative growth rate: the relative growth rate (RGR) of leaf number [Formula IX (described above)], rosette area [Formula VIII (described above)], plot coverage (Formula XIV, below) and harvest index [Formula IV (described above)] was calculated with the indicated formulas.
• 
  Relative growth rate of plot coverage=Regression coefficient of plot coverage along time course.  Formula XIV
• Seeds average weight—At the end of the experiment all seeds were collected. The seeds were scattered on a glass tray and a picture was taken. Using the digital analysis, the number of seeds in each sample was calculated.
• Dry weight and seed yield—On about day 80 from sowing, the plants were harvested and left to dry at 30° C. in a drying chamber. The biomass and seed weight of each plot were measured and divided by the number of plants in each plot. Dry weight=total weight of the vegetative portion above ground (excluding roots) after drying at 30° C. in a drying chamber; Seed yield per plant=total seed weight per plant (gr); 1000 seed weight (the weight of 1000 seeds) (gr.).
• The harvest index (HI) was calculated using Formula IV as described above.
• Oil percentage in seeds—At the end of the experiment all seeds from each plot were collected. Seeds from 3 plots were mixed grounded and then mounted onto the extraction chamber. 210 ml of n-Hexane (Cat No. 080951 Biolab Ltd.) were used as the solvent. The extraction was performed for 30 hours at medium heat 50° C. Once the extraction has ended the n-Hexane was evaporated using the evaporator at 35° C. and vacuum conditions. The process was repeated twice. The information gained from the Soxhlet extractor (Soxhlet, F. Die gewichtsanalytische Bestimmung des Milchfettes, Polytechnisches J. (Dingler's) 1879, 232, 461) was used to create a calibration curve for the Low Resonance NMR The content of oil of all seed samples was determined using the Low Resonance NMR (MARAN Ultra-Oxford Instrument) and its MultiQuant software package
• Silique length analysis—On day 50 from sowing, 30 siliques from different plants in each plot were sampled in block A. The chosen siliques were green-yellow in color and were collected from the bottom parts of a grown plant's stem. A digital photograph was taken to determine silique's length.
• Statistical analyses—To identify outperforming genes and constructs, results from the independent transformation events tested were analyzed separately. Data was analyzed using Student's t-test and results are considered significant if the p value was less than 0.1. The JMP statistics software package was used (Version 5.2.1, SAS Institute Inc., Cary, N.C., USA).
• Tables 56-60 summarize the observed phenotypes of transgenic plants exogenously expressing the gene constructs using the seed maturation (GH-SM) assays under normal conditions. Transgenic plants expressing these genes exhibit higher biomass (Tables 56, 57, 59), yield (Tables 59 and 60), vigor (Table 58), growth rate (Table 58), as compared to control plants grown under identical growth conditions. The evaluation of each gene was performed by testing the performance of different number of events. Event with p-value <0.1 was considered statistically significant.

• TABLE 56
  Genes showing improved plant performance at Normal growth
  conditions under regulation of At6669 promoter

  Inflorescence

  Dry Weight [mg]

  Flowering (days)

  Emergence (days)

  				%			%			%
  Gene Name	Event #	Ave.	P-Val.	Incr.	Ave.	P-Val.	Incr.	Ave.	P-Val.	Incr.
  LYD689	72710.2	—	—	—	39.7	0.25	−3	34.1	0.07	−3
  LYD689	72711.2	1157.7	0.15	12	37.9	L	−8	34.1	0.06	−3
  LYD689	72713.1	—	—	—	40.3	0.22	−2	34.5	0.17	−2
  LYD677	72223.1	—	—	—	—	—	—	34.2	0.08	−3
  LYD677	72223.6	—	—	—	39.3	0.10	−4	34.3	0.12	−3
  LYD677	72227.1	—	—	—	39.5	0.13	−4	34.1	0.07	−3
  LYD675	72644.3	—	—	—	—	—	—	34.6	0.23	−2
  LYD648	72834.2	1073.6	0.28	4	—	—	—	—	—	—
  LYD641	72632.2	—	—	—	—	—	—	34.1	0.07	−3
  LYD641	72635.2	—	—	—	—	—	—	34.2	0.09	−3
  LYD636	72204.1	—	—	—	40.4	0.28	−2	34.1	0.06	−3
  LYD625	72752.4	—	—	—	40.3	0.23	−2	34.5	0.17	−2
  LYD625	72755.1	1166.7	0.05	13	—	—	—	—	—	—
  LYD611	71991.1	—	—	—	—	—	—	34.5	0.18	−2
  LYD611	71992.6	—	—	—	—	—	—	34.7	0.28	−2
  LYD602	72613.3	—	—	—	—	—	—	34.3	0.12	−3
  LYD599	72270.5	—	—	—	39.3	0.05	−4	34.5	0.18	−2
  CONT.	—	1033.1	—	—	41.0	—	—	35.3	—	—
  LYD667	72030.1	1106.2	0.02	19	—	—	—	—	—	—
  LYD667	72035.2	—	—	—	—	—	—	34.1	0.21	−5
  LYD667	72035.6	—	—	—	—	—	—	34.5	0.13	−4
  LYD635	72626.1	1004.8	0.22	8	—	—	—	—	—	—
  LYD635	72626.2	1100.0	0.02	18	—	—	—	—	—	—
  LYD635	72630.2	1081.2	0.13	16	42.8	0.19	−2	35.2	0.29	−2
  LYD635	72630.4	1083.8	0.04	16	42.0	0.13	−4	34.5	0.10	−4
  LYD632	72771.1	1086.5	0.07	17	—	—	—	—	—	—
  LYD632	72774.4	1129.4	0.02	21	—	—	—	—	—	—
  LYD631	72542.3	—	—	—	41.4	0.13	−5	33.2	L	−7
  LYD627	72764.3	1070.4	0.21	15	—	—	—	—	—	—
  LYD627	72765.1	1031.9	0.16	11	—	—	—	—	—	—
  LYD627	72766.1	1190.6	0.08	28	—	—	—	—	—	—
  LYD623	71970.2	1049.4	0.07	13	41.5	L	−5	34.5	0.01	−4
  LYD623	71970.4	1027.5	0.14	10	42.2	0.06	−3	34.3	0.26	−4
  LYD623	71972.3	1057.5	0.09	14	—	—	—	—	—	—
  LYD623	71974.1	1199.4	L	29	—	—	—	—	—	—
  LYD621	72573.3	—	—	—	42.6	0.07	−2	33.9	0.02	−5
  LYD621	72574.1	1111.9	0.27	19	—	—	—	—	—	—
  LYD618	72622.2	1121.2	0.02	20	—	—	—	—	—	—
  LYD618	72623.1	1026.5	0.25	10	—	—	—	—	—	—
  LYD618	72624.4	1070.6	0.11	15	41.3	0.08	−5	34.3	0.14	−4
  LYD612	71818.3	1065.5	0.05	14	42.8	0.18	−2	—	—	—
  LYD603	72536.2	1036.2	0.10	11	—	—	—	—	—	—
  LYD603	72537.3	—	—	—	42.8	0.19	−2	35.2	0.16	−2
  LYD603	72537.5	—	—	—	41.1	0.20	−5	—	—	—
  LYD603	72537.7	1131.9	0.03	22	—	—	—	—	—	—
  LYD593	71953.4	1041.2	0.10	12	—	—	—	—	—	—
  LYD585	72986.1	1158.8	0.16	24	43.0	0.25	−1	—	—	—
  LYD585	72986.2	1137.5	L	22	42.9	0.19	−1	—	—	—
  LYD585	72986.4	1116.2	0.02	20	—	—	—	—	—	—
  LYD585	72988.1	1083.1	0.22	16	—	—	—	—	—	—
  LYD585	72988.3	1048.8	0.08	13	—	—	—	—	—	—
  LYD572	72385.1	1126.9	0.01	21	41.8	0.29	−4	34.4	L	−4
  LYD571	72357.5	—	—	—	41.5	0.18	−5	33.6	0.02	−6
  LYD571	72358.3	—	—	—	40.6	L	−7	32.6	L	−9
  LYD571	72360.2	1095.0	0.06	18	41.4	L	−5	—	—	—
  LYD551	71984.1	1171.9	0.17	26	—	—	—	—	—	—
  LYD551	71986.4	1185.0	0.06	27	40.5	L	−7	33.1	L	−8
  LYD551	71986.7	1078.8	0.03	16	42.8	0.19	−2	35.0	0.07	−2
  LYD551	71986.9	1027.5	0.14	10	—	—	—	—	—	—
  LYD548	72656.1	1006.9	0.21	8	42.8	0.19	−2	—	—	—
  LYD548	72656.2	1117.6	0.13	20	—	—	—	—	—	—
  LYD548	72676.1	—	—	—	42.9	0.21	−1	35.1	0.15	−2
  LYD548	72677.1	1168.8	L	26	—	—	—	—	—	—
  LYD531	71916.1	—	—	—	—	—	—	34.1	0.21	−5
  LYD531	71917.1	1026.9	0.13	10	41.9	0.07	−4	33.5	0.05	−7
  LYD531	71917.2	1160.6	0.06	25	—	—	—	—	—	—
  LYD531	71921.2	—	—	—	41.4	L	−5	33.5	L	−7
  LYD527	72241.3	1016.9	0.28	9	41.9	0.15	−4	33.9	0.25	−5
  LYD527	72243.3	—	—	—	42.4	0.05	−2	35.1	0.14	−2
  LYD527	72245.2	—	—	—	42.1	0.02	−3	34.2	0.28	−5
  LYD527	72246.3	1131.9	L	22	41.6	0.10	−4	33.9	0.18	−5
  CONT.	—	930.8	—	—	43.5	—	—	35.9	—	—
  LYD684	72271.2	—	—	—	40.5	0.21	−4	—	—	—
  LYD684	72274.3	—	—	—	39.9	L	−5	32.3	0.29	−7
  LYD666	72391.3	—	—	—	41.1	0.11	−3	—	—	—
  LYD666	72393.1	—	—	—	40.5	0.10	−4	—	—	—
  LYD666	72394.5	—	—	—	40.2	0.01	−5	33.0	0.05	−5
  LYD666	72396.2	1208.1	0.19	7	—	—	—	33.3	0.11	−4
  LYD662	72008.3	—	—	—	39.8	0.03	−6	32.0	0.16	−7
  LYD662	72011.2	—	—	—	41.0	0.10	−3	—	—	—
  LYD662	72011.4	—	—	—	40.3	0.14	−4	—	—	—
  LYD658	72279.1	—	—	—	41.0	0.08	−3	—	—	—
  LYD645	72341.2	—	—	—	41.3	0.15	−2	33.4	0.12	−3
  LYD632	72771.1	—	—	—	—	—	—	33.4	0.12	−3
  LYD632	72774.3	1219.4	0.04	8	—	—	—	—	—	—
  LYD631	72541.2	—	—	—	—	—	—	33.6	0.17	−3
  LYD631	72544.1	—	—	—	40.7	0.06	−4	—	—	—
  LYD631	72544.4	—	—	—	41.3	0.22	−2	33.3	0.11	−4
  LYD627	72766.1	—	—	—	40.3	0.02	−5	32.0	0.16	−7
  LYD627	72766.2	—	—	—	—	—	—	33.6	0.17	−3
  LYD627	72767.1	—	—	—	40.2	0.18	−5	—	—	—
  LYD586	71947.4	—	—	—	—	—	—	33.4	0.12	−3
  LYD586	71949.6	—	—	—	40.6	0.07	−4	33.3	0.09	−4
  LYD586	71949.7	—	—	—	40.5	0.10	−4	33.0	0.05	−5
  LYD571	72357.5	—	—	—	40.8	0.13	−3	—	—	—
  LYD571	72358.3	1205.0	0.07	7	39.9	0.24	−6	30.6	L	−12
  LYD571	72358.4	—	—	—	39.3	L	−7	32.1	0.23	−7
  LYD571	72360.2	—	—	—	40.6	0.07	−4	—	—	—
  LYD570	71934.2	—	—	—	—	—	—	33.4	0.12	−3
  LYD570	71936.2	—	—	—	40.7	0.15	−3	33.3	0.09	−4
  LYD570	71938.2	—	—	—	40.2	0.01	−5	33.3	0.11	−4
  LYD564	72182.4	—	—	—	39.6	L	−6	31.7	0.29	−8
  LYD564	72182.5	—	—	—	—	—	—	33.3	0.09	−4
  LYD564	72185.1	—	—	—	40.7	0.06	−4	33.3	0.11	−4
  LYD564	72186.2	—	—	—	40.5	0.10	−4	—	—	—
  LYD560	71924.1	—	—	—	—	—	—	33.6	0.17	−3
  LYD560	71925.1	—	—	—	39.9	L	−5	33.0	0.05	−5
  LYD560	71926.1	—	—	—	41.2	0.12	−2	—	—	—
  LYD560	71927.1	—	—	—	40.9	0.26	−3	—	—	—
  LYD545	72510.2	—	—	—	40.0	0.01	−5	33.1	0.06	−4
  LYD543	72251.2	—	—	—	—	—	—	31.8	0.28	−8
  LYD543	72252.1	—	—	—	39.6	L	−6	31.8	0.20	−8
  CONT.	—	1124.2	—	—	42.2	—	—	34.6	—	—
  LYD672	72346.4	—	—	—	41.5	0.14	−2	32.9	0.10	−5
  LYD672	72347.3	—	—	—	40.7	0.06	−4	32.8	0.03	−6
  LYD672	72348.1	—	—	—	41.0	0.21	−4	33.2	0.06	−5
  LYD668	72020.2	1169.4	L	15	—	—	—	—	—	—
  LYD664	72015.2	—	—	—	40.9	0.04	−4	32.8	L	−6
  LYD664	72016.2	—	—	—	40.6	0.24	−5	31.6	0.28	−9
  LYD664	72017.8	1065.6	0.12	5	—	—	—	—	—	—
  LYD661	72325.1	1112.5	0.20	10	—	—	—	—	—	—
  LYD661	72325.4	—	—	—	40.1	L	−6	33.1	0.06	−5
  LYD661	72326.1	—	—	—	40.1	L	−6	32.4	L	−7
  LYD661	72328.2	—	—	—	40.0	0.28	−6	32.5	0.14	−7
  LYD661	72329.2	—	—	—	40.2	0.25	−5	32.8	0.12	−6
  LYD657	72400.3	—	—	—	39.4	0.11	−7	32.4	L	−7
  LYD657	72402.1	—	—	—	41.4	0.01	−3	33.6	0.02	−3
  LYD580	72188.2	1070.0	0.09	5	40.2	L	−6	32.8	L	−6
  LYD580	72189.1	—	—	—	—	—	—	33.6	0.28	−3
  LYD580	72189.2	1090.2	0.23	7	—	—	—	—	—	—
  LYD573	72973.3	—	—	—	41.6	0.11	−2	34.3	0.25	−1
  LYD561	72178.1	—	—	—	40.7	0.12	−4	—	—	—
  LYD554	72169.2	—	—	—	41.4	L	−3	33.9	0.16	−2
  LYD553	72741.2	—	—	—	40.1	L	−6	32.5	L	−6
  LYD553	72742.3	1073.1	0.21	6	—	—	—	33.7	0.09	−3
  LYD547	71978.2	—	—	—	40.2	L	−6	32.8	L	−6
  LYD547	71978.3	—	—	—	—	—	—	33.1	0.09	−5
  LYD547	71980.1	—	—	—	39.8	0.08	−6	32.9	L	−5
  LYD547	71980.3	—	—	—	40.6	0.06	−5	33.4	0.22	−4
  LYD538	72839.5	—	—	—	40.8	0.03	−4	33.7	0.20	−3
  LYD528	72311.1	—	—	—	40.5	0.02	−5	32.5	0.07	−7
  LYD528	72312.3	—	—	—	—	—	—	34.2	0.16	−1
  LYD522	72720.1	—	—	—	40.9	0.15	−4	—	—	—
  LYD521	72607.1	—	—	—	40.0	L	−6	32.4	0.10	−7
  LYD521	72611.3	—	—	—	41.1	0.17	−3	33.4	0.01	−4
  CONT.	—	1014.5	—	—	42.5	—	—	34.8	—	—
  LYD682	72566.1	—	—	—	41.5	0.05	−2	34.8	0.03	−3
  LYD682	72568.2	—	—	—	41.0	0.02	−3	—	—	—
  LYD665	72211.2	—	—	—	40.2	0.06	−5	34.6	0.14	−4
  LYD665	72216.5	1077.6	0.18	6	—	—	—	—	—	—
  LYD650	72641.2	—	—	—	40.5	0.26	−5	—	—	—
  LYD644	72775.2	—	—	—	40.6	0.23	−4	—	—	—
  LYD644	72780.2	—	—	—	41.9	0.22	−1	35.3	0.27	−2
  LYD639	72548.4	—	—	—	41.1	0.06	−3	—	—	—
  LYD639	72549.3	1111.9	0.01	9	—	—	—	—	—	—
  LYD630	72404.3	1102.1	0.07	8	40.0	L	−6	34.7	0.09	−3
  LYD626	72002.1	1074.4	0.25	5	40.6	L	−4	—	—	—
  LYD606	72500.2	—	—	—	40.8	0.19	−4	—	—	—
  LYD606	72500.5	—	—	—	41.7	0.15	−2	—	—	—
  LYD577	72745.4	—	—	—	41.0	0.09	−3	35.3	0.27	−2
  LYD577	72750.4	—	—	—	40.7	0.19	−4	34.7	0.09	−3
  LYD542	72733.2	1153.8	L	13	—	—	—	—	—	—
  LYD526	72164.4	1081.9	0.07	6	—	—	—	—	—	—
  LYD526	72167.4	—	—	—	39.6	0.14	−7	35.3	0.27	−2
  LYD526	72168.1	—	—	—	40.6	L	−4	—	—	—
  CONT.	—	1019.8	—	—	42.5	—	—	35.9	—	—
  LYD683	72867.2	—	—	—	—	—	—	30.7	0.19	−3
  LYD683	72867.4	1178.1	0.27	4	—	—	—	—	—	—
  LYD674	72253.6	—	—	—	38.9	0.05	−2	30.2	0.06	−5
  LYD674	72255.1	—	—	—	—	—	—	30.5	0.12	−4
  LYD664	72015.2	—	—	—	—	—	—	30.7	0.19	−3
  LYD664	72016.2	—	—	—	—	—	—	30.3	0.07	−4
  LYD664	72017.8	—	—	—	38.2	0.14	−4	30.1	0.05	−5
  LYD643	72333.6	1229.9	0.17	8	—	—	—	—	—	—
  LYD643	72336.3	—	—	—	—	—	—	30.1	0.04	−5
  LYD642	71820.2	—	—	—	—	—	—	30.3	0.09	−4
  LYD642	71824.5	1192.5	0.18	5	—	—	—	30.0	0.04	−5
  LYD642	71825.1	—	—	—	38.4	0.25	−3	30.4	0.09	−4
  LYD634	71995.1	1339.4	0.04	18	37.7	L	−5	30.1	0.05	−5
  LYD634	71996.2	1319.4	L	16	—	—	—	—	—	—
  LYD634	71999.3	—	—	—	38.4	0.25	−3	30.4	0.09	−4
  LYD629	72198.2	—	—	—	38.9	0.05	−2	30.1	0.04	−5
  LYD629	72198.5	—	—	—	—	—	—	30.0	0.04	−5
  LYD622	72024.3	—	—	—	37.7	L	−5	30.2	0.06	−5
  LYD622	72027.5	—	—	—	38.2	0.14	−4	30.3	0.09	−4
  LYD617	71966.6	—	—	—	38.7	0.02	−2	30.2	0.06	−5
  LYD603	72537.3	—	—	—	—	—	—	30.2	0.05	−5
  LYD603	72537.5	—	—	—	39.2	0.20	−1	—	—	—
  LYD603	72537.7	—	—	—	—	—	—	30.8	0.21	−3
  LYD567	72495.3	—	—	—	—	—	—	30.5	0.10	−4
  LYD567	72496.2	—	—	—	39.0	0.08	−2	30.6	0.19	−3
  LYD561	72177.1	—	—	—	38.2	0.14	−4	30.1	0.04	−5
  LYD561	72178.2	—	—	—	—	—	—	30.5	0.10	−4
  LYD553	72743.1	1282.5	0.22	13	—	—	—	—	—	—
  LYD553	72743.2	—	—	—	—	—	—	30.5	0.10	−4
  LYD547	71978.3	—	—	—	—	—	—	30.1	0.04	−5
  LYD547	71980.3	—	—	—	—	—	—	30.5	0.10	−4
  LYD547	71981.2	—	—	—	37.6	L	−5	30.1	0.04	−5
  LYD534	72414.3	1199.4	0.12	6	—	—	—	—	—	—
  LYD531	71917.1	—	—	—	—	—	—	30.1	0.04	−5
  LYD531	71921.2	—	—	—	—	—	—	30.1	0.04	−5
  LYD531	71921.2	1236.9	0.04	9	—	—	—	30.1	0.04	−5
  LYD521	72610.2	—	—	—	—	—	—	30.6	0.19	−3
  CONT.	—	1135.4	—	—	39.7	—	—	31.7	—	—
  Table 56. “CONT.”—Control; “Ave.” —Average; “% Incr.” = % increment; “p-val.” —p-value, L—p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). “—” = results are still unavailable.

• TABLE 57
  Genes showing improved plant performance at Normal growth
  conditions under regulation of At6669 promoter

  Leaf Blade Area [cm2]

  Leaf Number

  Plot Coverage [cm2]

  				%			%			%
  Gene Name	Event #	Ave	P-Val.	Incr.	Ave	P-Val.	Incr.	Ave	P-Val.	Incr.
  LYD689	72711.2	0.9	0.01	19	—	—	—	46.8	0.29	15
  LYD689	72713.1	0.8	0.11	9	10.0	0.14	5	46.3	0.08	13
  LYD677	72223.3	0.8	0.05	13	—	—	—	46.4	0.16	14
  LYD677	72223.6	0.9	L	25	—	—	—	51.9	L	27
  LYD677	72227.1	0.8	0.17	8	—	—	—	—	—	—
  LYD675	72644.3	—	—	—	—	—	—	46.4	0.27	14
  LYD671	72880.1	0.8	0.26	6	—	—	—	—	—	—
  LYD648	72831.3	0.8	0.23	8	—	—	—	—	—	—
  LYD641	72635.2	0.8	0.03	15	—	—	—	46.1	0.19	13
  LYD636	72204.1	0.8	0.09	10	—	—	—	44.4	0.21	9
  LYD625	72752.4	0.8	0.21	7	—	—	—	44.4	0.25	9
  LYD625	72755.1	—	—	—	10.2	0.05	7	—	—	—
  LYD625	72755.4	0.8	0.22	13	—	—	—	—	—	—
  LYD602	72613.3	0.8	0.26	6	—	—	—	—	—	—
  LYD599	72270.5	—	—	—	10.1	0.16	5	46.1	0.28	13
  LYD598	72421.2	—	—	—	—	—	—	44.3	0.26	8
  LYD585	72986.1	0.8	0.15	16	—	—	—	—	—	—
  LYD573	72977.1	0.8	0.05	16	10.2	0.10	7	49.7	0.02	22
  CONT.	—	0.7	—	—	9.6	—	—	40.8	—	—
  LYD635	72630.2	—	—	—	12.4	0.16	14	69.9	0.28	18
  LYD635	72630.4	1.1	L	24	—	—	—	74.1	0.13	25
  LYD632	72769.2	1.0	0.15	6	—	—	—	—	—	—
  LYD631	72542.3	1.2	L	31	11.9	0.16	10	85.9	L	45
  LYD627	72764.3	1.0	0.02	11	—	—	—	66.8	0.01	12
  LYD627	72765.1	1.1	L	16	—	—	—	67.6	L	14
  LYD623	71970.2	1.1	0.03	18	—	—	—	71.0	0.09	19
  LYD623	71970.4	1.0	0.17	14	—	—	—	68.2	L	15
  LYD623	71972.3	1.1	0.14	23	11.4	0.03	6	74.9	0.19	26
  LYD621	72571.1	1.0	0.27	4	—	—	—	63.8	0.12	7
  LYD621	72573.3	1.2	0.19	29	11.8	0.22	9	80.2	0.20	35
  LYD621	72574.3	—	—	—	11.5	0.03	6	65.5	0.05	10
  LYD618	72621.2	1.0	0.10	8	—	—	—	—	—	—
  LYD618	72622.2	—	—	—	11.2	0.15	3	—	—	—
  LYD618	72622.3	—	—	—	11.3	0.07	4	—	—	—
  LYD618	72624.4	1.1	0.06	18	11.7	0.15	8	79.0	0.04	33
  LYD612	71817.3	—	—	—	—	—	—	67.5	0.01	14
  LYD612	71819.1	—	—	—	11.2	0.28	3	64.0	0.14	8
  LYD603	72535.2	1.0	0.08	8	—	—	—	67.9	0.03	14
  LYD603	72536.2	—	—	—	11.2	0.14	4	—	—	—
  LYD603	72537.5	1.0	0.20	10	—	—	—	—	—	—
  LYD585	72986.1	1.1	0.05	22	—	—	—	71.7	L	21
  LYD585	72986.2	1.0	0.05	9	—	—	—	65.6	0.11	10
  LYD585	72988.3	1.1	0.15	17	12.0	L	11	74.4	0.20	25
  LYD572	72385.1	1.0	0.22	10	11.8	0.22	9	70.1	0.22	18
  LYD572	72386.1	—	—	—	11.1	0.28	3	—	—	—
  LYD571	72357.5	1.1	L	20	—	—	—	75.0	0.02	26
  LYD571	72358.1	1.0	0.14	11	—	—	—	70.9	0.03	19
  LYD571	72358.3	1.3	L	41	11.7	L	8	86.4	L	45
  LYD571	72358.4	1.0	0.14	9	—	—	—	65.6	0.03	11
  LYD571	72360.2	—	—	—	11.6	0.01	7	70.5	0.04	19
  LYD551	71984.1	—	—	—	11.2	0.28	3	—	—	—
  LYD551	71986.4	1.1	L	19	—	—	—	—	—	—
  LYD551	71986.7	1.0	0.05	9	11.7	L	8	66.4	0.02	12
  LYD551	71986.9	—	—	—	—	—	—	63.2	0.27	6
  LYD548	72656.1	1.0	0.26	10	11.8	0.08	8	—	—	—
  LYD548	72673.3	—	—	—	11.7	0.04	8	64.7	0.06	9
  LYD548	72676.1	1.0	L	15	—	—	—	70.8	L	19
  LYD548	72677.1	1.0	0.13	6	—	—	—	—	—	—
  LYD531	71916.1	1.0	0.23	9	—	—	—	67.9	0.20	14
  LYD531	71917.1	1.1	L	18	11.5	0.15	6	72.6	L	22
  LYD531	71917.2	—	—	—	11.9	L	10	72.0	0.06	21
  LYD531	71921.2	1.1	0.02	18	11.9	0.06	10	76.7	L	29
  LYD527	72241.3	1.1	0.14	21	11.4	0.25	6	72.3	0.06	22
  LYD527	72243.3	1.0	L	14	11.4	0.07	5	68.8	L	16
  LYD527	72243.4	—	—	—	—	—	—	63.0	0.19	6
  LYD527	72245.2	1.0	0.05	9	—	—	—	69.9	L	18
  LYD527	72246.3	1.1	L	18	12.0	0.05	11	72.6	0.01	22
  CONT.	—	0.9	—	—	10.8	—	—	59.4	—	—
  LYD684	72271.2	—	—	—	10.4	0.22	4	48.0	0.25	9
  LYD684	72274.3	0.9	0.03	13	10.4	0.05	3	50.7	0.08	15
  LYD666	72391.3	0.8	0.14	7	—	—	—	—	—	—
  LYD666	72393.1	0.9	0.17	12	—	—	—	50.8	0.04	15
  LYD666	72396.2	—	—	—	10.3	0.11	3	—	—	—
  LYD662	72008.3	0.9	0.03	14	—	—	—	51.5	0.01	17
  LYD662	72011.4	0.9	0.02	12	—	—	—	46.9	0.24	6
  LYD658	72277.2	0.8	0.18	7	—	—	—	47.5	0.17	7
  LYD658	72282.1	0.8	0.04	11	—	—	—	50.0	0.04	13
  LYD645	72340.2	—	—	—	10.2	0.17	2	—	—	—
  LYD645	72341.2	0.9	0.10	14	—	—	—	51.6	0.14	17
  LYD632	72771.1	0.8	0.06	10	—	—	—	48.6	0.24	10
  LYD632	72774.4	0.8	0.27	7	—	—	—	—	—	—
  LYD631	72544.1	0.8	0.13	8	—	—	—	—	—	—
  LYD631	72544.3	—	—	—	10.4	0.03	4	—	—	—
  LYD631	72544.4	0.9	0.03	11	—	—	—	50.9	0.02	15
  LYD627	72764.3	0.8	0.16	7	—	—	—	—	—	—
  LYD627	72765.1	—	—	—	10.8	L	7	49.7	0.08	13
  LYD627	72766.1	1.0	0.04	30	—	—	—	58.7	L	33
  LYD601	72872.2	0.9	0.02	13	—	—	—	51.0	0.04	16
  LYD586	71949.6	0.8	0.09	8	—	—	—	—	—	—
  LYD586	71949.7	0.9	0.03	11	10.6	0.14	5	53.1	0.02	20
  LYD571	72357.5	0.8	0.25	8	—	—	—	51.1	0.07	16
  LYD571	72358.3	1.0	L	30	11.4	0.06	13	60.9	0.03	38
  LYD571	72358.4	0.9	0.21	15	—	—	—	49.9	0.10	13
  LYD564	72182.4	0.9	0.09	17	—	—	—	55.5	0.11	26
  LYD564	72182.5	0.8	0.15	6	—	—	—	—	—	—
  LYD564	72185.1	0.8	0.10	8	10.7	0.25	6	50.0	0.04	13
  LYD564	72186.2	—	—	—	10.3	0.11	3	—	—	—
  LYD560	71925.1	0.9	0.01	14	—	—	—	50.4	0.04	14
  LYD545	72510.2	0.9	0.15	13	10.2	0.17	2	52.3	0.12	18
  LYD543	72252.1	0.8	0.27	5	—	—	—	49.4	0.06	12
  CONT.	—	0.8	—	—	10.0	—	—	44.2	—	—
  LYD672	72346.4	0.8	0.12	7	—	—	—	47.5	0.18	14
  LYD672	72347.3	—	—	—	10.5	L	9	54.2	0.16	30
  LYD668	72023.3	0.8	0.29	8	—	—	—	46.7	0.04	12
  LYD664	72012.1	0.8	0.13	7	—	—	—	45.9	0.07	10
  LYD664	72015.2	—	—	—	—	—	—	44.8	0.22	8
  LYD664	72016.2	0.9	L	20	10.1	0.05	6	53.1	L	28
  LYD664	72017.8	0.8	0.22	13	9.9	0.25	3	47.3	0.16	14
  LYD661	72325.1	—	—	—	10.1	0.16	5	—	—	—
  LYD661	72325.4	—	—	—	10.2	0.10	6	—	—	—
  LYD661	72326.1	0.8	0.08	8	—	—	—	—	—	—
  LYD661	72328.2	0.9	0.14	21	10.4	0.24	8	56.0	0.28	35
  LYD661	72329.2	0.9	0.05	16	—	—	—	51.4	0.07	23
  LYD657	72400.3	0.9	0.17	27	10.5	L	9	54.8	0.26	32
  LYD580	72188.2	0.9	0.11	16	—	—	—	51.8	L	24
  LYD580	72189.1	0.8	0.05	12	10.3	0.06	8	48.7	0.01	17
  LYD580	72192.3	0.9	L	20	9.8	0.29	2	51.9	L	25
  LYD561	72177.1	0.8	0.30	13	—	—	—	—	—	—
  LYD561	72178.1	0.9	0.11	17	—	—	—	51.4	0.19	23
  LYD560	71925.1	0.8	0.12	7	—	—	—	48.6	0.25	17
  LYD554	72169.2	0.8	0.16	7	—	—	—	—	—	—
  LYD553	72741.2	0.8	0.09	8	—	—	—	45.1	0.29	8
  LYD547	71978.2	0.9	0.16	29	10.9	0.04	13	57.5	0.12	38
  LYD547	71978.3	—	—	—	10.0	0.12	4	50.9	0.29	22
  LYD547	71980.1	0.8	0.22	9	10.2	0.15	7	47.3	0.08	14
  LYD547	71980.3	0.8	0.09	8	10.1	0.05	6	47.6	0.07	14
  LYD538	72835.2	0.8	0.06	9	—	—	—	45.0	0.13	8
  LYD538	72839.5	—	—	—	10.1	0.04	5	—	—	—
  LYD528	72311.1	0.8	0.03	10	—	—	—	45.7	0.12	10
  LYD528	72312.3	0.8	0.06	14	—	—	—	45.5	0.11	9
  LYD522	72715.2	—	—	—	9.8	0.29	2	—	—	—
  LYD522	72720.1	0.9	L	16	10.1	0.03	6	49.8	0.02	20
  LYD522	72720.2	—	—	—	—	—	—	49.2	0.30	18
  LYD521	72607.1	0.9	0.03	23	10.2	0.15	7	55.1	0.07	32
  LYD521	72610.1	—	—	—	9.9	0.25	3	—	—	—
  LYD521	72610.2	—	—	—	10.1	0.03	6	58.3	0.22	40
  LYD521	72611.3	0.8	0.28	7	—	—	—	—	—	—
  CONT.	—	0.7	—	—	9.6	—	—	41.6	—	—
  LYD683	72870.1	0.8	0.02	16	—	—	—	44.3	0.05	26
  LYD682	72566.1	0.8	L	26	—	—	—	46.7	L	33
  LYD682	72568.2	0.8	L	21	—	—	—	45.9	0.02	31
  LYD678	72787.2	0.7	0.08	7	9.8	0.12	5	41.5	0.03	18
  LYD665	72211.2	0.8	L	20	—	—	—	44.6	L	27
  LYD650	72639.4	0.7	0.04	13	—	—	—	41.2	0.02	18
  LYD644	72775.1	0.7	0.01	13	—	—	—	41.1	0.03	17
  LYD644	72775.2	0.8	0.24	20	9.9	0.11	5	45.1	0.17	29
  LYD644	72780.2	0.7	0.03	13	—	—	—	42.3	0.12	21
  LYD639	72548.4	0.7	0.22	13	9.8	0.20	4	44.0	L	26
  LYD639	72548.6	—	—	—	—	—	—	40.6	0.29	16
  LYD639	72549.3	—	—	—	—	—	—	41.2	0.02	17
  LYD639	72551.1	0.7	0.21	13	—	—	—	40.9	0.22	17
  LYD639	72551.2	0.8	0.01	24	—	—	—	44.7	L	27
  LYD630	72404.3	0.9	L	34	—	—	—	50.9	L	45
  LYD626	72002.1	0.7	0.06	10	—	—	—	40.3	0.04	15
  LYD626	72004.4	—	—	—	—	—	—	40.6	0.08	16
  LYD606	72500.5	0.8	L	14	—	—	—	40.5	0.03	16
  LYD606	72501.1	0.7	0.16	7	—	—	—	—	—	—
  LYD577	72745.4	0.8	L	19	—	—	—	42.0	0.01	20
  LYD577	72747.4	0.7	0.11	7	—	—	—	38.4	0.11	10
  LYD577	72748.2	0.7	0.02	12	—	—	—	40.9	0.02	17
  LYD577	72750.4	—	—	—	—	—	—	44.2	0.29	26
  LYD536	72529.2	—	—	—	—	—	—	44.2	0.20	26
  LYD536	72529.5	0.8	0.15	15	—	—	—	44.1	L	26
  LYD536	72534.2	0.7	0.07	7	—	—	—	39.9	0.05	14
  LYD526	72164.4	0.8	0.24	21	—	—	—	47.5	0.13	36
  LYD526	72167.4	0.9	L	31	10.4	0.01	11	53.8	L	53
  LYD526	72168.1	0.7	0.02	12	—	—	—	42.4	0.01	21
  CONT.	—	0.7	—	—	9.4	—	—	35.1	—	—
  LYD683	72867.2	1.0	0.20	8	—	—	—	57.7	0.20	10
  LYD674	72253.6	—	—	—	10.9	0.25	6	58.4	0.24	11
  LYD664	72015.2	—	—	—	10.8	0.17	4	—	—	—
  LYD664	72016.2	1.0	0.13	12	—	—	—	57.9	0.21	10
  LYD664	72017.8	1.1	0.03	27	11.6	L	12	69.3	L	32
  LYD643	72336.3	—	—	—	—	—	—	68.0	0.22	30
  LYD642	71820.2	—	—	—	10.9	0.05	6	—	—	—
  LYD642	71824.5	1.0	0.17	10	11.4	0.05	10	58.2	0.16	11
  LYD634	71995.1	—	—	—	11.1	0.10	8	60.9	0.13	16
  LYD629	72195.1	—	—	—	11.1	0.19	7	58.9	0.13	12
  LYD629	72198.2	—	—	—	—	—	—	62.3	0.27	19
  LYD629	72198.5	1.1	0.02	28	11.6	L	12	71.0	L	35
  LYD622	72028.3	—	—	—	10.6	0.28	3	—	—	—
  LYD617	71966.6	1.0	0.08	12	—	—	—	—	—	—
  LYD603	72535.2	—	—	—	10.6	0.28	3	—	—	—
  LYD595	72907.4	1.0	0.18	9	—	—	—	—	—	—
  LYD595	72909.1	1.0	0.18	13	—	—	—	61.3	0.18	17
  LYD595	72910.3	1.0	0.18	9	11.1	0.10	8	59.0	0.13	12
  LYD567	72496.2	1.1	0.04	20	11.3	0.21	9	63.6	0.02	21
  LYD561	72175.4	—	—	—	11.2	0.02	8	—	—	—
  LYD561	72177.1	0.9	0.30	7	—	—	—	59.5	0.12	13
  LYD561	72178.2	—	—	—	10.9	0.05	6	—	—	—
  LYD553	72743.2	1.0	0.28	13	—	—	—	58.8	0.21	12
  LYD547	71978.3	1.0	0.23	8	—	—	—	61.1	0.06	16
  LYD547	71981.2	1.0	0.04	17	11.9	0.08	15	65.3	0.01	24
  LYD531	71921.2	1.0	0.04	16	11.6	0.16	12	65.4	0.06	25
  CONT.	—	0.9	—	—	10.3	—	—	52.5	—	—
  Table 57. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L—p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). “—” = results are still unavailable.

• TABLE 58
  Genes showing improved plant performance at Normal growth
  conditions under regulation of At6669 promoter

  	RGR Of Leaf	RGR Of Plot	RGR Of Rosette
  	Number (number/day)	Coverage (cm2/day)	Diameter (cm/day)

  				%			%			%
  Gene Name	Event #	Ave.	P-Val.	Incr.	Ave.	P-Val.	Incr.	Ave.	P-Val.	Incr.
  LYD689	72711.2	—	—	—	—	—	—	0.4	0.14	15
  LYD677	72223.6	—	—	—	6.4	0.08	26	0.4	0.29	10
  LYD625	72755.1	—	—	—	6.4	0.12	27	0.4	0.23	13
  LYD573	72977.1	—	—	—	6.2	0.14	22	—	—	—
  CONT.	—	—	—	—	5.1	—	—	0.4	—	—
  LYD635	72626.1	—	—	—	8.5	0.17	17	—	—	—
  LYD635	72626.2	—	—	—	8.2	0.29	13	—	—	—
  LYD635	72630.2	—	—	—	8.4	0.18	16	—	—	—
  LYD635	72630.4	—	—	—	9.0	0.04	24	0.5	0.09	17
  LYD632	72770.2	—	—	—	8.5	0.16	18	—	—	—
  LYD631	72542.3	0.8	0.27	16	10.6	L	46	0.5	0.04	20
  LYD627	72765.1	—	—	—	8.3	0.21	14	0.5	0.27	10
  LYD623	71970.2	—	—	—	8.7	0.08	20	0.5	0.25	11
  LYD623	71970.4	—	—	—	8.4	0.16	16	—	—	—
  LYD623	71972.3	—	—	—	9.0	0.04	25	0.5	0.21	13
  LYD621	72573.3	—	—	—	9.8	L	36	0.5	0.19	13
  LYD618	72624.4	—	—	—	9.5	0.01	31	—	—	—
  LYD612	71817.3	—	—	—	8.2	0.27	13	—	—	—
  LYD612	71818.3	0.8	0.23	19	—	—	—	—	—	—
  LYD603	72535.2	—	—	—	8.4	0.16	16	—	—	—
  LYD585	72986.1	—	—	—	8.8	0.05	22	0.5	0.30	10
  LYD585	72988.3	0.8	0.11	24	9.1	0.04	25	—	—	—
  LYD572	72385.1	—	—	—	8.6	0.10	20	—	—	—
  LYD572	72387.1	—	—	—	8.9	0.08	22	—	—	—
  LYD571	72357.5	—	—	—	9.1	0.03	26	0.5	0.21	12
  LYD571	72358.1	0.8	0.27	16	8.6	0.10	19	—	—	—
  LYD571	72358.3	—	—	—	10.5	L	45	0.5	0.04	20
  LYD571	72360.2	—	—	—	8.7	0.08	20	—	—	—
  LYD551	71986.2	0.8	0.26	16	—	—	—	—	—	—
  LYD551	71986.4	—	—	—	8.5	0.13	18	0.5	0.25	11
  LYD551	71986.7	0.8	0.26	17	—	—	—	—	—	—
  LYD548	72656.1	—	—	—	8.3	0.20	15	—	—	—
  LYD548	72673.3	0.8	0.25	16	—	—	—	—	—	—
  LYD548	72676.1	—	—	—	8.6	0.11	18	—	—	—
  LYD531	71916.1	—	—	—	8.2	0.24	13	—	—	—
  LYD531	71917.1	—	—	—	8.8	0.06	22	0.5	0.21	13
  LYD531	71917.2	—	—	—	8.7	0.08	20	0.5	0.21	12
  LYD531	71921.2	—	—	—	9.4	0.02	29	0.5	0.12	15
  LYD527	72241.3	—	—	—	8.8	0.06	22	0.5	0.27	11
  LYD527	72243.3	—	—	—	8.4	0.14	17	—	—	—
  LYD527	72245.2	—	—	—	8.5	0.14	17	—	—	—
  LYD527	72246.3	—	—	—	8.9	0.04	23	0.5	0.24	11
  CONT.	—	0.7	—	—	7.2	—	—	0.4	—	—
  LYD684	72274.3	—	—	—	6.3	0.11	15	—	—	—
  LYD666	72393.1	—	—	—	6.2	0.14	14	—	—	—
  LYD662	72008.3	—	—	—	6.3	0.08	17	0.4	0.21	9
  LYD662	72008.5	—	—	—	—	—	—	0.4	0.15	14
  LYD658	72277.2	0.7	0.28	14	—	—	—	—	—	—
  LYD658	72282.1	—	—	—	—	—	—	0.4	0.30	8
  LYD645	72341.2	—	—	—	6.3	0.09	16	0.4	0.29	8
  LYD632	72771.1	—	—	—	6.0	0.21	12	—	—	—
  LYD631	72544.1	0.6	0.30	12	—	—	—	—	—	—
  LYD631	72544.4	—	—	—	6.2	0.11	15	0.4	0.16	11
  LYD627	72764.3	0.7	0.27	14	—	—	—	0.4	0.18	11
  LYD627	72765.1	—	—	—	6.0	0.23	11	—	—	—
  LYD627	72766.1	—	—	—	7.1	L	30	0.4	0.13	12
  LYD601	72872.2	—	—	—	6.2	0.11	15	—	—	—
  LYD586	71949.7	—	—	—	6.5	0.04	20	—	—	—
  LYD571	72357.5	—	—	—	6.2	0.12	15	0.4	0.28	8
  LYD571	72358.3	—	—	—	7.5	L	38	0.4	0.02	19
  LYD571	72358.4	—	—	—	6.2	0.14	14	—	—	—
  LYD570	71934.2	0.7	0.23	15	—	—	—	—	—	—
  LYD570	71936.4	0.7	0.04	25	—	—	—	—	—	—
  LYD564	72182.4	—	—	—	6.6	0.03	23	—	—	—
  LYD564	72182.5	—	—	—	6.0	0.28	11	—	—	—
  LYD564	72185.1	—	—	—	6.1	0.18	13	0.4	0.20	10
  LYD560	71925.1	—	—	—	6.1	0.17	13	0.4	0.26	8
  LYD545	72510.2	—	—	—	6.5	0.05	20	—	—	—
  LYD543	72252.1	—	—	—	6.0	0.22	12	—	—	—
  CONT.	—	0.6	—	—	5.4	—	—	0.3	—	—
  LYD672	72346.4	—	—	—	6.0	0.26	16	—	—	—
  LYD672	72347.3	—	—	—	6.7	0.05	29	0.4	0.19	15
  LYD664	72012.1	—	—	—	—	—	—	0.4	0.27	12
  LYD664	72016.2	—	—	—	6.6	0.06	28	—	—	—
  LYD661	72325.1	—	—	—	6.2	0.20	19	—	—	—
  LYD661	72326.1	—	—	—	—	—	—	0.4	0.30	11
  LYD661	72328.2	—	—	—	6.9	0.04	34	0.4	0.30	13
  LYD661	72329.2	—	—	—	6.4	0.10	24	0.4	0.22	13
  LYD657	72400.3	0.7	0.29	16	6.8	0.05	31	0.4	0.15	18
  LYD580	72188.2	—	—	—	6.4	0.10	24	0.4	0.22	14
  LYD580	72189.1	—	—	—	6.0	0.24	16	—	—	—
  LYD580	72192.3	—	—	—	6.4	0.10	25	—	—	—
  LYD561	72177.1	—	—	—	6.0	0.29	15	—	—	—
  LYD561	72178.1	—	—	—	6.4	0.11	24	—	—	—
  LYD560	71925.1	—	—	—	6.0	0.28	16	—	—	—
  LYD554	72174.4	—	—	—	6.2	0.27	19	—	—	—
  LYD547	71978.2	—	—	—	7.1	0.01	38	0.4	0.14	16
  LYD547	71978.3	—	—	—	6.3	0.13	22	0.4	0.24	13
  LYD547	71981.2	—	—	—	6.4	0.14	23	—	—	—
  LYD538	72838.3	—	—	—	6.3	0.20	22	—	—	—
  LYD522	72715.2	—	—	—	6.2	0.23	19	—	—	—
  LYD522	72720.1	—	—	—	6.1	0.21	18	0.4	0.28	12
  LYD522	72720.2	—	—	—	6.2	0.20	19	—	—	—
  LYD521	72607.1	—	—	—	6.9	0.03	33	0.4	0.16	16
  LYD521	72610.2	—	—	—	7.2	0.02	39	0.4	0.29	12
  CONT.	—	0.6	—	—	5.2	—	—	0.3	—	—
  LYD683	72866.4	—	—	—	5.1	0.28	17	—	—	—
  LYD683	72870.1	—	—	—	5.5	0.09	27	0.4	0.23	11
  LYD682	72566.1	—	—	—	5.7	0.06	31	—	—	—
  LYD682	72568.2	—	—	—	5.6	0.05	30	0.4	0.14	13
  LYD678	72787.2	—	—	—	5.2	0.18	20	—	—	—
  LYD665	72211.2	—	—	—	5.4	0.08	26	—	—	—
  LYD650	72639.4	—	—	—	5.1	0.21	18	0.4	0.17	12
  LYD644	72775.1	—	—	—	5.1	0.20	19	0.4	0.15	12
  LYD644	72775.2	—	—	—	5.6	0.06	30	—	—	—
  LYD644	72780.2	—	—	—	5.2	0.17	21	—	—	—
  LYD639	72548.4	—	—	—	5.4	0.11	25	0.4	0.19	12
  LYD639	72549.3	—	—	—	5.1	0.24	17	—	—	—
  LYD639	72551.1	—	—	—	5.1	0.23	18	—	—	—
  LYD639	72551.2	—	—	—	5.5	0.06	28	0.4	0.03	19
  LYD630	72404.3	—	—	—	6.3	L	45	0.4	0.03	20
  LYD626	72002.1	—	—	—	5.0	0.28	15	0.4	0.23	11
  LYD626	72004.4	—	—	—	5.1	0.24	17	—	—	—
  LYD606	72500.2	—	—	—	5.2	0.21	20	—	—	—
  LYD606	72500.5	—	—	—	5.2	0.18	19	0.4	0.06	16
  LYD577	72745.4	—	—	—	5.2	0.18	20	0.4	0.15	13
  LYD577	72748.2	—	—	—	5.1	0.21	18	0.4	0.14	13
  LYD577	72750.4	—	—	—	5.5	0.09	27	0.4	0.27	10
  LYD536	72529.2	—	—	—	5.5	0.08	27	0.4	0.20	12
  LYD536	72529.5	—	—	—	5.5	0.07	27	—	—	—
  LYD536	72534.2	—	—	—	5.0	0.30	15	—	—	—
  LYD526	72164.4	—	—	—	5.9	0.03	36	0.4	0.22	12
  LYD526	72167.4	—	—	—	6.6	L	53	0.4	0.04	18
  LYD526	72168.1	—	—	—	5.3	0.14	21	—	—	—
  CONT.	—	—	—	—	4.3	—	—	0.3	—	—
  LYD664	72017.8	—	—	—	8.5	0.03	29	0.4	0.20	14
  LYD643	72336.3	—	—	—	8.3	0.05	27	—	—	—
  LYD629	72198.2	—	—	—	7.6	0.19	17	0.4	0.29	12
  LYD629	72198.5	0.7	0.28	17	8.7	0.01	33	0.4	0.11	17
  LYD595	72909.1	—	—	—	7.5	0.23	15	—	—	—
  LYD567	72496.2	—	—	—	8.0	0.08	22	0.4	0.21	13
  LYD561	72175.4	0.7	0.26	17	—	—	—	—	—	—
  LYD553	72743.2	—	—	—	—	—	—	0.4	0.20	14
  LYD547	71978.3	—	—	—	7.4	0.27	14	—	—	—
  LYD547	71981.2	0.7	0.21	21	8.0	0.08	22	0.4	0.14	16
  LYD531	71921.2	—	—	—	8.0	0.07	23	0.4	0.29	11
  CONT.	—	0.6	—	—	6.5	—	—	0.4	—	—
  Table 58. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L—p < 0.01. RGR = relative growth rate. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). “—” = results are still unavailable.

• TABLE 59
  Genes showing improved plant performance at Normal growth
  conditions under regulation of At6669 promoter

  Harvest Index

  Rosette Area [cm2]

  Rosette Diameter [cm]

  				%			%			%
  Gene Name	Event #	Ave.	P-Val.	Incr.	Ave.	P-Val.	Incr.	Ave.	P-Val.	Incr.
  LYD689	72711.2	—	—	—	6.2	0.02	22	4.5	0.04	14
  LYD689	72713.1	—	—	—	5.8	0.08	13	4.2	0.09	7
  LYD677	72223.3	—	—	—	5.8	0.16	14	4.3	0.05	9
  LYD677	72223.6	0.2	0.21	14	6.5	L	27	4.5	0.03	13
  LYD677	72227.1	0.2	0.22	17	—	—	—	—	—	—
  LYD675	72643.1	0.2	0.15	21	—	—	—	—	—	—
  LYD675	72644.3	0.2	0.03	32	5.8	0.27	14	4.2	0.28	6
  LYD648	72831.3	—	—	—	—	—	—	4.1	0.23	5
  LYD641	72632.2	0.2	0.04	27	—	—	—	—	—	—
  LYD641	72635.2	0.2	0.04	27	5.8	0.19	13	4.3	0.04	10
  LYD636	72204.1	—	—	—	5.6	0.21	9	—	—	—
  LYD625	72752.4	0.2	0.03	29	5.6	0.25	9	4.1	0.20	5
  LYD625	72755.4	—	—	—	—	—	—	4.3	0.18	8
  LYD611	71991.1	0.2	0.25	50	—	—	—	—	—	—
  LYD599	72270.5	0.2	0.18	15	5.8	0.28	13	—	—	—
  LYD598	72421.2	0.2	0.13	21	5.5	0.26	8	—	—	—
  LYD573	72977.1	0.2	0.05	26	6.2	0.02	22	4.3	0.08	9
  CONT.	—	0.2	—	—	5.1	—	—	3.9	—	—
  LYD667	72031.1	—	—	—	—	—	—	5.4	0.27	6
  LYD635	72626.1	—	—	—	—	—	—	5.6	0.21	11
  LYD635	72630.2	—	—	—	8.7	0.28	18	—	—	—
  LYD635	72630.4	—	—	—	9.3	0.13	25	5.8	L	16
  LYD632	72769.2	0.2	0.09	9	—	—	—	5.2	0.02	4
  LYD631	72541.5	—	—	—	—	—	—	5.3	0.01	4
  LYD631	72542.3	0.2	0.02	12	10.7	L	45	6.0	L	19
  LYD631	72544.1	0.2	0.02	13	—	—	—	5.2	0.14	3
  LYD627	72764.3	—	—	—	8.4	0.01	12	5.4	L	7
  LYD627	72765.1	—	—	—	8.4	L	14	5.5	0.11	8
  LYD627	72766.2	—	—	—	—	—	—	5.3	0.01	4
  LYD623	71970.2	—	—	—	8.9	0.09	19	5.6	0.20	11
  LYD623	71970.4	—	—	—	8.5	L	15	5.4	0.17	8
  LYD623	71972.2	0.2	0.12	11	—	—	—	—	—	—
  LYD623	71972.3	—	—	—	9.4	0.19	26	5.8	0.21	14
  LYD621	72571.1	—	—	—	8.0	0.12	7	5.3	L	6
  LYD621	72573.3	—	—	—	10.0	0.20	35	5.8	0.19	15
  LYD621	72574.3	0.2	0.06	9	8.2	0.05	10	5.5	L	8
  LYD618	72621.2	—	—	—	—	—	—	5.3	0.20	6
  LYD618	72622.2	0.2	0.12	9	—	—	—	—	—	—
  LYD618	72622.3	—	—	—	—	—	—	5.2	0.06	3
  LYD618	72623.1	—	—	—	—	—	—	5.2	0.05	4
  LYD618	72624.4	0.2	0.22	10	9.9	0.04	33	5.8	L	14
  LYD612	71817.3	0.2	L	16	8.4	0.01	14	5.4	0.03	7
  LYD612	71819.1	—	—	—	8.0	0.14	8	—	—	—
  LYD603	72535.2	—	—	—	8.5	0.03	14	5.5	0.06	8
  LYD603	72537.3	0.2	0.07	17	—	—	—	—	—	—
  LYD593	71957.5	—	—	—	—	—	—	5.2	0.06	3
  LYD585	72986.1	0.2	0.07	9	9.0	L	21	5.6	L	10
  LYD585	72986.2	0.2	0.10	8	8.2	0.11	10	5.3	L	5
  LYD585	72988.3	—	—	—	9.3	0.20	25	5.5	0.21	10
  LYD572	72385.1	—	—	—	8.8	0.22	18	—	—	—
  LYD572	72387.1	0.2	0.16	7	—	—	—	—	—	—
  LYD571	72357.5	0.2	L	26	9.4	0.02	26	5.7	L	12
  LYD571	72358.1	—	—	—	8.9	0.03	19	5.4	0.02	8
  LYD571	72358.3	0.2	0.08	26	10.8	L	45	6.0	L	20
  LYD571	72358.4	—	—	—	8.2	0.03	11	5.4	0.16	6
  LYD571	72360.2	—	—	—	8.8	0.04	19	5.4	0.06	8
  LYD551	71986.4	0.2	0.15	7	—	—	—	5.5	L	9
  LYD551	71986.7	—	—	—	8.3	0.02	12	—	—	—
  LYD551	71986.9	0.2	0.03	21	7.9	0.27	6	5.2	0.17	2
  LYD548	72673.3	—	—	—	8.1	0.06	9	5.3	L	6
  LYD548	72676.1	—	—	—	8.9	L	19	5.5	0.10	8
  LYD548	72677.1	—	—	—	—	—	—	5.3	0.24	5
  LYD531	71916.1	—	—	—	8.5	0.20	14	5.4	0.19	7
  LYD531	71917.1	0.2	0.23	13	9.1	L	22	5.6	0.03	11
  LYD531	71917.2	—	—	—	9.0	0.06	21	5.6	L	11
  LYD531	71921.2	—	—	—	9.6	L	29	5.7	L	14
  LYD527	72241.3	0.2	0.19	17	9.0	0.06	22	5.5	0.17	10
  LYD527	72243.3	—	—	—	8.6	L	16	5.4	0.04	7
  LYD527	72243.4	—	—	—	7.9	0.19	6	5.2	0.27	3
  LYD527	72245.2	0.2	L	34	8.7	L	18	5.4	L	7
  LYD527	72246.3	—	—	—	9.1	0.01	22	5.5	0.07	9
  CONT.	—	0.2	—	—	7.4	—	—	5.0	—	—
  LYD684	72271.2	—	—	—	6.0	0.25	9	4.3	0.17	3
  LYD684	72274.3	0.2	0.07	29	6.3	0.08	15	4.3	0.07	5
  LYD666	72391.3	—	—	—	—	—	—	4.2	0.28	2
  LYD666	72393.1	0.1	0.22	19	6.3	0.04	15	—	—	—
  LYD662	72008.3	—	—	—	6.4	0.01	17	4.5	0.11	10
  LYD662	72011.4	0.2	0.06	31	5.9	0.24	6	4.2	0.25	3
  LYD658	72277.2	—	—	—	5.9	0.17	7	4.3	0.15	4
  LYD658	72279.3	0.2	0.08	28	—	—	—	—	—	—
  LYD658	72282.1	—	—	—	6.2	0.04	13	4.5	L	8
  LYD645	72341.2	—	—	—	6.4	0.14	17	4.4	0.05	8
  LYD632	72771.1	0.1	0.27	18	6.1	0.24	10	4.3	0.06	5
  LYD631	72541.2	0.1	0.25	17	—	—	—	—	—	—
  LYD631	72544.3	—	—	—	—	—	—	4.2	0.27	3
  LYD631	72544.4	—	—	—	6.4	0.02	15	4.5	0.05	9
  LYD627	72764.3	—	—	—	—	—	—	4.4	0.04	6
  LYD627	72765.1	—	—	—	6.2	0.08	13	—	—	—
  LYD627	72766.1	—	—	—	7.3	L	33	4.8	0.05	15
  LYD618	72622.3	—	—	—	—	—	—	4.4	0.05	6
  LYD601	72872.2	—	—	—	6.4	0.04	16	4.5	0.13	8
  LYD586	71949.7	—	—	—	6.6	0.02	20	4.4	0.05	7
  LYD571	72357.5	—	—	—	6.4	0.07	16	4.5	0.15	8
  LYD571	72358.3	—	—	—	7.6	0.03	38	4.8	L	17
  LYD571	72358.4	0.2	0.04	38	6.2	0.10	13	4.3	0.24	5
  LYD571	72360.2	0.1	0.25	16	—	—	—	—	—	—
  LYD570	71936.2	0.1	0.30	19	—	—	—	—	—	—
  LYD564	72182.4	0.1	0.19	22	6.9	0.11	26	4.6	0.14	11
  LYD564	72182.5	—	—	—	—	—	—	4.3	0.19	4
  LYD564	72185.1	—	—	—	6.2	0.04	13	4.4	0.03	7
  LYD560	71925.1	0.2	0.07	29	6.3	0.04	14	4.4	0.01	8
  LYD560	71926.1	0.2	0.20	24	—	—	—	—	—	—
  LYD560	71927.1	0.2	0.10	26	—	—	—	—	—	—
  LYD545	72510.2	0.2	0.21	39	6.5	0.12	18	4.4	0.15	6
  LYD543	72251.2	0.2	0.11	34	—	—	—	—	—	—
  LYD543	72252.1	—	—	—	6.2	0.06	12	4.3	0.10	4
  CONT.	—	0.1	—	—	5.5	—	—	4.1	—	—
  LYD672	72346.4	0.2	0.28	26	5.9	0.18	14	4.2	0.17	5
  LYD672	72347.3	—	—	—	6.8	0.16	30	4.5	0.20	14
  LYD668	72020.4	0.2	0.14	13	—	—	—	—	—	—
  LYD668	72023.3	0.2	0.02	25	5.8	0.04	12	4.1	0.26	4
  LYD664	72012.1	0.3	0.10	37	5.7	0.07	10	4.3	0.06	7
  LYD664	72015.2	—	—	—	5.6	0.22	8	—	—	—
  LYD664	72016.2	—	—	—	6.6	L	28	4.4	0.01	11
  LYD664	72017.7	0.2	0.26	15	—	—	—	—	—	—
  LYD664	72017.8	0.2	0.09	22	5.9	0.16	14	—	—	—
  LYD661	72326.1	0.2	0.20	11	—	—	—	—	—	—
  LYD661	72328.2	—	—	—	7.0	0.28	35	4.6	0.27	14
  LYD661	72329.2	0.3	0.01	32	6.4	0.07	23	4.4	0.13	10
  LYD657	72400.1	0.2	0.01	22	—	—	—	—	—	—
  LYD657	72400.3	—	—	—	6.8	0.26	32	4.6	0.29	15
  LYD657	72401.2	0.3	L	29	—	—	—	4.2	0.27	5
  LYD657	72402.1	0.3	0.07	30	—	—	—	—	—	—
  LYD580	72188.2	0.2	0.03	18	6.5	L	24	4.5	0.08	12
  LYD580	72189.1	—	—	—	6.1	0.01	17	4.3	0.05	7
  LYD580	72191.1	0.2	0.10	17	—	—	—	—	—	—
  LYD580	72192.3	0.3	0.14	48	6.5	L	25	4.5	L	12
  LYD573	72973.2	0.2	0.11	12	—	—	—	—	—	—
  LYD573	72977.1	0.2	0.17	19	—	—	—	—	—	—
  LYD561	72177.1	0.2	0.28	12	—	—	—	4.2	0.28	6
  LYD561	72177.2	0.2	0.16	23	—	—	—	—	—	—
  LYD561	72178.1	—	—	—	6.4	0.19	23	4.3	0.15	9
  LYD560	71922.1	0.3	L	29	—	—	—	—	—	—
  LYD560	71925.1	0.2	0.11	16	6.1	0.25	17	—	—	—
  LYD560	71926.1	0.2	0.01	21	—	—	—	—	—	—
  LYD554	72174.4	0.2	0.10	24	—	—	—	—	—	—
  LYD553	72741.2	0.2	0.06	15	5.6	0.29	8	4.2	0.09	6
  LYD553	72743.2	0.2	0.26	9	—	—	—	—	—	—
  LYD547	71978.2	—	—	—	7.2	0.12	38	4.7	0.06	17
  LYD547	71978.3	—	—	—	6.4	0.29	22	4.4	0.28	12
  LYD547	71980.1	0.2	0.19	24	5.9	0.08	14	—	—	—
  LYD547	71980.3	0.2	0.25	21	5.9	0.07	14	4.2	0.14	5
  LYD538	72835.2	0.2	L	25	5.6	0.13	8	4.2	0.15	5
  LYD528	72310.1	0.3	L	39	—	—	—	—	—	—
  LYD528	72311.1	—	—	—	5.7	0.12	10	4.2	0.21	5
  LYD528	72312.2	0.2	0.07	24	—	—	—	—	—	—
  LYD528	72312.3	—	—	—	5.7	0.11	9	4.3	0.12	7
  LYD528	72312.4	0.2	0.16	18	—	—	—	—	—	—
  LYD522	72716.6	0.2	0.25	25	—	—	—	—	—	—
  LYD522	72720.1	—	—	—	6.2	0.02	20	4.3	0.02	9
  LYD522	72720.2	—	—	—	6.2	0.30	18	—	—	—
  LYD521	72607.1	0.3	0.24	34	6.9	0.07	32	4.5	0.10	13
  LYD521	72610.1	0.2	0.24	12	—	—	—	—	—	—
  LYD521	72610.2	0.3	0.23	28	7.3	0.22	40	—	—	—
  LYD521	72611.1	0.2	0.01	22	—	—	—	—	—	—
  CONT.	—	0.2	—	—	5.2	—	—	4.0	—	—
  LYD683	72870.1	—	—	—	5.5	0.05	26	4.1	L	13
  LYD682	72565.1	—	—	—	—	—	—	3.9	0.14	7
  LYD682	72566.1	—	—	—	5.8	L	33	4.2	L	15
  LYD682	72568.2	0.1	0.26	14	5.7	0.02	31	4.2	L	16
  LYD678	72787.2	—	—	—	5.2	0.03	18	3.9	0.05	8
  LYD665	72211.2	—	—	—	5.6	L	27	4.0	L	11
  LYD665	72216.5	—	—	—	—	—	—	3.8	0.07	5
  LYD650	72639.4	—	—	—	5.2	0.02	18	4.1	L	13
  LYD644	72775.1	—	—	—	5.1	0.03	17	3.9	0.03	8
  LYD644	72775.2	—	—	—	5.6	0.17	29	4.1	0.15	14
  LYD644	72780.2	0.1	0.19	42	5.3	0.12	21	4.0	0.03	10
  LYD639	72548.4	—	—	—	5.5	L	26	4.1	L	12
  LYD639	72548.6	—	—	—	5.1	0.29	16	3.9	0.22	8
  LYD639	72549.3	—	—	—	5.1	0.02	17	4.0	0.01	10
  LYD639	72551.1	—	—	—	5.1	0.22	17	—	—	—
  LYD639	72551.2	0.1	0.27	18	5.6	L	27	4.2	L	17
  LYD630	72404.3	—	—	—	6.4	L	45	4.5	L	23
  LYD626	72002.1	0.1	0.11	49	5.0	0.04	15	4.0	0.02	9
  LYD626	72004.4	0.1	0.23	26	5.1	0.08	16	3.9	0.07	8
  LYD606	72500.5	—	—	—	5.1	0.03	16	4.0	L	11
  LYD606	72501.1	—	—	—	—	—	—	3.8	0.26	4
  LYD577	72745.4	—	—	—	5.2	0.01	20	4.1	L	13
  LYD577	72747.4	—	—	—	4.8	0.11	10	3.9	0.03	8
  LYD577	72748.2	—	—	—	5.1	0.02	17	4.1	L	12
  LYD577	72750.4	0.1	0.26	32	5.5	0.29	26	4.1	0.21	13
  LYD536	72529.2	—	—	—	5.5	0.20	26	4.2	0.17	15
  LYD536	72529.5	—	—	—	5.5	L	26	4.1	L	13
  LYD536	72534.2	—	—	—	5.0	0.05	14	3.9	0.04	8
  LYD526	72164.4	—	—	—	5.9	0.13	36	4.2	0.11	17
  LYD526	72167.4	—	—	—	6.7	L	53	4.5	L	23
  LYD526	72168.1	0.1	0.07	33	5.3	0.01	21	4.0	0.10	9
  CONT.	—	0.1	—	—	4.4	—	—	3.6	—	—
  LYD683	72867.2	—	—	—	7.2	0.20	10	4.7	0.20	5
  LYD674	72253.6	0.2	0.12	17	7.3	0.24	11	—	—	—
  LYD674	72255.1	0.2	0.10	23	—	—	—	—	—	—
  LYD664	72016.2	—	—	—	7.2	0.21	10	4.7	0.23	5
  LYD664	72017.8	0.2	L	25	8.7	L	32	5.1	0.05	13
  LYD643	72336.3	0.2	0.02	10	8.5	0.22	30	—	—	—
  LYD642	71824.5	—	—	—	7.3	0.16	11	4.8	0.12	7
  LYD642	71825.1	0.2	L	14	—	—	—	—	—	—
  LYD634	71995.1	—	—	—	7.6	0.13	16	—	—	—
  LYD634	71999.3	0.2	L	17	—	—	—	—	—	—
  LYD629	72195.1	—	—	—	7.4	0.13	12	4.7	0.17	6
  LYD629	72198.2	0.2	L	19	7.8	0.27	19	4.9	0.27	9
  LYD629	72198.5	—	—	—	8.9	L	35	5.2	L	16
  LYD622	72027.5	0.2	L	24	—	—	—	—	—	—
  LYD617	71966.6	—	—	—	—	—	—	4.7	0.22	5
  LYD595	72909.1	—	—	—	7.7	0.18	17	4.8	0.17	8
  LYD595	72910.3	—	—	—	7.4	0.13	12	—	—	—
  LYD567	72496.2	0.2	0.02	12	8.0	0.02	21	4.8	0.09	7
  LYD567	72496.3	0.2	0.20	5	—	—	—	—	—	—
  LYD561	72175.4	0.2	0.11	11	—	—	—	—	—	—
  LYD561	72177.1	—	—	—	7.4	0.12	13	4.7	0.26	5
  LYD553	72743.2	0.2	0.01	16	7.4	0.21	12	4.9	0.10	9
  LYD547	71978.3	—	—	—	7.6	0.06	16	4.8	0.13	8
  LYD547	71981.2	—	—	—	8.2	0.01	24	5.0	0.02	12
  LYD531	71921.2	—	—	—	8.2	0.06	25	4.9	0.04	10
  CONT.	—	0.2	—	—	6.6	—	—	4.5	—	—
  Table 59. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L—p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). “—” = results are still unavailable.

• TABLE 60
  Genes showing improved plant performance at Normal growth
  conditions under regulation of At6669 promoter

  Seed Yield [mg]

  1000 Seed Weight [mg]

  				%			%
  Gene Name	Event #	Ave.	P-Val.	Incr.	Ave.	P-Val.	Incr.
  LYD689	72711.2	205.6	0.26	33	27.5	0.25	19
  LYD689	72713.1	171.1	0.25	10	25.2	0.02	9
  LYD677	72227.1	191.4	0.04	23	24.3	0.21	6
  LYD675	72643.1	175.7	0.16	13	—	—	—
  LYD675	72644.3	173.1	0.21	12	—	—	—
  LYD641	72632.2	198.5	0.10	28	—	—	—
  LYD641	72635.2	179.0	0.14	15	23.8	0.14	3
  LYD636	72204.1	—	—	—	27.0	0.27	17
  LYD625	72752.4	187.9	0.05	21	—	—	—
  LYD625	72756.2	—	—	—	25.3	0.21	10
  LYD599	72270.5	183.2	0.07	18	—	—	—
  LYD573	72977.1	186.6	0.25	20	—	—	—
  CONT.	—	155.2	—	—	23.1	—	—
  LYD667	72030.4	—	—	—	18.8	0.30	3
  LYD667	72035.6	175.8	0.11	13	—	—	—
  LYD635	72626.1	185.3	0.27	20	—	—	—
  LYD635	72630.2	—	—	—	21.7	0.22	19
  LYD632	72769.2	170.0	0.22	10	—	—	—
  LYD632	72770.2	—	—	—	19.3	0.06	5
  LYD632	72771.1	—	—	—	20.2	L	10
  LYD632	72774.4	204.8	0.05	32	—	—	—
  LYD631	72542.3	180.0	0.07	16	20.2	0.21	11
  LYD631	72544.1	174.3	0.26	13	—	—	—
  LYD631	72544.4	—	—	—	21.3	L	17
  LYD627	72764.3	—	—	—	20.3	0.14	11
  LYD627	72765.1	—	—	—	19.6	0.02	7
  LYD627	72766.1	—	—	—	19.8	0.06	8
  LYD623	71970.2	185.5	0.08	20	—	—	—
  LYD623	71974.1	215.8	0.26	39	19.1	0.12	4
  LYD618	72621.2	—	—	—	19.3	0.09	5
  LYD618	72622.2	202.6	0.04	31	—	—	—
  LYD618	72624.4	196.1	0.18	27	21.4	0.29	17
  LYD612	71817.3	186.8	0.07	21	—	—	—
  LYD603	72536.2	196.2	0.20	27	—	—	—
  LYD603	72537.3	180.7	0.06	17	—	—	—
  LYD603	72537.7	209.6	0.19	35	—	—	—
  LYD585	72986.1	209.3	0.09	35	—	—	—
  LYD585	72986.2	203.8	L	32	—	—	—
  LYD585	72986.4	188.1	0.02	21	—	—	—
  LYD585	72988.3	186.2	0.25	20	19.8	0.05	8
  LYD572	72387.1	176.6	0.24	14	—	—	—
  LYD572	72388.2	185.3	0.24	20	—	—	—
  LYD571	72357.5	210.4	L	36	—	—	—
  LYD571	72358.3	199.2	0.05	29	20.8	L	14
  LYD551	71986.4	209.9	0.02	35	—	—	—
  LYD551	71986.7	203.3	0.11	31	—	—	—
  LYD551	71986.9	206.2	0.04	33	—	—	—
  LYD531	71916.1	—	—	—	20.7	L	13
  LYD531	71917.1	193.3	0.11	25	—	—	—
  LYD531	71917.2	—	—	—	20.0	0.03	9
  LYD527	72241.3	197.2	L	27	—	—	—
  LYD527	72245.2	207.2	0.17	34	—	—	—
  LYD527	72246.3	190.5	0.04	23	—	—	—
  CONT.	—	154.9	—	—	18.3	—	—
  LYD684	72274.3	166.6	0.25	19	—	—	—
  LYD666	72393.1	163.6	0.29	17	—	—	—
  LYD662	72011.4	188.5	0.05	35	—	—	—
  LYD658	72282.1	—	—	—	20.6	0.02	5
  LYD632	72771.1	—	—	—	22.7	L	15
  LYD632	72774.3	—	—	—	20.5	0.05	4
  LYD631	72544.4	—	—	—	21.8	0.02	10
  LYD627	72764.3	—	—	—	21.7	0.18	10
  LYD627	72765.1	—	—	—	23.3	0.07	18
  LYD601	72872.2	—	—	—	20.2	0.23	2
  LYD571	72358.1	—	—	—	21.1	0.16	7
  LYD571	72358.3	173.9	0.28	24	22.8	0.03	16
  LYD571	72358.4	190.9	0.06	36	20.3	0.25	3
  LYD570	71935.1	—	—	—	20.8	L	6
  LYD570	71936.2	—	—	—	20.6	0.26	4
  LYD564	72182.4	172.7	0.28	23	—	—	—
  LYD564	72182.5	—	—	—	21.0	0.07	7
  LYD560	71925.1	179.4	0.10	28	—	—	—
  LYD560	71927.1	170.0	0.20	21	—	—	—
  LYD545	72510.2	183.4	0.23	31	—	—	—
  LYD543	72251.2	175.6	0.23	25	—	—	—
  CONT.	—	140.1	—	—	19.7	—	—
  LYD672	72347.2	268.4	L	36	—	—	—
  LYD672	72347.3	—	—	—	22.7	0.10	13
  LYD672	72348.1	220.3	0.15	11	—	—	—
  LYD668	72020.2	—	—	—	21.5	0.25	7
  LYD668	72023.1	—	—	—	21.6	0.16	8
  LYD668	72023.3	218.8	0.15	11	—	—	—
  LYD664	72012.1	244.8	0.01	24	—	—	—
  LYD664	72015.2	225.2	0.07	14	—	—	—
  LYD664	72017.7	227.5	0.06	15	—	—	—
  LYD664	72017.8	254.0	0.04	28	—	—	—
  LYD661	72325.1	—	—	—	23.6	0.11	18
  LYD661	72329.2	258.5	L	31	—	—	—
  LYD657	72400.1	222.1	0.15	12	—	—	—
  LYD657	72401.2	233.5	0.03	18	—	—	—
  LYD657	72402.1	249.7	0.04	26	—	—	—
  LYD580	72188.2	246.1	L	24	21.6	0.08	8
  LYD580	72189.2	248.5	0.24	26	—	—	—
  LYD580	72192.3	277.0	0.13	40	—	—	—
  LYD561	72177.2	246.7	L	25	—	—	—
  LYD561	72179.1	221.4	0.19	12	—	—	—
  LYD560	71922.1	239.6	0.14	21	—	—	—
  LYD560	71925.1	243.7	0.01	23	—	—	—
  LYD560	71926.1	238.5	0.06	20	—	—	—
  LYD554	72174.4	241.0	0.02	22	—	—	—
  LYD547	71978.2	—	—	—	22.5	0.06	12
  LYD547	71980.3	215.7	0.21	9	—	—	—
  LYD538	72835.2	243.9	0.02	23	—	—	—
  LYD528	72310.1	277.8	L	40	—	—	—
  LYD528	72312.2	236.6	0.17	19	—	—	—
  LYD528	72312.4	237.6	0.28	20	—	—	—
  LYD522	72716.2	244.8	0.19	24	—	—	—
  LYD522	72716.6	247.0	0.21	25	—	—	—
  LYD521	72611.1	237.8	0.28	20	—	—	—
  CONT.	—	198.0	—	—	20.0	—	—
  LYD682	72566.1	—	—	—	25.2	0.29	6
  LYD682	72568.2	100.2	0.17	17	—	—	—
  LYD665	72211.2	—	—	—	26.3	0.01	11
  LYD644	72780.2	126.2	0.29	48	—	—	—
  LYD630	72404.3	116.1	0.28	36	26.6	0.04	12
  LYD626	72002.1	134.7	0.05	58	—	—	—
  LYD626	72004.4	105.6	0.07	24	—	—	—
  LYD606	72500.2	—	—	—	24.9	0.12	5
  LYD577	72750.4	106.8	0.06	25	—	—	—
  LYD526	72167.4	—	—	—	24.8	0.14	5
  LYD526	72168.1	113.5	0.03	33	—	—	—
  CONT.	—	85.5	—	—	23.7	—	—
  LYD683	72866.4	—	—	—	20.4	0.29	4
  LYD674	72255.1	246.4	0.16	28	—	—	—
  LYD664	72015.2	208.6	L	9	20.1	0.24	3
  LYD664	72016.2	197.0	0.30	3	21.1	0.01	8
  LYD643	72333.2	—	—	—	20.1	0.25	3
  LYD643	72336.3	—	—	—	22.9	0.08	17
  LYD643	72336.6	—	—	—	21.4	0.05	9
  LYD642	71824.5	—	—	—	24.0	0.13	23
  LYD634	71995.1	—	—	—	25.0	0.08	28
  LYD634	71999.3	230.6	0.04	20	—	—	—
  LYD629	72195.1	—	—	—	20.4	0.29	4
  LYD629	72198.5	200.8	0.08	5	21.8	L	12
  LYD622	72027.5	—	—	—	20.9	0.17	7
  LYD622	72028.3	—	—	—	20.9	0.02	7
  LYD617	71964.2	—	—	—	20.0	0.26	3
  LYD617	71966.6	219.6	0.28	14	—	—	—
  LYD603	72537.3	215.9	0.21	12	—	—	—
  LYD595	72909.1	—	—	—	21.6	0.11	11
  LYD595	72910.3	206.8	0.04	8	—	—	—
  LYD567	72495.3	—	—	—	20.2	0.19	4
  LYD567	72496.2	217.3	L	13	—	—	—
  LYD561	72175.4	212.5	0.21	11	—	—	—
  LYD561	72177.1	215.3	0.04	12	—	—	—
  LYD561	72177.2	—	—	—	20.5	0.28	5
  LYD553	72743.1	252.4	0.29	31	—	—	—
  LYD547	71978.3	209.6	L	9	—	—	—
  LYD547	71980.3	—	—	—	20.3	0.19	4
  LYD547	71981.2	—	—	—	22.8	0.23	17
  LYD534	72411.2	—	—	—	20.3	0.12	4
  LYD534	72414.3	224.6	0.27	17	20.9	0.03	7
  LYD521	72607.1	—	—	—	20.2	0.22	4
  LYD521	72610.2	—	—	—	20.1	0.24	3
  CONT.	—	192.1	—	—	19.5	—	—
  Table 60. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L—p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). “—” = results are still unavailable.

Example 16 Evaluation of Transgenic Arabidopsis for Seed Yield and Plant Growth Rate Under Normal Conditions in Greenhouse Assays Until Bolting (GH-SB Assays)
• Assay 2: Plant performance improvement measured until boiling stage: plant biomass and plant growth rate under normal greenhouse conditions (GH-SB Assays)—This assay follows the plant biomass formation and the rosette area growth of plants grown in the greenhouse under normal growth conditions. Transgenic Arabidopsis seeds were sown in agar media supplemented with ½ MS medium and a selection agent (Kanamycin). The T₂ transgenic seedlings were then transplanted to 1.7 trays filled with peat and perlite in a 1:1 ratio. The tray's were irrigated with a solution containing of 6 mM inorganic nitrogen in the form of KNO₃ with 1 mM KH₂PO₄, 1 mM MgSO₄, 2 mM CaCl₂ and microelements. All plants were grown in the greenhouse until bolting stage. Plant biomass (the above ground tissue) was weight in directly after harvesting the rosette (plant fresh weight [FW]). Following plants were dried in an oven at 50° C. for 48 hours and weighted (plant dry weight [DW]).
• Each construct was validated at its T₂ generation. Transgenic plants transformed with a construct conformed by an empty vector carrying the 35S promoter and the selectable marker was used as control.
• The plants were analyzed for their overall size, growth rate, fresh weight and dry matter. Transgenic plants performance was compared to control plants grown in parallel under the same conditions. Mock-transgenic plants expressing the uidA reporter gene (GUS-Intron) or with no gene at all, under the same promoter were used as control.
• The experiment was planned in nested randomized plot distribution. For each gene of the invention three to five independent transformation events were analyzed from each construct.
• Digital imaging—A laboratory image acquisition system, which consists of a digital reflex camera (Canon EOS 300D) attached with a 55 mm focal length lens (Canon EF-S series), mounted on a reproduction device (Kaiser RS), which includes 4 light units (4×150 Watts light bulb) was used for capturing images of plant samples.
• The image capturing process was repeated every 2 days starting from day 1 after transplanting till day 15. Same camera, placed in a custom made iron mount, was used for capturing images of larger plants sawn in white tubs in an environmental controlled greenhouse. The tubs were square shape include 1.7 liter trays. During the capture process, the tubes were placed beneath the iron mount, while avoiding direct sun light and casting of shadows.
• An image analysis system was used, which consists of a personal desktop computer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ 1.39 [Java based image processing program which was developed at the U.S. National Institutes of Health and freely available on the internet at Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/]. Images were captured in resolution of 10 Mega Pixels (3888×2592 pixels) and stored in a low compression JPEG (Joint Photographic Experts Group standard) format. Next, analyzed data was saved to text files and processed using the JMP statistical analysis software (SAS institute).
• Leaf analysis—Using the digital analysis leaves data was calculated, including leaf number, rosette area, rosette diameter, and leaf blade area.
• Vegetative growth rate: the relative growth rate (RGR) of leaf number (Formula IX, described above), rosette area (Formula VIII described above) and plot coverage (Formula XIV, described above) were calculated using the indicated formulas.
• Plant Fresh and Dry weight—On about day 80 from sowing, the plants were harvested and directly weight for the determination of the plant fresh weight (FW) and left to dry at 50° C. in a drying chamber for about 48 hours before weighting to determine plant dry weight (DW).
• Statistical analyses—To identify outperforming genes and constructs, results from the independent transformation events tested were analyzed separately. Data was analyzed using Student's t-test and results are considered significant if the p value was less than 0.1. The JMP statistics software package was used (Version 5.2.1, SAS Institute Inc., Cary, N.C. USA).
• Experimental Results:
• Tables 61-63 summarize the observed phenotypes of transgenic plants expressing the genes constructs using the GH-SB Assays.
• The genes listed in Tables 61-63 improved plant performance when grown at normal conditions. These genes produced larger plants with a larger photosynthetic area, biomass (fresh weight, dry weight, rosette diameter, rosette area and plot coverage), and relative growth rate (of leaf number, plot coverage and rosette diameter) as compared to control plants grown under identical growth conditions. The genes were cloned under the regulation of a constitutive At6669 promoter (SEQ ID NO:4111). The evaluation of each gene was performed by testing the performance of different number of events. Event with p-value <0.1 was considered statistically significant.

• TABLE 61
  Genes showing improved plant performance at Normal growth
  conditions under regulation of At6669 promoter

  Dry Weight [mg]

  Fresh Weight [mg]

  Leaf Number

  				%			%			%
  Gene Name	Event #	Ave.	P-Val.	Incr.	Ave.	P-Val.	Incr.	Ave.	P-Val.	Incr.

  LYD684	72271.4	377.2	0.04	13	4795.5	0.01	11	—	—	—
  LYD684	72274.1	379.4	L	14	4718.8	L	9	11.1	0.03	7
  LYD672	72347.3	364.8	L	9	4987.5	L	15	—	—	—
  LYD667	72030.1	368.8	0.07	11	4643.8	L	7	—	—	—
  LYD667	72031.1	371.9	0.03	11	4575.0	0.02	6	—	—	—
  LYD661	72325.1	366.2	L	10	4831.2	L	12	11.9	0.17	14
  LYD661	72328.1	358.3	0.02	7	—	—	—	11.1	0.23	6
  LYD661	72328.2	—	—	—	—	—	—	10.8	0.11	4
  LYD651	73026.4	—	—	—	4675.0	L	8	—	—	—
  LYD626	72004.4	—	—	—	—	—	—	11.2	0.01	8
  LYD620	73066.3	359.4	L	8	4681.2	L	8	11.4	0.07	9
  LYD617	71966.2	349.4	0.05	5	4581.2	0.10	6	—	—	—
  LYD617	71966.3	358.1	0.04	7	4600.0	0.11	6	—	—	—
  LYD617	71966.6	345.6	0.11	4	4568.8	0.15	6	11.4	0.02	10
  LYD612	71814.5	—	—	—	4618.8	0.01	7	—	—	—
  LYD612	71818.3	350.6	0.07	5	—	—	—	—	—	—
  LYD609	73124.4	—	—	—	4943.8	0.01	14	11.2	0.22	8
  LYD609	73125.3	—	—	—	4581.2	0.29	6	—	—	—
  LYD609	73125.4	365.6	0.10	10	4543.8	0.06	5	10.9	0.05	5
  LYD596	73639.1	360.0	0.01	8	4506.2	0.19	4	—	—	—
  LYD593	71952.1	365.0	0.03	9	4593.8	0.02	6	—	—	—
  LYD593	71957.5	347.1	0.09	4	—	—	—	—	—	—
  LYD574	73118.4	376.9	0.02	13	4783.0	L	11	11.1	0.03	7
  LYD574	73122.3	371.9	L	11	4625.0	L	7	—	—	—
  LYD564	72182.4	—	—	—	4437.5	0.23	3	—	—	—
  LYD558	73112.3	390.0	0.16	17	5143.8	L	19	11.4	0.18	9
  LYD558	73114.3	—	—	—	4600.9	L	6	11.2	0.01	8
  LYD527	72241.3	—	—	—	4662.5	0.22	8	—	—	—
  LYD527	72243.4	—	—	—	4581.2	0.07	6	—	—	—
  LYD527	72246.3	378.1	0.11	13	4781.2	L	11	—	—	—
  LYD526	72164.4	367.5	0.17	10	4518.8	0.13	5	—	—	—
  LYD526	72164.5	—	—	—	—	—	—	10.8	0.11	4
  LYD526	72167.4	—	—	—	4687.5	0.06	8	10.9	0.27	4
  LYD526	72168.1	—	—	—	4475.0	0.10	4	—	—	—
  CONT.	—	333.6	—	—	4322.7	—	—	10.4	—	—
  LYD680	72230.2	—	—	—	—	—	—	9.8	0.26	5
  LYD680	72232.1	—	—	—	—	—	—	10.2	0.06	10
  LYD668	72019.2	—	—	—	—	—	—	9.8	L	6
  LYD668	72019.3	—	—	—	—	—	—	9.9	0.03	7
  LYD668	72020.2	257.1	0.03	15	3474.1	0.29	11	9.6	0.02	4
  LYD668	72023.3	262.0	0.07	17	3536.6	0.17	13	—	—	—
  LYD664	72012.1	277.9	0.12	24	3435.7	0.28	9	9.9	0.20	7
  LYD664	72015.2	—	—	—	—	—	—	9.9	0.03	7
  LYD664	72016.2	235.0	0.30	5	3450.0	0.01	10	9.9	0.03	7
  LYD664	72017.8	260.0	0.03	16	3356.2	0.05	7	9.9	0.10	7
  LYD661	72325.1	—	—	—	3386.6	0.17	8	9.6	0.12	4
  LYD661	72325.4	236.9	0.28	6	3400.0	0.19	8	—	—	—
  LYD661	72328.2	258.1	0.01	15	3700.0	L	18	9.9	0.03	7
  LYD661	72329.2	—	—	—	3481.2	0.29	11	—	—	—
  LYD657	72400.1	236.2	0.26	6	—	—	—	—	—	—
  LYD657	72400.3	—	—	—	3630.4	0.13	16	—	—	—
  LYD657	72401.1	280.5	0.04	25	3461.6	0.16	10	—	—	—
  LYD657	72401.2	—	—	—	3325.0	0.14	6	—	—	—
  LYD642	71820.2	—	—	—	—	—	—	9.7	0.02	5
  LYD642	71824.5	290.0	0.23	30	3868.8	0.23	23	10.8	0.15	17
  LYD642	71825.1	—	—	—	3368.8	0.28	7	9.9	0.03	7
  LYD642	71825.3	—	—	—	3356.2	0.06	7	9.7	0.20	5
  LYD631	72541.2	—	—	—	—	—	—	9.6	0.07	3
  LYD631	72544.3	268.2	0.10	20	3484.5	0.08	11	—	—	—
  LYD631	72544.4	—	—	—	3318.8	0.17	6	—	—	—
  LYD621	72571.1	248.1	0.06	11	3431.2	0.17	9	—	—	—
  LYD621	72573.6	272.5	0.01	22	3681.2	0.21	17	9.8	0.25	6
  LYD621	72574.1	—	—	—	3468.8	0.14	11	—	—	—
  LYD618	72621.2	—	—	—	3393.8	0.03	8	9.6	0.02	4
  LYD618	72622.2	—	—	—	3562.5	0.20	13	—	—	—
  LYD618	72622.3	247.5	0.14	11	3550.0	0.16	13	—	—	—
  LYD618	72624.4	255.7	0.13	14	3592.9	0.03	14	9.9	0.03	7
  LYD603	72535.2	—	—	—	3393.8	0.05	8	—	—	—
  LYD603	72536.1	—	—	—	3318.8	0.17	6	—	—	—
  LYD603	72537.7	—	—	—	3487.5	L	11	—	—	—
  LYD572	72388.2	240.6	0.18	8	—	—	—	9.4	0.25	2
  LYD572	72390.3	—	—	—	—	—	—	9.9	L	7
  LYD568	71930.1	240.6	0.16	8	3487.5	L	11	9.7	0.02	5
  LYD568	71931.2	—	—	—	3406.2	0.20	9	—	—	—
  LYD568	71931.4	—	—	—	3581.2	L	14	9.6	0.12	4
  LYD561	72175.4	—	—	—	—	—	—	9.8	L	6
  LYD561	72177.1	—	—	—	3362.5	0.24	7	10.1	0.20	9
  LYD561	72179.1	—	—	—	—	—	—	9.8	0.06	5
  LYD551	71986.9	238.1	0.20	6	3312.5	0.11	6	10.0	0.02	8
  LYD531	71916.3	—	—	—	3343.8	0.06	7	9.8	0.26	5
  LYD531	71917.1	—	—	—	3406.2	0.06	9	—	—	—
  LYD531	71917.2	—	—	—	3400.0	0.22	8	9.8	L	6
  LYD531	71918.1	258.8	0.08	16	3562.5	0.03	13	10.4	0.09	12
  LYD531	71921.2	255.0	0.03	14	3418.8	0.04	9	9.9	0.20	7
  LYD528	72310.1	—	—	—	3325.9	0.08	6	—	—	—
  LYD528	72312.4	245.6	0.12	10	3556.2	0.19	13	9.5	0.27	3
  LYD522	72716.2	—	—	—	3456.2	0.27	10	10.1	0.01	9
  LYD522	72716.6	274.9	L	23	3799.1	0.12	21	—	—	—
  LYD522	72720.1	—	—	—	3437.5	0.11	10	—	—	—
  LYD522	72720.2	241.9	0.12	8	3450.0	0.02	10	9.9	0.03	7
  CONT.	—	223.6	—	—	3138.8	—	—	9.3	—	—
  LYD688	73129.1	—	—	—	—	—	—	11.4	0.30	5
  LYD688	73133.1	371.2	0.01	15	4818.8	0.04	11	11.8	0.04	8
  LYD688	73133.3	—	—	—	—	—	—	11.4	0.30	5
  LYD688	73133.6	368.1	0.17	14	4987.5	0.01	15	—	—	—
  LYD670	73346.2	350.0	0.20	8	4675.0	0.17	7	—	—	—
  LYD670	73347.4	—	—	—	4912.5	0.07	13	—	—	—
  LYD670	73348.1	—	—	—	—	—	—	12.2	0.28	12
  LYD670	73350.2	376.2	0.12	16	5050.0	L	16	11.5	0.08	5
  LYD662	72008.3	—	—	—	4637.5	0.17	7	11.8	0.02	8
  LYD643	72336.3	354.8	0.10	10	4816.7	0.21	11	—	—	—
  LYD629	72198.3	—	—	—	—	—	—	11.8	0.03	8
  LYD623	71972.3	—	—	—	4575.0	0.28	5	—	—	—
  LYD606	72500.2	—	—	—	—	—	—	11.5	0.10	5
  LYD606	72500.5	341.2	0.25	6	—	—	—	—	—	—
  LYD599	72266.2	375.0	0.01	16	4831.2	0.04	11	12.1	L	11
  LYD594	73307.4	—	—	—	—	—	—	11.4	0.28	4
  LYD562	73484.1	—	—	—	—	—	—	11.4	0.17	5
  LYD562	73484.2	351.2	0.16	9	4781.2	0.06	10	11.5	0.10	5
  LYD562	73486.3	350.0	0.13	8	4756.2	0.13	9	—	—	—
  LYD562	73489.1	352.5	0.09	9	4687.5	0.13	8	—	—	—
  LYD549	73029.2	363.1	0.03	12	4806.2	0.07	10	—	—	—
  LYD549	73032.1	—	—	—	—	—	—	11.5	0.19	5
  CONT.	—	323.4	—	—	4352.3	—	—	10.9	—	—
  LYD669	72217.2	—	—	—	4262.5	0.11	17	—	—	—
  LYD660	73929.2	395.6	0.23	30	—	—	—	11.9	0.17	13
  LYD660	73933.5	374.4	0.11	23	4137.5	0.01	13	12.2	0.05	16
  LYD654	73924.4	328.8	0.15	8	3875.0	0.29	6	—	—	—
  LYD643	72333.1	—	—	—	3843.8	0.29	5	—	—	—
  LYD643	72333.2	—	—	—	—	—	—	11.0	0.19	4
  LYD643	72333.6	—	—	—	4231.2	0.03	16	—	—	—
  LYD643	72336.3	—	—	—	—	—	—	11.2	0.11	6
  LYD634	71995.1	—	—	—	4012.5	0.07	10	11.4	0.04	8
  LYD634	71996.1	—	—	—	3829.2	0.23	5	—	—	—
  LYD634	71996.2	—	—	—	3931.2	0.19	8	—	—	—
  LYD629	72195.1	—	—	—	4075.0	0.15	12	11.9	L	13
  LYD629	72198.3	328.8	0.17	8	—	—	—	11.4	0.20	8
  LYD622	72024.3	—	—	—	3868.8	0.21	6	—	—	—
  LYD614	73916.4	340.6	0.12	12	4231.2	0.04	16	—	—	—
  LYD614	73917.1	—	—	—	4156.2	0.05	14	—	—	—
  LYD614	73917.3	337.5	0.18	11	—	—	—	—	—	—
  LYD609	73125.4	—	—	—	—	—	—	11.4	0.09	8
  LYD609	73128.5	—	—	—	3875.0	0.16	6	—	—	—
  LYD603	72537.7	330.0	0.13	8	4131.2	0.01	13	—	—	—
  LYD584	73915.2	—	—	—	—	—	—	11.4	0.09	8
  LYD584	73915.4	—	—	—	—	—	—	11.3	0.07	7
  LYD580	72188.2	—	—	—	4237.5	L	16	10.9	0.23	4
  LYD580	72189.1	—	—	—	3837.5	0.23	5	—	—	—
  LYD570	71937.3	323.1	0.29	6	4043.8	0.06	11	12.1	0.20	15
  LYD561	72177.2	—	—	—	3868.8	0.21	6	—	—	—
  LYD556	72903.5	—	—	—	—	—	—	11.4	0.09	8
  LYD556	72903.6	—	—	—	4062.5	0.02	11	—	—	—
  LYD556	72904.3	—	—	—	4131.2	0.01	13	—	—	—
  LYD534	72409.2	—	—	—	3912.5	0.15	7	—	—	—
  CONT.	—	305.2	—	—	3651.8	—	—	10.6	—	—
  LYD674	72254.1	—	—	—	3581.2	0.14	8	—	—	—
  LYD672	72347.3	—	—	—	—	—	—	9.6	0.03	6
  LYD635	72626.2	—	—	—	3737.5	0.03	13	9.4	0.21	4
  LYD635	72630.1	—	—	—	—	—	—	9.7	0.01	7
  LYD635	72630.2	—	—	—	—	—	—	10.1	0.06	12
  LYD635	72630.4	—	—	—	—	—	—	9.6	0.02	7
  LYD632	72770.2	—	—	—	3617.9	0.10	9	9.4	0.11	4
  LYD627	72765.1	—	—	—	—	—	—	10.1	L	12
  LYD627	72767.1	—	—	—	3568.8	0.16	8	—	—	—
  LYD623	71970.2	—	—	—	—	—	—	9.9	L	10
  LYD623	71972.2	—	—	—	—	—	—	9.4	0.07	4
  LYD623	71972.3	—	—	—	—	—	—	9.8	0.13	8
  LYD623	71974.3	271.9	0.19	15	—	—	—	9.8	L	8
  LYD593	71957.1	—	—	—	3714.3	0.06	12	9.6	0.13	6
  LYD593	71957.5	283.1	0.11	20	—	—	—	9.3	0.19	3
  LYD580	72188.2	—	—	—	—	—	—	9.9	L	10
  LYD580	72189.1	—	—	—	—	—	—	9.7	0.08	7
  LYD580	72189.2	288.8	0.02	22	3793.8	0.02	15	9.9	L	9
  LYD571	72357.5	—	—	—	—	—	—	9.6	0.18	7
  LYD571	72358.1	278.1	0.12	18	3675.0	0.06	11	—	—	—
  LYD571	72358.3	287.0	0.22	22	3955.4	0.03	20	10.1	L	12
  LYD571	72360.2	—	—	—	—	—	—	9.4	0.07	4
  LYD560	71925.1	265.9	0.19	13	—	—	—	9.5	0.26	5
  LYD554	72169.2	—	—	—	—	—	—	9.6	0.04	7
  LYD554	72173.2	—	—	—	—	—	—	9.6	0.13	6
  LYD553	72742.1	—	—	—	—	—	—	9.6	0.18	7
  LYD553	72743.2	—	—	—	—	—	—	9.3	0.19	3
  LYD548	72656.1	—	—	—	—	—	—	9.6	0.30	6
  LYD548	72656.2	—	—	—	—	—	—	9.5	0.26	5
  LYD548	72673.3	—	—	—	—	—	—	9.5	0.04	5
  LYD548	72677.1	276.9	0.28	17	—	—	—	—	—	—
  LYD547	71978.3	—	—	—	—	—	—	9.8	L	9
  LYD547	71980.1	—	—	—	—	—	—	10.0	0.08	11
  LYD547	71980.3	—	—	—	3590.2	0.26	9	—	—	—
  LYD547	71981.2	—	—	—	—	—	—	10.0	L	11
  LYD538	72835.2	273.8	0.08	16	3837.5	0.17	16	9.9	0.22	9
  LYD538	72835.4	262.9	0.16	11	—	—	—	9.4	0.18	4
  LYD538	72839.1	—	—	—	—	—	—	9.7	0.23	7
  LYD538	72839.5	—	—	—	—	—	—	9.7	0.08	7
  LYD527	72241.3	—	—	—	—	—	—	9.6	0.30	6
  LYD527	72243.4	—	—	—	—	—	—	9.3	0.19	3
  LYD527	72245.2	—	—	—	—	—	—	9.4	0.18	4
  LYD527	72246.3	—	—	—	—	—	—	9.5	0.08	5
  LYD521	72607.1	—	—	—	—	—	—	9.8	0.13	8
  LYD521	72610.2	—	—	—	—	—	—	9.9	0.22	9
  LYD521	72611.3	—	—	—	—	—	—	9.4	0.21	4
  CONT.	—	236.0	—	—	3306.4	—	—	9.0	—	—
  LYD680	72230.2	—	—	—	3043.8	0.03	15	—	—	—
  LYD680	72231.2	281.9	L	30	3675.0	L	39	—	—	—
  LYD680	72232.1	275.6	L	27	3568.8	L	35	9.8	0.13	6
  LYD678	72787.2	304.4	L	41	3562.5	0.01	35	—	—	—
  LYD678	72788.1	—	—	—	3081.2	0.25	17	—	—	—
  LYD678	72790.1	—	—	—	—	—	—	9.6	0.15	4
  LYD674	72254.3	—	—	—	3387.5	0.17	28	—	—	—
  LYD674	72255.1	261.2	0.03	21	3550.0	L	34	9.7	0.04	4
  LYD674	72256.3	244.4	0.06	13	—	—	—	—	—	—
  LYD664	72015.2	250.6	0.10	16	3455.4	0.16	31	—	—	—
  LYD664	72017.7	286.9	L	33	3668.8	L	39	9.6	0.15	4
  LYD642	71821.4	275.0	L	27	3662.5	L	39	—	—	—
  LYD642	71824.5	—	—	—	—	—	—	9.7	0.21	4
  LYD642	71825.1	270.0	0.03	25	3568.8	L	35	—	—	—
  LYD642	71825.3	—	—	—	—	—	—	9.7	0.04	4
  LYD641	72632.2	—	—	—	2881.2	0.08	9	9.5	0.19	2
  LYD641	72633.4	302.5	L	40	3950.0	L	50	—	—	—
  LYD641	72635.2	244.4	0.08	13	3256.2	0.01	23	—	—	—
  LYD637	73684.1	273.1	L	26	3475.0	L	32	—	—	—
  LYD637	73685.1	271.9	0.14	26	3781.2	L	43	—	—	—
  LYD637	73685.2	—	—	—	3231.2	L	22	—	—	—
  LYD637	73685.3	262.5	L	21	3293.8	L	25	—	—	—
  LYD624	73382.3	—	—	—	3256.2	0.11	23	—	—	—
  LYD624	73385.3	264.9	0.14	22	—	—	—	—	—	—
  LYD621	72571.1	—	—	—	—	—	—	9.8	0.07	5
  LYD621	72574.1	245.8	0.19	14	—	—	—	—	—	—
  LYD621	72574.3	—	—	—	—	—	—	9.6	0.06	4
  LYD617	71964.2	—	—	—	3437.5	L	30	—	—	—
  LYD617	71966.2	264.4	0.25	22	3525.0	0.06	33	—	—	—
  LYD617	71966.6	258.1	L	19	3243.8	L	23	9.5	0.19	2
  LYD617	71967.1	244.4	0.03	13	3268.8	L	24	—	—	—
  LYD616	73057.1	239.4	0.13	11	2981.2	0.21	13	—	—	—
  LYD616	73057.4	—	—	—	3425.0	L	30	9.5	0.19	2
  LYD616	73058.4	265.6	L	23	3425.0	L	30	—	—	—
  LYD616	73059.1	—	—	—	3475.0	0.09	32	—	—	—
  LYD616	73059.4	—	—	—	—	—	—	9.6	0.12	3
  LYD588	73852.1	233.8	0.15	8	—	—	—	—	—	—
  LYD588	73852.2	241.9	0.14	12	3062.5	0.01	16	—	—	—
  LYD572	72387.1	258.1	L	19	3381.2	L	28	—	—	—
  LYD572	72390.3	276.2	L	28	3625.0	L	37	—	—	—
  LYD567	72495.3	255.6	0.20	18	3637.5	0.08	38	—	—	—
  LYD567	72495.4	—	—	—	—	—	—	10.0	0.28	8
  LYD567	72496.2	—	—	—	—	—	—	9.5	0.19	2
  LYD567	72496.3	259.4	0.04	20	3518.8	0.01	33	—	—	—
  LYD559	73623.3	—	—	—	3412.5	0.22	29	—	—	—
  LYD559	73624.1	—	—	—	—	—	—	9.6	0.15	4
  LYD559	73626.1	—	—	—	2916.1	0.29	10	—	—	—
  LYD538	72835.4	260.0	L	20	3281.2	L	24	9.8	0.07	5
  LYD537	73628.1	279.4	0.02	29	3631.2	L	37	—	—	—
  LYD537	73633.1	265.6	0.01	23	3212.5	L	22	—	—	—
  LYD537	73633.4	238.3	0.06	10	2902.1	0.08	10	—	—	—
  LYD537	73633.5	248.8	0.12	15	2981.2	0.02	13	—	—	—
  LYD521	72607.1	277.5	L	28	3368.8	L	28	—	—	—
  LYD521	72610.1	240.0	0.05	11	3043.8	0.03	15	9.8	0.27	5
  LYD521	72610.2	—	—	—	—	—	—	9.6	0.06	4
  LYD521	72611.1	241.2	0.04	12	—	—	—	9.7	0.04	4
  LYD521	72611.3	294.4	L	36	3406.2	L	29	—	—	—
  CONT.	—	216.3	—	—	2641.6	—	—	9.3	—	—
  LYD689	72711.2	—	—	—	5537.5	0.02	12	10.6	0.05	5
  LYD689	72712.3	465.0	0.01	17	5575.0	0.11	13	—	—	—
  LYD689	72713.1	446.2	0.26	12	5656.2	0.04	15	10.4	0.16	3
  LYD682	72566.2	460.6	0.05	16	5618.8	0.02	14	—	—	—
  LYD682	72568.2	474.3	L	19	5596.4	0.01	13	—	—	—
  LYD677	72223.6	—	—	—	—	—	—	10.8	0.18	8
  LYD677	72223.7	461.1	0.04	16	5209.8	0.21	6	—	—	—
  LYD677	72227.1	—	—	—	—	—	—	10.5	0.27	4
  LYD669	73327.1	471.4	0.09	19	5750.0	L	17	10.9	0.25	9
  LYD666	72394.3	—	—	—	5631.2	0.01	14	—	—	—
  LYD657	72400.1	453.8	0.29	14	5868.8	0.01	19	—	—	—
  LYD657	72400.3	426.4	0.19	7	5291.1	0.13	7	—	—	—
  LYD657	72401.1	421.9	0.27	6	5293.8	0.12	7	—	—	—
  LYD620	73063.3	—	—	—	5291.1	0.19	7	—	—	—
  LYD620	73066.3	—	—	—	5262.5	0.30	7	10.6	0.14	5
  LYD602	72613.1	—	—	—	5443.8	0.04	10	—	—	—
  LYD602	72613.2	429.3	0.17	8	—	—	—	—	—	—
  LYD598	72421.1	—	—	—	5250.0	0.28	6	—	—	—
  LYD598	72446.4	446.9	0.09	12	5187.5	0.24	5	—	—	—
  LYD595	72907.4	—	—	—	—	—	—	10.5	0.07	4
  LYD595	72907.5	434.4	0.16	9	5743.8	L	16	—	—	—
  LYD574	73118.3	447.5	0.22	13	5300.0	0.12	7	—	—	—
  LYD574	73118.4	—	—	—	5237.5	0.18	6	—	—	—
  LYD574	73119.1	463.8	0.25	17	5525.0	0.05	12	10.9	0.22	8
  LYD574	73121.2	461.0	0.28	16	5226.8	0.22	6	10.3	0.26	3
  LYD574	73122.3	466.9	0.15	17	5881.2	L	19	—	—	—
  LYD562	73484.2	—	—	—	—	—	—	10.7	0.02	6
  LYD549	73029.1	—	—	—	—	—	—	10.3	0.26	3
  LYD549	73029.4	457.1	0.02	15	—	—	—	—	—	—
  LYD549	73032.1	424.8	0.20	7	—	—	—	—	—	—
  LYD549	73032.2	—	—	—	5481.2	0.06	11	—	—	—
  LYD542	72733.2	425.6	0.25	7	5425.0	0.04	10	—	—	—
  LYD542	72735.4	426.7	0.23	7	5600.0	0.01	13	10.3	0.26	3
  LYD542	72736.3	423.8	0.29	7	—	—	—	—	—	—
  LYD542	72736.4	—	—	—	—	—	—	10.6	0.03	6
  LYD542	72736.7	433.0	0.11	9	5530.4	0.02	12	—	—	—
  LYD536	72531.3	424.4	0.24	7	5493.8	0.07	11	—	—	—
  LYD533	72726.2	—	—	—	5268.8	0.18	7	—	—	—
  CONT.	—	397.4	—	—	4934.9	—	—	10.1	—	—
  LYD688	73133.1	449.2	0.02	11	5805.4	0.08	5	—	—	—
  LYD688	73134.6	455.0	0.07	13	5831.2	0.03	6	10.5	0.02	7
  LYD681	73184.1	—	—	—	—	—	—	10.6	L	8
  LYD681	73184.3	—	—	—	—	—	—	10.4	0.11	6
  LYD681	73186.2	—	—	—	5762.5	0.06	5	10.5	0.02	7
  LYD675	72644.1	435.0	0.02	8	5893.8	0.01	7	11.1	0.12	13
  LYD675	72644.3	—	—	—	—	—	—	10.4	0.04	6
  LYD675	72648.1	460.0	0.15	14	—	—	—	—	—	—
  LYD671	72877.1	427.5	0.21	6	—	—	—	—	—	—
  LYD671	72878.2	425.0	0.25	5	—	—	—	—	—	—
  LYD671	72879.2	464.4	0.29	15	5862.5	0.13	6	—	—	—
  LYD665	72216.5	435.6	0.29	8	—	—	—	—	—	—
  LYD665	72216.6	426.9	0.06	6	—	—	—	—	—	—
  LYD652	72559.1	—	—	—	—	—	—	10.1	0.17	3
  LYD652	72560.1	—	—	—	5817.0	0.03	6	—	—	—
  LYD651	73021.3	451.2	0.10	12	6031.2	L	10	—	—	—
  LYD648	72831.3	420.0	0.23	4	—	—	—	—	—	—
  LYD648	72832.2	442.2	0.02	10	—	—	—	—	—	—
  LYD644	72775.1	476.6	L	18	5875.9	0.01	7	—	—	—
  LYD644	72778.1	420.6	0.11	4	—	—	—	—	—	—
  LYD644	72778.2	421.3	0.28	4	—	—	—	—	—	—
  LYD639	72548.4	—	—	—	—	—	—	10.0	0.20	2
  LYD639	72549.3	—	—	—	—	—	—	10.2	0.08	4
  LYD639	72551.3	440.6	L	9	—	—	—	—	—	—
  LYD596	73635.1	—	—	—	5756.2	0.06	5	—	—	—
  LYD596	73635.3	—	—	—	5700.0	0.15	4	—	—	—
  LYD596	73636.1	453.6	0.25	12	—	—	—	—	—	—
  LYD596	73637.1	440.0	0.18	9	6206.2	L	13	—	—	—
  LYD594	73303.1	416.2	0.21	3	—	—	—	—	—	—
  LYD594	73307.1	462.5	0.21	15	6068.8	0.11	10	—	—	—
  LYD594	73307.3	434.4	0.02	8	—	—	—	—	—	—
  LYD594	73307.4	475.0	0.08	18	—	—	—	10.2	0.03	4
  LYD577	72747.4	481.2	L	19	—	—	—	—	—	—
  LYD577	72748.2	—	—	—	—	—	—	10.1	0.17	3
  LYD577	72748.3	—	—	—	—	—	—	10.2	0.24	4
  LYD577	72750.4	430.0	0.06	7	—	—	—	—	—	—
  LYD545	72506.2	448.8	L	11	5956.2	L	8	—	—	—
  LYD545	72508.2	429.2	0.10	6	—	—	—	—	—	—
  LYD545	72508.5	428.8	0.19	6	—	—	—	—	—	—
  LYD541	72729.1	432.3	0.25	7	—	—	—	—	—	—
  LYD541	72729.2	439.4	0.15	9	—	—	—	—	—	—
  LYD541	72732.1	452.7	0.03	12	—	—	—	—	—	—
  LYD534	72409.2	—	—	—	—	—	—	10.2	0.24	4
  LYD534	72414.3	—	—	—	—	—	—	10.1	0.05	3
  LYD522	72715.2	474.4	0.23	18	—	—	—	—	—	—
  LYD522	72720.1	—	—	—	—	—	—	10.2	0.03	4
  CONT.	—	403.4	—	—	5506.6	—	—	9.8	—	—
  Table 61. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L—p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). “—” = results are still unavailable.

• TABLE 62
  Genes showing improved plant performance at Normal growth
  conditions under regulation of At6669 promoter

  	Plot	Rosette	Rosette
  	Coverage [cm2]	Area [cm2]	Diameter [cm]

  				%			%			%
  Gene Name	Event #	Ave.	P-Val.	Incr.	Ave.	P-Val.	Incr.	Ave.	P-Val.	Incr.

  LYD684	72271.4	—	—	—	—	—	—	4.8	0.24	7
  LYD684	72272.3	57.6	0.17	9	7.2	0.17	9	—	—	—
  LYD684	72274.1	73.6	0.13	39	9.2	0.13	39	5.1	0.14	13
  LYD681	73188.3	62.4	0.24	18	7.8	0.24	18	4.8	0.22	6
  LYD667	72030.4	58.0	0.22	9	7.2	0.22	9	—	—	—
  LYD661	72325.1	63.0	L	19	7.9	L	19	4.9	0.07	7
  LYD661	72328.1	70.3	L	32	8.8	L	32	5.1	0.01	14
  LYD661	72328.2	67.7	0.04	28	8.5	0.04	28	5.1	0.12	13
  LYD651	73026.4	60.2	0.11	13	7.5	0.11	13	—	—	—
  LYD626	72002.1	—	—	—	—	—	—	4.8	0.27	7
  LYD626	72003.1	—	—	—	—	—	—	4.9	0.14	9
  LYD620	73066.3	67.2	L	26	8.4	L	26	5.1	L	13
  LYD617	71964.2	58.2	0.12	10	7.3	0.12	10	4.8	0.22	6
  LYD617	71966.3	56.1	0.28	6	7.0	0.28	6	—	—	—
  LYD617	71966.6	70.1	L	32	8.8	L	32	5.0	L	11
  LYD612	71818.3	58.0	0.08	9	7.3	0.08	9	4.7	0.12	5
  LYD609	73125.3	61.6	0.28	16	7.7	0.28	16	4.9	0.22	7
  LYD609	73125.4	61.1	0.08	15	7.6	0.08	15	4.8	0.14	5
  LYD609	73128.5	59.9	0.23	13	7.5	0.23	13	4.9	0.05	7
  LYD596	73635.1	—	—	—	—	—	—	5.1	0.02	12
  LYD596	73639.1	61.5	0.08	16	7.7	0.08	16	5.1	0.03	12
  LYD593	71952.1	62.5	0.26	18	7.8	0.26	18	—	—	—
  LYD593	71952.2	58.4	0.06	10	7.3	0.06	10	4.7	0.28	4
  LYD593	71957.5	58.9	0.05	11	7.4	0.05	11	—	—	—
  LYD574	73118.4	70.3	L	32	8.8	L	32	5.1	L	13
  LYD574	73119.1	58.2	0.17	10	7.3	0.17	10	—	—	—
  LYD564	72182.4	62.0	0.17	17	7.8	0.17	17	—	—	—
  LYD564	72182.5	56.0	0.26	5	7.0	0.26	5	—	—	—
  LYD558	73112.3	71.0	0.07	34	8.9	0.07	34	5.2	L	15
  LYD558	73113.1	60.3	0.02	14	7.5	0.02	14	4.7	0.19	4
  LYD558	73114.3	58.1	0.21	9	7.3	0.21	9	—	—	—
  LYD558	73114.6	58.5	0.17	10	7.3	0.17	10	4.7	0.19	4
  LYD527	72246.1	56.0	0.27	5	7.0	0.27	5	—	—	—
  LYD527	72246.3	67.2	0.29	26	8.4	0.29	26	—	—	—
  LYD526	72164.5	63.0	L	19	7.9	L	19	4.9	0.01	9
  LYD526	72167.4	67.9	0.10	28	8.5	0.10	28	5.1	0.03	13
  LYD526	72168.1	59.6	0.06	12	7.5	0.06	12	4.8	0.25	6
  LYD526	72168.4	64.1	L	21	8.0	L	21	4.9	0.02	9
  CONT.	—	53.1	—	—	6.6	—	—	4.5	—	—
  LYD680	72232.1	53.7	0.29	16	6.7	0.29	16	—	—	—
  LYD664	72012.1	52.0	0.02	12	6.5	0.02	12	4.3	0.11	4
  LYD664	72015.2	54.4	0.29	17	6.8	0.29	17	4.5	0.25	8
  LYD661	72325.1	54.7	0.25	18	6.8	0.25	18	4.4	0.28	6
  LYD661	72328.2	57.9	0.01	25	7.2	0.01	25	4.5	0.06	8
  LYD657	72401.1	50.7	0.02	9	6.3	0.02	9	—	—	—
  LYD642	71820.2	49.8	0.14	7	6.2	0.14	7	4.4	0.10	6
  LYD642	71821.4	51.0	0.02	10	6.4	0.02	10	4.5	0.01	7
  LYD642	71824.5	64.5	0.08	39	8.1	0.08	39	4.9	0.06	17
  LYD642	71825.1	48.2	0.25	4	6.0	0.25	4	—	—	—
  LYD631	72544.4	54.4	0.20	17	6.8	0.20	17	4.5	0.09	8
  LYD621	72571.1	53.2	L	15	6.7	L	15	4.5	L	9
  LYD618	72621.2	57.2	0.20	23	7.1	0.20	23	4.6	0.29	10
  LYD618	72622.2	49.8	0.23	7	6.2	0.23	7	—	—	—
  LYD572	72390.3	54.2	L	17	6.8	L	17	4.5	0.04	8
  LYD568	71930.1	57.5	0.22	24	7.2	0.22	24	4.7	0.13	13
  LYD568	71931.4	53.7	0.01	16	6.7	0.01	16	4.4	0.12	7
  LYD561	72177.1	51.2	0.01	10	6.4	0.01	10	4.3	0.14	4
  LYD551	71984.1	50.0	0.27	8	6.2	0.27	8	—	—	—
  LYD551	71986.9	52.7	L	14	6.6	L	14	4.4	0.15	5
  LYD531	71917.1	52.2	0.10	13	6.5	0.10	13	4.6	0.01	9
  LYD531	71917.2	52.6	0.17	13	6.6	0.17	13	4.4	0.10	5
  LYD531	71918.1	59.7	0.15	29	7.5	0.15	29	4.7	0.03	13
  LYD531	71921.2	—	—	—	—	—	—	4.4	0.21	5
  LYD528	72312.2	49.5	0.08	7	6.2	0.08	7	4.3	0.16	3
  LYD522	72715.2	48.9	0.13	6	6.1	0.13	6	4.3	0.21	3
  LYD522	72720.1	51.5	0.29	11	6.4	0.29	11	—	—	—
  LYD522	72720.2	53.8	0.12	16	6.7	0.12	16	—	—	—
  CONT.	—	46.4	—	—	5.8	—	—	4.2	—	—
  LYD688	73129.1	74.6	0.07	22	9.3	0.07	22	5.4	0.05	13
  LYD688	73133.1	75.8	0.03	24	9.5	0.03	24	5.3	0.04	10
  LYD688	73133.3	—	—	—	—	—	—	5.2	0.27	8
  LYD688	73133.6	67.7	0.26	11	8.5	0.26	11	—	—	—
  LYD670	73346.2	70.3	0.17	15	8.8	0.17	15	5.2	0.08	9
  LYD670	73347.4	—	—	—	—	—	—	5.1	0.20	5
  LYD670	73348.1	77.6	0.22	27	9.7	0.22	27	5.4	0.10	11
  LYD662	72008.3	74.8	0.04	22	9.4	0.04	22	5.5	L	14
  LYD646	73040.5	—	—	—	—	—	—	5.0	0.24	5
  LYD646	73042.4	75.7	0.07	24	9.5	0.07	24	5.4	0.09	13
  LYD643	72336.3	72.6	0.07	19	9.1	0.07	19	5.3	0.07	9
  LYD643	72336.6	72.1	0.12	18	9.0	0.12	18	5.3	0.03	10
  LYD629	72198.3	72.8	0.07	19	9.1	0.07	19	5.3	0.15	10
  LYD623	71972.3	70.0	0.15	15	8.8	0.15	15	5.2	0.10	7
  LYD622	72026.1	68.2	0.26	12	8.5	0.26	12	5.1	0.17	6
  LYD599	72266.2	81.3	0.04	33	10.2	0.04	33	5.5	0.11	15
  LYD594	73307.4	71.2	0.22	16	8.9	0.22	16	5.2	0.26	8
  LYD562	73484.1	71.5	0.15	17	8.9	0.15	17	5.2	0.29	8
  LYD562	73484.2	74.9	0.10	23	9.4	0.10	23	5.4	0.08	12
  LYD562	73486.3	—	—	—	—	—	—	5.1	0.12	7
  LYD551	71986.9	71.9	0.08	18	9.0	0.08	18	5.4	0.02	12
  LYD549	73029.4	—	—	—	—	—	—	5.3	0.06	11
  LYD549	73032.1	—	—	—	—	—	—	5.3	0.03	10
  LYD528	72312.4	—	—	—	—	—	—	5.2	0.10	8
  CONT.	—	61.1	—	—	7.6	—	—	4.8	—	—
  LYD669	73330.2	65.0	0.19	11	8.1	0.19	11	—	—	—
  LYD660	73929.2	70.6	0.05	21	8.8	0.05	21	4.9	0.25	9
  LYD660	73933.4	—	—	—	—	—	—	4.8	0.05	7
  LYD660	73933.5	78.5	L	34	9.8	L	34	5.2	L	16
  LYD654	73924.5	—	—	—	—	—	—	4.9	0.04	9
  LYD654	73926.3	63.7	0.20	9	8.0	0.20	9	4.8	0.11	6
  LYD643	72336.3	67.8	0.08	16	8.5	0.08	16	4.8	0.24	8
  LYD634	71995.1	64.0	0.13	9	8.0	0.13	9	—	—	—
  LYD629	72195.1	69.2	0.05	18	8.7	0.05	18	—	—	—
  LYD629	72198.2	65.7	0.15	12	8.2	0.15	12	4.8	0.08	6
  LYD629	72198.3	73.0	0.02	25	9.1	0.02	25	4.9	0.02	9
  LYD629	72198.5	65.6	0.17	12	8.2	0.17	12	—	—	—
  LYD614	73916.4	68.0	0.02	16	8.5	0.02	16	4.8	0.18	6
  LYD614	73916.5	—	—	—	—	—	—	5.0	0.28	10
  LYD614	73917.3	63.0	0.20	8	7.9	0.20	8	—	—	—
  LYD609	73125.4	63.8	0.15	9	8.0	0.15	9	4.8	0.11	6
  LYD584	73912.3	—	—	—	—	—	—	4.7	0.14	5
  LYD584	73915.2	66.8	0.15	14	8.3	0.15	14	4.8	0.28	8
  LYD584	73915.4	68.4	0.02	17	8.5	0.02	17	4.8	0.05	7
  LYD580	72188.2	67.7	0.03	16	8.5	0.03	16	4.8	0.12	7
  LYD570	71937.3	71.1	L	22	8.9	L	22	4.9	0.08	9
  LYD561	72177.2	—	—	—	—	—	—	4.9	0.26	10
  LYD556	72903.5	—	—	—	—	—	—	4.7	0.27	4
  LYD534	72414.4	62.8	0.22	7	7.9	0.22	7	—	—	—
  CONT.	—	58.5	—	—	7.3	—	—	4.5	—	—
  LYD672	72348.2	—	—	—	—	—	—	4.1	0.06	7
  LYD635	72626.2	44.4	0.02	13	5.5	0.02	13	4.0	0.02	6
  LYD632	72771.1	45.1	0.07	15	5.6	0.07	15	4.1	0.01	7
  LYD632	72774.3	—	—	—	—	—	—	4.1	0.12	7
  LYD632	72774.4	42.8	0.25	9	5.3	0.25	9	—	—	—
  LYD627	72766.1	44.0	0.09	12	5.5	0.09	12	4.0	0.25	5
  LYD627	72767.1	—	—	—	—	—	—	4.2	0.25	11
  LYD593	71957.5	42.8	0.05	9	5.3	0.05	9	4.0	0.06	5
  LYD580	72188.2	44.2	0.10	12	5.5	0.10	12	—	—	—
  LYD571	72357.5	47.7	L	21	6.0	L	21	4.1	L	8
  LYD571	72358.1	47.9	L	22	6.0	L	22	4.2	L	11
  LYD571	72358.3	54.2	0.20	38	6.8	0.20	38	4.4	0.18	17
  LYD571	72358.4	46.7	0.08	19	5.8	0.08	19	4.1	0.19	8
  LYD554	72174.4	45.3	0.18	15	5.7	0.18	15	—	—	—
  LYD553	72741.2	44.2	0.15	12	5.5	0.15	12	4.1	0.03	6
  LYD548	72656.2	—	—	—	—	—	—	4.0	0.13	4
  LYD548	72677.1	43.9	0.27	12	5.5	0.27	12	—	—	—
  LYD547	71980.1	47.4	L	20	5.9	L	20	—	—	—
  LYD538	72835.2	52.6	L	34	6.6	L	34	4.5	0.07	18
  LYD538	72835.4	41.7	0.06	6	5.2	0.06	6	—	—	—
  LYD538	72839.5	41.4	0.10	5	5.2	0.10	5	—	—	—
  LYD527	72246.3	44.2	L	12	5.5	L	12	4.2	L	10
  LYD521	72610.2	42.6	0.02	8	5.3	0.02	8	—	—	—
  CONT.	—	39.4	—	—	4.9	—	—	3.8	—	—
  LYD680	72231.2	—	—	—	—	—	—	3.4	0.26	5
  LYD680	72232.1	32.4	0.11	11	4.0	0.11	11	—	—	—
  LYD680	72232.4	31.3	0.29	7	3.9	0.29	7	3.6	0.07	9
  LYD678	72787.2	32.1	0.13	10	4.0	0.13	10	—	—	—
  LYD678	72790.1	33.7	0.15	16	4.2	0.15	16	3.5	0.07	6
  LYD664	72016.2	—	—	—	—	—	—	3.4	0.23	4
  LYD664	72017.7	35.1	0.06	20	4.4	0.06	20	3.5	0.11	8
  LYD642	71824.5	33.3	0.05	14	4.2	0.05	14	3.7	L	13
  LYD642	71825.1	31.4	0.22	8	3.9	0.22	8	3.4	0.16	4
  LYD641	72632.2	31.4	0.24	8	3.9	0.24	8	—	—	—
  LYD641	72633.4	41.0	0.11	41	5.1	0.11	41	3.9	0.08	19
  LYD637	73683.1	32.6	0.17	12	4.3	0.02	19	3.6	0.01	11
  LYD637	73685.3	—	—	—	—	—	—	3.4	0.12	5
  LYD624	73382.4	—	—	—	—	—	—	3.6	0.02	10
  LYD621	72571.1	32.2	0.11	11	4.0	0.11	11	3.5	0.03	8
  LYD621	72573.6	32.3	0.11	11	4.0	0.11	11	3.5	0.24	6
  LYD621	72574.3	32.5	0.09	12	4.1	0.09	12	3.5	0.08	6
  LYD617	71966.6	—	—	—	—	—	—	3.4	0.28	4
  LYD616	73058.4	36.6	L	26	4.6	L	26	3.6	0.02	10
  LYD616	73059.4	—	—	—	—	—	—	3.5	0.14	6
  LYD588	73855.2	35.1	0.23	20	4.4	0.23	20	3.6	0.20	12
  LYD588	73855.3	32.5	0.14	11	4.1	0.14	11	3.5	0.04	8
  LYD567	72495.3	—	—	—	—	—	—	3.4	0.19	4
  LYD567	72495.4	31.6	0.19	9	4.0	0.19	9	3.4	0.11	5
  LYD567	72496.3	32.4	0.09	11	4.1	0.09	11	3.4	0.11	5
  LYD559	73624.1	32.6	0.08	12	4.1	0.08	12	3.5	0.09	6
  LYD538	72839.2	31.8	0.15	9	4.0	0.15	9	—	—	—
  LYD537	73630.3	—	—	—	—	—	—	3.5	0.12	8
  LYD521	72611.1	32.0	0.21	10	4.0	0.21	10	—	—	—
  LYD521	72611.3	33.0	0.28	13	4.1	0.28	13	3.5	0.19	7
  CONT.	—	29.1	—	—	3.6	—	—	3.3	—	—
  LYD689	72711.2	58.6	0.29	10	7.3	0.29	10	—	—	—
  LYD689	72713.1	64.0	0.03	20	8.0	0.03	20	5.0	0.02	8
  LYD682	72566.2	60.5	0.24	14	7.6	0.24	14	—	—	—
  LYD677	72223.6	64.3	0.03	21	8.0	0.03	21	4.9	0.05	7
  LYD669	72217.2	61.8	0.06	16	7.7	0.06	16	4.9	0.04	8
  LYD669	73330.1	64.3	0.29	21	8.0	0.29	21	—	—	—
  LYD666	72394.3	64.7	L	22	8.1	L	22	5.0	0.02	9
  LYD666	72396.2	60.8	0.04	14	7.6	0.04	14	4.8	0.15	6
  LYD650	72640.1	57.3	0.18	8	7.2	0.18	8	4.7	0.26	3
  LYD620	73066.3	65.2	0.12	23	8.1	0.12	23	5.1	0.08	11
  LYD620	73068.2	58.0	0.14	9	7.3	0.14	9	—	—	—
  LYD602	72613.1	58.5	0.10	10	7.3	0.10	10	4.8	0.14	5
  LYD598	72421.1	62.7	0.01	18	7.8	0.01	18	4.9	0.09	8
  LYD598	72445.1	62.0	0.13	17	7.8	0.13	17	4.9	0.14	6
  LYD598	72446.4	61.4	0.02	16	7.7	0.02	16	4.9	0.05	7
  LYD574	73118.4	—	—	—	—	—	—	5.0	0.05	9
  LYD574	73119.1	67.1	0.04	26	8.4	0.04	26	5.0	0.07	9
  LYD562	73484.2	62.5	0.27	18	7.8	0.27	18	—	—	—
  LYD562	73489.4	65.4	L	23	8.2	L	23	5.0	0.28	8
  LYD549	73029.4	63.4	0.06	19	7.9	0.06	19	4.9	0.06	6
  CONT.	—	53.1	—	—	6.6	—	—	4.6	—	—
  LYD688	73129.1	—	—	—	—	—	—	4.6	0.27	9
  LYD688	73133.1	68.7	L	45	8.6	L	45	5.2	L	24
  LYD688	73134.6	62.9	0.13	33	7.9	0.13	33	4.9	L	16
  LYD681	73184.1	58.5	L	24	7.3	L	24	4.7	L	11
  LYD681	73184.2	56.7	0.27	20	7.1	0.27	20	4.7	0.09	12
  LYD681	73184.3	55.2	0.02	17	6.9	0.02	17	4.5	0.04	7
  LYD681	73186.2	58.5	0.21	24	7.3	0.21	24	4.8	0.19	13
  LYD681	73188.3	54.6	0.20	15	6.8	0.20	15	4.6	0.04	8
  LYD675	72644.1	64.2	0.12	36	8.0	0.12	36	4.9	0.07	16
  LYD675	72644.3	59.0	L	25	7.4	L	25	4.7	0.01	12
  LYD671	72878.2	54.3	0.16	15	6.8	0.16	15	4.6	0.09	8
  LYD665	72216.5	—	—	—	—	—	—	4.6	0.07	8
  LYD652	72559.1	53.6	0.05	13	6.7	0.05	13	4.7	0.14	11
  LYD652	72560.1	53.6	0.05	13	6.7	0.05	13	4.5	0.12	6
  LYD652	72563.1	51.9	0.26	10	6.5	0.26	10	4.4	0.16	5
  LYD651	73021.3	57.4	L	21	7.2	L	21	4.7	L	11
  LYD651	73021.5	55.3	0.02	17	6.9	0.02	17	4.6	0.01	9
  LYD651	73026.4	55.9	0.18	18	7.0	0.18	18	4.6	0.09	10
  LYD648	72834.1	—	—	—	—	—	—	4.4	0.22	5
  LYD644	72775.1	55.7	0.10	18	7.0	0.10	18	4.6	0.02	9
  LYD639	72548.4	—	—	—	—	—	—	4.7	0.22	11
  LYD639	72549.3	52.6	0.10	11	6.6	0.10	11	4.5	0.11	7
  LYD596	73635.1	—	—	—	—	—	—	4.4	0.22	4
  LYD596	73637.1	50.7	0.26	7	6.3	0.26	7	4.6	0.02	9
  LYD594	73307.1	57.6	0.19	22	7.2	0.19	22	4.9	0.18	15
  LYD594	73307.4	56.0	0.12	19	7.0	0.12	19	4.6	0.06	8
  LYD577	72745.4	—	—	—	—	—	—	4.5	0.17	7
  LYD577	72748.3	57.1	0.11	21	7.1	0.11	21	4.8	0.14	13
  LYD545	72506.2	—	—	—	—	—	—	4.6	0.13	8
  LYD545	72508.5	50.6	0.25	7	6.3	0.25	7	4.4	0.21	4
  LYD541	72729.1	52.6	0.18	11	6.6	0.18	11	4.5	0.06	7
  LYD534	72409.1	59.7	0.29	26	7.5	0.29	26	4.9	0.11	16
  LYD534	72414.3	55.1	0.06	17	6.9	0.06	17	4.6	0.15	8
  LYD524	72859.3	57.6	L	22	7.2	L	22	4.8	L	14
  LYD524	72864.4	—	—	—	—	—	—	4.5	0.11	5
  LYD522	72716.2	—	—	—	—	—	—	4.7	0.10	11
  CONT.	—	47.3	—	—	5.9	—	—	4.2	—	—
  Table 62. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L—p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). “—” = results are still unavailable.

• TABLE 63
  Genes showing improved plant performance at Normal growth
  conditions under regulation of At6669 promoter

  	RGR Of Leaf	RGR Of Plot	RGR Of Rosette
  	Number	Coverage	Diameter
  	(number/day)	(cm2/day)	(cm/day)

  				%			%			%
  Gene Name	Event #	Ave.	P-Val.	Incr.	Ave.	P-Val.	Incr.	Ave.	P-Val.	Incr.
  LYD684	72274.1	—	—	—	8.6	0.02	39	0.4	0.17	15
  LYD681	73186.2	—	—	—	7.6	0.16	23	—	—	—
  LYD681	73188.3	—	—	—	7.2	0.23	18	—	—	—
  LYD672	72347.3	—	—	—	7.6	0.20	24	—	—	—
  LYD667	72030.1	—	—	—	7.2	0.26	17	—	—	—
  LYD661	72325.1	0.7	0.13	21	7.3	0.19	19	—	—	—
  LYD661	72328.1	—	—	—	8.4	0.02	37	0.4	0.23	13
  LYD661	72328.2	—	—	—	7.8	0.08	27	—	—	—
  LYD626	72002.1	0.7	0.29	16	—	—	—	—	—	—
  LYD626	72003.1	—	—	—	—	—	—	0.4	0.27	13
  LYD620	73066.3	0.7	0.25	15	7.8	0.07	27	0.4	0.21	13
  LYD620	73066.5	0.7	0.10	22	—	—	—	—	—	—
  LYD617	71966.6	0.7	0.11	21	8.2	0.03	34	0.4	0.24	13
  LYD617	71967.1	0.7	0.23	16	—	—	—	—	—	—
  LYD609	73124.4	0.7	0.28	15	8.0	0.08	29	0.4	0.29	12
  LYD609	73125.3	—	—	—	7.3	0.24	18	—	—	—
  LYD609	73125.4	0.7	0.18	18	7.2	0.25	17	—	—	—
  LYD596	73639.1	—	—	—	7.2	0.22	18	—	—	—
  LYD593	71952.1	—	—	—	7.3	0.21	19	—	—	—
  LYD593	71952.2	0.7	0.27	15	—	—	—	—	—	—
  LYD574	73118.3	—	—	—	7.3	0.24	19	—	—	—
  LYD574	73118.4	—	—	—	8.2	0.03	33	—	—	—
  LYD574	73122.3	—	—	—	7.2	0.28	17	—	—	—
  LYD564	72182.4	—	—	—	7.1	0.28	16	—	—	—
  LYD564	72184.1	—	—	—	7.8	0.17	26	—	—	—
  LYD558	73112.3	—	—	—	8.2	0.03	33	0.4	0.25	13
  LYD558	73113.1	—	—	—	7.1	0.26	16	—	—	—
  LYD558	73114.3	0.7	0.12	21	—	—	—	—	—	—
  LYD527	72246.3	—	—	—	7.8	0.09	26	—	—	—
  LYD526	72164.5	—	—	—	7.3	0.22	18	—	—	—
  LYD526	72167.4	—	—	—	8.1	0.03	31	—	—	—
  LYD526	72168.1	0.7	0.19	17	—	—	—	—	—	—
  LYD526	72168.4	—	—	—	7.4	0.16	21	—	—	—
  CONT.	—	0.6	—	—	6.2	—	—	0.4	—	—
  LYD680	72232.1	0.7	0.28	13	6.6	0.19	15	0.4	0.12	13
  LYD668	72023.3	—	—	—	7.1	0.07	24	—	—	—
  LYD664	72012.1	—	—	—	6.5	0.27	12	—	—	—
  LYD664	72015.2	—	—	—	6.7	0.14	17	0.4	0.16	11
  LYD661	72325.1	—	—	—	6.7	0.17	16	—	—	—
  LYD661	72328.2	—	—	—	7.2	0.04	24	—	—	—
  LYD642	71820.2	—	—	—	—	—	—	0.4	0.26	9
  LYD642	71821.4	0.7	0.23	14	—	—	—	0.4	0.11	12
  LYD642	71824.5	0.7	0.09	21	8.0	L	38	0.4	0.01	20
  LYD642	71825.1	0.7	0.16	17	—	—	—	—	—	—
  LYD631	72544.4	—	—	—	6.6	0.18	15	—	—	—
  LYD621	72571.1	—	—	—	6.5	0.22	13	0.4	0.21	10
  LYD621	72574.3	0.7	0.29	13	—	—	—	—	—	—
  LYD618	72621.2	—	—	—	7.1	0.04	24	0.4	0.10	13
  LYD572	72390.3	—	—	—	6.8	0.13	17	0.4	0.09	13
  LYD568	71930.1	—	—	—	7.2	0.04	25	0.4	0.03	17
  LYD568	71931.4	—	—	—	6.7	0.15	16	0.4	0.27	8
  LYD568	71932.2	0.7	0.27	13	—	—	—	—	—	—
  LYD561	72175.4	—	—	—	6.7	0.15	17	—	—	—
  LYD561	72177.1	0.7	0.27	13	—	—	—	—	—	—
  LYD561	72177.2	—	—	—	6.8	0.12	19	0.4	0.25	9
  LYD561	72179.1	—	—	—	6.6	0.19	15	—	—	—
  LYD551	71986.9	—	—	—	6.6	0.18	14	0.4	0.26	8
  LYD531	71916.3	0.7	0.29	13	—	—	—	—	—	—
  LYD531	71917.1	—	—	—	6.4	0.29	12	0.4	0.07	14
  LYD531	71918.1	—	—	—	7.3	0.03	27	0.4	0.08	13
  LYD531	71921.2	—	—	—	6.4	0.30	12	—	—	—
  LYD528	72312.4	0.7	0.22	15	—	—	—	—	—	—
  LYD522	72715.2	—	—	—	—	—	—	0.4	0.24	8
  LYD522	72716.6	—	—	—	6.6	0.23	14	0.4	0.18	11
  LYD522	72720.1	—	—	—	—	—	—	0.4	0.27	8
  LYD522	72720.2	0.7	0.21	15	6.7	0.15	16	—	—	—
  CONT.	—	0.6	—	—	5.8	—	—	0.3	—	—
  LYD688	73129.1	—	—	—	8.7	0.27	22	—	—	—
  LYD688	73133.1	—	—	—	8.8	0.23	24	—	—	—
  LYD670	73348.1	—	—	—	9.1	0.19	27	—	—	—
  LYD662	72008.3	—	—	—	8.7	0.26	22	—	—	—
  LYD646	73042.4	—	—	—	8.7	0.30	21	—	—	—
  LYD599	72266.2	—	—	—	9.4	0.13	31	—	—	—
  LYD562	73484.2	—	—	—	8.8	0.25	23	—	—	—
  CONT.	—	—	—	—	7.2	—	—	—	—	—
  LYD660	73929.2	0.8	0.09	21	8.5	0.14	21	—	—	—
  LYD660	73933.5	0.8	0.30	14	9.4	0.03	34	0.4	0.18	15
  LYD629	72195.1	0.8	0.13	20	8.2	0.22	18	—	—	—
  LYD629	72198.3	—	—	—	8.7	0.09	25	—	—	—
  LYD614	73916.4	—	—	—	8.1	0.27	16	—	—	—
  LYD614	73916.5	—	—	—	8.2	0.26	17	0.4	0.18	16
  LYD609	73128.5	—	—	—	8.4	0.21	19	0.4	0.13	19
  LYD584	73915.4	—	—	—	8.1	0.25	16	—	—	—
  LYD570	71937.3	0.8	0.16	18	8.5	0.15	21	—	—	—
  LYD561	72177.2	—	—	—	—	—	—	0.4	0.28	13
  CONT.	—	0.7	—	—	7.0	—	—	0.3	—	—
  LYD672	72348.2	—	—	—	—	—	—	0.3	0.18	10
  LYD635	72626.2	—	—	—	5.5	0.17	14	0.3	0.07	12
  LYD632	72770.2	—	—	—	5.7	0.10	19	0.3	0.17	11
  LYD632	72771.1	—	—	—	5.6	0.11	17	0.3	0.07	13
  LYD632	72774.4	—	—	—	5.3	0.27	11	—	—	—
  LYD627	72765.1	—	—	—	6.0	0.04	25	—	—	—
  LYD627	72766.1	—	—	—	5.4	0.20	13	—	—	—
  LYD627	72767.1	—	—	—	5.8	0.06	22	0.3	0.08	14
  LYD623	71970.2	0.7	0.21	21	—	—	—	—	—	—
  LYD623	71974.3	0.7	0.28	18	—	—	—	—	—	—
  LYD580	72188.2	—	—	—	5.4	0.24	12	—	—	—
  LYD580	72189.2	—	—	—	5.5	0.16	15	0.3	0.06	14
  LYD571	72357.5	—	—	—	5.9	0.04	23	0.3	0.09	11
  LYD571	72358.1	—	—	—	5.9	0.04	22	0.3	0.05	14
  LYD571	72358.3	—	—	—	6.7	L	39	0.4	0.02	18
  LYD571	72358.4	—	—	—	5.7	0.06	20	0.3	0.29	7
  LYD560	71925.1	—	—	—	6.2	0.02	28	0.3	0.16	12
  LYD554	72174.4	—	—	—	5.6	0.11	17	—	—	—
  LYD553	72741.2	—	—	—	5.4	0.20	13	0.3	0.22	8
  LYD553	72741.3	—	—	—	—	—	—	0.3	0.22	10
  LYD548	72656.1	—	—	—	5.7	0.07	19	0.3	0.13	12
  LYD548	72677.1	—	—	—	5.4	0.20	13	—	—	—
  LYD547	71980.1	—	—	—	5.8	0.04	21	—	—	—
  LYD538	72835.2	—	—	—	6.4	L	33	0.4	L	20
  LYD527	72241.3	—	—	—	5.4	0.21	13	—	—	—
  LYD527	72245.2	—	—	—	5.5	0.19	14	—	—	—
  LYD527	72246.3	—	—	—	5.4	0.24	12	0.3	0.06	14
  LYD521	72610.1	—	—	—	5.8	0.07	20	0.3	0.22	10
  CONT.	—	0.6	—	—	4.8	—	—	0.3	—	—
  LYD678	72790.1	—	—	—	4.2	0.27	16	—	—	—
  LYD664	72017.7	—	—	—	4.4	0.17	21	—	—	—
  LYD641	72633.4	—	—	—	5.0	0.01	39	0.3	0.15	14
  LYD641	72635.2	0.7	0.23	14	—	—	—	—	—	—
  LYD624	73382.4	—	—	—	—	—	—	0.3	0.27	10
  LYD616	73058.4	—	—	—	4.5	0.09	25	—	—	—
  LYD588	73855.2	—	—	—	4.4	0.18	21	—	—	—
  LYD567	72495.4	0.7	0.29	14	—	—	—	—	—	—
  LYD559	73624.1	0.7	0.22	14	—	—	—	—	—	—
  LYD538	72835.4	0.7	0.28	13	—	—	—	0.3	0.25	11
  LYD537	73630.3	—	—	—	—	—	—	0.3	0.22	12
  LYD521	72607.1	—	—	—	4.3	0.21	19	—	—	—
  CONT.	—	0.6	—	—	3.6	—	—	0.3	—	—
  LYD689	72713.1	—	—	—	7.5	0.23	19	—	—	—
  LYD682	72568.2	0.7	0.28	14	—	—	—	—	—	—
  LYD677	72223.6	—	—	—	7.6	0.19	21	—	—	—
  LYD669	72217.2	—	—	—	7.4	0.24	18	—	—	—
  LYD669	73327.1	0.7	0.14	21	—	—	—	—	—	—
  LYD669	73330.1	—	—	—	7.8	0.15	24	0.4	0.20	12
  LYD666	72394.3	—	—	—	7.6	0.20	21	0.4	0.28	9
  LYD650	72642.5	0.7	0.11	21	—	—	—	—	—	—
  LYD620	73066.3	—	—	—	7.7	0.15	22	0.4	0.26	10
  LYD598	72421.1	—	—	—	7.3	0.27	17	0.4	0.30	9
  LYD598	72445.1	—	—	—	7.4	0.27	18	—	—	—
  LYD574	73119.1	0.7	0.29	14	8.0	0.10	27	—	—	—
  LYD574	73121.2	0.7	0.26	15	—	—	—	—	—	—
  LYD562	73484.2	0.7	0.27	15	7.4	0.26	18	—	—	—
  LYD562	73489.4	—	—	—	7.8	0.13	24	—	—	—
  LYD549	73029.4	—	—	—	7.5	0.21	20	—	—	—
  LYD542	72733.2	0.7	0.24	17	7.4	0.27	18	—	—	—
  LYD542	72735.4	0.7	0.19	18	—	—	—	—	—	—
  LYD542	72736.4	0.7	0.21	16	—	—	—	—	—	—
  LYD536	72531.3	0.7	0.09	23	—	—	—	—	—	—
  CONT.	—	0.6	—	—	6.3	—	—	0.4	—	—
  LYD688	73133.1	—	—	—	8.1	0.01	44	0.4	0.03	25
  LYD688	73134.6	—	—	—	7.4	0.05	33	0.4	0.12	17
  LYD681	73184.1	—	—	—	6.8	0.18	22	0.4	0.16	15
  LYD681	73184.2	—	—	—	6.7	0.23	20	0.4	0.21	14
  LYD681	73186.2	—	—	—	6.9	0.16	24	—	—	—
  LYD675	72644.1	—	—	—	7.6	0.04	36	0.4	0.14	16
  LYD675	72644.3	0.7	0.22	17	6.9	0.15	24	0.4	0.23	13
  LYD675	72648.1	0.7	0.20	18	6.9	0.20	24	—	—	—
  LYD671	72882.3	0.7	0.14	19	—	—	—	—	—	—
  LYD651	73021.3	—	—	—	6.7	0.22	20	—	—	—
  LYD651	73026.4	—	—	—	6.6	0.27	18	0.4	0.27	12
  LYD644	72775.1	0.7	0.25	16	6.5	0.29	17	—	—	—
  LYD639	72548.4	—	—	—	6.6	0.28	19	0.4	0.23	13
  LYD594	73307.1	—	—	—	6.8	0.18	22	0.4	0.20	15
  LYD594	73307.3	—	—	—	6.6	0.28	19	—	—	—
  LYD594	73307.4	—	—	—	6.6	0.26	18	—	—	—
  LYD577	72748.3	—	—	—	6.7	0.21	21	0.4	0.24	13
  LYD545	72508.2	0.7	0.30	13	—	—	—	—	—	—
  LYD534	72409.1	—	—	—	7.0	0.15	25	0.4	0.15	16
  LYD534	72414.3	—	—	—	6.6	0.28	18	—	—	—
  LYD524	72859.3	—	—	—	6.8	0.20	21	0.4	0.21	13
  LYD524	72859.4	0.7	0.12	20	—	—	—	—	—	—
  LYD522	72720.1	0.7	0.27	14	—	—	—	—	—	—
  CONT.	—	0.6	—	—	5.6	—	—	0.3	—	—
  Table 63. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L—p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). “—” = results are still unavailable.

Example 17 Evaluating Transgenic Arabidopsis Under Normal Conditions Using In Vitro Assays [Tissue Culture T2 and T1 Plants, TC-T2 and TC-T1 Assays]
• Surface sterilized seeds were sown in basal media [50% Murashige-Skoog medium (MS) supplemented with 0.8% plant agar as solidifying agent] in the presence of Kanamycin (used as a selecting agent). After sowing, plates were transferred for 2-3 days for stratification at 4° C. and then grown at 25° C. under 12-hour light 12-hour dark daily cycles for 7 to 10 days. At this time point, seedlings randomly chosen were carefully transferred to plates containing %4 MS media (15 mM N). For experiments performed in T₂ lines, each plate contained 5 seedlings of the same transgenic event, and 3-4 different plates (replicates) for each event. For each polynucleotide of the invention at least four-five independent transformation events were analyzed from each construct. For experiments performed in T₁ lines, each plate contained 5 seedlings of 5 independent transgenic events and 3-4 different plates (replicates) were planted. In total, for T₁ lines, 20 independent events were evaluated. Plants expressing the polynucleotides of the invention were compared to the average measurement of the control plants (empty vector or GUS reporter gene under the same promoter) used in the same experiment.
• Digital imaging—A laboratory image acquisition system, which consists of a digital reflex camera (Canon EOS 300D) attached with a 55 mm focal length lens (Canon EF-S series), mounted on a reproduction device (Kaiser RS), which includes 4 light units (4×150 Watts light bulb) and located in a darkroom, was used for capturing images of plantlets sawn in agar plates.
• The image capturing process was repeated every 3-4 days starting at day 1 till day 10 (see for example the images in FIGS. 3A-3F). An image analysis system was used, which consists of a personal desktop computer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ 1.39 [Java based image processing program which was developed at the U.S. National Institutes of Health and freely available on the internet at Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/]. Images were captured in resolution of 10 Mega Pixels (3888×2592 pixels) and stored in a low compression JPEG (Joint Photographic Experts Group standard) format. Next, analyzed data was saved to text files and processed using the JMP statistical analysis software (SAS institute).
• Seedling analysis—Using the digital analysis seedling data was calculated, including leaf area, root coverage and root length.
• The relative growth rate for the various seedling parameters was calculated according to the following formulas XV (RGR leaf area), and XVI (RGR root length).
• 
  Relative growth rate of leaf area=Regression coefficient of leaf area along time course.  Formula XV:
• 
  Relative growth rate of root length=Regression coefficient of root length along time course.  Formula XVI:
• At the end of the experiment, plantlets were removed from the media and weighed for the determination of plant fresh weight. Plantlets were then dried for 24 hours at 60° C., and weighed again to measure plant dry weight for later statistical analysis. The fresh and dry weights are provided for each Arabidopsis plant. Growth rate was determined by comparing the leaf area coverage, root coverage and root length, between each couple of sequential photographs, and results were used to resolve the effect of the gene introduced on plant vigor under optimal conditions. Similarly, the effect of the gene introduced on biomass accumulation, under optimal conditions, was determined by comparing the plants' fresh and dry weight to that of control plants (containing an empty vector or the GUS reporter gene under the same promoter). From every construct created, 3-5 independent transformation events were examined in replicates.
• Statistical analyses—To identify genes conferring significantly improved plant vigor or enlarged root architecture, the results obtained from the transgenic plants were compared to those obtained from control plants. To identify outperforming genes and constructs, results from the independent transformation events tested were analyzed separately. To evaluate the effect of a gene event over a control the data was analyzed by Student's t-test and the p value was calculated. Results were considered significant if p≤0.1. The JMP statistics software package was used (Version 5.2.1, SAS Institute Inc., Cary, N.C., USA).
• Experimental Results:
• Results from T2 Plants
• Tables 64-66 summarize the observed phenotypes of transgenic plants expressing the gene constructs using the TC-T2 Assays.
• The genes presented in Table 64 showed a significant improvement as they produced larger plant biomass (plant fresh and dry weight) in T2 generation when grown under normal growth conditions, as compared to control plants grown under identical growth conditions. The genes were cloned under the regulation of a constitutive promoter (At6669, SEQ ID NO:4111).
• The evaluation of each gene was carried out by testing the performance of different number of events. Some of the genes were evaluated in more than one tissue culture assay. The results obtained in these second experiments were significantly positive as well.

• TABLE 64
  Genes showing improved plant performance at Normal growth
  conditions under regulation of At6669 promoter

  Dry Weight [mg]

  Fresh Weight [mg]

  Gene Name	Event #	Ave.	P-Val.	% Incr.	Ave.	P-Val.	% Incr.

  LYD686	72796.2	6.6	L	83	119.8	0.01	51
  LYD686	72798.1	6.8	L	88	127.7	L	61
  LYD685	72458.3	5.8	0.22	61	—	—	—
  LYD685	72458.5	6.5	0.06	80	116.9	0.09	48
  LYD685	72459.1	5.5	0.11	52	125.7	0.27	59
  LYD685	72462.4	—	—	—	105.5	0.09	33
  LYD685	72462.5	4.8	0.14	33	103.3	0.12	30
  LYD673	72662.2	5.2	0.02	44	—	—	—
  LYD673	72664.1	4.8	0.24	33	—	—	—
  LYD673	72666.1	4.5	0.23	23	—	—	—
  LYD663	72856.3	5.4	L	48	102.2	0.29	29
  LYD663	72856.5	5.6	0.01	54	106.3	0.03	34
  LYD663	72858.1	5.6	L	55	98.7	0.07	25
  LYD663	72858.3	4.9	0.07	34	—	—	—
  LYD655	72209.1	—	—	—	106.5	0.21	34
  LYD655	72210.1	4.8	0.26	33	—	—	—
  LYD640	72556.3	6.6	0.01	81	106.2	0.07	34
  LYD640	72557.2	4.6	0.07	27	—	—	—
  LYD640	72558.2	6.2	L	71	105.2	0.04	33
  LYD638	72451.1	6.3	L	73	109.6	0.02	38
  LYD638	72456.2	4.2	0.25	17	—	—	—
  LYD615	72260.1	6.1	0.06	68	104.8	0.17	32
  LYD615	72264.2	5.3	0.02	46	92.9	0.22	17
  LYD613	72512.3	5.0	0.08	37	—	—	—
  LYD613	72514.2	6.1	0.16	68	109.0	0.29	38
  LYD613	72515.4	4.9	0.13	34	99.0	0.24	25
  LYD608	72883.2	5.9	L	63	95.7	0.12	21
  LYD608	72888.2	6.4	L	77	119.5	L	51
  LYD607	71961.1	7.3	L	103	133.1	L	68
  LYD607	71963.1	6.3	0.02	73	119.2	0.04	51
  LYD607	71963.2	5.7	0.09	58	128.8	0.11	63
  LYD607	71963.4	5.1	0.08	40	—	—	—
  LYD597	72419.1	5.1	0.18	41	—	—	—
  LYD597	72419.2	4.1	0.17	13	—	—	—
  LYD597	72419.3	6.6	L	81	106.7	0.01	35
  LYD597	72420.1	4.9	L	34	—	—	—
  LYD597	72443.4	5.8	0.23	59	—	—	—
  LYD583	71943.1	4.7	0.04	30	—	—	—
  LYD579	72350.3	5.1	0.03	40	92.1	0.23	16
  LYD579	72354.1	5.7	0.14	57	104.6	0.15	32
  LYD563	72319.2	4.1	0.19	13	—	—	—
  LYD563	72319.4	6.5	0.02	78	110.3	0.12	39
  LYD563	72321.2	4.8	0.17	32	—	—	—
  LYD563	72323.1	5.0	0.07	38	—	—	—
  CONT.	—	3.6	—	—	79.2	—	—
  LYD676	73880.1	4.9	0.17	43	97.8	0.17	41
  LYD676	73884.1	—	—	—	85.6	0.16	23
  LYD660	73932.1	5.1	0.03	49	107.4	L	54
  LYD654	73924.4	4.7	0.06	36	96.9	0.05	39
  LYD654	73926.3	4.3	0.17	25	84.0	0.20	21
  LYD647	72784.3	5.6	0.09	64	116.9	0.07	68
  LYD647	72785.2	4.8	0.04	38	103.7	L	49
  LYD628	73678.3	4.5	0.25	30	92.9	0.15	34
  LYD628	73679.2	7.6	0.11	120	136.4	0.11	96
  LYD614	73917.1	4.8	0.04	38	106.8	0.04	54
  LYD614	73919.3	6.2	0.04	78	128.1	0.05	84
  LYD611	71988.3	4.6	0.07	35	93.1	0.04	34
  LYD611	71992.5	5.2	0.02	51	104.8	0.13	51
  LYD611	71992.6	5.7	0.07	66	92.1	0.13	32
  LYD605	73643.1	5.8	0.05	67	104.0	0.07	50
  LYD605	73644.2	5.1	0.04	47	106.8	0.07	54
  LYD605	73645.2	—	—	—	79.8	0.29	15
  LYD598	72421.2	5.8	L	67	104.4	0.04	50
  LYD598	72423.2	4.6	0.07	33	—	—	—
  LYD598	72423.3	4.8	0.16	38	92.8	0.04	33
  LYD591	73907.3	5.0	0.04	46	91.2	0.24	31
  LYD589	73898.1	5.5	L	61	119.7	0.08	72
  LYD589	73902.3	4.6	0.24	35	—	—	—
  LYD589	73903.3	5.5	L	61	111.2	0.02	60
  LYD588	73852.2	4.7	0.22	37	—	—	—
  LYD588	73854.1	5.2	0.10	51	111.9	0.03	61
  LYD588	73855.3	5.8	0.03	69	115.6	0.04	66
  LYD584	73910.2	4.5	0.08	30	99.5	0.01	43
  LYD584	73915.4	—	—	—	84.7	0.24	22
  LYD566	73482.4	6.4	L	85	127.5	L	83
  LYD566	73483.5	4.8	0.13	40	101.1	0.11	45
  LYD535	72850.5	5.0	0.21	45	95.7	0.29	38
  LYD535	72851.6	4.9	0.04	43	98.1	0.06	41
  LYD535	72852.1	6.2	L	79	121.1	L	74
  CONT.	—	3.4	—	—	69.5	—	—
  LYD682	72565.2	—	—	—	83.8	0.10	23
  LYD682	72566.1	—	—	—	91.7	0.02	35
  LYD665	72215.2	4.5	0.22	18	—	—	—
  LYD665	72216.4	5.3	0.18	39	95.8	0.03	41
  LYD650	72641.2	—	—	—	86.2	0.21	27
  LYD644	72775.1	—	—	—	96.4	0.03	41
  LYD644	72780.2	—	—	—	92.4	0.11	36
  LYD626	72001.1	—	—	—	82.2	0.10	21
  LYD626	72001.3	5.1	0.15	35	96.4	0.09	42
  LYD626	72002.1	—	—	—	102.3	L	50
  LYD555	74193.5	—	—	—	92.1	0.02	35
  LYD555	74194.1	4.8	0.17	26	100.6	L	48
  LYD555	74197.1	—	—	—	95.5	L	40
  LYD542	72733.1	4.9	0.17	28	96.4	0.15	41
  LYD542	72733.2	—	—	—	99.1	0.15	45
  LYD542	72736.4	—	—	—	101.3	0.14	49
  LYD540	74182.4	—	—	—	84.0	0.18	23
  LYD540	74183.3	—	—	—	91.9	0.23	35
  LYD536	72529.5	—	—	—	90.3	0.03	33
  LYD536	72532.2	4.8	0.06	26	—	—	—
  LYD533	72721.1	5.0	0.23	30	97.7	0.19	43
  LYD533	72721.2	4.7	0.20	23	95.2	0.02	40
  LYD533	72722.1	—	—	—	89.2	0.09	31
  LYD533	72723.1	5.8	0.29	51	117.9	0.07	73
  LYD526	72164.4	4.7	0.11	24	96.3	0.12	41
  CONT.	—	3.8	—	—	68.1	—	—
  LYD679	72650.6	8.6	0.03	56	151.9	0.09	33
  LYD645	72339.2	10.2	0.01	85	192.3	0.02	68
  LYD636	72200.3	9.2	0.02	68	160.6	0.05	40
  LYD634	71998.2	9.9	0.03	80	197.9	0.05	73
  LYD634	71999.3	7.5	0.24	36	137.0	0.30	20
  LYD567	72496.3	8.8	0.21	59	—	—	—
  LYD556	72904.3	9.1	0.06	65	184.3	0.09	61
  LYD552	72983.2	9.5	0.01	73	170.6	0.02	49
  CONT.	—	5.5	—	—	114.7	—	—
  LYD689	72712.3	5.5	0.24	37	—	—	—
  LYD689	72713.1	9.6	0.05	141	174.7	L	118
  LYD675	72643.1	7.3	0.08	82	142.2	0.08	77
  LYD675	72644.3	8.7	0.01	119	174.8	L	118
  LYD675	72646.1	9.6	L	140	165.4	0.01	106
  LYD671	72877.1	—	—	—	100.3	0.12	25
  LYD671	72878.2	6.8	0.02	69	119.2	0.16	49
  LYD671	72880.1	—	—	—	104.4	0.05	30
  LYD654	73922.3	6.6	L	65	119.5	0.03	49
  LYD654	73924.5	5.7	0.16	44	—	—	—
  LYD652	72560.2	7.3	0.03	83	141.0	0.04	76
  LYD652	72561.5	7.4	0.02	86	161.3	0.06	101
  LYD652	72563.1	9.1	0.06	129	163.1	0.02	103
  LYD648	72834.2	9.2	L	130	177.1	L	121
  LYD641	72633.4	5.8	0.22	44	116.2	0.22	45
  LYD641	72635.2	7.4	0.06	86	142.4	0.03	78
  LYD636	72199.3	7.8	0.10	95	135.9	0.08	69
  LYD636	72202.3	6.0	0.28	49	—	—	—
  LYD602	72613.1	6.1	0.19	52	134.4	0.13	68
  LYD602	72614.2	7.5	L	87	158.5	L	98
  LYD599	72265.3	6.3	0.07	59	—	—	—
  LYD599	72266.4	7.8	0.03	96	131.4	L	64
  LYD599	72270.4	8.8	L	121	157.8	L	97
  LYD555	74194.1	6.7	0.01	67	131.9	0.01	64
  LYD555	74197.1	7.9	L	98	137.4	0.03	71
  LYD555	74197.4	7.9	0.03	97	158.8	0.02	98
  LYD555	74197.6	5.0	0.09	27	94.8	0.06	18
  LYD548	72655.3	8.9	0.03	123	152.2	0.07	90
  LYD548	72656.2	5.3	0.14	34	97.7	0.20	22
  LYD541	72729.2	6.8	0.06	71	136.9	0.12	71
  LYD541	72729.7	5.2	0.29	32	—	—	—
  LYD541	72731.4	6.5	0.14	62	109.5	0.27	37
  LYD540	74182.2	5.0	0.20	26	98.0	0.17	22
  LYD540	74182.7	6.8	L	71	133.2	0.03	66
  LYD524	72859.1	9.6	L	141	178.9	L	123
  LYD524	72859.4	8.0	0.06	100	129.9	0.09	62
  CONT.	—	4.0	—	—	80.2	—	—
  LYD683	72866.4	11.2	L	159	211.9	L	147
  LYD683	72870.1	6.9	0.10	59	117.4	0.12	37
  LYD683	72870.4	5.5	0.12	28	—	—	—
  LYD654	73922.4	5.2	0.26	20	107.6	0.16	25
  LYD654	73924.4	6.6	0.21	53	120.2	0.30	40
  LYD654	73924.5	5.8	0.08	33	114.2	0.01	33
  LYD654	73926.3	7.9	0.01	82	146.8	L	71
  LYD628	73679.2	5.8	0.22	34	114.2	0.23	33
  LYD628	73680.2	5.5	0.21	26	—	—	—
  LYD628	73681.5	8.7	0.06	100	152.2	0.06	77
  LYD624	73181.3	5.8	0.15	34	114.2	0.22	33
  LYD624	73382.3	5.9	0.30	36	116.6	0.22	36
  LYD624	73383.1	6.3	L	45	124.5	0.01	45
  LYD624	73385.3	5.6	0.22	29	117.8	0.11	37
  LYD605	73642.3	6.2	L	44	114.7	0.09	33
  LYD604	73045.1	6.9	0.17	60	125.7	0.22	46
  LYD604	73045.4	6.5	L	49	120.0	0.04	40
  LYD604	73048.2	6.6	0.26	51	119.3	0.28	39
  LYD598	72421.1	6.2	0.26	42	—	—	—
  LYD598	72445.1	6.0	0.01	39	112.0	0.07	30
  LYD581	73107.1	5.9	0.03	37	108.6	0.10	27
  LYD581	73107.5	5.5	0.27	27	—	—	—
  LYD581	73109.2	7.7	0.04	78	144.2	L	68
  LYD581	73109.3	8.5	L	95	142.1	0.04	65
  LYD581	73110.1	7.8	L	81	135.5	L	58
  LYD566	73480.4	7.7	0.03	78	143.1	0.07	67
  LYD566	73482.4	7.2	L	65	123.7	L	44
  LYD566	73483.6	5.0	0.26	15	—	—	—
  LYD554	72171.1	9.1	0.01	109	153.4	0.01	79
  LYD554	72174.4	7.2	0.17	65	126.6	0.20	47
  LYD550	74186.3	6.5	0.14	50	—	—	—
  LYD550	74187.1	6.2	L	44	110.1	0.11	28
  LYD550	74187.2	6.3	0.12	45	121.3	0.13	41
  LYD548	72655.3	6.1	0.03	41	109.7	0.10	28
  LYD548	72673.3	5.2	0.28	20	106.8	0.26	24
  LYD540	74181.2	8.7	L	101	157.3	L	83
  LYD540	74182.2	7.2	L	67	134.2	L	56
  LYD540	74182.4	7.0	0.05	61	129.8	0.01	51
  LYD540	74182.7	5.9	0.27	35	117.9	0.10	37
  LYD535	72850.5	6.8	0.07	57	116.6	0.14	36
  LYD535	72851.4	6.1	0.15	40	—	—	—
  LYD535	72852.2	5.2	0.25	21	—	—	—
  LYD530	73052.3	9.5	L	120	153.3	L	79
  LYD530	73053.3	9.0	L	107	152.0	L	77
  LYD530	73053.5	7.1	0.03	64	127.7	0.07	49
  LYD530	73054.3	5.3	0.22	22	108.0	0.21	26
  CONT.	—	4.3	—	—	85.9	—	—
  LYD637	73685.1	9.0	0.15	42	173.7	0.13	53
  LYD637	73685.2	8.0	0.18	26	142.9	0.25	26
  LYD637	73685.3	9.8	0.03	54	183.6	0.05	62
  LYD605	73642.3	—	—	—	149.8	0.17	32
  LYD605	73644.2	8.2	0.14	29	142.8	0.22	26
  LYD605	73645.2	10.2	0.03	60	168.6	0.12	49
  LYD585	72986.1	8.5	0.13	34	167.2	0.08	48
  LYD585	72986.4	9.1	0.09	44	161.4	0.09	42
  LYD573	72977.1	—	—	—	151.0	0.24	33
  LYD573	72978.2	—	—	—	151.0	0.24	33
  LYD559	73627.2	8.3	0.24	31	140.9	0.28	24
  LYD537	73633.4	8.8	0.24	39	—	—	—
  LYD537	73633.5	—	—	—	136.2	0.29	20
  CONT.	—	6.3	—	—	113.3	—	—
  LYD683	72868.1	7.2	0.28	24	—	—	—
  LYD647	72785.3	8.2	0.11	41	161.8	0.10	35
  LYD611	71992.5	9.7	0.02	65	188.8	L	57
  LYD611	71992.6	8.2	0.11	40	149.9	0.21	25
  LYD585	72987.2	7.5	0.29	27	—	—	—
  LYD573	72973.2	8.4	0.11	44	161.1	0.11	34
  LYD550	74188.2	7.6	0.07	30	152.9	0.07	27
  CONT.	—	5.9	—	—	120.2	—	—
  LYD686	72796.2	5.3	0.28	26	—	—	—
  LYD673	72662.2	6.5	0.03	55	130.2	0.04	42
  LYD663	72853.5	6.5	0.17	55	—	—	—
  LYD655	72209.1	7.1	0.11	70	141.0	0.07	54
  LYD638	72432.2	6.5	0.19	55	117.7	0.20	29
  LYD638	72451.1	—	—	—	128.8	0.23	41
  LYD615	72262.1	6.0	0.06	44	140.9	0.06	54
  LYD613	72512.1	—	—	—	120.1	0.21	31
  LYD608	72885.3	6.7	0.08	59	124.6	0.08	36
  LYD608	72887.1	8.8	0.03	110	174.5	0.05	91
  LYD608	72888.2	5.3	0.28	27	112.6	0.24	23
  LYD607	71961.1	5.9	0.08	40	125.3	0.09	37
  LYD607	71963.2	5.9	0.08	40	116.2	0.22	27
  LYD597	72419.2	7.8	0.02	85	151.2	0.04	65
  LYD597	72419.3	7.2	0.08	73	121.1	0.17	32
  LYD597	72420.1	8.0	L	91	158.4	0.02	73
  LYD583	71943.1	5.8	0.23	39	116.7	0.24	28
  LYD583	71943.5	5.5	0.28	30	—	—	—
  LYD579	72350.3	6.9	0.05	64	162.1	0.02	77
  LYD579	72354.1	8.3	0.02	98	169.3	0.05	85
  LYD563	72319.2	6.9	0.01	65	124.5	0.06	36
  LYD563	72324.2	8.0	0.12	90	182.8	0.04	100
  CONT.	—	4.2	—	—	91.5	—	—
  LYD592	74348.3	—	—	—	157.0	0.27	29
  LYD592	74350.1	—	—	—	212.2	0.13	75
  LYD592	74351.1	—	—	—	153.7	0.14	26
  LYD592	74353.3	—	—	—	230.9	L	90
  CONT.	—	—	—	—	121.6	—	—
  LYD676	73881.2	5.8	0.15	16	131.1	0.29	51
  LYD591	73905.1	5.9	0.13	16	97.4	0.24	12
  CONT.	—	5.0	—	—	86.9	—	—
  LYD665	72211.2	6.8	L	97	127.0	L	82
  LYD665	72216.4	5.0	0.11	45	97.7	0.14	40
  LYD665	72216.5	6.3	0.13	84	120.8	0.17	74
  LYD665	72216.6	5.3	0.13	54	100.8	0.25	45
  LYD592	74348.3	6.6	0.02	93	122.9	0.02	77
  LYD592	74348.4	8.3	0.02	143	149.5	0.02	115
  LYD592	74349.2	6.2	0.06	80	112.5	0.07	62
  LYD592	74350.1	9.6	L	179	175.3	L	152
  LYD592	74351.1	9.8	0.10	185	196.6	0.09	183
  LYD532	74343.2	5.6	L	64	108.0	L	55
  LYD532	74344.2	4.8	0.20	40	84.0	0.26	21
  LYD532	74345.1	4.7	0.08	36	89.0	0.05	28
  LYD532	74345.3	6.5	0.01	90	135.9	0.01	95
  LYD525	74229.2	6.4	0.04	87	117.9	0.02	69
  LYD525	74230.2	7.8	0.09	128	141.5	0.09	103
  LYD525	74233.1	4.3	0.16	25	81.1	0.28	17
  CONT.	—	3.4	—	—	69.6	—	—
  LYD679	72652.3	6.7	0.03	55	153.5	0.11	41
  LYD670	73346.2	4.9	0.20	13	—	—	—
  LYD670	73348.1	5.7	0.04	33	—	—	—
  LYD646	73040.3	6.5	0.19	52	143.2	0.26	32
  LYD646	73040.4	5.6	L	31	134.8	0.17	24
  LYD646	73042.4	5.1	0.23	19	—	—	—
  LYD616	73057.4	5.1	0.20	19	—	—	—
  LYD609	73124.2	8.7	0.04	101	200.8	0.07	85
  LYD609	73128.5	5.4	0.23	26	—	—	—
  LYD604	73047.3	5.8	0.08	34	—	—	—
  LYD596	73634.2	5.4	0.09	26	127.1	0.26	17
  LYD581	73107.1	7.2	L	67	164.9	0.07	52
  LYD558	73112.3	5.5	0.01	28	137.2	0.12	26
  LYD558	73113.1	5.1	0.13	18	—	—	—
  LYD558	73114.3	6.5	0.21	51	163.2	0.26	50
  LYD552	72981.3	6.9	L	60	168.9	L	56
  LYD552	72981.4	5.9	0.17	37	145.5	0.05	34
  LYD530	73052.3	5.2	0.06	21	—	—	—
  LYD529	72899.7	6.4	L	48	135.5	0.08	25
  CONT.	—	4.3	—	—	108.5	—	—
  Table 64. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L—p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). “—” = results are still unavailable.

• The genes presented in Tables 65 and 66 show a significant improvement in plant performance since they produced a larger leaf biomass (leaf are) and root biomass (root length and root coverage) (Table 65) and a higher relative growth rate of leaf area, root coverage and root length (Table 66) when grown under normal growth conditions, as compared to control plants grown under identical growth conditions. Plants producing larger root biomass have better possibilities to absorb larger amount of nitrogen from soil. Plants producing larger leaf biomass have better ability to produce assimilates. The genes were cloned under the regulation of a constitutive promoter (At6669). The evaluation of each gene was performed by testing the performance of different number of events. Some of the genes were evaluated in more than one N tissue culture assay. This second experiment confirmed the significant increment in leaf and root performance. Event with p-value <0.1 was considered statistically significant.

• TABLE 65
  Genes showing improved plant performance at Normal growth
  conditions under regulation of At6669 promoter

  Leaf Area [cm2]

  Roots Coverage [cm2]

  Roots Length [cm]

  			P-	%		P-	%		P-	%
  Gene Name	Event #	Ave.	Val.	Incr.	Ave.	Val.	Incr.	Ave.	Val.	Incr.
  LYD686	72796.2	0.5	L	56	10.9	0.03	48	7.8	0.23	6
  LYD686	72798.1	0.5	L	59	—	—	—	—	—	—
  LYD685	72458.3	0.5	0.10	46	—	—	—	—	—	—
  LYD685	72458.5	0.5	L	58	12.4	0.02	67	8.4	L	15
  LYD685	72459.1	0.4	0.08	33	8.8	0.18	19	—	—	—
  LYD685	72462.4	0.5	0.08	45	—	—	—	—	—	—
  LYD685	72462.5	0.5	0.05	43	10.0	0.18	36	—	—	—
  LYD673	72662.2	0.4	0.06	29	9.3	0.17	25	8.0	L	9
  LYD673	72663.3	0.4	0.07	27	—	—	—	—	—	—
  LYD673	72664.1	0.4	0.15	26	—	—	—	—	—	—
  LYD673	72666.1	0.4	0.14	25	8.8	0.23	20	7.8	0.19	6
  LYD663	72856.3	0.5	0.04	43	10.6	0.07	43	—	—	—
  LYD663	72856.5	0.5	0.01	44	10.4	L	40	—	—	—
  LYD663	72858.1	0.5	L	42	9.9	0.07	33	—	—	—
  LYD663	72858.3	0.4	0.12	22	9.9	0.03	33	—	—	—
  LYD655	72210.1	0.4	0.21	34	9.5	0.21	29	—	—	—
  LYD640	72556.3	0.5	0.02	57	11.3	0.03	53	—	—	—
  LYD640	72557.2	0.4	L	30	9.2	0.05	24	—	—	—
  LYD640	72558.2	0.5	L	55	11.4	0.04	54	8.1	0.05	10
  LYD638	72432.2	—	—	—	8.1	0.18	10	7.8	0.11	7
  LYD638	72451.1	0.5	L	66	12.0	L	63	8.1	L	10
  LYD615	72259.2	0.4	0.19	32	—	—	—	—	—	—
  LYD615	72260.1	0.5	0.05	58	11.1	0.01	50	8.3	L	13
  LYD615	72264.2	0.4	0.02	32	—	—	—	—	—	—
  LYD613	72512.3	0.4	0.05	28	8.7	0.11	18	—	—	—
  LYD613	72514.2	0.5	0.11	53	—	—	—	—	—	—
  LYD613	72515.4	0.4	0.01	24	—	—	—	—	—	—
  LYD608	72883.2	0.5	L	40	9.9	L	34	—	—	—
  LYD608	72888.2	0.5	0.01	44	12.9	L	74	8.1	0.01	11
  LYD607	71961.1	0.6	L	73	11.5	L	56	—	—	—
  LYD607	71963.1	0.5	0.02	59	9.7	0.23	32	—	—	—
  LYD607	71963.2	0.5	0.02	43	11.6	L	57	—	—	—
  LYD607	71963.4	0.4	0.05	32	—	—	—	—	—	—
  LYD597	72419.3	0.5	L	37	8.6	0.19	16	—	—	—
  LYD597	72420.1	0.4	0.16	11	—	—	—	—	—	—
  LYD583	71943.1	0.4	0.10	13	—	—	—	—	—	—
  LYD579	72350.2	0.4	0.03	18	8.0	0.15	8	—	—	—
  LYD579	72350.3	0.5	L	37	10.9	0.06	47	7.8	0.19	6
  LYD579	72354.1	0.5	0.02	43	11.2	0.01	51	8.0	0.03	9
  LYD563	72319.2	0.4	0.02	20	8.8	0.19	19	—	—	—
  LYD563	72319.4	0.5	0.04	54	11.4	0.01	54	7.8	0.17	6
  LYD563	72321.2	0.4	0.24	25	—	—	—	—	—	—
  LYD563	72323.1	0.4	0.04	33	11.8	0.08	59	—	—	—
  LYD563	72324.2	—	—	—	—	—	—	7.8	0.15	7
  CONT.	—	0.3	—	—	7.4	—	—	7.3	—	—
  LYD676	73880.1	0.5	0.18	26	—	—	—	—	—	—
  LYD676	73884.1	—	—	—	—	—	—	7.7	0.23	5
  LYD660	73932.1	0.5	0.20	18	—	—	—	—	—	—
  LYD654	73924.4	0.5	0.11	21	7.5	0.24	25	7.7	0.15	6
  LYD647	72784.3	0.6	0.13	45	10.3	0.08	71	8.2	0.01	12
  LYD647	72785.2	0.5	0.04	28	7.5	0.19	25	—	—	—
  LYD628	73678.3	0.5	0.27	20	—	—	—	—	—	—
  LYD628	73679.2	0.6	0.10	54	10.7	0.08	77	8.0	0.04	9
  LYD628	73681.1	—	—	—	—	—	—	7.8	0.12	7
  LYD614	73917.1	0.5	0.09	35	—	—	—	—	—	—
  LYD614	73919.3	0.6	0.09	60	—	—	—	—	—	—
  LYD611	71988.3	—	—	—	7.4	0.22	23	7.8	0.18	7
  LYD611	71992.3	—	—	—	—	—	—	7.9	0.08	8
  LYD611	71992.5	0.5	0.05	33	—	—	—	7.8	0.18	7
  LYD611	71992.6	0.6	0.03	43	9.0	0.12	49	8.0	0.07	9
  LYD605	73643.1	0.5	0.17	26	—	—	—	—	—	—
  LYD605	73644.2	0.5	0.05	30	7.3	0.25	21	—	—	—
  LYD598	72421.2	0.5	0.01	38	7.6	0.27	27	8.1	0.02	11
  LYD598	72423.3	—	—	—	8.9	0.03	47	7.8	0.12	7
  LYD591	73907.3	0.5	0.09	27	8.1	0.09	34	7.9	0.18	9
  LYD591	73907.4	—	—	—	—	—	—	7.8	0.13	7
  LYD589	73898.1	0.6	0.01	43	8.3	0.09	37	7.7	0.19	6
  LYD589	73903.3	0.5	0.08	35	—	—	—	7.8	0.11	7
  LYD588	73854.1	0.6	0.01	52	8.5	0.12	40	8.5	L	16
  LYD588	73855.3	0.5	0.03	37	8.6	0.08	42	7.6	0.28	5
  LYD584	73910.2	0.4	0.26	14	—	—	—	—	—	—
  LYD584	73915.4	—	—	—	—	—	—	7.8	0.11	8
  LYD566	73480.4	—	—	—	—	—	—	7.8	0.21	7
  LYD566	73482.4	0.6	L	59	8.7	0.07	44	7.8	0.18	7
  LYD566	73483.5	0.5	0.22	21	7.6	0.16	26	—	—	—
  LYD535	72851.6	0.5	0.06	26	—	—	—	7.8	0.09	7
  LYD535	72852.1	0.6	L	42	9.4	0.01	56	—	—	—
  CONT.	—	0.4	—	—	6.0	—	—	7.3	—	—
  LYD682	72566.1	0.5	0.12	13	—	—	—	—	—	—
  LYD665	72215.2	0.5	0.08	27	8.5	0.09	19	7.9	0.07	8
  LYD665	72216.4	0.5	0.11	29	9.6	0.10	33	8.0	0.04	10
  LYD650	72639.4	—	—	—	—	—	—	8.1	L	10
  LYD650	72641.2	0.5	0.19	17	8.7	0.06	21	7.7	0.17	5
  LYD644	72775.1	0.5	L	27	9.3	0.11	29	—	—	—
  LYD644	72778.1	—	—	—	—	—	—	7.9	0.03	7
  LYD644	72780.2	0.5	0.18	20	9.1	0.11	27	7.8	0.14	7
  LYD639	72548.6	—	—	—	—	—	—	7.7	0.18	5
  LYD639	72549.3	—	—	—	—	—	—	8.2	L	12
  LYD639	72551.1	0.5	0.14	16	8.8	0.20	23	8.0	0.05	9
  LYD626	72001.3	0.5	0.02	28	—	—	—	—	—	—
  LYD626	72002.1	0.6	L	37	11.1	L	54	8.3	0.03	13
  LYD626	72004.4	—	—	—	8.5	0.15	19	8.0	0.07	9
  LYD606	72500.3	—	—	—	—	—	—	7.9	0.02	8
  LYD555	74193.5	0.5	0.13	13	9.7	0.09	35	8.0	0.05	8
  LYD555	74194.1	0.5	0.09	24	—	—	—	7.7	0.21	5
  LYD555	74197.1	0.5	0.05	17	—	—	—	—	—	—
  LYD542	72733.1	0.5	0.08	24	—	—	—	—	—	—
  LYD542	72733.2	0.5	0.29	14	—	—	—	—	—	—
  LYD542	72736.1	—	—	—	—	—	—	7.9	0.02	8
  LYD542	72736.4	0.5	0.16	26	8.9	0.15	24	7.9	0.15	8
  LYD540	74182.2	0.5	0.10	26	—	—	—	—	—	—
  LYD540	74182.4	—	—	—	8.2	0.14	14	—	—	—
  LYD536	72529.5	0.5	0.18	16	—	—	—	—	—	—
  LYD536	72532.2	0.5	0.06	21	8.6	0.20	20	8.0	0.09	8
  LYD533	72721.1	0.5	0.06	27	9.5	0.08	33	8.4	L	14
  LYD533	72721.2	0.5	0.05	21	9.0	0.03	25	—	—	—
  LYD533	72722.1	0.5	0.17	15	—	—	—	—	—	—
  LYD533	72723.1	0.5	0.09	34	9.8	0.14	36	7.9	0.06	8
  LYD526	72164.4	—	—	—	8.2	0.25	15	—	—	—
  LYD526	72168.4	—	—	—	—	—	—	7.6	0.29	4
  CONT.	—	0.4	—	—	7.2	—	—	7.3	—	—
  LYD679	72650.6	0.7	0.01	39	11.6	0.17	29	—	—	—
  LYD679	72652.3	0.6	0.25	25	11.4	0.29	27	—	—	—
  LYD645	72339.2	0.7	0.01	47	11.8	0.13	31	—	—	—
  LYD636	72200.3	0.7	0.03	33	11.8	0.10	31	—	—	—
  LYD634	71998.2	0.7	0.03	45	15.0	0.06	67	8.2	0.16	5
  LYD634	71999.3	0.6	0.20	18	—	—	—	—	—	—
  LYD567	72496.3	0.7	0.15	37	—	—	—	—	—	—
  LYD556	72904.3	0.7	0.03	44	12.9	0.03	44	—	—	—
  LYD552	72979.3	—	—	—	—	—	—	8.1	0.15	4
  LYD552	72983.2	0.6	0.03	32	12.2	0.04	36	—	—	—
  LYD529	72898.2	0.6	0.21	27	—	—	—	—	—	—
  CONT.	—	0.5	—	—	9.0	—	—	7.8	—	—
  LYD689	72711.2	—	—	—	—	—	—	7.5	0.18	6
  LYD689	72712.3	—	—	—	8.2	0.21	31	—	—	—
  LYD689	72713.1	0.7	0.01	72	12.6	L	101	8.4	L	20
  LYD675	72643.1	0.6	0.14	43	11.6	0.06	86	7.7	0.19	9
  LYD675	72644.1	—	—	—	—	—	—	7.7	0.13	10
  LYD675	72644.3	0.7	L	86	13.3	L	113	8.3	L	18
  LYD675	72646.1	0.7	L	68	12.5	0.02	100	7.7	0.15	10
  LYD671	72877.1	0.5	0.06	29	9.1	0.09	46	8.0	L	14
  LYD671	72878.2	0.6	0.05	50	11.4	0.09	82	8.1	0.02	16
  LYD671	72880.1	0.5	0.19	28	9.8	0.12	58	8.1	0.03	15
  LYD654	73922.3	0.6	L	54	9.8	L	56	7.9	L	13
  LYD654	73924.4	—	—	—	—	—	—	7.7	0.29	10
  LYD654	73924.5	0.5	0.20	18	9.2	0.01	47	8.0	L	14
  LYD652	72560.1	—	—	—	—	—	—	7.8	0.06	12
  LYD652	72560.2	0.6	0.04	48	12.2	L	96	8.4	L	19
  LYD652	72561.5	0.6	0.02	52	9.7	0.03	56	7.8	0.06	11
  LYD652	72563.1	0.6	0.02	64	12.4	0.04	98	8.5	L	21
  LYD648	72831.3	—	—	—		—	—	7.3	0.28	4
  LYD648	72834.1	—	—	—	8.6	0.16	38	8.1	L	15
  LYD648	72834.2	0.7	L	73	14.8	L	136	8.0	0.09	14
  LYD641	72632.2	—	—	—	—	—	—	7.4	0.27	6
  LYD641	72633.4	0.5	0.11	28	9.6	0.02	54	8.2	L	17
  LYD641	72635.2	0.6	0.04	41	10.6	0.13	70	8.0	0.16	13
  LYD636	72199.3	0.6	0.09	54	10.7	0.11	71	—	—	—
  LYD636	72200.3	—	—	—	—	—	—	7.6	0.11	9
  LYD636	72202.3	—	—	—	8.6	0.15	38	7.4	0.18	6
  LYD602	72613.1	0.5	0.19	34	8.6	0.19	37	—	—	—
  LYD602	72614.2	0.6	L	51	11.3	0.04	81	7.9	0.01	13
  LYD599	72265.3	0.5	0.24	23	—	—	—	—	—	—
  LYD599	72266.4	0.5	0.06	38	—	—	—	—	—	—
  LYD599	72270.4	0.7	L	72	8.0	0.05	29	—	—	—
  LYD555	74193.1	0.5	0.28	15	—	—	—	7.7	0.15	10
  LYD555	74194.1	0.6	L	56	13.0	L	109	8.4	L	20
  LYD555	74197.1	0.7	L	80	9.6	0.04	54	7.6	0.12	9
  LYD555	74197.4	0.7	L	66	11.8	0.01	89	7.9	0.01	12
  LYD555	74197.6	0.5	0.08	28	8.5	0.02	36	7.9	0.10	12
  LYD548	72655.3	0.7	0.01	84	11.6	0.02	85	8.2	0.03	17
  LYD548	72656.2	0.5	0.27	17	8.9	0.04	42	7.8	0.04	11
  LYD548	72673.3	—	—	—	7.8	0.10	24	7.6	0.06	8
  LYD548	72677.1	—	—	—	7.1	0.24	14	7.5	0.06	8
  LYD541	72729.2	0.6	0.07	55	10.4	0.12	67	7.6	0.26	9
  LYD541	72729.7	0.5	0.16	28	—	—	—	8.0	0.02	14
  LYD541	72731.4	0.6	0.03	45	7.9	0.26	26	—	—	—
  LYD541	72732.1	0.4	0.15	9	—	—	—	7.7	0.06	9
  LYD540	74182.2	0.5	0.17	30	—	—	—	—	—	—
  LYD540	74182.7	0.6	L	54	10.1	0.03	61	7.7	0.02	10
  LYD524	72859.1	0.7	0.01	68	9.9	0.01	59	—	—	—
  LYD524	72859.4	0.6	0.02	63	9.9	0.11	58	7.7	0.22	10
  LYD524	72864.4	—	—	—	—	—	—	7.7	0.05	10
  CONT.	—	0.4	—	—	6.2	—	—	7.0	—	—
  LYD683	72866.4	0.7	L	75	13.8	L	79	—	—	—
  LYD683	72870.1	0.5	0.12	27	11.3	L	47	7.9	0.20	7
  LYD683	72870.4	0.5	0.05	24	11.0	0.05	44	7.9	0.27	6
  LYD654	73922.4	0.5	0.22	14	9.1	0.21	19	—	—	—
  LYD654	73924.4	0.5	0.20	25	11.4	0.09	49	8.0	0.19	8
  LYD654	73924.5	0.5	0.05	19	12.0	L	57	8.4	0.02	13
  LYD654	73926.3	0.6	L	50	12.4	L	62	8.2	0.05	11
  LYD628	73678.3	—	—	—	9.7	0.24	27	—	—	—
  LYD628	73679.2	—	—	—	10.7	0.17	39	8.1	0.19	9
  LYD628	73681.5	0.6	0.02	46	11.9	0.05	56	7.9	0.28	7
  LYD624	73181.3	0.6	0.08	32	10.0	0.10	31	8.1	0.10	9
  LYD624	73383.1	0.6	L	34	9.1	0.06	19	—	—	—
  LYD624	73385.1	0.5	0.22	24	—	—	—	—	—	—
  LYD624	73385.3	0.5	0.07	29	11.0	L	43	8.1	0.12	9
  LYD605	73642.3	0.5	0.06	28	8.7	0.19	14	—	—	—
  LYD604	73045.1	0.6	0.23	31	10.2	0.22	33	8.1	0.10	9
  LYD604	73045.4	0.6	L	31	9.4	L	22	—	—	—
  LYD604	73048.2	—	—	—	9.9	0.11	29	7.9	0.28	6
  LYD598	72421.2	—	—	—	—	—	—	8.0	0.21	8
  LYD598	72445.1	0.5	0.27	14	10.7	0.24	39	8.1	0.18	9
  LYD581	73107.1	0.5	0.06	22	—	—	—	—	—	—
  LYD581	73109.2	0.5	0.07	30	11.2	0.03	46	8.1	0.10	8
  LYD581	73109.3	0.6	0.02	49	10.2	0.08	33	—	—	—
  LYD581	73110.1	0.6	L	51	12.7	L	66	8.0	0.22	7
  LYD566	73480.4	0.7	0.02	56	9.0	0.14	17	—	—	—
  LYD566	73482.4	0.7	L	56	10.5	0.03	37	8.0	0.17	8
  LYD566	73483.6	—	—	—	9.2	0.14	20	8.0	0.10	8
  LYD554	72171.1	0.6	0.02	51	12.1	0.09	57	8.2	0.15	11
  LYD554	72174.4	—	—	—	11.7	0.12	52	8.0	0.26	8
  LYD550	74186.3	0.6	0.16	36	—	—	—	—	—	—
  LYD550	74187.1	0.5	L	29	—	—	—	—	—	—
  LYD550	74187.2	0.6	0.09	42	10.7	0.10	39	8.0	0.26	7
  LYD548	72655.3	0.5	0.05	20	10.3	0.04	35	—	—	—
  LYD548	72673.3	0.5	0.25	11	9.2	0.28	20	8.3	0.04	12
  LYD540	74181.2	0.7	L	58	13.0	L	69	8.5	0.02	14
  LYD540	74182.2	0.6	L	36	10.6	L	38	—	—	—
  LYD540	74182.4	0.5	0.06	20	10.8	0.03	41	8.3	0.05	11
  LYD540	74182.7	0.5	0.25	25	10.0	0.20	30	—	—	—
  LYD535	72850.5	0.6	0.02	33	9.3	0.14	22	—	—	—
  LYD535	72851.4	0.5	0.18	23	—	—	—	—	—	—
  LYD535	72852.2	—	—	—	—	—	—	7.9	0.28	7
  LYD530	73052.3	0.7	L	63	13.5	L	76	8.2	0.04	11
  LYD530	73053.3	0.7	L	61	13.1	L	71	8.1	0.11	9
  LYD530	73053.4	—	—	—	10.1	0.16	32	8.1	0.12	9
  LYD530	73053.5	0.6	0.05	40	12.5	L	63	8.2	0.05	11
  LYD530	73054.3	—	—	—	9.1	0.21	19	8.1	0.09	9
  CONT.	—	0.4	—	—	7.7	—	—	7.4	—	—
  LYD677	72223.1	—	—	—	13.3	0.25	15	8.6	0.02	5
  LYD677	72223.6	0.7	0.04	27	14.2	0.13	23	8.6	0.10	5
  LYD677	72223.7	—	—	—	—	—	—	8.5	0.23	4
  LYD637	73685.1	0.7	0.08	44	14.3	0.23	24	8.6	0.10	5
  LYD637	73685.2	0.7	0.03	30	—	—	—	—	—	—
  LYD637	73685.3	0.8	0.02	47	13.9	0.25	21	—	—	—
  LYD625	72756.1	0.6	0.16	23	—	—	—	—	—	—
  LYD605	73641.1	0.6	0.19	21	—	—	—	—	—	—
  LYD605	73642.3	0.7	0.15	34	—	—	—	—	—	—
  LYD605	73644.2	0.7	0.02	33	—	—	—	—	—	—
  LYD605	73645.2	0.8	L	62	14.8	0.08	28	—	—	—
  LYD585	72986.1	0.7	0.04	38	14.5	0.06	26	8.8	0.03	7
  LYD585	72986.4	0.7	0.01	45	13.9	0.11	21	8.7	0.14	6
  LYD585	72988.3	0.7	0.10	38	—	—	—	—	—	—
  LYD573	72974.2	0.6	0.25	15	14.2	0.09	23	8.4	0.20	2
  LYD573	72977.1	0.6	0.26	20	—	—	—	—	—	—
  LYD573	72978.2	0.7	0.12	35	—	—	—	—	—	—
  LYD566	73481.2	0.6	0.10	24	—	—	—	—	—	—
  LYD566	73483.6	—	—	—	—	—	—	8.4	0.21	3
  LYD559	73627.2	0.7	0.06	34	—	—	—	8.7	0.01	7
  LYD537	73628.1	0.6	0.28	20	—	—	—	—	—	—
  LYD537	73633.1	0.6	0.12	26	—	—	—	8.7	0.13	6
  LYD537	73633.4	0.7	0.13	36	15.3	0.10	33	8.6	0.08	5
  LYD537	73633.5	0.7	0.05	28	13.1	0.24	14	—	—	—
  CONT.	—	0.5	—	—	11.5	—	—	8.2	—	—
  LYD683	72866.4	—	—	—	—	—	—	7.9	0.15	6
  LYD647	72784.3	—	—	—	—	—	—	7.9	0.15	6
  LYD647	72785.3	0.7	0.05	29	12.9	0.15	21	—	—	—
  LYD647	72785.4	—	—	—	—	—	—	8.0	0.23	7
  LYD647	72786.1	—	—	—	—	—	—	8.2	0.01	10
  LYD611	71991.5	—	—	—	—	—	—	7.9	0.05	7
  LYD611	71992.5	0.8	L	55	13.0	0.17	22	—	—	—
  LYD611	71992.6	0.7	0.02	29	—	—	—	—	—	—
  LYD585	72986.1	—	—	—	—	—	—	7.9	0.11	7
  LYD585	72986.4	—	—	—	—	—	—	8.2	0.06	10
  LYD585	72987.2	—	—	—	—	—	—	7.9	0.22	6
  LYD585	72988.1	0.7	L	29	14.3	L	34	7.9	0.10	6
  LYD573	72973.2	0.6	0.06	26	13.0	0.19	22	7.9	0.17	7
  LYD573	72974.2	—	—	—	—	—	—	7.8	0.22	6
  LYD573	72978.1	0.6	0.18	18	—	—	—	8.2	L	11
  LYD550	74188.2	0.6	0.04	25	—	—	—	—	—	—
  CONT.	—	0.5	—	—	10.7	—	—	7.4	—	—
  LYD686	72796.2	0.5	0.28	12	—	—	—	—	—	—
  LYD673	72662.2	0.6	0.03	29	10.5	0.13	25	—	—	—
  LYD663	72858.1	0.6	0.25	29	—	—	—	7.9	0.27	4
  LYD655	72209.1	0.6	0.08	41	10.3	0.11	23	7.8	0.14	4
  LYD655	72210.1	0.6	0.17	40	11.5	0.02	36	—	—	—
  LYD640	72557.2	0.6	L	40	11.8	0.07	40	7.9	0.27	4
  LYD640	72558.3	0.5	0.10	20	10.0	0.19	19	—	—	—
  LYD638	72432.2	0.6	0.12	28	—	—	—	—	—	—
  LYD638	72451.1	0.6	L	42	11.9	0.05	42	8.0	0.05	6
  LYD615	72262.1	0.6	0.07	35	12.2	0.05	46	8.2	0.13	8
  LYD613	72515.1	0.6	0.07	44	—	—	—	—	—	—
  LYD613	72516.1	0.6	0.06	26	—	—	—	—	—	—
  LYD608	72885.3	—	—	—	—	—	—	8.1	0.02	7
  LYD608	72887.1	0.7	0.04	60	12.4	0.02	47	—	—	—
  LYD608	72888.1	—	—	—	—	—	—	7.9	0.10	4
  LYD608	72888.2	0.5	0.17	17	9.9	0.20	17	8.2	0.06	8
  LYD607	71961.1	0.5	0.12	22	10.5	0.13	25	—	—	—
  LYD607	71963.2	0.5	0.08	23	10.3	0.19	23	7.8	0.19	4
  LYD607	71963.4	—	—	—	—	—	—	7.8	0.20	3
  LYD597	72419.2	0.6	0.06	28	—	—	—	—	—	—
  LYD597	72420.1	0.7	L	48	11.1	0.04	32	—	—	—
  LYD583	71943.1	—	—	—	—	—	—	7.8	0.25	3
  LYD579	72350.3	0.6	0.05	42	11.4	0.04	35	8.1	L	7
  LYD579	72354.1	0.7	0.03	62	12.1	0.05	44	8.2	0.01	8
  LYD563	72319.2	0.6	0.01	37	11.5	0.02	37	8.1	0.05	7
  LYD563	72319.4	—	—	—	—	—	—	7.8	0.21	4
  LYD563	72324.2	0.7	0.10	63	—	—	—	8.4	0.01	11
  CONT.	—	0.4	—	—	8.4	—	—	7.6	—	—
  LYD592	74348.3	0.7	0.15	29	—	—	—	8.6	0.12	8
  LYD592	74349.2	0.7	0.29	15	—	—	—	—	—	—
  LYD592	74350.1	0.8	0.08	40	13.6	0.13	27	—	—	—
  LYD592	74351.1	0.7	0.02	28	13.6	0.04	27	8.3	0.20	4
  LYD592	74353.3	0.9	L	65	16.3	L	52	8.8	L	10
  LYD525	74230.2	0.7	0.19	15	—	—	—	8.4	0.30	5
  CONT.	—	0.6	—	—	10.7	—	—	8.0	—	—
  LYD676	73881.2	0.6	0.14	22	10.4	0.19	32	—	—	—
  LYD591	73905.1	—	—	—	10.3	L	29	8.2	L	11
  CONT.	—	0.5	—	—	7.9	—	—	7.4	—	—
  LYD665	72211.2	0.6	L	72	10.5	0.02	39	8.3	0.02	13
  LYD665	72216.4	0.5	0.16	32	—	—	—	7.7	0.30	5
  LYD665	72216.5	0.5	0.18	31	—	—	—	—	—	—
  LYD665	72216.6	0.4	0.27	24	9.1	0.30	20	7.9	0.21	8
  LYD592	74348.3	0.6	L	70	11.2	L	49	8.0	0.06	9
  LYD592	74348.4	0.6	L	86	14.8	L	97	8.8	L	19
  LYD592	74349.2	0.6	0.04	58	—	—	—	—	—	—
  LYD592	74350.1	0.7	L	109	14.3	L	90	8.3	0.03	13
  LYD592	74351.1	0.7	0.07	96	13.3	0.09	76	8.2	0.05	12
  LYD532	74343.2	0.5	L	51	9.5	0.05	25	—	—	—
  LYD532	74345.1	0.4	0.06	23	9.2	0.12	22	—	—	—
  LYD532	74345.3	0.6	L	78	11.7	L	55	8.0	0.09	8
  LYD525	74229.2	0.5	0.01	56	—	—	—	—	—	—
  LYD525	74230.2	0.6	0.05	83	12.1	0.18	61	8.3	0.05	13
  LYD525	74233.1	0.4	0.13	17	—	—	—	—	—	—
  CONT.	—	0.3	—	—	7.5	—	—	7.3	—	—
  LYD679	72652.3	0.6	0.06	27	13.1	L	36	—	—	—
  LYD670	73348.1	0.5	0.21	9	—	—	—	—	—	—
  LYD646	73040.3	0.6	0.17	29	—	—	—	—	—	—
  LYD646	73040.4	0.6	L	26	12.8	L	33	8.4	L	8
  LYD624	73181.3	0.5	0.12	9	—	—	—	—	—	—
  LYD616	73057.4	0.5	0.26	9	—	—	—	—	—	—
  LYD616	73058.4	—	—	—	—	—	—	8.3	0.09	7
  LYD609	73124.2	0.7	0.06	50	12.1	0.19	26	—	—	—
  LYD609	73128.5	0.6	0.16	18	—	—	—	—	—	—
  LYD604	73045.4	0.6	0.10	19	—	—	—	—	—	—
  LYD604	73047.3	0.6	L	24	10.7	0.24	11	—	—	—
  LYD581	73107.1	0.6	L	29	13.3	L	38	—	—	—
  LYD558	73112.3	0.6	0.23	18	—	—	—	—	—	—
  LYD558	73114.3	0.7	0.11	46	—	—	—	8.2	0.02	6
  LYD552	72981.3	0.7	L	36	11.4	0.17	18	—	—	—
  LYD552	72981.4	0.6	0.03	31	11.8	0.08	22	—	—	—
  LYD552	72983.1	0.6	0.17	26	—	—	—	—	—	—
  LYD530	73052.3	0.6	0.11	21	—	—	—	—	—	—
  LYD529	72899.7	0.6	0.03	25	11.5	0.06	20	8.1	0.06	4
  CONT.	—	0.5	—	—	9.6	—	—	7.8	—	—
  Table 65. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment “p-val.”—p-value, L—p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). “—” = results are still unavailable.

• TABLE 66
  Genes showing improved plant performance at Normal growth
  conditions under regulation of At6669 promoter

  	RGR Of Leaf Area	RGR Of Roots Coverage	RGR Of Root Length
  	(cm2/day)	(cm2/day)	(cm/day)

  			P-	%		P-	%		P-	%
  Gene Name	Event #	Ave.	Val.	Incr.	Ave.	Val.	Incr.	Ave.	Val.	Incr.
  LYD686	72796.2	0.1	L	67	1.3	L	49	0.8	0.16	8
  LYD686	72798.1	0.1	L	61	—	—	—	—	—	—
  LYD685	72458.3	0.0	0.02	45	—	—	—	—	—	—
  LYD685	72458.5	0.1	L	65	1.5	L	68	0.8	0.06	11
  LYD685	72459.1	0.0	0.03	32	1.1	0.17	18	—	—	—
  LYD685	72462.4	0.0	L	46	1.2	0.12	31	—	—	—
  LYD685	72462.5	0.0	L	48	1.2	0.03	36	—	—	—
  LYD673	72662.2	0.0	0.01	36	1.1	0.09	26	0.8	0.01	13
  LYD673	72663.3	0.0	0.04	28	—	—	—	—	—	—
  LYD673	72664.1	0.0	0.06	28	—	—	—	—	—	—
  LYD673	72666.1	0.0	0.05	30	1.1	0.16	20	0.8	0.23	7
  LYD663	72856.3	0.0	L	43	1.3	L	44	—	—	—
  LYD663	72856.5	0.0	L	49	1.3	L	41	—	—	—
  LYD663	72858.1	0.0	L	46	1.2	0.02	34	—	—	—
  LYD663	72858.3	0.0	0.05	25	1.2	0.02	34	—	—	—
  LYD655	72207.3	0.0	0.21	17	—	—	—	—	—	—
  LYD655	72210.1	0.0	0.05	37	1.2	0.08	30	—	—	—
  LYD640	72556.3	0.1	L	60	1.4	L	54	—	—	—
  LYD640	72557.2	0.0	L	32	1.1	0.06	25	—	—	—
  LYD640	72557.4	0.0	0.30	20	—	—	—	—	—	—
  LYD640	72558.2	0.1	L	64	1.4	L	54	0.8	0.24	7
  LYD640	72558.3	0.0	0.30	15	—	—	—	—	—	—
  LYD638	72432.2	—	—	—	—	—	—	0.8	0.18	7
  LYD638	72451.1	0.1	L	63	1.5	L	64	0.8	0.19	7
  LYD615	72259.2	0.0	0.07	33	—	—	—	—	—	—
  LYD615	72260.1	0.1	L	66	1.4	L	51	0.8	0.02	14
  LYD615	72264.2	0.0	0.01	31	—	—	—	—	—	—
  LYD613	72512.3	0.0	0.03	31	1.1	0.15	18	—	—	—
  LYD613	72514.2	0.1	0.01	55	1.1	0.17	23	—	—	—
  LYD613	72515.4	0.0	0.02	28	—	—	—	—	—	—
  LYD608	72883.2	0.0	L	46	1.2	L	35	—	—	—
  LYD608	72888.2	0.0	L	48	1.6	L	75	0.8	0.19	7
  LYD607	71961.1	0.1	L	80	1.4	L	54	—	—	—
  LYD607	71963.1	0.1	L	64	1.2	0.07	31	—	—	—
  LYD607	71963.2	0.0	L	46	1.4	L	57	—	—	—
  LYD607	71963.4	0.0	L	37	—	—	—	—	—	—
  LYD597	72419.3	0.0	L	35	1.1	0.20	17	0.8	0.21	7
  LYD597	72420.1	0.0	0.27	13	—	—	—	—	—	—
  LYD597	72443.4	0.0	0.19	26	—	—	—	—	—	—
  LYD583	71943.1	0.0	0.29	12	—	—	—	—	—	—
  LYD579	72350.2	0.0	0.10	19	—	—	—	—	—	—
  LYD579	72350.3	0.0	L	41	1.3	L	48	—	—	—
  LYD579	72354.1	0.0	L	42	1.4	L	52	0.8	0.19	7
  LYD563	72319.2	0.0	0.29	12	1.1	0.16	19	—	—	—
  LYD563	72319.4	0.1	L	62	1.4	L	55	—	—	—
  LYD563	72321.2	0.0	0.15	24	1.1	0.18	21	—	—	—
  LYD563	72323.1	0.0	L	40	1.4	L	60	—	—	—
  CONT.	—	0.0	—	—	0.9	—	—	0.7	—	—
  LYD676	73880.1	0.0	0.21	27	—	—	—	0.8	0.28	8
  LYD676	73884.1	—	—	—	—	—	—	0.8	0.12	12
  LYD654	73924.4	0.0	0.18	25	0.9	0.23	28	0.8	0.05	15
  LYD647	72784.3	0.1	0.05	49	1.3	0.01	74	0.8	0.12	13
  LYD647	72785.2	0.1	0.09	33	0.9	0.24	26	—	—	—
  LYD628	73679.2	0.1	0.01	68	1.3	L	79	—	—	—
  LYD628	73681.1	—	—	—	—	—	—	0.8	0.17	10
  LYD614	73917.1	0.1	0.05	42	—	—	—	—	—	—
  LYD614	73919.3	0.1	0.04	55	—	—	—	—	—	—
  LYD611	71988.3	—	—	—	0.9	0.26	25	0.8	0.12	12
  LYD611	71992.3	—	—	—	—	—	—	0.8	0.03	16
  LYD611	71992.5	0.1	0.10	32	—	—	—	0.8	0.28	8
  LYD611	71992.6	0.1	0.04	44	1.1	0.05	51	0.8	0.08	14
  LYD605	73643.1	0.1	0.14	31	—	—	—	—	—	—
  LYD605	73644.2	0.1	0.13	29	0.9	0.30	23	—	—	—
  LYD598	72421.2	0.1	0.06	37	0.9	0.25	27	0.8	0.13	12
  LYD598	72423.3	—	—	—	1.1	0.03	50	0.7	0.30	8
  LYD591	73907.3	0.1	0.14	29	1.0	0.11	36	0.8	0.21	11
  LYD591	73907.4	—	—	—	—	—	—	0.8	0.04	15
  LYD589	73898.1	0.1	0.04	45	1.0	0.09	40	0.8	0.18	11
  LYD589	73903.3	0.1	0.08	38	—	—	—	0.8	0.19	11
  LYD588	73851.2	—	—	—	—	—	—	0.8	0.19	11
  LYD588	73852.1	—	—	—	—	—	—	0.8	0.10	13
  LYD588	73852.2	0.0	0.28	25	—	—	—	0.8	0.20	12
  LYD588	73854.1	0.1	0.02	51	1.0	0.08	42	0.8	0.01	20
  LYD588	73855.3	0.1	0.04	40	1.0	0.06	44	0.8	0.25	9
  LYD584	73915.4	—	—	—	—	—	—	0.8	0.10	12
  LYD566	73480.4	—	—	—	—	—	—	0.8	0.02	20
  LYD566	73481.2	—	—	—	—	—	—	0.8	0.09	13
  LYD566	73482.4	0.1	L	59	1.1	0.05	47	0.8	0.28	9
  LYD566	73483.5	0.0	0.28	22	0.9	0.20	28	—	—	—
  LYD566	73483.6	—	—	—	—	—	—	0.8	0.08	13
  LYD535	72851.6	0.0	0.22	23	—	—	—	0.8	0.22	10
  LYD535	72852.1	0.1	0.02	45	1.2	0.01	59	0.8	0.20	11
  CONT.	—	0.0	—	—	0.7	—	—	0.7	—	—
  LYD682	72566.1	0.0	0.30	15	—	—	—	—	—	—
  LYD665	72215.2	0.1	0.07	29	1.0	0.18	20	0.8	0.13	9
  LYD665	72216.4	0.1	0.08	30	1.2	0.05	34	0.8	0.15	9
  LYD650	72639.4	—	—	—	—	—	—	0.8	0.06	11
  LYD650	72641.2	0.0	0.16	22	1.1	0.14	22	0.8	0.10	10
  LYD644	72775.1	0.1	0.03	32	1.1	0.07	29	—	—	—
  LYD644	72778.1	—	—	—	—	—	—	0.8	0.29	6
  LYD644	72780.2	0.0	0.22	20	1.1	0.09	27	—	—	—
  LYD639	72549.3	—	—	—	—	—	—	0.8	0.21	7
  LYD639	72551.1	0.1	0.13	22	1.1	0.15	24	0.9	0.02	15
  LYD626	72001.1	—	—	—	—	—	—	0.8	0.28	7
  LYD626	72001.3	0.1	0.06	29	—	—	—	—	—	—
  LYD626	72002.1	0.1	0.03	35	1.4	L	55	—	—	—
  LYD626	72004.4	—	—	—	1.0	0.22	19	0.8	0.18	8
  LYD555	74193.5	—	—	—	1.2	0.04	35	—	—	—
  LYD555	74194.1	0.1	0.08	27	—	—	—	—	—	—
  LYD555	74197.1	0.0	0.28	15	—	—	—	—	—	—
  LYD542	72733.1	0.0	0.17	21	—	—	—	—	—	—
  LYD542	72736.4	0.1	0.14	25	1.1	0.13	24	0.8	0.19	9
  LYD540	74182.2	0.1	0.09	28	—	—	—	—	—	—
  LYD536	72532.2	0.0	0.16	21	1.1	0.19	21	0.8	0.05	13
  LYD533	72721.1	0.1	0.06	31	1.2	0.05	32	0.8	0.06	11
  LYD533	72721.2	0.1	0.10	24	1.1	0.09	25	—	—	—
  LYD533	72722.1	0.0	0.28	15	—	—	—	—	—	—
  LYD533	72723.1	0.1	0.02	41	1.2	0.05	37	0.8	0.08	10
  CONT.	—	0.0	—	—	0.9	—	—	0.7	—	—
  LYD679	72650.6	0.1	0.06	38	1.4	0.17	29	—	—	—
  LYD679	72652.3	0.1	0.18	30	1.4	0.23	27	—	—	—
  LYD645	72339.2	0.1	L	55	1.4	0.14	31	—	—	—
  LYD636	72200.3	0.1	0.06	37	1.4	0.13	30	—	—	—
  LYD634	71998.2	0.1	0.01	55	1.8	L	67	—	—	—
  LYD567	72496.3	0.1	0.10	39	—	—	—	—	—	—
  LYD556	72903.5	—	—	—	1.4	0.28	24	—	—	—
  LYD556	72904.3	0.1	0.04	44	1.6	0.04	45	—	—	—
  LYD552	72979.3	—	—	—	—	—	—	0.8	0.29	7
  LYD552	72983.2	0.1	0.04	40	1.5	0.07	36	—	—	—
  LYD529	72898.2	0.1	0.17	31	—	—	—	—	—	—
  CONT.	—	0.1	—	—	1.1	—	—	0.7	—	—
  LYD689	72712.3	0.0	0.17	19	1.0	0.09	32	—	—	—
  LYD689	72713.1	0.1	L	82	1.5	L	99	0.8	0.08	16
  LYD675	72643.1	0.1	L	54	1.4	L	87	—	—	—
  LYD675	72644.1	—	—	—	—	—	—	0.7	0.27	10
  LYD675	72644.3	0.1	L	99	1.6	L	114	—	—	—
  LYD675	72646.1	0.1	L	82	1.5	L	102	—	—	—
  LYD671	72877.1	0.1	L	34	1.1	0.01	48	0.8	0.03	19
  LYD671	72878.2	0.1	L	62	1.3	L	80	0.7	0.20	12
  LYD671	72880.1	0.1	0.02	34	1.2	0.01	59	0.8	0.15	14
  LYD654	73922.3	0.1	L	65	1.2	L	54	0.8	0.10	14
  LYD654	73924.4	0.0	0.13	29	1.0	0.14	40	—	—	—
  LYD654	73924.5	0.0	0.07	22	1.1	0.01	44	—	—	—
  LYD652	72560.1	—	—	—	—	—	—	0.8	0.14	14
  LYD652	72560.2	0.1	L	60	1.5	L	97	—	—	—
  LYD652	72561.5	0.1	L	63	1.2	L	56	—	—	—
  LYD652	72563.1	0.1	L	75	1.5	L	97	0.8	0.04	20
  LYD648	72832.2	0.1	0.02	33	1.0	0.15	33	—	—	—
  LYD648	72834.1	0.0	0.18	16	1.0	0.06	38	0.7	0.21	11
  LYD648	72834.2	0.1	L	91	1.8	L	139	—	—	—
  LYD641	72633.4	0.1	0.01	33	1.1	L	52	—	—	—
  LYD641	72635.2	0.1	L	49	1.2	0.01	67	—	—	—
  LYD636	72199.3	0.1	L	63	1.3	L	69	—	—	—
  LYD636	72202.3	0.1	0.05	35	1.0	0.08	34	—	—	—
  LYD602	72613.1	0.1	L	45	1.0	0.06	38	—	—	—
  LYD602	72613.3	0.0	0.30	15	—	—	—	—	—	—
  LYD602	72614.2	0.1	L	66	1.4	L	82	—	—	—
  LYD602	72617.3	0.0	0.11	22	—	—	—	—	—	—
  LYD599	72265.3	0.1	0.01	36	—	—	—	0.8	0.03	23
  LYD599	72266.4	0.1	L	50	—	—	—	—	—	—
  LYD599	72270.4	0.1	L	91	1.0	0.07	29	—	—	—
  LYD555	74193.1	0.0	0.27	12	—	—	—	0.7	0.24	11
  LYD555	74194.1	0.1	L	72	1.5	L	107	0.7	0.23	11
  LYD555	74197.1	0.1	L	86	1.1	L	53	—	—	—
  LYD555	74197.4	0.1	L	70	1.4	L	89	—	—	—
  LYD555	74197.6	0.1	L	34	1.0	0.04	33	—	—	—
  LYD548	72655.3	0.1	L	101	1.4	L	81	—	—	—
  LYD548	72656.2	0.1	0.01	30	1.1	0.02	42	—	—	—
  LYD548	72673.3	0.0	0.18	16	0.9	0.13	23	—	—	—
  LYD541	72729.2	0.1	L	67	1.3	L	70	0.8	0.17	13
  LYD541	72729.7	0.1	L	42	0.9	0.26	25	0.7	0.29	10
  LYD541	72731.4	0.1	L	48	0.9	0.18	24	—	—	—
  LYD541	72732.1	0.0	0.03	19	—	—	—	—	—	—
  LYD540	74182.2	0.1	0.03	32	—	—	—	—	—	—
  LYD540	74182.7	0.1	L	60	1.2	L	60	—	—	—
  LYD524	72859.1	0.1	L	77	1.2	L	59	—	—	—
  LYD524	72859.4	0.1	L	70	1.2	0.01	57	—	—	—
  LYD524	72864.4	—	—	—	—	—	—	0.7	0.20	11
  CONT.	—	0.0	—	—	0.7	—	—	0.7	—	—
  LYD683	72866.3	—	—	—	1.1	0.26	20	—	—	—
  LYD683	72866.4	0.1	L	79	1.7	L	80	—	—	—
  LYD683	72870.1	0.1	0.05	32	1.4	L	49	0.8	0.27	9
  LYD683	72870.4	0.1	0.09	25	1.3	L	45	—	—	—
  LYD654	73922.4	—	—	—	1.1	0.21	19	—	—	—
  LYD654	73924.4	0.1	0.10	29	1.4	0.01	48	—	—	—
  LYD654	73924.5	0.1	0.09	23	1.5	L	57	—	—	—
  LYD654	73926.3	0.1	L	53	1.5	L	64	0.8	0.13	13
  LYD628	73678.3	0.1	0.24	26	1.2	0.13	28	0.8	0.13	17
  LYD628	73679.2	0.1	0.16	25	1.3	0.05	38	—	—	—
  LYD628	73680.2	—	—	—	1.1	0.30	15	—	—	—
  LYD628	73681.5	0.1	L	50	1.5	L	56	—	—	—
  LYD624	73181.3	0.1	0.04	35	1.2	0.06	31	0.8	0.28	9
  LYD624	73383.1	0.1	0.02	34	1.1	0.15	19	—	—	—
  LYD624	73385.1	0.1	0.10	29	—	—	—	—	—	—
  LYD624	73385.3	0.1	0.06	30	1.3	L	45	0.8	0.16	12
  LYD605	73642.3	0.1	0.08	27	1.1	0.29	15	—	—	—
  LYD604	73045.1	0.1	0.08	36	1.2	0.08	32	—	—	—
  LYD604	73045.4	0.1	0.06	29	1.1	0.10	23	0.8	0.22	11
  LYD604	73048.2	0.1	0.23	24	1.2	0.07	29	—	—	—
  LYD598	72421.2	—	—	—	1.1	0.29	17	—	—	—
  LYD598	72445.1	0.1	0.18	20	1.3	0.08	37	—	—	—
  LYD581	73107.1	0.1	0.09	24	—	—	—	—	—	—
  LYD581	73107.5	—	—	—	1.1	0.21	22	—	—	—
  LYD581	73109.2	0.1	0.02	37	1.4	L	46	—	—	—
  LYD581	73109.3	0.1	L	56	1.2	0.04	31	—	—	—
  LYD581	73110.1	0.1	L	52	1.6	L	67	—	—	—
  LYD566	73480.4	0.1	L	52	1.1	0.21	18	—	—	—
  LYD566	73482.4	0.1	L	59	1.3	0.02	39	0.8	0.08	16
  LYD566	73483.6	—	—	—	1.1	0.19	19	—	—	—
  LYD554	72171.1	0.1	L	54	1.5	L	56	0.8	0.28	11
  LYD554	72174.4	0.1	0.17	28	1.4	0.01	52	—	—	—
  LYD550	74186.3	0.1	0.08	34	—	—	—	—	—	—
  LYD550	74187.1	0.1	0.02	34	—	—	—	—	—	—
  LYD550	74187.2	0.1	0.03	42	1.3	0.03	41	0.8	0.15	14
  LYD548	72655.3	0.1	0.17	20	1.3	0.02	35	—	—	—
  LYD548	72656.2	—	—	—	—	—	—	0.8	0.11	15
  LYD548	72673.3	—	—	—	1.1	0.20	20	0.8	0.06	16
  LYD540	74181.2	0.1	L	57	1.6	L	69	0.8	0.11	15
  LYD540	74182.2	0.1	L	42	1.3	0.01	37	—	—	—
  LYD540	74182.4	0.1	0.10	23	1.3	L	42	—	—	—
  LYD540	74182.7	0.1	0.21	23	1.2	0.08	31	—	—	—
  LYD535	72850.5	0.1	0.03	33	1.1	0.12	23	—	—	—
  LYD535	72851.4	0.1	0.13	24	—	—	—	—	—	—
  LYD530	73052.3	0.1	L	69	1.6	L	76	0.8	0.19	11
  LYD530	73053.3	0.1	L	74	1.6	L	71	0.8	0.08	16
  LYD530	73053.4	—	—	—	1.2	0.08	32	0.8	0.25	11
  LYD530	73053.5	0.1	0.02	42	1.5	L	64	0.8	0.16	12
  LYD530	73054.3	—	—	—	1.1	0.22	18	—	—	—
  CONT.	—	0.0	—	—	0.9	—	—	0.7	—	—
  LYD677	72223.1	—	—	—	—	—	—	0.8	0.26	7
  LYD677	72223.6	0.1	0.04	34	1.7	0.14	23	—	—	—
  LYD637	73684.1	—	—	—	—	—	—	0.8	0.26	8
  LYD637	73685.1	0.1	0.05	40	1.7	0.18	24	—	—	—
  LYD637	73685.2	0.1	0.06	31	—	—	—	0.8	0.26	7
  LYD637	73685.3	0.1	0.02	47	1.7	0.22	21	—	—	—
  LYD625	72756.1	0.1	0.16	25	—	—	—	—	—	—
  LYD605	73641.1	0.1	0.24	20	—	—	—	0.9	0.03	14
  LYD605	73642.3	0.1	0.16	28	—	—	—	—	—	—
  LYD605	73644.2	0.1	0.06	32	—	—	—	—	—	—
  LYD605	73645.2	0.1	L	65	1.8	0.08	29	0.8	0.27	8
  LYD585	72986.1	0.1	0.04	37	1.7	0.11	25	—	—	—
  LYD585	72986.4	0.1	0.02	45	1.7	0.20	20	0.8	0.29	8
  LYD585	72988.3	0.1	0.06	38	—	—	—	—	—	—
  LYD573	72974.2	0.1	0.29	18	1.7	0.15	22	—	—	—
  LYD573	72977.1	0.1	0.24	21	—	—	—	—	—	—
  LYD573	72978.2	0.1	0.08	35	—	—	—	—	—	—
  LYD566	73481.2	0.1	0.20	22	—	—	—	—	—	—
  LYD559	73627.2	0.1	0.03	39	—	—	—	0.9	0.03	16
  LYD537	73628.1	0.1	0.26	21	—	—	—	—	—	—
  LYD537	73633.1	0.1	0.12	28	—	—	—	—	—	—
  LYD537	73633.4	0.1	0.06	39	1.9	0.06	33	—	—	—
  LYD537	73633.5	0.1	0.08	29	—	—	—	—	—	—
  CONT.	—	0.1	—	—	1.4	—	—	0.7	—	—
  LYD683	72866.4	—	—	—	—	—	—	0.8	0.07	15
  LYD683	72867.4	—	—	—	—	—	—	0.8	0.20	11
  LYD683	72868.1	0.1	0.27	18	—	—	—	—	—	—
  LYD647	72784.3	—	—	—	—	—	—	0.8	0.25	9
  LYD647	72785.3	0.1	0.03	37	1.6	0.17	21	—	—	—
  LYD647	72786.1	—	—	—	—	—	—	0.8	0.12	12
  LYD611	71991.5	—	—	—	—	—	—	0.8	0.22	9
  LYD611	71992.2	—	—	—	—	—	—	0.8	0.19	11
  LYD611	71992.5	0.1	L	66	1.6	0.14	23	0.8	0.11	12
  LYD611	71992.6	0.1	0.02	36	—	—	—	0.8	0.27	9
  LYD585	72986.4	0.1	0.26	17	—	—	—	—	—	—
  LYD585	72987.2	0.1	0.26	20	—	—	—	—	—	—
  LYD585	72988.1	0.1	0.02	33	1.7	0.02	34	—	—	—
  LYD573	72973.2	0.1	0.04	33	1.6	0.17	21	0.8	0.07	14
  LYD573	72974.2	—	—	—	—	—	—	0.8	0.11	13
  LYD573	72978.1	0.1	0.22	19	—	—	—	0.8	0.06	15
  LYD550	74188.2	0.1	0.07	28	—	—	—	—	—	—
  CONT.	—	0.1	—	—	1.3	—	—	0.7	—	—
  LYD686	72796.2	0.1	0.29	17	—	—	—	—	—	—
  LYD673	72662.2	0.1	0.08	29	1.3	0.16	25	—	—	—
  LYD673	72663.3	0.1	0.27	20	—	—	—	—	—	—
  LYD663	72853.5	0.1	0.28	22	—	—	—	—	—	—
  LYD663	72858.1	0.1	0.15	32	—	—	—	—	—	—
  LYD655	72209.1	0.1	0.03	46	1.3	0.17	24	0.8	0.15	10
  LYD655	72210.1	0.1	0.05	47	1.4	0.04	38	—	—	—
  LYD640	72557.2	0.1	0.02	40	1.4	0.04	41	—	—	—
  LYD640	72558.3	0.1	0.14	25	1.2	0.24	21	—	—	—
  LYD638	72432.2	0.1	0.11	31	—	—	—	—	—	—
  LYD638	72451.1	0.1	0.01	45	1.4	0.04	40	—	—	—
  LYD615	72260.1	0.1	0.29	20	—	—	—	—	—	—
  LYD615	72262.1	0.1	0.03	45	1.5	0.02	47	—	—	—
  LYD613	72512.1	—	—	—	—	—	—	0.8	0.13	12
  LYD613	72515.1	0.1	0.02	52	—	—	—	—	—	—
  LYD613	72516.1	0.1	0.14	26	—	—	—	—	—	—
  LYD608	72887.1	0.1	L	65	1.5	0.01	49	—	—	—
  LYD608	72888.2	0.1	0.29	18	1.2	0.29	19	0.8	0.09	14
  LYD607	71961.1	0.1	0.15	25	1.3	0.15	26	—	—	—
  LYD607	71963.2	0.1	0.05	34	1.2	0.20	23	—	—	—
  LYD597	72419.2	0.1	0.07	32	—	—	—	—	—	—
  LYD597	72420.1	0.1	L	60	1.4	0.06	34	—	—	—
  LYD583	71943.2	0.1	0.29	21	1.3	0.22	25	—	—	—
  LYD579	72350.3	0.1	0.02	48	1.4	0.05	36	—	—	—
  LYD579	72354.1	0.1	L	72	1.5	0.03	45	—	—	—
  LYD563	72319.2	0.1	0.02	42	1.4	0.04	37	—	—	—
  LYD563	72324.2	0.1	0.04	56	1.3	0.20	33	—	—	—
  CONT.	—	0.0	—	—	1.0	—	—	0.7	—	—
  LYD592	74348.3	0.1	0.13	29	—	—	—	—	—	—
  LYD592	74350.1	0.1	0.04	42	1.6	0.17	25	—	—	—
  LYD592	74351.1	0.1	0.08	29	1.6	0.13	25	—	—	—
  LYD592	74353.3	0.1	L	66	2.0	L	51	—	—	—
  CONT.	—	0.1	—	—	1.3	—	—	—	—	—
  LYD676	73881.2	0.1	0.06	27	1.3	0.05	33	0.8	0.27	10
  LYD591	73905.1	—	—	—	1.3	0.02	30	0.8	0.03	13
  CONT.	—	0.0	—	—	1.0	—	—	0.7	—	—
  LYD665	72211.2	0.1	L	78	1.3	0.02	38	0.9	0.15	10
  LYD665	72216.4	0.0	0.03	39	1.1	0.28	19	—	—	—
  LYD665	72216.5	0.1	0.02	43	1.1	0.25	23	—	—	—
  LYD665	72216.6	0.0	0.08	31	1.1	0.24	20	0.9	0.23	9
  LYD592	74348.3	0.1	L	79	1.4	L	47	0.9	0.21	8
  LYD592	74348.4	0.1	L	95	1.8	L	96	0.9	0.16	10
  LYD592	74349.2	0.1	L	59	1.1	0.26	20	—	—	—
  LYD592	74350.1	0.1	L	116	1.7	L	86	—	—	—
  LYD592	74351.1	0.1	L	103	1.6	L	72	—	—	—
  LYD532	74343.2	0.1	L	51	1.2	0.11	26	—	—	—
  LYD532	74345.1	0.0	0.04	28	1.1	0.21	20	—	—	—
  LYD532	74345.3	0.1	L	84	1.4	L	51	—	—	—
  LYD525	74229.2	0.1	L	53	—	—	—	—	—	—
  LYD525	74230.2	0.1	L	90	1.5	0.03	58	—	—	—
  CONT.	—	0.0	—	—	0.9	—	—	0.8	—	—
  LYD679	72652.3	0.1	L	32	1.6	L	37	—	—	—
  LYD670	73347.4	0.1	0.21	14	—	—	—	—	—	—
  LYD670	73348.1	0.1	0.20	11	—	—	—	—	—	—
  LYD646	73040.3	0.1	0.04	31	1.3	0.26	14	—	—	—
  LYD646	73040.4	0.1	L	29	1.5	L	33	0.8	0.18	10
  LYD646	73042.3	0.1	0.22	14	—	—	—	—	—	—
  LYD624	73181.3	0.1	0.21	10	—	—	—	—	—	—
  LYD624	73382.4	0.1	0.22	17	—	—	—	—	—	—
  LYD609	73124.2	0.1	L	55	1.5	0.06	26	—	—	—
  LYD609	73128.5	0.1	0.22	13	—	—	—	—	—	—
  LYD604	73045.4	0.1	0.05	20	—	—	—	—	—	—
  LYD604	73047.3	0.1	L	29	1.3	0.28	12	—	—	—
  LYD581	73107.1	0.1	L	31	1.6	L	38	—	—	—
  LYD581	73107.5	0.1	0.13	17	—	—	—	—	—	—
  LYD558	73112.3	0.1	0.13	18	—	—	—	—	—	—
  LYD558	73114.3	0.1	L	52	1.4	0.14	23	—	—	—
  LYD552	72981.3	0.1	L	38	1.4	0.14	17	—	—	—
  LYD552	72981.4	0.1	L	31	1.4	0.06	22	—	—	—
  LYD552	72983.1	0.1	0.05	26	—	—	—	—	—	—
  LYD530	73052.3	0.1	0.02	27	—	—	—	—	—	—
  LYD529	72897.1	—	—	—	—	—	—	0.8	0.15	9
  LYD529	72899.7	0.1	L	30	1.4	0.08	20	—	—	—
  LYD529	72900.2	—	—	—	—	—	—	0.8	0.28	7
  CONT.	—	0.0	—	—	1.2	—	—	0.7	—	—
  Table 66. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L—p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). “—” = results are still unavailable.

• Results from T1 Plants
• The genes presented in Tables 67-69 showed a significant improvement in plant biomass and root development since they produced a higher biomass (dry and fresh weight, Table 67), a larger leaf and root biomass (leaf area, root length and root coverage) (Table 68), and a higher relative growth rate of leaf area, root coverage and root length (Table 69) when grown under normal growth conditions, as compared to control plants grown under identical growth conditions. Plants producing larger root biomass have better possibilities to absorb larger amount of nitrogen from soil. Plants producing larger leaf biomass has better ability to produce assimilates). The genes were cloned under the regulation of a constitutive promoter (At6669; SEQ ID NO:4111). The evaluation of each gene was performed by testing the performance of different number of events. Some of the genes were evaluated in more than one tissue culture assay. This second experiment confirmed the significant increment in leaf and root performance. Event with p-value <0.1 was considered statistically significant.
• Tables 67-69 summarize the observed phenotypes of transgenic plants expressing the gene constructs using the TC-T1 Assays.

• TABLE 67
  Genes showing improved plant performance at Normal growth
  conditions under regulation of A6669 promoter

  Dry Weight [mg]

  Fresh Weight [mg]

  Gene Name	Ave.	P-Val.	% Incr.	Ave.	P-Val.	% Incr.

  LYD690	4.6	0.01	26	108.9	L	26
  LYD550	4.8	L	30	121.0	L	40
  LYD525	4.6	0.09	24	108.4	0.17	26
  CONT.	3.7	—	—	86.3	—	—
  LYD592	4.9	0.02	37	99.6	L	42
  CONT.	3.6	—	—	70.2	—	—
  LYD633	10.6	L	25	200.2	0.06	25
  LYD619	10.8	0.03	28	194.8	0.03	21
  LYD587	9.8	0.04	17	—	—	—
  LYD565	10.2	0.19	21	—	—	—
  CONT.	8.4	—	—	160.5	—	—
  LYD659	8.8	0.07	11	160.8	0.12	12
  CONT.	8.0	—	—	143.9	—	—
  LYD659	5.9	L	64	136.1	0.02	64
  LYD578	4.3	0.27	20	96.3	0.18	16
  LYD532	4.6	0.15	29	101.3	0.12	22
  CONT.	3.6	—	—	82.8	—	—
  LYD532	6.6	0.08	48	205.1	0.06	80
  CONT.	4.4	—	—	114.2	—	—
  LYD539_H11	7.8	0.20	25	—	—	—
  CONT.	6.2	—	—	—	—	—
  LYD575	6.5	0.19	29	159.5	0.22	27
  CONT.	5.0	—	—	125.1	—	—
  Table 67. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L—p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). “—” = results are still unavailable.

• TABLE 68
  Genes showing improved plant performance at Normal growth
  conditions under regulation of At6669 promoter

  Leaf Area [cm2]

  Roots Coverage [cm2]

  Roots Length [cm]

  		P-	%		P-	%		P-	%
  Gene Name	Ave.	Val.	Incr.	Ave.	Val.	Incr.	Ave.	Val.	Incr.

  LYD690	0.4	L	30	3.8	0.04	26	—	—	—
  LYD550	0.4	L	31	—	—	—	—	—	—
  LYD525	0.4	0.15	21	—	—	—	—	—	—
  CONT.	0.3	—	—	3.0	—	—	—	—	—
  LYD592	0.5	0.05	41	4.2	0.17	26	—	—	—
  LYD575	0.4	0.05	12	—	—	—	—	—	—
  LYD539_H11	0.4	0.18	21	4.5	0.23	34	4.9	0.26	12
  CONT.	0.3	—	—	3.4	—	—	4.4	—	—
  LYD633	0.8	0.14	26	—	—	—	7.2	0.14	20
  LYD619	0.7	0.01	21	—	—	—	6.7	0.14	12
  LYD587	0.7	0.05	16	7.6	0.24	17	7.1	0.08	19
  LYD565	0.7	0.23	18	—	—	—	—	—	—
  CONT.	0.6	—	—	6.5	—	—	6.0	—	—
  LYD659	0.8	0.17	11	—	—	—	—	—	—
  CONT.	0.7	—	—	—	—	—	—	—	—
  LYD659	0.5	L	34	4.5	0.12	37	—	—	—
  LYD578	0.5	0.21	16	4.6	0.24	40	—	—	—
  LYD532	0.4	0.28	11	—	—	—	—	—	—
  CONT.	0.4	—	—	3.3	—	—	—	—	—
  LYD576	0.5	0.12	22	—	—	—	6.7	0.09	11
  LYD532	0.7	0.04	54	7.4	0.13	43	7.2	0.04	19
  CONT.	0.4	—	—	5.2	—	—	6.0	—	—
  LYD539_H11	0.6	0.25	19	—	—	—	—	—	—
  CONT.	0.5	—	—	—	—	—	—	—	—
  LYD575	0.7	0.26	26	10.3	0.26	20	—	—	—
  CONT.	0.5	—	—	8.6	—	—	—	—	—
  Table 68. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L—p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). “—” = results are still unavailable.

• TABLE 69
  Genes showing improved plant performance at Normal growth
  conditions under regulation of At6669 promoter

  	RGR Of Leaf Area	RGR Of Roots Coverage	RGR Of Root Length
  	(cm2/day)	(cm2/day)	(cm/day)

  		P-	%		P-	%		P-	%
  Gene Name	Ave.	Val.	Incr.	Ave.	Val.	Incr.	Ave.	Val.	Incr.

  LYD690	0.0	0.02	25	0.5	L	28	—	—	—
  LYD550	0.0	L	28	—	—	—	—	—	—
  LYD525	0.0	0.14	18	—	—	—	—	—	—
  CONT.	0.0	—	—	0.4	—	—	—	—	—
  LYD592	0.0	L	46	0.5	0.07	26	—	—	—
  LYD539_H11	0.0	0.05	26	0.5	0.07	34	0.5	0.27	11
  CONT.	0.0	—	—	0.4	—	—	0.5	—	—
  LYD633	0.1	0.13	26	—	—	—	0.8	0.15	22
  LYD619	0.1	0.05	24	—	—	—	0.8	0.15	15
  LYD587	0.1	0.15	18	0.9	0.28	18	0.8	0.07	20
  LYD565	0.1	0.11	24	—	—	—	—	—	—
  CONT.	0.1	—	—	0.8	—	—	0.7	—	—
  LYD659	0.1	L	39	0.6	0.02	41	—	—	—
  LYD578	0.0	0.13	18	0.6	0.04	41	—	—	—
  LYD532	0.0	0.20	14	—	—	—	—	—	—
  CONT.	0.0	—	—	0.4	—	—	—	—	—
  LYD576	0.1	0.14	21	—	—	—	0.7	0.09	16
  LYD532	0.1	L	56	0.9	0.03	45	0.8	0.02	25
  CONT.	0.0	—	—	0.6	—	—	0.6	—	—
  LYD575	0.1	0.23	22	—	—	—	—	—	—
  LYD539_H11	0.1	0.20	21	—	—	—	—	—	—
  CONT.	0.1	—	—	—	—	—	—	—	—
  LYD575	0.1	0.08	31	1.3	0.21	20	—	—	—
  CONT.	0.1	—	—	1.1	—	—	—	—	—
  Table 69. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L—p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). “—” = results are still unavailable.

• These results demonstrate that the polynucleotides of the invention are capable of improving yield and additional valuable important agricultural traits such as increase of biomass, abiotic stress tolerance, nitrogen use efficiency, yield, vigor, fiber yield and/or quality. Thus, transformed plants showing improved fresh and dry weight demonstrate the gene capacity to improve biomass a key trait of crops for forage and plant productivity; transformed plants showing improvement of seed yield demonstrate the genes capacity to improve plant productivity; transformed plants showing improvement of plot coverage and rosette diameter demonstrate the genes capacity to improve plant drought resistance as they reduce the loss of soil water by simple evaporation and reduce the competition with weeds; hence reduce the need to use herbicides to control weeds. Transformed plants showing improvement of relative growth rate of various organs (leaf and root) demonstrate the gene capacity to promote plant growth and hence shortening the needed growth period and/or alternatively improving the utilization of available nutrients and water leading to increase of land productivity; Transformed plants showing improvement of organ number as demonstrated by the leaf number parameter exhibit a potential to improve biomass yield important for forage crops and improve the plant productivity, Transformed plants showing increased root length and coverage demonstrate the gene capacity to improve drought resistance and better utilization of fertilizers as the roots can reach larger soil volume; Transformed plants showing improvement of leaf petiole relative area and leaf blade area demonstrate the genes capacity to cope with limited light intensities results from increasing the plant population densities and hence improve land productivity.
• Although the invention has been described in conjunction with specific embodiments thereof, it is evident that many alternatives, modifications and variations will be apparent to those skilled in the art. Accordingly, it is intended to embrace all such alternatives, modifications and variations that fall within the spirit and broad scope of the appended claims.
• It is the intent of the Applicant(s) that all publications, patents and patent applications referred to in this specification are to be incorporated in their entirety by reference into the specification, as if each individual publication, patent or patent application was specifically and individually noted when referenced that it is to be incorporated herein by reference. In addition, citation or identification of any reference in this application shall not be construed as an admission that such reference is available as prior art to the present invention. To the extent that section headings are used, they should not be construed as necessarily limiting. In addition, any priority document(s) of this application is/are hereby incorporated herein by reference in its/their entirety.

Claims (23)

What is claimed is:

1. A method of increasing yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress tolerance of a plant and/or reducing time to flowering and/or time to inflorescence emergence of a plant, comprising over-expressing within the plant a polypeptide comprising an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 362-387, 389-419, 421-442, 444-467, 469-552, 554-569, 571-601, 2429-2656, 2663-3132, 3136-3646, 3648-4085 or 4086, thereby increasing the yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress tolerance of the plant and/or reducing time to flowering and/or time to inflorescence emergence of the plant.

2. The method of claim 1, wherein said over-expressing of said polypeptide is performed by transforming the plant with an exogenous polynucleotide comprising a nucleic acid sequence encoding said polypeptide.

3. The method of claim 2, wherein said exogenous polynucleotide is operably linked to a promoter capable of directing expression of said exogenous polynucleotide in a plant cell.

4. The method of claim 1, wherein said amino acid sequence exhibits at least 90% sequence identity to the polypeptide set forth by SEQ ID NO: 362-387, 389-419, 421-442, 444-467, 469-552, 554-569, 571-601, 2429-2656, 2663-3132, 3136-3646, 3648-4085 or 4086.

5. The method of claim 1, wherein said amino acid sequence exhibits at least 95% sequence identity to the polypeptide set forth by SEQ ID NO: 362-387, 389-419, 421-442, 444-467, 469-552, 554-569, 571-601, 2429-2656, 2663-3132, 3136-3646, 3648-4085 or 4086.

6. The method of claim 2, wherein said amino acid sequence exhibits at least 95% sequence identity to the polypeptide set forth by SEQ ID NO: 362-387, 389-419, 421-442, 444-467, 469-552, 554-569, 571-601, 2429-2656, 2663-3132, 3136-3646, 3648-4085 or 4086.

7. The method of claim 1, wherein said amino acid sequence is selected from the group consisting of SEQ ID NOs: 362-387, 389-419, 421-442, 444-467, 469-552, 554-569, 571-601, 2429-2656, 2663-3132, 3136-3646, 3648-4085 and 4086.

8. The method of claim 3, wherein said promoter is heterologous to said plant cell and/or to said exogenous polynucleotide.

9. The method of claim 2, wherein said nucleic acid sequence is selected from the group consisting of SEQ ID NOs: 1-26, 28-58, 60-81, 83-106, 108-189, 191-225, 227-257, 259-279, 281-304, 306-361, 602-853, 860-1379, 1383-2427 and 2428, or a codon-optimized sequence thereof.

10. The method of claim 1, further comprising selecting a plant over-expressing said polypeptide for an increased trait selected from the group consisting of: yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and abiotic stress tolerance as compared to a native plant of the same species which is grown under the same growth conditions.

11. The method of claim 1, further comprising selecting a plant over-expressing said polypeptide for a decreased trait selected from the group consisting of: time to flowering and time to inflorescence emergence as compared to a native plant of the same species which is grown under the same growth conditions.

12. The method of claim 1, further comprising growing the plant over-expressing said polypeptide under nitrogen-limiting conditions.

13. The method of claim 1, further comprising growing the plant over-expressing said polypeptide under the abiotic stress.

14. The method of claim 1, wherein said abiotic stress is selected from the group consisting of salinity, drought, osmotic stress, water deprivation, flood, etiolation, low temperature, high temperature, heavy metal toxicity, anaerobiosis, nutrient deficiency, nutrient excess, atmospheric pollution and UV irradiation.

15. A method of producing a crop, comprising growing a crop of a plant expressing an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide comprising an amino acid sequence exhibiting at least 80% sequence identity to the amino acid sequence set forth by SEQ ID NO: 362-387, 389-419, 421-442, 444467, 469-552, 554-569, 571-601, 2429-2656, 2663-3132, 3136-3646, 36484085 or 4086, wherein said plant is derived from a plant selected for increased yield, increased growth rate, increased biomass, increased vigor, increased oil content, increased seed yield, increased fiber yield, increased fiber quality, increased nitrogen use efficiency, increased abiotic stress tolerance, reduced time to flowering and/or reduced time to inflorescence emergence as compared to a control plant of the same species under the same growth conditions, thereby producing the crop.

16. The method of claim 15, wherein said amino acid sequence is selected from the group consisting of SEQ ID NOs: 362-387, 389-419, 421-442, 444-467, 469-552, 554-569, 571-601, 2429-2656, 2663-3132, 3136-3646, 3648-4085 and 4086.

17. The method of claim 15, wherein said nucleic acid sequence is selected from the group consisting of SEQ ID NOs: 1-26, 28-58, 60-81, 83-106, 108-189, 191-225, 227-257, 259-279, 281-304, 306-361, 602-853, 860-1379, 1383-2427 and 2428, or a codon-optimized sequence thereof.

18. A nucleic acid construct comprising an isolated polynucleotide comprising a nucleic acid sequence encoding a polypeptide which comprises an amino acid sequence exhibiting at least 80% sequence identity to the amino acid sequence set forth in SEQ ID NO: 362-387, 389-419, 421-442, 444-467, 469-552, 554-569, 571-601, 2429-2656, 2663-3132, 3136-3646, 36484085 or 4086, and a heterologous promoter for directing transcription of said nucleic acid sequence in a host cell, wherein said amino acid sequence is capable of increasing yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant and/or reducing time to flowering and/or reducing time to inflorescence emergence of a plant.

19. The nucleic acid construct of claim 18, wherein said amino acid sequence is selected from the group consisting of SEQ ID NOs: 362-387, 389-419, 421-442, 444-467, 469-552, 554-569, 571-601, 2429-2656, 2663-3132, 3136-3646, 3648-4085 and 4086.

20. The nucleic acid construct of claim 18, wherein said nucleic acid sequence is selected from the group consisting of SEQ ID NOs: 1-26, 28-58, 60-81, 83-106, 108-189, 191-225, 227-257, 259-279, 281-304, 306-361, 602-853, 860-1379, 1383-2427 and 2428, or a codon-optimized sequence thereof.

21. A plant cell transformed with the nucleic acid construct of claim 18.

22. A plant transformed with the nucleic acid construct of claim 18.

23. A method of growing a crop, the method comprising seeding seeds and/or planting plantlets of a plant transformed with the nucleic acid construct of claim 18, wherein the plant is derived from plants selected for at least one trait selected from the group consisting of: increased yield, increased growth rate, increased biomass, increased vigor, increased oil content, increased seed yield, increased fiber yield, increased fiber quality, increased nitrogen use efficiency, increased abiotic stress tolerance, reduced time to flowering and reduced time to inflorescence emergence as compared to a non-transformed plant, thereby growing the crop.

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