US20070294782A1 - Transgenic plants with enhanced agronomic traits - Google Patents

Transgenic plants with enhanced agronomic traits Download PDF

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Publication number
US20070294782A1
US20070294782A1 US11/311,940 US31194005A US2007294782A1 US 20070294782 A1 US20070294782 A1 US 20070294782A1 US 31194005 A US31194005 A US 31194005A US 2007294782 A1 US2007294782 A1 US 2007294782A1
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enhanced
seed
plant
plants
protein
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Mark Abad
Adrian Lund
Terry Bradshaw
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Monsanto Technology LLC
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Monsanto Technology LLC
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Priority to US11/311,940 priority Critical patent/US20070294782A1/en
Assigned to MONSANTO TECHNOLOGY LLC reassignment MONSANTO TECHNOLOGY LLC ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: BRADSHAW, TERRY, LUND, ADRIAN, ABAD, MARK
Publication of US20070294782A1 publication Critical patent/US20070294782A1/en
Priority to US14/121,455 priority patent/US9862959B2/en
Priority to US15/732,668 priority patent/US20180327759A1/en
Abandoned legal-status Critical Current

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    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
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Definitions

  • Folder hmmer-2.3.2 and 67 pfamDir are contained on a compact disc and is hereby incorporated herein by reference in their entirety.
  • Folder hmmer-2.3.2 contains the source code and other associated file for implementing the HMMer software for Pfam analysis.
  • Folder 67 pfamDir contains 67 Pfam Hidden Markov Models. Both folders were created on the disk on December 13, 2005, having a total size of 7.7 megabytes (measured in MS-WINDOWS).
  • inventions in the field of plant genetics and developmental biology More specifically, the present inventions provide plant cells with recombinant DNA for providing an enhanced trait in a transgenic plant, plants comprising such cells, seed and pollen derived from such plants, methods of making and using such cells, plants, seeds and pollen.
  • Transgenic plants with improved agronomic traits such as yield, environmental stress tolerance, pest resistance, herbicide tolerance, improved seed compositions, and the like are desired by both farmers and consumers.
  • agronomic traits such as yield, environmental stress tolerance, pest resistance, herbicide tolerance, improved seed compositions, and the like are desired by both farmers and consumers.
  • the ability to introduce specific DNA into plant genomes provides further opportunities for generation of plants with improved and/or unique traits.
  • Merely introducing recombinant DNA into a plant genome doesn't always produce a transgenic plant with an enhanced agronomic trait. Methods to select individual transgenic events from a population are required to identify those transgenic events that are characterized by the enhanced agronomic trait.
  • This invention employs recombinant DNA for expression of proteins that are useful for imparting enhanced agronomic traits to the transgenic plants.
  • Recombinant DNA in this invention is provided in a construct comprising a promoter that is functional in plant cells and that is operably linked to DNA that encodes a protein having at least one amino acid domain in a sequence that exceeds the Pfam gathering cutoff for amino acid sequence alignment with a protein domain family identified by a Pfam name in the group of Pfam names as identified in Table 28.
  • the protein expressed in plant cells has an amino acid sequence with at least 90% identity to a consensus amino acid sequence in the group of consensus amino acid sequences consisting of the consensus amino acid sequence constructed for SEQ ID NO:84 and homologs thereof listed in Table 2 through the consensus amino acid sequence constructed for SEQ ID NO: 166 and homologs thereof listed in Table 2.
  • the protein expressed in plant cells is a protein selected from the group of proteins identified in Table 1.
  • transgenic plant cells comprising the recombinant DNA of the invention, transgenic plants comprising a plurality of such plant cells, progeny transgenic seed and transgenic pollen from such plants.
  • plant cells are selected from a population of transgenic plants regenerated from plant cells transformed with recombinant DNA and that express the protein by screening transgenic plants in the population for an enhanced trait as compared to control plants that do not have said recombinant DNA, where the enhanced trait is selected from group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • the plant cells, plants, seeds and pollen further comprise DNA expressing a protein that provides tolerance from exposure to an herbicide applied at levels that are lethal to a wild type of said plant cell.
  • a protein that provides tolerance is especially useful not only as a advantageous trait in such plants but is also useful in a selection step in the methods of the invention.
  • the agent of such herbicide is a glyphosate, dicamba, or glufosinate compound.
  • transgenic plants which are homozygous for the recombinant DNA and transgenic seed of the invention from corn, soybean, cotton, canola, alfalfa, wheat or rice plants.
  • the recombinant DNA is provided in plant cells derived from corn lines that that are and maintain resistance to the Mal de Rio Cuarto virus or the Puccina sorghi fungus or both.
  • This invention also provides methods for manufacturing non-natural, transgenic seed that can be used to produce a crop of transgenic plants with an enhanced trait resulting from expression of stably-integrated, recombinant DNA for expressing a protein having at least one domain of amino acids in a sequence that exceeds the Pfam gathering cutoff for amino acid sequence alignment with a protein domain family identified by a Pfam name in the group of Pfam names identified in Table 28.
  • the method comprises (a) screening a population of plants for an enhanced trait and a recombinant DNA, where individual plants in the population can exhibit the trait at a level less than, essentially the same as or greater than the level that the trait is exhibited in control plants which do not express the recombinant DNA, (b) selecting from the population one or more plants that exhibit the trait at a level greater than the level that said trait is exhibited in control plants, (c) verifying that the recombinant DNA is stably integrated in said selected plants, (d) analyzing tissue of a selected plant to determine the production of a protein having the function of a protein encoded by nucleotides in a sequence of one of SEQ ID NO: 1-83; and (e) collecting seed from a selected plant.
  • the plants in the population further comprise DNA expressing a protein that provides tolerance to exposure to an herbicide applied at levels that are lethal to wild type plant cells and the selecting is effected by treating the population with the herbicide, e.g. a glyphosate, dicamba, or glufosinate compound.
  • the plants are selected by identifying plants with the enhanced trait. The methods are especially useful for manufacturing corn, soybean, cotton, alfalfa, wheat or rice seed.
  • Another aspect of the invention provides a method of producing hybrid corn seed comprising acquiring hybrid corn seed from a herbicide tolerant corn plant which also has stably-integrated, recombinant DNA comprising a promoter that is (a) functional in plant cells and (b) is operably linked to DNA that encodes a protein having at least one domain of amino acids in a sequence that exceeds the Pfam gathering cutoff for amino acid sequence alignment with a protein domain family identified by a Pfam name in the group of Pfam names identified in Table 28.
  • the methods further comprise producing corn plants from said hybrid corn seed, wherein a fraction of the plants produced from said hybrid corn seed is homozygous for said recombinant DNA, a fraction of the plants produced from said hybrid corn seed is hemizygous for said recombinant DNA, and a fraction of the plants produced from said hybrid corn seed has none of said recombinant DNA; selecting corn plants which are homozygous and hemizygous for said recombinant DNA by treating with an herbicide; collecting seed from herbicide-treated-surviving corn plants and planting said seed to produce further progeny corn plants; repeating the selecting and collecting steps at least once to produce an inbred corn line; and crossing the inbred corn line with a second corn line to produce hybrid seed.
  • this invention provides methods of growing a corn, cotton or soybean crop without irrigation water comprising planting seed having plant cells of the invention which are selected for enhanced water use efficiency.
  • methods comprise applying reduced irrigation water, e.g. providing up to 300 millimeters of ground water during the production of a corn crop.
  • This invention also provides methods of growing a corn cotton or soybean crop without added nitrogen fertilizer comprising planting seed having plant cells of the invention which are selected for enhanced nitrogen use efficiency.
  • FIG. 1 is a DNA sequence.
  • FIGS. 2 and 3 are alignments of amino acid sequence.
  • a “plant cell” means a plant cell that is transformed with stably-integrated, non-natural, recombinant DNA, e.g. by Agrobacterium -mediated transformation or by baombardment using microparticles coated with recombinant DNA or other means.
  • a plant cell of this invention can be an originally-transformed plant cell that exists as a microorganism or as a progeny plant cell that is regenerated into differentiated tissue, e.g. into a transgenic plant with stably-integrated, non-natural recombinant DNA, or seed or pollen derived from a progeny transgenic plant.
  • transgenic plant means a plant whose genome has been altered by the stable integration of recombinant DNA.
  • a transgenic plant includes a plant regenerated from an originally-transformed plant cell and progeny transgenic plants from later generations or crosses of a transformed plant.
  • recombinant DNA means DNA which has been a genetically engineered and constructed outside of a cell including DNA containing naturally occurring DNA or cDNA or synthetic DNA.
  • Consensus sequence means an artificial sequence of amino acids in a conserved region of an alignment of amino acid sequences of homologous proteins, e.g. as determined by a CLUSTALW alignment of amino acid sequence of homolog proteins.
  • homolog means a protein in a group of proteins that perform the same biological function, e.g. proteins that belong to the same Pfam protein family and that provide a common enhanced trait in transgenic plants of this invention.
  • homologs are expressed by homologous genes.
  • homologous genes include naturally occurring alleles and artificially-created variants. Degeneracy of the genetic code provides the possibility to substitute at least one base of the protein encoding sequence of a gene with a different base without causing the amino acid sequence of the polypeptide produced from the gene to be changed.
  • a polynucleotide useful in the present invention may have any base sequence that has been changed from SEQ ID NO: 1 through SEQ ID NO:83 by substitution in accordance with degeneracy of the genetic code.
  • Homologs are proteins that, when optimally aligned, have at least 60% identity, more preferably about 70% or higher, more preferably at least 80% and even more preferably at least 90% identity over the full length of a protein identified as being associated with imparting an enhanced trait when expressed in plant cells.
  • Homologs include proteins with an amino acid sequence that has at least 90% identity to a consensus amino acid sequence of proteins and homologs disclosed herein.
  • Homologs are be identified by comparison of amino acid sequence, e.g. manually or by use of a computer-based tool using known homology-based search algorithms such as those commonly known and referred to as BLAST, FASTA, and Smith-Waterman.
  • a local sequence alignment program e.g. BLAST
  • BLAST can be used to search a database of sequences to find similar sequences, and the summary Expectation value (E-value) used to measure the sequence base similarity.
  • E-value Expectation value
  • a reciprocal query is used in the present invention to filter hit sequences with significant E-values for ortholog identification.
  • the reciprocal query entails search of the significant hits against a database of amino acid sequences from the base organism that are similar to the sequence of the query protein.
  • a hit is a likely ortholog, when the reciprocal query's best hit is the query protein itself or a protein encoded by a duplicated gene after speciation.
  • a further aspect of the invention comprises functional homolog proteins that differ in one or more amino acids from those of disclosed protein as the result of conservative amino acid substitutions, for example substitutions are among: acidic (negatively charged) amino acids such as aspartic acid and glutamic acid; basic (positively charged) amino acids such as arginine, histidine, and lysine; neutral polar amino acids such as glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine; neutral nonpolar (hydrophobic) amino acids such as alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine; amino acids having aliphatic side chains such as glycine, alanine, valine, leucine, and isoleucine; amino acids having aliphatic-hydroxyl side chains such as serine and threonine; amino acids having amide-containing side chains such as asparagine and glut
  • percent identity means the extent to which two optimally aligned DNA or protein segments are invariant throughout a window of alignment of components, for example nucleotide sequence or amino acid sequence.
  • An “identity fraction” for aligned segments of a test sequence and a reference sequence is the number of identical components that are shared by sequences of the two aligned segments divided by the total number of sequence components in the reference segment over a window of alignment which is the smaller of the full test sequence or the full reference sequence. “Percent identity” (“% identity”) is the identity fraction times 100.
  • Pfam refers to a large collection of multiple sequence alignments and hidden Markov models covering many common protein families, e.g. Pfam version 18.0 (August 2005) contains alignments and models for 7973 protein families and is based on the Swissprot 47.0 and SP-TrEMBL 30.0 protein sequence databases. See S. R. Eddy, “Profile Hidden Markov Models”, Bioinformatics 14:755-763, 1998. Pfam is currently maintained and updated by a Pfam Consortium. The alignments represent some evolutionary conserved structure that has implications for the protein's function.
  • Profile hidden Markov models (profile HMMs) built from the Pfam alignments are useful for automatically recognizing that a new protein belongs to an existing protein family even if the homology by alignment appears to be low.
  • Candidate proteins meeting the gathering cutoff for the alignment of a particular Pfam are in the protein family and have cognate DNA that is useful in constructing recombinant DNA for the use in the plant cells of this invention.
  • Hidden Markov Model databases for use with HMMER software in identifying DNA expressing protein in a common Pfam for recombinant DNA in the plant cells of this invention are also included in the appended computer listing.
  • the HMMER software and Pfam databases are version 18.0 and were used to identify known domains in the proteins corresponding to amino acid sequence of SEQ ID NO:84 through SEQ ID NO:166. All DNA encoding proteins that have scores higher than the gathering cutoff disclosed in Table 27 by Pfam analysis disclosed herein can be used in recombinant DNA of the plant cells of this invention, e.g. for selecting transgenic plants having enhanced agronomic traits.
  • the relevant Pfams for use in this invention are AAA, AP2, Aldo ket red, Alpha-amylase, Aminotran 1 2, Ank, ArfGap, Asn synthase, BRO1, CBFD NFYB HMF, Catalase, CorA, Cpn60 TCP1, Cystatin, DNA photolyase, DSPc, DUF1685, DUF296, Dil9, E2F TDP, FAD binding 7, FA desaturase, FBPase, GAF, GATA, GATase 2, Glyco hydro 1, Glyoxalase, Got1, HATPase c, HSF DNA-bind, HSP20, HisKA, Homeobox, Hpt, Isoamylase N, K-box, Lactamase B, Metallophos, MtN3 slv, NAF, NAM, NIF, Oxidored FMN, PAS, PDZ, PRA1, Peptidase C15
  • promoter means regulatory DNA for initializing transcription.
  • a “plant promoter” is a promoter capable of initiating transcription in plant cells whether or not its origin is a plant cell, e.g. is it well known that Agrobacterium promoters are functional in plant cells.
  • plant promoters include promoter DNA obtained from plants, plant viruses and bacteria such as Agrobacterium and Braidyrhizobium bacteria.
  • Examples of promoters under developmental control include promoters that preferentially initiate transcription in certain tissues, such as leaves, roots, or seeds. Such promoters are referred to as “tissue preferred”. Promoters that initiate transcription only in certain tissues are referred to as “tissue specific”.
  • a “cell type” specific promoter primarily drives expression in certain cell types in one or more organs, for example, vascular cells in roots or leaves.
  • An “inducible” or “repressible” promoter is a promoter which is under environmental control. Examples of environmental conditions that may effect transcription by inducible promoters include anaerobic conditions, or certain chemicals, or the presence of light. Tissue specific, tissue preferred, cell type specific, and inducible promoters constitute the class of “non-constitutive” promoters.
  • a “constitutive” promoter is a promoter which is active under most conditions.
  • operably linked means the association of two or more DNA fragments in a DNA construct so that the function of one, e.g. protein-encoding DNA, is controlled by the other, e.g. a promoter.
  • expressed means produced, e.g. a protein is expressed in a plant cell when its cognate DNA is transcribed to mRNA that is translated to the protein.
  • control plant means a plant that does not contain the recombinant DNA that expressed a protein that impart an enhanced trait.
  • a control plant is to identify and select a transgenic plant that has an enhance trait.
  • a suitable control plant can be a non-transgenic plant of the parental line used to generate a transgenic plant, i.e. devoid of recombinant DNA.
  • a suitable control plant may in some cases be a progeny of a hemizygous transgenic plant line that is does not contain the recombinant DNA, known as a negative segregant.
  • an “enhanced trait” means a characteristic of a transgenic plant that includes, but is not limited to, an enhance agronomic trait characterized by enhanced plant morphology, physiology, growth and development, yield, nutritional enhancement, disease or pest resistance, or environmental or chemical tolerance.
  • enhanced trait is selected from group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • the enhanced trait is enhanced yield including increased yield under non-stress conditions and increased yield under environmental stress conditions.
  • Stress conditions may include, for example, drought, shade, fungal disease, viral disease, bacterial disease, insect infestation, nematode infestation, cold temperature exposure, heat exposure, osmotic stress, reduced nitrogen nutrient availability, reduced phosphorus nutrient availability and high plant density.
  • Yield can be affected by many properties including without limitation, plant height, pod number, pod position on the plant, number of internodes, incidence of pod shatter, grain size, efficiency of nodulation and nitrogen fixation, efficiency of nutrient assimilation, resistance to biotic and abiotic stress, carbon assimilation, plant architecture, resistance to lodging, percent seed germination, seedling vigor, and juvenile traits. Yield can also affected by efficiency of germination (including germination in stressed conditions), growth rate (including growth rate in stressed conditions), ear number, seed number per ear, seed size, composition of seed (starch, oil, protein) and characteristics of seed fill.
  • Increased yield of a transgenic plant of the present invention can be measured in a number of ways, including test weight, seed number per plant, seed weight, seed number per unit area (i.e. seeds, or weight of seeds, per acre), bushels per acre, tonnes per acre, tons per acre, kilo per hectare.
  • maize yield may be measured as production of shelled corn kernels per unit of production area, for example in bushels per acre or metric tons per hectare, often reported on a moisture adjusted basis, for example at 15.5 percent moisture.
  • Increased yield may result from improved utilization of key biochemical compounds, such as nitrogen, phosphorous and carbohydrate, or from improved responses to environmental stresses, such as cold, heat, drought, salt, and attack by pests or pathogens.
  • Recombinant DNA used in this invention can also be used to provide plants having improved growth and development, and ultimately increased yield, as the result of modified expression of plant growth regulators or modification of cell cycle or photosynthesis pathways. Also of interest is the generation of transgenic plants that demonstrate enhanced yield with respect to a seed component that may or may not correspond to an increase in overall plant yield. Such properties include enhancements in seed oil, seed molecules such as tocopherol, protein and starch, or oil particular oil components as may be manifest by an alterations in the ratios of seed components.
  • a subset of the nucleic molecules of this invention includes fragments of the disclosed recombinant DNA consisting of oligonucleotides of at least 15, preferably at least 16 or 17, more preferably at least 18 or 19, and even more preferably at least 20 or more, consecutive nucleotides.
  • oligonucleotides are fragments of the larger molecules having a sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO:83, and find use, for example as probes and primers for detection of the polynucleotides of the present invention.
  • a dominant negative mutant of a native gene is generated to achieve the desired effect.
  • “dominant negative mutant” means a mutant gene whose gene product adversely affects the normal, wild-type gene product within the same cell, usually by dimerizing (combining) with it. In cases of polymeric molecules, such as collagen, dominant negative mutations are often more deleterious than mutations causing the production of no gene product (null mutations or null alleles).
  • SEQ ID NO: 6 and SEQ ID NO: 7 are constructed to encode agl11 protein with K-box deleted and MADs 3 protein with MAD box deleted, respectively. MADS box proteins similar to AGL11 can be considered as having three functional domains.
  • the MADS box N-terminal DNA-binding domain
  • the K-box more distal dimerization domain
  • the C-terminal domain that is usually involved in interactions with other proteins.
  • the region between the MADS box and the K-box has been shown to be important for DNA binding in some proteins and is often referred to as the I-box (Fan et al., 1997).
  • I-box an N-terminal DNA-binding domain
  • Several different classes of dominant negative constructs are considered. Deletion or inactivation of the DNA-binding domain can create proteins that are able to dimerize with their native full length counterparts as well as other natural dimerization partners.
  • removal of the C-terminal domain can allow dimerization with both the native protein and it's natural dimerization partners. In both cases these types of constructs disable both the target protein and any other protein capable of interacting with the K-box.
  • a constitutively active mutant is constructed to achieve the desired effect.
  • SEQ ID NO:3 encodes only the kinase domain from a calcium-dependent protein kinase (CDPK).
  • CDPK1 has a domain structure similar to other calcium-dependant protein kinases in which the protein kinase domain is separated from four efhand domains by 42 amino acid “spacer” region.
  • Calcium-dependant protein kinases are thought to be activated by a calcium-induced conformational change that results in movement of an autoinhibitory domain away from the protein kinase active site (Yokokura et al., 1995).
  • constitutively active proteins can be made by over expressing the protein kinase domain alone.
  • DNA constructs are assembled using methods well known to persons of ordinary skill in the art and typically comprise a promoter operably linked to DNA, the expression of which provides the enhanced agronomic trait.
  • Other construct components may include additional regulatory elements, such as 5′ leasders and introns for enhancing transcription, 3′ untranslated regions (such as polyadenylation signals and sites), DNA for transit or signal peptides.
  • promoters that are active in plant cells have been described in the literature. These include promoters present in plant genomes as well as promoters from other sources, including nopaline synthase (NOS) promoter and octopine synthase (OCS) promoters carried on tumor-inducing plasmids of Agrobacterium tumefaciens , caulimovirus promoters such as the cauliflower mosaic virus.
  • NOS nopaline synthase
  • OCS octopine synthase
  • caulimovirus promoters such as the cauliflower mosaic virus.
  • CaMV35S constitutive promoter derived from cauliflower mosaic virus
  • U.S. Pat. No. 5,641,876, which discloses a rice actin promoter U.S.
  • Patent Application Publication 2002/0192813A1 which discloses 5′, 3′ and intron elements useful in the design of effective plant expression vectors
  • U.S. patent application Ser. No. 09/757,089 which discloses a maize chloroplast aldolase promoter
  • U.S. patent application Ser. No. 08/706,946 which discloses a rice glutelin promoter
  • U.S. patent application Ser. No.09/757,089 which discloses a maize aldolase (FDA) promoter
  • U.S. patent application Ser. No. 60/310,370 which discloses a maize nicotianamine synthase promoter, all of which are incorporated herein by reference.
  • These and numerous other promoters that function in plant cells are known to those skilled in the art and available for use in recombinant polynucleotides of the present invention to provide for expression of desired genes in transgenic plant cells.
  • promoters for use for seed composition modification include promoters from seed genes such as napin (U.S. Pat. No. 5,420,034), zein Z27 and glutelin1 (Russell et al. (1997) Transgenic Res. 6(2):157-166), peroxiredoxin antioxidant (Per1) (Stacy et al. (1996) Plant Mol Biol. 31(6): 1205-1216)., maize L3 oleosin (U.S. Pat. No. 6,433,252), globulin 1 (Belanger et al (1991) Genetics 129:863-872).
  • Promoters of interest for such uses include those from (genes such as Arabidopsis thaliana ribulose-1,5-bisphosphate carboxylase (Rubisco) small subunit (Fischhoff et al. (1992) Plant Mol Biol. 20:81-93), aldolase and pyruvate orthophosphate dikinase (PPDK) (Taniguchi et al. (2000) Plant Cell Physiol. 41(1):42-48).
  • Rubisco Arabidopsis thaliana ribulose-1,5-bisphosphate carboxylase
  • PPDK pyruvate orthophosphate dikinase
  • the promoters may be altered to contain multiple “enhancer sequences” to assist in elevating gene expression.
  • enhancers are known in the art.
  • the expression of the selected protein may be enhanced.
  • These enhancers often are found 5′ to the start of transcription in a promoter that functions in eukaryotic cells, but can often be inserted upstream (5′) or downstream (3′) to the coding sequence.
  • these 5′ enhancing elements are introns.
  • Particularly useful as enhancers are the 5′ introns of the rice actin 1 (see U.S. Pat. No. 5,641,876)and rice actin 2 genes, the maize alcohol dehydrogenase gene intron, the maize heat shock protein 70 gene intron (U.S. Pat. No. 5,593,874) and the maize shrunken 1 gene.
  • promoters for use for seed composition modification include promoters from seed genes such as napin (U.S. Pat. No. 5,420,034), maize L3 oleosin (U.S. Pat. No. 6,433,252), zein Z27 (Russell et al. (1997) Transgenic Res. 6(2): 157-166), globulin 1 (Belanger et al (1991) Genetics 129:863-872), glutelin 1 (Russell (1997) supra), and peroxiredoxin antioxidant (Per1) (Stacy et al. (1996) Plant Mol Biol. 31(6):1205-1216).
  • seed genes such as napin (U.S. Pat. No. 5,420,034), maize L3 oleosin (U.S. Pat. No. 6,433,252), zein Z27 (Russell et al. (1997) Transgenic Res. 6(2): 157-166), globulin 1 (Belanger et al (1991) Genetic
  • Recombinant DNA constructs prepared in accordance with the invention will also generally include a 3′ element that typically contains a polyadenylation signal and site.
  • 3′ elements include those from Agrobacterium tumefaciens genes such as nos 3′, tml 3′, tmr 3′, tms 3′, ocs 3′, tr7 3′, for example disclosed in U.S. Pat. No.
  • 3′ elements from plant genes such as wheat ( Triticum aesevitum ) heat shock protein 17 (Hsp17 3′), a wheat ubiquitin gene, a wheat fructose-1,6-biphosphatase gene, a rice glutelin gene a rice lactate dehydrogenase gene and a rice beta-tubulin gene, all of which are disclosed in U.S. published patent application 2002/0192813 A1, incorporated herein by reference; and the pea ( Pisum sativum ) ribulose biphosphate carboxylase gene (rbs 3′), and 3′ elements from the genes within the host plant.
  • wheat Triticum aesevitum
  • Hsp17 3′ heat shock protein 17
  • a wheat ubiquitin gene a wheat fructose-1,6-biphosphatase gene
  • rice glutelin gene a rice lactate dehydrogenase gene
  • rbs 3′ the pea ( Pisum sativ
  • Constructs and vectors may also include a transit peptide for targeting of a gene target to a plant organelle, particularly to a chloroplast, leucoplast or other plastid organelle.
  • a transit peptide for targeting of a gene target to a plant organelle, particularly to a chloroplast, leucoplast or other plastid organelle.
  • chloroplast transit peptides see U.S. Pat. No. 5,188,642 and U.S. Pat. No. 5,728,925, incorporated herein by reference.
  • the transit peptide region of an Arabidopsis EPSPS gene useful in the present invention, see Klee, H. J. et al (MGG (1987) 210:437-442).
  • Transgenic plants comprising or derived from plant cells of this invention transformed with recombinant DNA can be further enhanced with stacked traits, e.g. a crop plant having an enhanced trait resulting from expression of DNA disclosed herein in combination with herbicide and/or pest resistance traits.
  • genes of the current invention can be stacked with other traits of agronomic interest, such as a trait providing herbicide resistance, or insect resistance, such as using a gene from Bacillus thuringensis to provide resistance against lepidopteran, coliopteran, homopteran, hemiopteran, and other insects.
  • Herbicides for which transgenic plant tolerance has been demonstrated and the method of the present invention can be applied include, but are not limited to, glyphosate, dicamba, glufosinate, sulfonylurea, bromoxynil and norflurazon herbicides.
  • Polynucleotide molecules encoding proteins involved in herbicide tolerance are well-known in the art and include, but are not limited to, a polynucleotide molecule encoding 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) disclosed in U.S. Pat. Nos.
  • EPSPS 5-enolpyruvylshikimate-3-phosphate synthase
  • Patent Application publication 2003/0135879 A1 for imparting dicamba tolerance a polynucleotide molecule encoding bromoxynil nitrilase (Bxn) disclosed in U.S. Pat. No. 4,810,648 for imparting bromoxynil tolerance; a polynucleotide molecule encoding phytoene desaturase (crtl) described in Misawa et al, (1993) Plant J. 4:833-840 and Misawa et al, (1994) Plant J.
  • Bxn bromoxynil nitrilase
  • crtl phytoene desaturase
  • Patent Application Publication 2003/010609 A1 for imparting N-amino methyl phosphonic acid tolerance polynucleotide molecules disclosed in U.S. Pat. No. 6,107,549 for impartinig pyridine herbicide resistance; molecules and methods for imparting tolerance to multiple herbicides such as glyphosate, atrazine, ALS inhibitors, isoxoflutole and glufosinate herbicides are disclosed in U.S. Pat. No. 6,376,754 and U.S. Patent Application Publication 2002/0112260, all of said U.S. Patents and Patent Application Publications are incorporated herein by reference. Molecules and methods for imparting insect/nematode/virus resistance is disclosed in U.S. Pat. Nos. 5,250,515; 5,880,275; 6,506,599; 5,986,175 and U.S. Patent Application Publication 2003/0150017 A1, all of which are incorporated herein by reference.
  • the inventors contemplate the use of antibodies, either monoclonal or polyclonal which bind to the proteins disclosed herein.
  • Means for preparing and characterizing antibodies are well known in the art (See, e.g., Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988; incorporated herein by reference).
  • the methods for generating monoclonal antibodies (mAbs) generally begin along the same lines as those for preparing polyclonal antibodies. Briefly, a polyclonal antibody is prepared by immunizing an animal with an immunogenic composition in accordance with the present invention and collecting antisera from that immunized animal. A wide range of animal species can be used for the production of antisera.
  • the animal used for production of anti-antisera is a rabbit, a mouse, a rat, a hamster, a guinea pig or a goat. Because of the relatively large blood volume of rabbits, a rabbit is a preferred choice for production of polyclonal antibodies.
  • a given composition may vary in its immunogenicity. It is often necessary therefore to boost the host immune system, as may be achieved by coupling a peptide or polypeptide immunogen to a carrier.
  • exemplary and preferred carriers are keyhole limpet hemocyanin (KLH) and bovine serum albumin (BSA). Other albumins such as ovalbumin, mouse serum albumin or rabbit serum albumin can also be used as carriers.
  • KLH keyhole limpet hemocyanin
  • BSA bovine serum albumin
  • Other albumins such as ovalbumin, mouse serum albumin or rabbit serum albumin can also be used as carriers.
  • Means for conjugating a polypeptide to a carrier protein are well known in the art and include using glutaraldehyde, m-maleimidobencoyl-N-hydroxysuccinimide ester, carbodiimide and bis-biazotized benzidine.
  • the immunogenicity of a particular immunogen composition can be enhanced by the use of non-specific stimulators of the immune response, known as adjuvants.
  • adjuvants include complete Freund's adjuvant (a non-specific stimulator of the immune response containing killed Mycobacterium tuberculosis ), incomplete Freund's adjuvants and aluminum hydroxide adjuvant.
  • the amount of immunogen composition used in the production of polyclonal antibodies varies upon the nature of the immunogen as well as the animal used for immunization.
  • a variety of routes can be used to administer the immunogen (subcutaneous, intramuscular, intradermal, intravenous and intraperitoneal).
  • the production of polyclonal antibodies may be monitored by sampling blood of the immunized animal at various points following immunization. A second, booster, injection may also be given. The process of boosting and titering is repeated until a suitable titer is achieved.
  • the immunized animal can be bled and the serum isolated and stored, and/or the animal can be used to generate mAbs.
  • mAbs may be readily prepared through use of well-known techniques, such as those exemplified in U.S. Pat. No. 4,196,265, incorporated herein by reference.
  • this technique involves immunizing a suitable animal with a selected immunogen composition, e.g., a purified or partially purified antifungal protein, polypeptide or peptide.
  • the immunizing composition is administered in a manner effective to stimulate antibody producing cells.
  • Rodents such as mice and rats are preferred animals, however, the use of rabbit, sheep, or frog cells is also possible.
  • the use of rats may provide certain advantages (Goding, 1986, pp. 60-61), but mice are preferred, with the BALB/c mouse being most preferred as this is most routinely used and generally gives a higher percentage of stable fusions.
  • somatic cells with the potential for producing antibodies, specifically B lymphocytes (B cells), are selected for use in the mAb generating protocol.
  • B cells B lymphocytes
  • These cells may be obtained from biopsied spleens, tonsils or lymph nodes, or from a peripheral blood sample. Spleen cells and peripheral blood cells are preferred, the former because they are a rich source of antibody-producing cells that are in the dividing plasmablast stage, and the latter because peripheral blood is easily accessible.
  • a panel of animals will have been immunized and the spleen of animal with the highest antibody titer will be removed and the spleen lymphocytes obtained by homogenizing the spleen with a syringe.
  • a spleen from an immunized mouse contains approximately 5 ⁇ 10 7 to 2 ⁇ 10 8 lymphocytes.
  • the antibody-producing B lymphocytes from the immunized animal are then fused with cells of an immortal myeloma cell, generally one of the same species as the animal that was immunized.
  • Myeloma cell lines suited for use in hybridoma-producing fusion procedures preferably are non-antibody-producing, have high fusion efficiency, and enzyme deficiencies that render them incapable of growing in certain selective media which support the growth of only the desired fused cells (hybridomas).
  • any one of a number of myeloma cells may be used, as are known to those of skill in the art (Goding, 1986, pp. 65-66; Campbell, 1984, pp. 75-83).
  • the immunized animal is a mouse
  • P3-X63/Ag8, X63-Ag8.653, NS1/1.Ag 4 1, Sp210-Ag14, FO, NSO/U, MPC-11, MPC11-X45-GTG1.7 and S194/5XX0 Bul for rats, one may use R210.RCY3, Y3-Ag1.2.3, IR983F and 4B210; and U-266, GM1500-GRG2, LICR-LON-HMy2 and UC729-6 are all useful in connection with human cell fusions.
  • NS-1 myeloma cell line also termed P3-NS-1-Ag4-1
  • P3-NS-1-Ag4-1 Another mouse myeloma cell line that may be used is the 8-azaguanine-resistant mouse murine myeloma SP2/0 non-producer cell line.
  • Methods for generating hybrids of antibody-producing spleen or lymph node cells and myeloma cells usually comprise mixing somatic cells with myeloma cells in a 2:1 ratio, though the ratio may vary from about 20:1 to about 1:1, respectively, in the presence of an agent or agents (chemical or electrical) that promote the fusion of cell membranes.
  • Fusion methods using Spend virus have been described (Kohler and Milstein, 1975; 1976), and those using polyethylene glycol (PEG), such as 37% (v/v) PEG, (Gefter et al., 1977).
  • PEG polyethylene glycol
  • the use of electrically induced fusion methods is also appropriate (Goding, 1986, pp. 71-74).
  • Fusion procedures usually produce viable hybrids at low frequencies, about 1 ⁇ 10 ⁇ 6 to 1 ⁇ 10 ⁇ 8 . However, this does not pose a problem, as the viable, fused hybrids are differentiated from the parental, unfused cells (particularly the unfused myeloma cells that would normally continue to divide indefinitely) by culturing in a selective medium.
  • the selective medium is generally one that contains an agent that blocks the de novo synthesis of nucleotides in the tissue culture media.
  • Exemplary and preferred agents are aminopterin, methotrexate, and azasenne. Aminopterin and methotrexate block de novo synthesis of both purines and pyrimidines, whereas azasenne blocks only purine synthesis.
  • the media is supplemented with hypoxanthine and thymidine as a source of nucleotides (HAT medium).
  • HAT medium a source of nucleotides
  • azaserine the media is supplemented with hypoxanthine.
  • the preferred selection medium is HAT. Only cells capable of operating nucleotide salvage pathways are able to survive in HAT medium.
  • the myeloma cells are defective in key enzymes of the salvage pathway, e.g., hypoxanthine phosphoribosyl transferase (HPRT), and they cannot survive.
  • HPRT hypoxanthine phosphoribosyl transferase
  • the B-cells can operate this pathway, but they have a limited life span in culture and generally die within about two weeks. Therefore, the only cells that can survive in the selective media are those hybrids formed from myeloma and B-cells.
  • This culturing provides a population of hybridomas from which specific hybridomas are selected.
  • selection of hybridomas is performed by culturing the cells by single-clone dilution in microtiter plates, followed by testing the individual clonal supernatants (after about two to three weeks) for the desired reactivity.
  • the assay should be sensitive, simple and rapid, such as radioimmunoassays, enzyme immunoassays, cytotoxicity assays, plaque assays, dot immunobinding assays, and the like.
  • the selected hybridomas would then be serially diluted and cloned into individual antibody-producing cell lines, which clones can then be propagated indefinitely to provide mAbs.
  • the cell lines may be exploited for mAb production in two basic ways.
  • a sample of the hybridoma can be injected (often into the peritoneal cavity) into a histocompatible animal of the type that was used to provide the somatic and myeloma cells for the original fusion.
  • the injected animal develops tumors secreting the specific monoclonal antibody produced by the fused cell hybrid.
  • the body fluids of the animal such as serum or ascites fluid, can then be tapped to provide mAbs in high concentration.
  • the individual cell lines could also be cultured in vitro, where the mAbs are naturally secreted into the culture medium from which they can be readily obtained in high concentrations.
  • mAbs produced by either means may be further purified, if desired, using filtration, centrifugation and various chromatographic methods such as HPLC or affinity chromatography.
  • Transformation methods of this invention are preferably practiced in tissue culture on media and in a controlled environment.
  • Media refers to the numerous nutrient mixtures that are used to grow cells in vitro, that is, outside of the intact living organism.
  • Recipient cell targets include, but are not limited to, meristem cells, callus, immature embryos and gametic cells such as microspores, pollen, sperm and egg cells. It is contemplated that any cell from which a fertile plant may be regenerated is useful as a recipient cell. Callus may be initiated from tissue sources including, but not limited to, immature embryos, seedling apical meristems, microspores and the like. Cells capable of proliferating as callus are also recipient cells for genetic transformation.
  • transgenic plants of this invention for example various media and recipient target cells, transformation of immature embryo cells and subsequent regeneration of fertile transgenic plants are disclosed in U.S. Pat. Nos. 6,194,636 and 6,232,526, which are incorporated herein by reference.
  • transgenic plants can be harvested from fertile transgenic plants and be used to grow progeny generations of transformed plants of this invention including hybrid plants line for selection of plants having an enhanced trait.
  • transgenic plants can be prepared by crossing a first plant having a recombinant DNA with a second plant lacking the DNA.
  • recombinant DNA can be introduced into first plant line that is amenable to transformation to produce a transgenic plant which can be crossed with a second plant line to introgress the recombinant DNA into the second plant line.
  • a transgenic plant with recombinant DNA providing an enhanced trait e.g.
  • transgenic plant line having other recombinant DNA that confers another trait for example herbicide resistance or pest resistance
  • progeny plants having recombinant DNA that confers both traits Typically, in such breeding for combining traits the transgenic plant donating the additional trait is a male line and the transgenic plant carrying the base traits is the female line.
  • the progeny of this cross will segregate such that some of the plants will carry the DNA for both parental traits and some will carry DNA for one parental trait; such plants can be identified by markers associated with parental recombinant DNA, e.g.
  • marker identification by analysis for recombinant DNA or, in the case where a selectable marker is linked to the recombinant, by application of the selecting agent such as a herbicide for use with a herbicide tolerance marker, or by selection for the enhanced trait.
  • Progeny plants carrying DNA for both parental traits can be crossed back into the female parent line multiple times, for example usually 6 to 8 generations, to produce a progeny plant with substantially the same genotype as one original transgenic parental line but for the recombinant DNA of the other transgenic parental line.
  • Marker genes are used to provide an efficient system for identification of those cells that are stably transformed by receiving and integrating a transgenic DNA construct into their genomes.
  • Preferred marker genes provide selective markers which confer resistance to a selective agent, such as an antibiotic or herbicide. Any of the herbicides to which plants of this invention may be resistant are useful agents for selective markers.
  • Potentially transformed cells are exposed to the selective agent. In the population of surviving cells will be those cells where, generally, the resistance-conferring gene is integrated and expressed at sufficient levels to permit cell survival. Cells may be tested further to confirm stable integration of the exogenous DNA.
  • selective marker genes include those conferring resistance to antibiotics such as kanamycin and paromomycin (nptII), hygromycin B (aph IV) and gentamycin (aac3 and aacC4) or resistance to herbicides such as glufosinate (bar or pat) and glyphosate (aroA or EPSPS). Examples of such selectable are illustrated in U.S. Pat. Nos. 5,550,318; 5,633,435; 5,780,708 and 6,118,047, all of which are incorporated herein by reference.
  • Selectable markers which provide an ability to visually identify transformants can also be employed, for example, a gene expressing a colored or fluorescent protein such as a luciferase or green fluorescent protein (GFP) or a gene expressing a beta-glucuronidase or uidA gene (GUS) for which various chromogenic substrates are known.
  • a gene expressing a colored or fluorescent protein such as a luciferase or green fluorescent protein (GFP) or a gene expressing a beta-glucuronidase or uidA gene (GUS) for which various chromogenic substrates are known.
  • Plant cells that survive exposure to the selective agent, or plant cells that have been scored positive in a screening assay, may be cultured in regeneration media and allowed to mature into plants.
  • Developing plantlets regenerated from transformed plant cells can be transferred to plant growth mix, and hardened off, for example, in an environmentally controlled chamber at about 85% relative humidity, 600 ppm CO 2 , and 25-250 microeinsteins m ⁇ 2 s ⁇ 1 of light, prior to transfer to a greenhouse or growth chamber for maturation.
  • Plants are regenerated from about 6 weeks to 10 months after a transformant is identified, depending on the initial tissue.
  • Plants may be pollinated using conventional plant breeding methods known to those of skill in the art and seed produced, for example self-pollination is commonly used with transgenic corn.
  • the regenerated transformed plant or its progeny seed or plants can be tested for expression of the recombinant DNA and selected for the presence of enhanced agronomic trait.
  • Transgenic plants derived from the plant cells of this invention are grown to generate transgenic plants having an enhanced trait as compared to a control plant and produce transgenic seed and haploid pollen of this invention. Such plants with enhanced traits are identified by selection of transformed plants or progeny seed for the enhanced trait. For efficiency a selection method is designed to evaluate multiple transgenic plants (events) comprising the recombinant DNA, for example multiple plants from 2 to 20 or more transgenic events. Transgenic plants grown from transgenic seed provided herein demonstrate improved agronomic traits that contribute to increased yield or other trait that provides increased plant value, including, for example, improved seed quality. Of particular interest are plants having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • Table 1 provides a list of protein encoding DNA (“genes”) that are useful as recombinant DNA for production of transgenic plants with enhanced agronomic trait, the elements of Table 1 are described by reference to:
  • “Plasmid ID” which identifies an arbitrary name for the plant transformation plasmid comprising recombinant DNA for expressing the recombinant DNA in plant cells.
  • PEP NUC SEQ SEQ ID ID NO NO Base Vector PROTEIN NAME Enhanced trait(s)
  • Plasmid ID 84 1 pMON65154 lactoylglutathione lyase Enhanced seed protein pMON69462 85 2 pMON72472 rab7c Enhanced cold tolerance pMON69456 86 3 pMON65154 CDPK kinase domain Enhanced water use pMON67754 efficiency 87 4 pMON72472 SCOF-1 Enhanced water use pMON72494 efficiency and enhanced cold tolerance 88 5 pMON72472 Synechococcus sp.
  • PCC Increased yield, enhanced pMON68399 6301 Delta9 desaturase cold tolerance and enhanced water use efficiency 89 6 pMON72472 Arabidopsis agl11 delta Improved cold tolerance pMON73765 K-box 90 7 pMON72472 rice MADS3 delta Enhanced cold tolerance pMON73829 MADS-box - L37528 91 8 pMON72472 corn MADS box Enhanced nitrogen use pMON73816 protein 110 efficiency and enhance cold tolerance 92 9 pMON72472 Arabidopsis Enhanced cold tolerance pMON75305 homeodomain transcription factor- 93 10 pMON72472 Arabidopsis AP2 Enhanced cold tolerance pMON75306 domain transcription factor 94 11 pMON72472 Arabidopsis GATA Enhanced cold tolerance pMON75309 domain transcription factor 95 12 pMON72472 Arabidopsis AT-hook Enhanced cold tolerance pMON75312 domain transcription factor- 96 13 pMON72472 rice DET1-
  • Transgenic plants having enhanced traits are selected from populations of plants regenerated or derived from plant cells transformed as described herein by evaluating the plants in a variety of assays to detect an enhanced trait, e.g. enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. These assays also may take many forms including, but not limited to, direct screening for the trait in a greenhouse or field trial or by screening for a surrogate trait.
  • Such analyses can be directed to detecting changes in the chemical composition, biomass, physiological properties, morphology of the plant.
  • Changes in chemical compositions such as nutritional composition of grain can be detected by analysis of the seed composition and content of protein, free amino acids, oil, free fatty acids, starch or tocopherols.
  • Changes in biomass characteristics can be made on greenhouse or field grown plants and can include plant height, stem diameter, root and shoot dry weights; and, for corn plants, ear length and diameter.
  • Changes in physiological properties can be identified by evaluating responses to stress conditions, for example assays using imposed stress conditions such as water deficit, nitrogen deficiency, cold growing conditions, pathogen or insect attack or light deficiency, or increased plant density.
  • Changes in morphology can be measured by visual observation of tendency of a transformed plant with an enhanced agronomic trait to also appear to be a normal plant as compared to changes toward bushy, taller, thicker, narrower leaves, striped leaves, knotted trait, chlorosis, albino, anthocyanin production, or altered tassels, ears or roots.
  • Other selection properties include days to pollen shed, days to silking, leaf extension rate, chlorophyll content, leaf temperature, stand, seedling vigor, internode length, plant height, leaf number, leaf area, tillering, brace roots, stay green, stalk lodging, root lodging, plant health, barreness/prolificacy, green snap, and pest resistance.
  • phenotypic characteristics of harvested grain may be evaluated, including number of kernels per row on the ear, number of rows of kernels on the ear, kernel abortion, kernel weight, kernel size, kernel density and physical grain quality.
  • plant cells and methods of this invention can be applied to any plant cell, plant, seed or pollen, e.g. any fruit, vegetable, grass, tree or ornamental plant
  • the various aspects of the invention are preferably applied to corn, soybean, cotton, canola, alfalfa, wheat and rice plants.
  • the invention is applied to corn plants that are inherently resistant to disease from the Mal de Rio Cuarto virus or the Puccina sorghi fungus or both.
  • This example illustrates the construction of plasmids for transferring recombinant DNA into plant cells which can be regenerated into transgenic plants of this invention.
  • Primers for PCR amplification of protein coding nucleotides of recombinant DNA were designed at or near the start and stop codons of the coding sequence, in order to eliminate most of the 5′ and 3′ untranslated regions.
  • Each recombinant DNA coding for a protein identified in Table 1 was amplified by PCR prior to insertion into the insertion site of one of the base vectors as referenced in Table 1.
  • a base plant transformation vector pMON65154 was fabricated for use in preparing recombinant DNA for transformation into corn tissue using GATEWAYTM Destination plant expression vector systems (available from Invitrogen Life Technologies, Carlsbad, Calif.).
  • pMON65 154 comprises a selectable marker expression cassette and a template recombinant DNA expression cassette.
  • the marker expression cassette comprises a CaMV 35S promoter operably linked to a gene encoding neomycin phosphotransferase II (nptII) followed by a 3′ region of an Agrobacterium tumefaciens nopaline synthase gene (nos).
  • the template recombinant DNA expression cassette is positioned tail to tail with the marker expression cassette.
  • the template recombinant DNA expression cassette comprises 5′ regulatory DNA including a rice actin 1 promoter, exon and intron, followed by a GATEWAYTM insertion site for recombinant DNA, followed by a 3′ region of a potato proteinase inhibitor II (pinII) gene.
  • pinII potato proteinase inhibitor II
  • a similar base vector plasmid pMON72472 (SEQ ID NO: 10025) was constructed for use in Agrobacterium -mediated methods of plant transformation similar to pMON65154 except (a) the 5′ regulatory DNA in the template recombinant DNA expression cassette was a rice actin promoter and a rice actin intron, (b) left and right T-DNA border sequences from Agrobacterium are added with the right border sequence is located 5′ to the rice actin 1 promoter and the left border sequence is located 3′ to the 35S promoter and (c) DNA is added to facilitate replication of the plasmid in both E. coli and Agroacterium tumefaciens .
  • the DNA added to the plasmid outside of the T-DNA border sequences includes an oriV wide host range origin of DNA replication functional in Agrobacterium , a pBR322 origin of replication functional in E. coli , and a spectinomycin/stretptomycin resistance gene for selection in both E. coli and Agrobacterium.
  • SEQ ID NO: 10026 Another base vector pMON82060 (SEQ ID NO: 10026), illustrated in Table 4, was assembled using the technology known in the art. TABLE 4 Coordinates of SEQ ID function name Annotation NO: 10026 Agro B-AGRtu.right border Agro right border sequence, essential for 5235-5591 transformation transfer of T-DNA.
  • cassette I-Os.Act1 First intron and flanking UTR exon sequences from the rice actin 1 gene T-St.Pis4 The 3′ non-translated region of the 7084-8026 potato proteinase inhibitor II gene which functions to direct polyadenylation of the mRNA Plant P-CaMV.35S CaMV 35S promoter 8075-8398 selectable L-CaMV.35S 5′ UTR from the 35S RNA of CaMV marker CR-Ec.nptII-Tn5 nptII selectable marker that confers 8432-9226 expression resistance to neomycin and kanamycin cassette T-AGRtu.nos A 3′ non-translated region of the 9255-9507 nopaline synthase gene of Agrobacterium tumefaciens Ti plasmid which functions to direct polyadenylation of the mRNA.
  • OR-Ec.oriV-RK2 The vegetative origin of replication from 567-963 in E. coli plasmid RK2.
  • OR-Ec.ori-ColE1 The minimal origin of replication from 3091-3679 the E. coli plasmid ColE1.
  • Tn7 adenylyltransferase 4210-4251 AAD(3′′)
  • CR-Ec.aadA- Coding region for Tn7 4252-5040 SPC/STR adenylyltransferase AAD(3′′)
  • conferring spectinomycin and streptomycin resistance AAD(3′′)
  • SEQ ID NO: 10028 Another base vector pMON82053 (SEQ ID NO: 10028), illustrated in Table 6, was assembled using the technology known in the art. TABLE 6 Coordinates of SEQ ID Function Name Annotation NO: 10028 Agro B-AGRtu.left border Agro left border 6144-6585 transforamtion sequence, essential for transfer of T-DNA.
  • Plant P-At.Act7 Promoter from the 6624-7861 selectable arabidopsis actin 7 gene marker L-At.Act7 5′UTR of Arabidopsis expression Act7 gene cassette I-At.Act7 Intron from the Arabidopsis actin7 gene TS-At.ShkG-CTP2 Transit peptide region of 7864-8091 Arabidopsis EPSPS CR-AGRtu.aroA- Synthetic CP4 coding 8092-9459 CP4.nno_At region with dicot preferred codon usage.
  • T-AGRtu.nos A 3′ non-translated region 9466-9718 of the nopaline synthase gene of Agrobacterium tumefaciens Ti plasmid which functions to direct polyadenylation of the mRNA.
  • Gene of P-CaMV.35S-enh Promoter for 35S RNA 1-613 interest from CaMV containing a expression duplication of the ⁇ 90 to ⁇ 350 cassette region.
  • T-Gb.E6-3b 3′ untranslated region 688-1002 from the fiber protein E6 gene of sea-island cotton; Agro B-AGRtu.right border Agro right border 1033-1389 transformation sequence, essential for transfer of T-DNA.
  • OR-Ec.oriV-RK2 The vegetative origin of 5661-6057 in E. coli replication from plasmid RK2.
  • OR-Ec.ori-ColE1 The minimal origin of 2945-3533 replication from the E. coli plasmid ColE1.
  • Protein coding segments of recombinant DNA are amplified by PCR prior to insertion into vectors at the insertion site.
  • Primers for PCR amplification are designed at or near the start and stop codons of the coding sequence, in order to eliminate most of the 5′ and 3′ untranslated regions.
  • This example illustrates plant cell transformation methods useful in producing transgenic corn plant cells, plants, seeds and pollen of this invention and the production and identification of transgenic corn plants and seed with an enhanced trait, i.e. enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • Plasmid vectors were prepared by cloning DNA identified in Table 1 in the identified base vectors for use in corn transformation of corn plant cells to produce transgenic corn plants and progeny plants, seed and pollen.
  • corn plants of a readily transformable line (designated LH59) is grown in the greenhouse and ears harvested when the embryos are 1.5 to 2.0 mm in length. Ears are surface sterilized by spraying or soaking the ears in 80% ethanol, followed by air drying. Immature embryos are isolated from individual kernels on surface sterilized ears. Prior to inoculation of maize cells, Agrobacterium cells are grown overnight at room temperature. Immature maize embryo cells are inoculated with Agrobacterium shortly after excision, and incubated at room temperature with Agrobacterium for 5-20 minutes. Immature embryo plant cells are then co-cultured with Agrobacterium for 1 to 3 days at 23° C. in the dark.
  • LH59 readily transformable line
  • Co-cultured embryos are transferred to selection media and cultured for approximately two weeks to allow embryogenic callus to develop.
  • Embryogenic callus is transferred to culture medium containing 100 mg/L paromomycin and subcultured at about two week intervals.
  • Transformed plant cells are recovered 6 to 8 weeks after initiation of selection.
  • immature embryos are cultured for approximately 8-21 days after excision to allow callus to develop. Callus is then incubated for about 30 minutes at room temperature with the Agrobacterium suspension, followed by removal of the liquid by aspiration. The callus and Agrobacterium are co-cultured without selection for 3-6 days followed by selection on paromomycin for approximately 6 weeks, with biweekly transfers to fresh media, and paromomycin resistant callus identified as containing the recombinant DNA in an expression cassette.
  • transgenic corn plants To regenerate transgenic corn plants a callus of transgenic plant cells resulting from transformation is placed on media to initiate shoot development in plantlets which are transferred to potting soil for initial growth in a growth chamber at 26 degrees C. followed by a mist bench before transplanting to 5 inch pots where plants are grown to maturity.
  • the regenerated plants are self fertilized and seed is harvested for use in one or more methods to select seed, seedlings or progeny second generation transgenic plants (R2 plants) or hybrids, e.g. by selecting transgenic plants exhibiting an enhanced trait as compared to a control plant.
  • Transgenic corn plant cells were transformed with recombinant DNA from each of the genes identified in Table 1. Progeny transgenic plants and seed of the transformed plant cells were screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil as reported in Example 5.
  • This example illustrates plant transformation useful in producing the transgenic soybean plants of this invention and the production and identification of transgenic seed for transgenic soybean having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • soybean seeds are germinated overnight and the meristem explants excised.
  • the meristems and the explants are placed in a wounding vessel.
  • Soybean explants and induced Agrobacterium cells from a strain containing plasmid DNA with the gene of interest cassette and a plant selectable marker cassette are mixed no later than 14 hours from the time of initiation of seed germination and wounded using sonication.
  • explants are placed in co-culture for 2-5 days at which point they are transferred to selection media for 6-8 weeks to allow selection and growth of transgenic shoots.
  • Trait positive shoots are harvested approximately 6-8 weeks and placed into selective rooting media for 2-3 weeks. Shoots producing roots are transferred to the greenhouse and potted in soil.
  • a DNA construct can be transferred into the genome of a soybean cell by particle bombardment and the cell regenerated into a fertile soybean plant as described in U.S. Pat. No. 5,015,580, herein incorporated by reference.
  • Transgenic soybean plant cells were transformed with recombinant DNA from each of the genes identified in Table 1. Progeny transgenic plants and seed of the transformed plant cells were screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil as reported in Example 5.
  • This example illustrates the identification of homologs of proteins encoded by the DNA identified in Table 1 which is used to provide transgenic seed and plants having enhanced agronomic traits. From the sequence of the homologs, homologous DNA sequence can be identified for preparing additional transgenic seeds and plants of this invention with enhanced agronomic traits.
  • An “All Protein Database” was constructed of known protein sequences using a proprietary sequence database and the National Center for Biotechnology Information (NCBI) non-redundant amino acid database (nr.aa). For each organism from which a polynucleotide sequence provided herein was obtained, an “Organism Protein Database” was constructed of known protein sequences of the organism; it is a subset of the All Protein Database based on the NCBI taxonomy ID for the organism.
  • NCBI National Center for Biotechnology Information
  • the All Protein Database was queried using amino acid sequences provided herein as SEQ ID NO: 84 through SEQ ID NO: 166 using NCBI “blastp” program with E-value cutoff of 1e-8. Up to 1000 top hits were kept, and separated by organism names. For each organism other than that of the query sequence, a list was kept for hits from the query organism itself with a more significant E-value than the best hit of the organism. The list contains likely duplicated genes of the polynucleotides provided herein, and is referred to as the Core List. Another list was kept for all the hits from each organism, sorted by E-value, and referred to as the Hit List.
  • the Organism Protein Database was queried using polypeptide sequences provided herein as SEQ ID NO:84 through SEQ ID NO:166 using NCBI “blastp” program with E-value cutoff of 1e-4. Up to 1000 top hits were kept. A BLAST searchable database was constructed based on these hits, and is referred to as “SubDB”. SubDB was queried with each sequence in the Hit List using NCBI “blastp” program with E-value cutoff of 1e-8. The hit with the best E-value was compared with the Core List from the corresponding organism. The hit is deemed a likely ortholog if it belongs to the Core List, otherwise it is deemed not a likely ortholog and there is no further search of sequences in the Hit List for the same organism.
  • Transgenic corn seed and plants with recombinant DNA identified in Table 1 were prepared by plant cells transformed with DNA that was stably integrated into the genome of the corn cell.
  • the transgenic seed, plantlets and progeny plants were selected using the methods that measure Transgenic corn plant cells were transformed with recombinant DNA from each of the genes identified in Table 1.
  • Progeny transgenic plants and seed of the transformed plant cells were screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil as compared to control plants.
  • the physiological efficacy of transgenic corn plants can be tested for nitrogen use efficiency (NUE) traits in a high-throughput nitrogen (N) selection method.
  • NUE nitrogen use efficiency
  • the collected data are compared to the measurements from wildtype controls using a statistical model to determine if the changes are due to the transgene.
  • Raw data were analyzed by SAS software. Results shown herein are the comparison of transgenic plants relative to the wildtype controls.
  • Planting materials used Metro Mix 200 (vendor: Hummert) Cat. #10-0325, Scotts Micro Max Nutrients (vendor: Hummert) Cat. #07-6330, OS 41 ⁇ 3′′ ⁇ 37 ⁇ 8′′ pots (vendor: Hummert) Cat. #16-1415, OS trays (vendor: Hummert) Cat. #16-1515, Hoagland's macronutrients solution, Plastic 5′′ stakes (vendor: Hummert) yellow Cat. #49-1569, white Cat. #49-1505, Labels with numbers indicating material contained in pots. Fill 500 pots to rim with Metro Mix 200 to a weight of ⁇ 140g/pot. Pots are filled uniformly by using a balancer. Add 0.4 g of Micro Max nutrients to each pot. Stir ingredients with spatula to a depth of 3 inches while preventing material loss.
  • Seed Germination Each pot is lightly atered twice using reverse osmosis purified water. The first watering is scheduled to occur just before planting; and the second watering, after the seed has been planted in the pot. Ten Seeds of each entry (1 seed per pot) are planted to select eight healthy uniform seedlings. Additional wild type controls are planted for use as border rows. Alternatively, 15 seeds of each entry (1 seed per pot) are planted to select 12 healthy uniform seedlings (this larger number of plantings is used for the second, or confirmation, planting). Place pots on each of the 12 shelves in the Conviron growth chamber for seven days. This is done to allow more uniform germination and early seedling growth.
  • the following growth chamber settings are 25° C./day and 22° C./night, 14 hours light and ten hours dark, humidity ⁇ 80%, and light intensity ⁇ 350 ⁇ mol/m 2 /s (at pot level). Watering is done via capillary matting similar to greenhouse benches with duration of ten minutes three times a day.
  • Seedling transfer After seven days, the best eight or 12 seedlings for the first or confirmation pass runs, respectively, are chosen and transferred to greenhouse benches.
  • the pots are spaced eight inches apart (center to center) and are positioned on the benches using the spacing patterns printed on the capillary matting.
  • the Vattex matting creates a 384-position grid, randomizing all range, row combinations. Additional pots of controls are placed along the outside of the experimental block to reduce border effects.
  • Plants are allowed to grow for 28 days under the low N run or for 23 days under the high N run.
  • the macronutrients are dispensed in the form of a macronutrient solution (see composition below) containing precise amounts of N added (2 mM NH 4 NO 3 for limiting N selection and 20 mM NH 4 NO 3 for high N selection runs).
  • Each pot is manually dispensed 100 ml of nutrient solution three times a week on alternate days starting at eight and ten days after planting for high N and low N runs, respectively.
  • two 20 min waterings at 05:00 and 13:00 are skipped.
  • the vattex matting should be changed every third run to avoid N accumulation and buildup of root matter.
  • Table 7 shows the amount of nutrients in the nutrient solution for either the low or high nitrogen selection.
  • 2 mM NH 4 NO 3 20 mM NH 4 NO 3 (high (Low Nitrogen Growth Nitrogen Growth Condition, Low N) Condition, High N) Nutrient Stock mL/L mL/L 1 M NH 4 N0 3 2 20 1 M KH 2 PO 4 0.5 0.5 1 M MgSO 4 •7H 2 O 2 2 1 M CaCl 2 2.5 2.5 1 M K 2 SO 4 1 1
  • Leaf fresh mass is recorded for an excised V6 leaf, the leaf is placed into a paper bag.
  • the paper bags containing the leaves are then placed into a forced air oven at 80° C. for 3 days. After 3 days, the paper bags are removed from the oven and the leaf dry mass measurements are taken.
  • Leaf chlorophyll area which is a product of V6 relative chlorophyll content and its leaf area (relative units).
  • Leaf chlorophyll area leaf chlorophyll X leaf area. This parameter gives an indication of the spread of chlorophyll over the entire leaf area;
  • specific leaf area LSA is calculated as the ratio of V6 leaf area to its dry mass (cm 2 /g dry mass), a parameter also recognized as a measure of NUE.
  • Table 8 The data are shown in Table 8.
  • Transgenic plants provided by the present invention are planted in field without any nitrogen source being applied.
  • Transgenic plants and control plants are grouped by genotype and construct with controls arranged randomly within genotype blocks. Each type of transgenic plants are tested by 3 replications and across 5 locations.
  • Nitrogen levels in the fields are analyzed in early April pre-planting by collecting 30 sample soil cores from 0-24′′ and 24 to 48′′ soil layer. Soil samples are analyzed for nitrate-nitrogen, phosphorus(P), Potassium(K), organic matter and pH to provide baseline values. P, K and micronutrients are applied based upon soil test recommendations.
  • Transgenic plants provided by the present invention are planted in field with three levels of nitrogen (N) fertilizer being applied, i.e. low level (0 N), medium level (80 lb/ac) and high level (180 lb/ac). Liquid 28% or 32% UAN (Urea, Ammonium Nitrogen) are used as the N source and apply by broadcast boom and incorporate with a field cultivator with rear rolling basket in the same direction as intended crop rows. Although there is no N applied to the 0 N treatment the soil should still be disturbed in the same fashion as the treated area. Transgenic plants and control plants are grouped by genotype and construct with controls arranged randomly within genotype blocks. Each type of transgenic plants is tested by 3 replications and across 4 locations.
  • N nitrogen
  • UAN Ultra, Ammonium Nitrogen
  • Nitrogen levels in the fields are analyzed in early April pre-planting by collecting 30 sample soil cores from 0-24′′ and 24 to 48′′ soil layer. Soil samples are analyzed for nitrate-nitrogen, phosphorus(P), Potassium(K), organic matter and pH to provide baseline values. P, K and micronutrients are applied based upon soil test recommendations. TABLE 9 Genes increase seed yield in transgenic plants at different nitrogen levels.
  • transgenic plants of this invention exhibit improved yield as compared to a control plant. Improved yield can result from enhanced seed sink potential, i.e. the number and size of endosperm cells or kernels and/or enhanced sink strength, i.e. the rate of starch biosynthesis. Sink potential can be established very early during kernel development, as endosperm cell number and size are determined within the first few days after pollination.
  • Effective yield selection of enhanced yielding transgenic corn events uses hybrid progeny of the transgenic event over multiple locations with plants grown under optimal production management practices, and maximum pest control.
  • a useful target for improved yield is a 5% to 10% increase in yield as compared to yield produced by plants grown from seed for a control plant.
  • Selection methods may be applied in multiple and diverse geographic locations, for example up to 16 or more locations, over one or more plating seasons, for example at least two planting seasons to statistically distinguish yield improvement from natural environmental effects. It is to plant multiple transgenic plants, positive and negative control plants, and pollinator plants in standard plots, for example 2 row plots, 20 feet long by 5 feet wide with 30 inches distance between rows and a 3 foot alley between ranges.
  • Transgenic events can be grouped by recombinant DNA constructs with groups randomly placed in the field.
  • a pollinator plot of a high quality corn line is planted for every two plots to allow open pollination when using male sterile transgenic events.
  • a useful planting density is about 30,000 plants/acre.
  • High planting density is greater than 30,000 plants/acre; preferably about 40,000 plants/acre, more preferably about 42,000 plants/acre, most preferably about 45,000 plants/acre.
  • Surrogate indicators for yield improvement include source capacity (biomass), source output (sucrose and photosynthesis), sink components (kernel size, ear size, starch in the seed), development (light response, height, density tolerance), maturity, early flowering trait and physiological responses to high density planting, for example at 45,000 plants per acre, for example as illustrated in Table 10 and 11. TABLE 10 Timing Evaluation Description comments V2-3 Early stand Can be taken any time after germination and prior to removal of any plants. Pollen shed GDU to 50% shed GDU to 50% plants shedding 50% tassel. Silking GDU to 50% silk GDU to 50% plants showing silks. Maturity Plant height Height from soil surface to 10 plants per plot - Yield flag leaf attachment (inches).
  • team assistance Maturity Ear height Height from soil surface to 10 plants per plot - Yield primary ear attachment node.
  • team assistance Maturity Leaves above ear visual scores: erect, size, rolling Maturity Tassel size Visual scores +/ ⁇ vs. WT Pre-Harvest Final Stand Final stand count prior to harvest, exclude tillers Pre-Harvest Stalk lodging No. of stalks broken below the primary ear attachment. Exclude leaning tillers Pre-Harvest Root lodging No. of stalks leaning >45° angle from perpendicular. Pre-Harvest Stay green After physiological maturity and when differences among genotypes are evident: Scale 1 (90-100% tissue green) - 9 (0-19% tissue green). Harvest Grain Yield Grain yield/plot (Shell weight)
  • Electron transport rates (ETR) and CO2 exchange rates (CER) were measured with Li640LCF (Licor, Lincoln, Nebr.) around V9-R1 stages. Leaf chlorophyll fluorescence is a quick way to monitor the source activity and was reported to be highly correlated with CO 2 assimilation under varies conditions (Photosyn Research, 37: 89-102). The youngest fully expanded leaf or 2 leaves above the ear leaf was measured with actinic light 1500 (with 10% blue light) micromol m ⁇ 2 s ⁇ 1 , 28° C., CO2 levels 450 ppm. Ten plants were measured in each event. There were 2 readings for each plant.
  • a hand-held chlorophyll meter SPAD-502 (Minolta-Japan) was used to measure the total chlorophyll level on live transgenic plants and the wild type counterparts a. Three trifoliates from each plant were analyzed, and each trifoliate were analyzed three times. Then 9 data points were averaged to obtain the chlorophyll level. The number of analyzed plants of each genotype ranged from 5 to 8.
  • a useful statistical measurement approach comprises three components, i.e. modeling spatial autocorrelation of the test field separately for each location, adjusting traits of recombinant DNA events for spatial dependence for each location, and conducting an across location analysis.
  • the first step in modeling spatial autocorrelation is estimating the covariance parameters of the semivariogram.
  • a spherical covariance model is assumed to model the spatial autocorrelation. Because of the size and nature of the trial, it is likely that the spatial autocorrelation may change. Therefore, anisotropy is also assumed along with spherical covariance structure. The following set of equations describes the statistical form of the anisotropic spherical covariance model.
  • ⁇ (v, ⁇ 2 , ⁇ , ⁇ n , ⁇ j ), where v is the nugget effect, ⁇ 2 is the partial sill, ⁇ is a rotation in degrees clockwise from north, ⁇ n is a scaling parameter for the minor axis and ⁇ j is a scaling parameter for the major axis of an anisotropical ellipse of equal covariance.
  • the five covariance parameters that defines the spatial trend will then be estimated by using data from heavily replicated pollinator plots via restricted maximum likelihood approach. In a multi-location field trial, spatial trend are modeled separately for each location.
  • a variance-covariance structure is generated for the data set to be analyzed.
  • This variance-covariance structure contains spatial information required to adjust yield data for spatial dependence.
  • a nested model that best represents the treatment and experimental design of the study is used along with the variance-covariance structure to adjust the yield data.
  • the nursery or the seed batch effects can also be modeled and estimated to adjust the yields for any yield parity caused by seed batch differences.
  • all adjusted data is combined and analyzed assuming locations as replications. In this analysis, intra and inter-location variances are combined to estimate the standard error of yield from transgenic plants and control plants. Relative mean comparisons are used to indicate statistically significant yield improvements.
  • Described in this example is a high-throughput method for greenhouse selection of transgenic corn plants to wild type corn plants (tested as inbreds or hybrids) for water use efficiency.
  • This selection process imposes 3 drought/re-water cycles on plants over a total period of 15 days after an initial stress free growth period of 11 days. Each cycle consists of 5 days, with no water being applied for the first four days and a water quenching on the 5 th day of the cycle.
  • the primary phenotypes analyzed by the selection method are the changes in plant growth rate as determined by height and biomass during a vegetative drought treatment. The hydration status of the shoot tissues following the drought is also measured. The plant height are measured at three time points.
  • SIH shoot initial height
  • SWH shoot wilt height
  • SWM shoot wilted biomass
  • STM shoot turgid weight
  • SDM shoot dry biomass
  • Transgenic plants transformed with pMON67754 comprising the recombinant DNA as set forth in SEQ ID NO: 3 were tested in field with moderate drought conditions in Sananta, Ill. and Dixon Calif.
  • SPAD readings on leaves under a moderate drought stress showed a significant increase in chlorophyll level in the transgenic plants as compared to the control plants.
  • Two events showed a significant increase in SPAD reading for chlorophyll level, indicating an improvement in drought tolerance.
  • 2 events (ZM_M16396 and ZM_M16401) out of 6 tested, showed significantly (p ⁇ 0.1) improved leaf SPAD readings in two different locations, indicating an improvement in drought tolerance.
  • Corn kernels are placed embryo side down on blotter paper within an individual cell (8.9 ⁇ 8.9 cm) of a germination tray (54 ⁇ 36 cm). Ten seeds from an event are placed into one cell of the germination tray. Each tray can hold 21 transgenic events and 3 replicates of wildtype (LH244SDms+LH59), which is randomized in a complete block design. For every event there are five replications (five trays). The trays are placed at 9.7C for 24 days (no light) in a Convrion growth chamber (Conviron Model PG V36, Controlled Environments, Winnipeg, Canada). Two hundred and fifty milliliters of deionized water are added to each germination tray.
  • Convrion growth chamber Convrion Model PG V36, Controlled Environments, Winnipeg, Canada
  • Germination counts are taken 10th, 11th, 12th, 13th, 14th, 17th, 19th, 21st, and 24th day after start date of the experiment. Seeds are considered germinated if the emerged radicle size is 1 cm. From the germination counts germination index is calculated.
  • Germination index ( ⁇ ([ T+ 1 ⁇ n i ]*[P i ⁇ P i ⁇ 1 ]))/ T
  • T is the total number of days for which the germination assay is performed.
  • the number of days after planting is defined by n. “i” indicated the number of times the germination had been counted, including the current day.
  • P is the percentage of seeds germinated during any given rating.
  • Statistical differences are calculated between transgenic events and wild type control. After statistical analysis, the events that show a statistical significance at the p level of less than 0.1 relative to wild-type controls will advance to a secondary cold selection.
  • the secondary cold screen is conducted in the same manner of the primary selection only increasing the number of repetitions to ten.
  • Statistical analysis of the data from the secondary selection is conducted to identify the events that show a statistical significance at the p level of less than 0.05 relative to wild-type controls.
  • Pots were filled with Metro Mix 200 soil-less media containing 19:6:12 fertilizer (6 lbs/cubic yard) (Metro Mix, Pots and Flat are obtained from Hummert International, Earth City, Mo.).
  • Metro Mix 200 soil-less media containing 19:6:12 fertilizer (6 lbs/cubic yard) (Metro Mix, Pots and Flat are obtained from Hummert International, Earth City, Mo.).
  • pots were placed in a growth chamber set at 23° C., relative humidity of 65% with 12 hour day and night photoperiod (300 uE/m2-min). Planted seeds were watered for 20 minute every other day by sub-irrigation and flats were rotated every third day in a growth chamber for growing corn seedlings.
  • transgenic positive and wild-type negative (WT) plants were positioned in flats in an alternating pattern. Chlorophyll fluorescence of plants was measured on the 10 th day during the dark period of growth by using a PAM-2000 portable fluorometer as per the manufacturer's instructions (Walz, Germany). After chlorophyll measurements, leaf samples from each event were collected for confirming the expression of genes of the present invention. For expression analysis six VI leaf tips from each selection were randomly harvested. The flats were moved to a growth chamber set at 5° C. All other conditions such as humidity, day/night cycle and light intensity were held constant in the growth chamber. The flats were sub-irrigated every day after transfer to the cold temperature.
  • V3 leaf growth, V2 leaf necrosis and fluorescence during pre-shock and cold shock can be used for estimation of cold shock damage on corn plants.
  • Seeds were grown in germination paper for the early seedling growth assay. Three 12′′ ⁇ 18′′ pieces of germination paper (Anchor Paper #SD7606) were used for each entry in the test (three repetitions per transgenic event). The papers were wetted in a solution of 0.5% KNO 3 and 0.1% Thyram.
  • the wet paper was rolled up starting from one of the short ends. The paper was rolled evenly and tight enough to hold the seeds in place. The roll was secured into place with two large paper clips, one at the top and one at the bottom.
  • the rolls were incubated in a growth chamber at 23° C. for three days in a randomized complete block design within an appropriate container. The chamber was set for 65% humidity with no light cycle. For the cold stress treatment the rolls were then incubated in a growth chamber at 12° C. for twelve days. The chamber was set for 65% humidity with no light cycle.
  • the germination papers were unrolled and the seeds that did not germinate were discarded.
  • the lengths of the radicle and coleoptile for each seed were measured through an automated imaging program that automatically collects and processes the images.
  • the imaging program automatically measures the shoot length, root length, and whole seedling length of every individual seedling and then calculates the average of each roll.
  • the events that show a statistical significance at the p level of less than 0.1 relative to wild-type controls will advance to a secondary cold selection.
  • the secondary cold selection is conducted in the same manner of the primary selection only increasing the number of repetitions to five.
  • Statistical analysis of the data from the secondary selection is conducted to identify the events that show a statistical significance at the p level of less than 0.05 relative to wild-type controls.
  • This example sets forth a cold field efficacy trial to identify gene constructs that confer enhanced cold vigor at germination and early seedling growth under early spring planting field conditions in conventional-till and simulated no-till environments. Seeds are planted into the ground around two weeks before local farmers are beginning to plant corn so that a significant cold stress is exerted onto the crop, named as cold treatment. Seeds also are planted under local optimal planting conditions such that the crop has little or no exposure to cold condition, named as normal treatment. The cold field efficacy trials are carried out in five locations, including Glyndon Minn. Mason Mich., Monmouth Ill., Dayton Iowa, Mystic Conn. At each location, seeds are planted under both cold and normal conditions with 3 repetitions per treatment, 20 kernels per row and single row per plot. Seeds are planted 1.5 to 2 inch deep into soil to avoid muddy conditions. Two temperature monitors are set up at each location to monitor both air and soil temperature daily.
  • This example sets forth a high-throughput selection for identifying plant seeds with improvement in seed composition using the Infratec 1200 series Grain Analyzer, which is a near-infrared transmittance spectrometer used to determine the composition of a bulk seed sample.
  • Near infrared analysis is a non-destructive, high-throughput method that can analyze multiple traits in a single sample scan.
  • An NIR calibration for the analytes of interest is used to predict the values of an unknown sample.
  • the NIR spectrum is obtained for the sample and compared to the calibration using a complex chemometric software package that provides a predicted values as well as information on how well the sample fits in the calibration.
  • Infratec Model 1221, 1225, or 1227 with transport module by Foss North America is used with cuvette, item #1000-4033, Foss North America or for small samples with small cell cuvette, Foss standard cuvette modified by Leon Girard Co. Corn and soy check samples of varying composition maintained in check cell cuvettes are supplied by Leon Girard Co. NIT collection software is provided by Maximum Consulting Inc. Software. Calculations are preformed automatically by the software. Seed samples are received in packets or containers with barcode labels from the customer. The seed is poured into the cuvettes and analyzed as received.
  • Typical sample(s) Whole grain corn and soybean seeds Analytical time to run Less than 0.75 min per sample method: Total elapsed time per run: 1.5 minute per sample Typical and minimum sample Corn typical: 50 cc; minimum 30 cc size: Soybean typical: 50 cc; minimum 5 cc Typical analytical range: Determined in part by the specific calibration. Corn - moisture 5-15%, oil 5-20%, protein 5-30%, starch 50-75%, and density 1.0-1.3%. Soybean - moisture 5-15%, oil 15-25%, and protein 35-50%.
  • This example illustrates the preparation of transgenic plant cells containing recombinant DNA (SEQ ID NO:82) expressing a maize phytochrome A protein (PHYA).
  • SEQ ID NO:82 recombinant DNA
  • PHYA phytochrome A protein
  • a full-length cDNA encoding a corn PHYA protein was cloned from corn.
  • the cDNA clone contained 3396 bp of nucleotides encoding a 1131 amino acid PHYA protein with molecular weight at 125.2 kD.
  • primers were designed to clone a genomic DNA, illustrated in FIG. 1 , from a maize inbred LH172 genomic library.
  • Recombinant DNA comprising a rice actin promoter operably linked to the genomic DNA encoding the corn PHYA protein followed by a Hsp 17 terminator was inserted into transformation vector of pMON74916 as set forth in SEQ ID NO: 10030.
  • Corn plant cells were transformed with recombinant DNA expressing PHA using pMON74916 and used to regenerate a population of transgenic plants.
  • Transgenic plants were regenerated from about 100 events of transformed plant cells; plants from 90 of the events with various expression levels were selected for pollination to produce R1and F1 seeds; and plants from 31 events were selected for screening for an enhanced trait.
  • Transgenic plants were grown in fields at three densities: high density at 42,000 plants per acre; medium density at 35,000 plants per acre; and low density at 28,000 plants per acre. Plants from three plant cell events expressing PHYA were selected for studying physiological and yield responses to different densities.
  • the physiological data from the density trial Y1130 is summarized in the Table 23 shown below.
  • Event ZM_S83483 under high planting density showed significant decrease in plant height, ear height, and internode length and had a significant increase in chlorophyll content.
  • events ZM_S83444, ZM_S83446, ZM_S83473, ZM_S83480, ZM_S83483, and ZM_S83907 show significant increases in single kernel weight.
  • Event ZM_S83452 shows significant increases in single kernel weight and total kernel weight.
  • the screening data show that plant cells with stably-integrated, non-natural, recombinant DNA expressing a phytochrome A protein can be regenerated into plants exhibiting increased yield as compared to control plants.
  • This example illustrates the preparation of transgenic plant cells containing recombinant DNA (SEQ ID NO:77) expressing a soybean MADS box transcription factor protein and identified as G1760.
  • the DNA encoding the soybean MADS box transcription factor was cloned from a soybean library and inserted into a recombinant DNA construct comprising a CaMV 35S promoter operably linked to the DNA encoding the transcription factor followed by a terminator.
  • the recombinant DNA construct was inserted into a transformation vector plasmid to produce plasmid pMON74470, as set forth in SEQ ID NO: 10029 which was used for Agrobacterium -mediated transformation of soybean plant cells.
  • Soybean plant cells were transformed with recombinant DNA expressing the MADS box transcription factor using MON74470 and used to regenerate a population of transgenic plants.
  • Transgenic soybean plants were regenerated and selected for screening for an enhanced trait.
  • Transgenic soybean plants exhibited flowers with highly enlarged sepals and a winding stem. The main stem exhibited reduced lateral branching and increased raceme formation. Flowering time was decreased by about 2 to 4 days as compared to control plants under short day (10 hr) and long day (14 hr) conditions. Transgenic plants also flowered by 5 weeks when placed under non-inductive 20 hr light; wild-type control plants did not flower under such conditions. Floral and pod abscission was greatly reduced in the transgenic plants resulting in an increase in the number of pods per plant. Wild type control plants produced on the order of 100 pods, specific transgenic plants produced at least 125 pods per plant and plants regenerated from plant cells of one transgenic event produced greater than 200 pods per plant.
  • R0 plants regenerated from one transgenic plant cell event (28877) of 41 transgenic plant cells events produced a large number of pods per node and seeds/plant ⁇ 531 R1 seeds per plant compared to an average of 150 seeds per plant, i.e. increased yield.
  • This example illustrates the identification of consensus amino acid sequence for the proteins and homologs encoded by DNA that is used to prepare the transgenic seed and plants of this invention having enhanced agronomic traits.
  • FIG. 2 shows the sequences of SEQ ID NO: 136, its homologs and the consensus sequence (SEQ ID NO: 10031) at the end.
  • SEQ ID NO: 151 shows the sequences of SEQ ID NO: 151, its homologs and the consensus sequence (SEQ ID NO: 10032) at the end.
  • the consensus amino acid sequence can be used to identify DNA corresponding to the full scope of this invention that is useful in providing transgenic plants, for example corn and soybean plants with enhanced agronomic traits, for example improved nitrogen use efficiency, improved yield, improved water use efficiency and/or improved growth under cold stress, due to the expression in the plants of DNA encoding a protein with amino acid sequence identical to the consensus amino acid sequence.
  • the amino acid sequence of the expressed proteins that were shown to be associated with an enhanced trait were analyzed for Pfam protein family against the current Pfam collection of multiple sequence alignments and hidden Markov models using the HMMER software in the appended computer listing.
  • the Pfam protein families for the proteins of SEQ ID NO:84 through 166 are shown in Table 26.
  • the Hidden Markov model databases for the identified patent families are also in the appended computer listing allowing identification of other homologous proteins and their cognate encoding DNA to enable the full breadth of the invention for a person of ordinary skill in the art.
  • Certain proteins are identified by a single Pfam domain and others by multiple Pfam domains. For instance, the protein with amino acids of SEQ ID NO: 91 is characterized by two Pfam domains, i.e.
  • SRF-TF and K-box the protein with amino acids of SEQ ID NO: 165 is characterized by six Pfam domains, i.e. GAF, Phytochrome, PAS, a repeated PAS, HisKA, and HATPase.
  • This example illustrates the preparation and identification by selection of transgenic seeds and plants derived from transgenic plant cells of this invention where the plants and seed are identified by screening a having an enhanced agronomic trait imparted by expression of a protein selected from the group including the homologous proteins identified in Example 4, SEQ ID NO: 121, 128, 152-160, 162 and 164.
  • Transgenic plant cells of corn, soybean, cotton, canola, wheat and rice are transformed with recombinant DNA for expressing each of the homologs identified in Example 4. Plants are regenerated from the transformed plant cells and used to produce progeny plants and seed that are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. Plants are identified exhibiting enhanced traits imparted by expression of the homologous proteins.

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