US20100313297A1

US20100313297A1 - Phosphate use efficiency

Info

Publication number: US20100313297A1
Application number: US12/541,607
Authority: US
Inventors: Julissa Sosa; Greg Nadzan
Original assignee: Ceres Inc
Current assignee: Ceres Inc
Priority date: 2004-05-27
Filing date: 2009-08-14
Publication date: 2010-12-09
Also published as: EP1759002A2; US7576260B2; AU2005250442A1; WO2005118820A3; BRPI0510652A; CN101001954B; MXPA06013747A; CA2567983A1; WO2005118820A8; WO2005118820A2; CN101001954A; US20060294622A1

Abstract

Isolated polynucleotides and polypeptides encoded thereby are described, together with the use of those products for making transgenic plants with increased tolerance to pH or increased phosphorus efficiency.

Description

This application is a Continuation of co-pending application Ser. No. 11/140,347, filed on May 27, 2005, the entire contents of which are hereby incorporated by reference and for which priority is claimed under 35 U.S.C. §120.
Co-pending application Ser. No. 11/140,347 claims priority under 35 U.S.C. §119(e) on U.S. Provisional Application No(s). 60/575,309 filed on May 27, 2004, the entire contents of which are hereby incorporated by reference.

FIELD OF THE INVENTION

The present invention relates to isolated polynucleotides, polypeptides encoded thereby, and the use of those sequences for making transgenic plants with modulated pH response and phosphate use efficiency.

BACKGROUND OF THE INVENTION

Plants are constantly exposed to a variety of biotic (i.e., pathogen infection and insect herbivory) and abiotic (e.g., high pH, low phosphate) stresses. To survive these challenges, plants have developed elaborate mechanisms to perceive external signals and environmental stresses and to manifest adaptive responses with proper physiological and morphological changes (Bohnert et al., 1995). Plants exposed to low or high pH conditions typically have low yields of plant material, seeds, fruit and other edible products. Extreme soil pH conditions have a major influence on nutrient availability resulting in severe agronomic losses. Plants exposed to low pH soil conditions develop deficiencies in nutrients such as copper, molybdate, potassium, sulfur, and nitrogen. Also, plants exposed to high pH soil conditions develop iron, copper, manganese, and zinc deficiencies (FIG. 1). Phosphate deficiency is a problem in both high and low pH soil conditions. Essential mineral nutrients are required in substantial amounts to sustain plant growth and maximize plant yields.
Consequently, agricultural and horticultural entities routinely alter the rhizosphere to maximize and maintain crop yields; these frequently result in more pollution and unbalancing of the natural soil mineral balance (National Research Council. (1989) Alternative Agriculture. National Academic Press, Washington D.C.). Excessive over-liming of acid soils, for instance, has resulted in the induction of iron, manganese, copper, and zinc deficiencies; deficiencies commonly observed in calcareous soil.
It would, therefore, be of great interest and importance to be able to identify genes that confer improved phosphate efficiency characteristics to thereby enable one to create transformed plants (such as crop plants) with improved phosphate efficiency characteristics to thereby better survive low and high pH conditions.
In the field of agriculture and forestry efforts are constantly being made to produce plants with an increased growth potential in order to feed the ever-increasing world population and to guarantee the supply of reproducible raw materials. This is done conventionally through plant breeding. The breeding process is, however, both time-consuming and labor-intensive. Furthermore, appropriate breeding programs must be performed for each relevant plant species.
Progress has been made in part by the genetic manipulation of plants; that is by introducing and expressing recombinant nucleic acid molecules in plants. Such approaches have the advantage of not usually being limited to one plant species, but instead being transferable among plant species. (Zhang et al. (2004) Plant Physiol. 135:615). There is a need for generally applicable processes that improve forest or agricultural plant growth potential. Therefore, the present invention relates to a process for increasing the abiotic stress tolerance and consequently the growth potential in plants, characterized by expression of recombinant DNA molecules stably integrated into the plant genome.

SUMMARY OF THE INVENTION

The present invention, therefore, relates to isolated polynucleotides, polypeptides encoded thereby, and the use of those sequences for making transgenic plants with modulated pH tolerance or phosphate use efficiency.
The present invention also relates to processes for increasing the growth potential in plants under abnormal pH or phosphate conditions, recombinant nucleic acid molecules and polypeptides used for these processes and their uses, as well as to plants themselves.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows the relationship between soil pH and nutrient uptake.

FIG. 2 shows pH recovery as measured by volume of seeds collected from a plant containing cDNA 1248777 compared to pH treated and un-treated controls.

DETAILED DESCRIPTION OF THE INVENTION

1. Definitions

The following terms are utilized throughout this application:

Constitutive Promoter: Promoters referred to herein as “constitutive promoters” actively promote transcription under most, but not necessarily all, environmental conditions and states of development or cell differentiation. Examples of constitutive promoters include the cauliflower mosaic virus (CaMV) 35S transcript initiation region and the 1′ or 2′ promoter derived from T-DNA of Agrobacterium tumefaciens, and other transcription initiation regions from various plant genes, such as the maize ubiquitin-1 promoter, known to those of skill.
Domain: Domains are fingerprints or signatures that can be used to characterize protein families and/or parts of proteins. Such fingerprints or signatures can comprise conserved (1) primary sequence, (2) secondary structure, and/or (3) three-dimensional conformation. Generally, each domain has been associated with either a family of proteins or motifs. Typically, these families and/or motifs have been correlated with specific in-vitro and/or in-vivo activities. A domain can be any length, including the entirety of the sequence of a protein. Detailed descriptions of the domains, associated families and motifs, and correlated activities of the polypeptides of the instant invention are described below. Usually, the polypeptides with designated domain(s) can exhibit at least one activity that is exhibited by any polypeptide that comprises the same domain(s).
Endogenous: The term “endogenous,” within the context of the current invention refers to any polynucleotide, polypeptide or protein sequence which is a natural part of a cell or organisms regenerated from said cell.
Exogenous: “Exogenous,” as referred to within, is any polynucleotide, polypeptide or protein sequence, whether chimeric or not, that is initially or subsequently introduced into the genome of an individual host cell or the organism regenerated from said host cell by any means other than by a sexual cross. Examples of means by which this can be accomplished are described below, and include Agrobacterium-mediated transformation (of dicots—e.g. Salomon et al. EMBO J. 3:141 (1984); Herrera-Estrella et al. EMBO J. 2:987 (1983); of monocots, representative papers are those by Escudero et al., Plant J. 10:355 (1996), Ishida et al., Nature Biotechnology 14:745 (1996), May et al., Bio/Technology 13:486 (1995)), biolistic methods (Armaleo et al., Current Genetics 17:97 1990)), electroporation, in planta techniques, and the like. Such a plant containing the exogenous nucleic acid is referred to here as a T₀for the primary transgenic plant and T₁for the first generation. The term “exogenous” as used herein is also intended to encompass inserting a naturally found element into a non-naturally found location.
Functionally Comparable Proteins: This phrase describes those proteins that have at least one characteristic in common. Such characteristics include sequence similarity, biochemical activity, transcriptional pattern similarity and phenotypic activity. Typically, the functionally comparable proteins share some sequence similarity or at least one biochemical and within this definition, homologs, orthologs and analogs are considered to be functionally comparable. In addition, functionally comparable proteins generally share at least one biochemical and/or phenotypic activity.

Functionally comparable proteins will give rise to the same characteristic to a similar, but not necessarily to the same degree. Typically, comparable proteins give the same characteristics where the quantitative measurement due to one of the comparables is at lest 20% of the other; more typically, between 30 to 40%; even more typically, between 50-60%; even more typically, 70 to 80%; even more typically between 90 to 100%.

Heterologous sequences: “Heterologous sequences” are those that are not operatively linked or are not contiguous to each other in nature. For example, a promoter from corn is considered heterologous to an Arabidopsis coding region sequence. Also, a promoter from a gene encoding a growth factor from corn is considered heterologous to a sequence encoding the corn receptor for the growth factor. Regulatory element sequences, such as UTRs or 3′ end termination sequences that do not originate in nature from the same gene as the coding sequence originates from, are considered heterologous to said coding sequence. Elements operatively linked in nature and contiguous to each other are not heterologous to each other. On the other hand, these same elements remain operatively linked but become heterologous if other filler sequence is placed between them. Thus, the promoter and coding sequences of a corn gene expressing an amino acid transporter are not heterologous to each other, but the promoter and coding sequence of a corn gene operatively linked in a novel manner are heterologous.
High pH: “High pH” can be defined as a non-optimal and terminal alkaline pH value when a given plant can no longer make use of certain essential nutrients, such as phosphate, available in the soil. For instance, if a plant grows optimally at pH of 4.0-5.0, high pH would be any pH greater than 5. If the optimal pH were in the range of 6-6.5, high pH would be a pH greater than pH 6.5. As an example, if a corn crop under optimal pH conditions would yield 134 bushels per acre and all other conditions were held constant, a high pH tolerant variety would produce similar yields at pH 9 or above.
Inducible Promoter: An “inducible promoter” in the context of the current invention refers to a promoter which is regulated under certain conditions, such as light, chemical concentration, protein concentration, conditions in an organism, cell, or organelle, etc. A typical example of an inducible promoter, which can be utilized with the polynucleotides of the present invention, is PARSK1, the promoter from the Arabidopsis gene encoding a serine-threonine kinase enzyme, and which promoter is induced by dehydration, abscissic acid and sodium chloride (Wang and Goodman, Plant 1 8:37 (1995)). Examples of environmental conditions that may affect transcription by inducible promoters include anaerobic conditions, elevated temperature, or the presence of light.
Low Nitrogen: “Low nitrogen” can be defined as a quantity of nitrogen, whether in the form of ammonium or nitrate, which is insufficient to sustain normal growth and yield for a given plant. The need for nitrogen fertilizers varies considerably among plants. Further, the type of soil and the conditions in the soil have a significant impact on the ability of a plant to take up nitrogen. Supplemental nitrogen fertilizers are often added to soil or applied directly to plants to enhance their growth or appearance. Even with normal fertilizer applications, the amount of nitrogen available to a plant at any given time may be too low to support optimal growth. Hence, low nitrogen must be defined in terms of the specific plant and environment in which the plant is being grown. For example, if under a given set of conditions with a specific corn hybrid the optimal nitrogen level was 160 pounds of nitrogen fertilizer per acre and under such conditions the hybrid were able to achieve a yield of 134 bushels per acre, a low nitrogen tolerant hybrid would grow optimally and produce the same yield with at least10% less or at least 20% less or at least 30% less or at least 40% less or at least 50% less nitrogen. Further, the low nitrogen hybrid would grow better after much of the initial nitrogen had been depleted and would not require multiple applications of nitrogen.
Low pH: “Low pH” can be defined as that non-optimal and terminal acidic pH value when a given plant can no longer make use of certain essential nutrients, such as potassium, available in the soil. If a plant grows optimally at pH of 4.0-5.0, low pH is any pH less than 4. If the optimal pH is in the range of 6-8, low pH would be a pH less than 6. For example, if a corn crop under optimal pH conditions would yield 134 bushels per acre and all other conditions were held constant, a low pH tolerant variety would produce similar yields at pH 5, or pH 4.
Low Phosphate: “Low phosphate” can be defined as a quantity of phosphate which is insufficient to sustain normal growth and yield for a given plant. The level of phosphate required for optimal plant growth differs among plant species and depends on the condition of the soil and other environmental conditions. To determine a level of phosphate that is low, comparative experiments are needed. For example, if a corn hybrid in a particular field treated with 40 pounds of phosphate per acre would yield 134 bushels per acre and all other conditions were held constant, a low phosphate tolerant hybrid would produce similar yields at 35 or less pounds of phosphate per acre or 30 or less pounds of phosphate per acre or 25 or less pounds of phosphate per acre or 20 or less pounds of phosphate per acre.
Masterpool: The “master pools” discussed in these experiments are a pool of seeds from five different transgenic plants transformed with the same exogenous gene.
Misexpression: The term “misexpression” refers to an increase or a decrease in the transcription of a coding region into a complementary RNA sequence as compared to the wild-type. This term also encompasses expression of a gene or coding region for a different time period as compared to the wild-type and/or from a non-natural location within the plant genome.
Percentage of sequence identity: “Percentage of sequence identity,” as used herein, is determined by comparing two optimally aligned sequences over a comparison window, where the fragment of the polynucleotide or amino acid sequence in the comparison window may comprise additions or deletions (e.g., gaps or overhangs) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity. Optimal alignment of sequences for comparison may be conducted by the local homology algorithm of Smith and Waterman Add. APL. Math. 2:482 (1981), by the homology alignment algorithm of Needleman and Wunsch J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson and Lipman Proc. Natl. Acad. Sci. (USA) 85: 2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, BLAST, PASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.), or by inspection. Given that two sequences have been identified for comparison, GAP and BESTFIT are preferably employed to determine their optimal alignment. Typically, the default values of 5.00 for gap weight and 0.30 for gap weight length are used. The term “substantial sequence identity” between polynucleotide or polypeptide sequences refers to polynucleotide or polypeptide comprising a sequence that has at least 80% sequence identity, preferably at least 85%, more preferably at least 90% and most preferably at least 95%, even more preferably, at least 96%, 97%, 98% or 99% sequence identity compared to a reference sequence using the programs.

Query nucleic acid and amino acid sequences were searched against subject nucleic acid or amino acid sequences residing in public or proprietary databases. Such searches were done using the Washington University Basic Local Alignment Search Tool Version 1.83 (WU-Blast2) program. The WU-Blast2 program is available on the internet from Washington University. A WU-Blast2 service for Arabidopsis can also be found on the internet. Typically the following parameters of WU-Blast2 were used: Filter options were set to “default,” Output format was set to “gapped alignments,” the Comparison Matrix was set to “BLOSUM62,” Cutoff Score (S value) was set to “default,” the Expect (E threshold) was set to “default,” the Number of best alignments to show was set to “100,” and the “Sort output” option was set to sort the output by “pvalue.”

Plant Promoter: A “plant promoter” is a promoter capable of initiating transcription in plant cells and can drive or facilitate transcription of a nucleotide sequence or fragment thereof of the instant invention. Such promoters need not be of plant origin. For example, promoters derived from plant viruses, such as the CaMV35S promoter or from Agrobacterium tumefaciens such as the T-DNA promoters, can be plant promoters. A typical example of a plant promoter of plant origin is the maize ubiquitin-1 (ubi-1) promoter known to those of skill.
Specific Promoter: In the context of the current invention, “specific promoters” refers to promoters that have a high preference for being active in a specific tissue or cell and/or at a specific time during development of an organism. By “high preference” is meant at least 3-fold, preferably 5-fold, more preferably at least 10-fold still more preferably at least 20-fold, 50-fold or 100-fold increase in transcription in the desired tissue over the transcription in any other tissue. Typical examples of temporal and/or tissue specific promoters of plant origin that can be used with the polynucleotides of the present invention, are: SH-EP from Vigna mungo and EP-C1 from Phaseolus vulgaris (Yamauchi et al. (1996) Plant Mol Biol. 30(2):321-9.); RCc2 and RCc3, promoters that direct root-specific gene transcription in rice (Xu et al., Plant Mol. Biol. 27:237 (1995) and TobRB27, a root-specific promoter from tobacco (Yamamoto et al., Plant Cell 3:371 (1991)).
Stringency: “Stringency” as used herein is a function of probe length, probe composition (G+C content), and salt concentration, organic solvent concentration, and temperature of hybridization or wash conditions. Stringency is typically compared by the parameter T_m, which is the temperature at which 50% of the complementary molecules in the hybridization are hybridized, in terms of a temperature differential from T_m. High stringency conditions are those providing a condition of T_m−5° C. to T_m−10° C. Medium or moderate stringency conditions are those providing T_m−20° C. to T_m−29° C. Low stringency conditions are those providing a condition of T_m−40° C. to T_m−48° C. The relationship of hybridization conditions to T_m(in ° C.) is expressed in the mathematical equation

T _m=81.5−16.6(log₁₀[Na⁺])+0.41(% G+C)−(600/N) (1)
where N is the length of the probe. This equation works well for probes 14 to 70 nucleotides in length that are identical to the target sequence. The equation below for T_mof DNA-DNA hybrids is useful for probes in the range of 50 to greater than 500 nucleotides, and for conditions that include an organic solvent (formamide).
T _m=81.5+16.6 log {[Na⁺]/(1+0.7[Na⁺])}±0.41(% G+C)−500/L 0.63(% formamide) (2)
where L is the length of the probe in the hybrid. (P. Tijessen, “Hybridization with Nucleic Acid Probes” in Laboratory Techniques in Biochemistry and Molecular Biology, P. C. vand der Vliet, ed., c. 1993 by Elsevier, Amsterdam.) The T_mof equation (2) is affected by the nature of the hybrid; for DNA-RNA hybrids T_mis 10-15° C. higher than calculated, for RNA-RNA hybrids T_mis 20-25° C. higher. Because the T_mdecreases about 1° C. for each 1% decrease in homology when a long probe is used (Bonner et al., J. Mol. Biol. 81:123 (1973)), stringency conditions can be adjusted to favor detection of identical genes or related family members.
Equation (2) is derived assuming equilibrium and therefore, hybridizations according to the present invention are most preferably performed under conditions of probe excess and for sufficient time to achieve equilibrium. The time required to reach equilibrium can be shortened by inclusion of a hybridization accelerator such as dextran sulfate or another high volume polymer in the hybridization buffer.
Stringency can be controlled during the hybridization reaction or after hybridization has occurred by altering the salt and temperature conditions of the wash solutions used. The formulas shown above are equally valid when used to compute the stringency of a wash solution. Preferred wash solution stringencies lie within the ranges stated above; high stringency is 5-8° C. below T_m, medium or moderate stringency is 26-29° C. below T_mand low stringency is 45-48° C. below T_m.

Superpool: As used in the context of the current invention, a “superpool” refers to a mixture of seed from 100 different “master pools”. Thus, the superpool contains an equal amount of seed from 500 different events, but only represents 100 transgenic plants with a distinct exogenous nucleotide sequence transformed into them, because the master pools are of 5 different events with the same exogenous nucleotide sequence transformed into them.
T₀: As used in the current application, the term “T₀” refers to the whole plant, explant, or callous tissue inoculated with the transformation medium.
T₁: As used in the current application, the term T₁refers to the either the progeny of the T₀plant, in the case of whole-plant transformation, or the regenerated seedling in the case of explant or callous tissue transformation.
T₂: As used in the current application, the term T₂refers to the progeny of the T₁plant. T₂progeny are the result of self-fertilization or cross pollination of a T₁plant.
T₃: As used in the current application, the term T₃refers to second generation progeny of the plant that is the direct result of a transformation experiment. T₃progeny are the result of self-fertilization or cross pollination of a T₂plant.
Zero Nitrogen: Nitrogen is not present in any amount.
Zero Phosphorus: Phosphorus is not present in any amount.

2. Important Characteristics of the Polynucleotides and Polypeptides of the Invention

The polynucleotides and polypeptides of the present invention are of interest because when they are misexpressed (i.e. when expressed at a non-natural location or in an increased or decreased amount) they produce plants with modified pH tolerance or phosphate use efficiency. “Phosphate use efficiency” is a term that includes various responses to environmental conditions that affect the amount of phosphate available to the plant. For example, under both low and high pH conditions phosphate is bound within the soil, resulting in a decrease of available phosphate for maintaining or initiating physiological processes. As used herein, modulating phosphate use efficiency is intended to encompass all of these situations as well as other environmental situations that affect the plant's ability to use and/or maintain phosphate effectively (e.g. osmotic stress, etc.).
The polynucleotides and polypeptides of the invention, as discussed below and as evidenced by the results of various experiments, are useful for modulating pH tolerance or phosphate use efficiency. These traits can be used to exploit or maximize plant products for agricultural, ornamental or forestry purposes in different environment conditions of water supply. Modulating the expression of the nucleotides and polypeptides of the present invention leads to transgenic plants that will be less sensitive to variations in pH and that require less phosphate, resulting in better yields under these types of adverse conditions. Both categories of transgenic plants lead to reduced costs for the farmer and better yield in their respective environmental conditions.

3. The Polynucleotides and Polypeptides of the Invention

The polynucleotides of the invention, and the proteins expressed thereby, are set forth in the sequences present in the Sequence Listing. Some of these sequences are functionally comparable proteins.
Functionally comparable proteins are those proteins that have at least one characteristic in common. Such characteristics can include sequence similarity, biochemical activity and phenotypic activity. Typically, the functionally comparable proteins share some sequence similarity and generally share at least one biochemical and/or phenotypic activity. For example, biochemical functionally comparable proteins are proteins that act on the same reactant to give the same product.
Another class of functionally comparable proteins is phenotypic functionally comparable proteins. The members of this class regulate the same physical characteristic, such as increased drought tolerance. Proteins can be considered phenotypic functionally comparable proteins even if the proteins give rise to the same physical characteristic, but to a different degree.
The polypeptides of the invention also include those comprising the consensus sequences described in Tables 1-5, 2-6 and 3-5. A consensus sequence defines the important conserved amino acids and/or domains within a polypeptide. Thus, all those sequences that conform to the consensus sequence are suitable for the same purpose. Polypeptides comprised of a sequence within and defined by one of the consensus sequences can be utilized for the purposes of the invention namely to make transgenic plants with improved tolerance to heat or high or low water conditions.

4. Use of the Polynucleotides and Polypeptides to Make Transgenic Plants

To use the sequences of the present invention or a combination of them or parts and/or mutants and/or fusions and/or variants of them, recombinant DNA constructs are prepared which comprise the polynucleotide sequences of the invention inserted into a vector, and which are suitable for transformation of plant cells. The construct can be made using standard recombinant DNA techniques (Sambrook et al. 1989) and can be introduced to the species of interest by Agrobacterium-mediated transformation or by other means of transformation as referenced below.
The vector backbone can be any of those typical in the art such as plasmids, viruses, artificial chromosomes, BACs, YACs and PACs and vectors of the sort described by

(a) BAC: Shizuya et al., Proc. Natl. Acad. Sci. USA 89: 8794-8797 (1992); Hamilton et al., Proc. Natl. Acad. Sci. USA 93: 9975-9979 (1996);
(b) YAC: Burke et al., Science 236:806-812 (1987);
(c) PAC: Sternberg N. et al., Proc Natl Acad Sci USA. January; 87(1):103-7 (1990);
(d) Bacteria-Yeast Shuttle Vectors: Bradshaw et al., Nucl Acids Res 23: 4850-4856 (1995);
(e) Lambda Phage Vectors: Replacement Vector, e.g., Frischauf et al., J. Mol Biol 170: 827-842 (1983); or Insertion vector, e.g., Huynh et al., In: Glover N M (ed) DNA Cloning: A practical Approach, Vol. 1 Oxford: IRL Press (1985); T-DNA gene fusion vectors :Walden et al., Mol Cell Biol 1: 175-194 (1990); and
(g) Plasmid vectors: Sambrook et al., infra.

Typically, the construct comprises a vector containing a sequence of the present invention with any desired transcriptional and/or translational regulatory sequences, such as promoters, UTRs, and 3′ end termination sequences. Vectors can also include origins of replication, scaffold attachment regions (SARs), markers, homologous sequences, introns, etc. The vector may also comprise a marker gene that confers a selectable phenotype on plant cells. The marker typically encodes biocide resistance, particularly antibiotic resistance, such as resistance to kanamycin, bleomycin, hygromycin, or herbicide resistance, such as resistance to glyphosate, chlorosulfuron or phosphinotricin.
A plant promoter is used that directs transcription of the gene in all tissues of a regenerated plant and may be a constitutive promoter, such as p326 or CaMV35S. Alternatively, the plant promoter directs transcription of a sequence of the invention in a specific tissue manner (tissue-specific promoter) or is otherwise under more precise environmental control (inducible promoter). Various plant promoters, including constitutive, tissue-specific and inducible, are known to those skilled in the art and can be utilized in the present invention. Typically, preferred promoters to use in the present invention are those that are induced by heat or low water conditions Such as the RD29a promoter (Kasuga et al., Plant Cell Physiol. 45:346 (2004) and Yamaguchi-Shinozaki and Shinozaki, Mol Gen Genet. 236: 331 (1993)) or other DRE-containing (dehydration-responsive elements) promoters (Liu et al, Cell 10: 1391 (1998)). Another preferred embodiment of the present invention is the use of root specific promoters such as those present in the AtXTH17, AtXTH18, AtXTH19 and AtXTH20 genes of Arabidopsis (Vissenberg et al. (2005) Plant Cell Physiol 46:192) or guard cell specific promoters such as TGG1 or KST1 (Husebye et al. (2002) Plant Physiol 128:1180; Plesch et al. (2001) Plant J 28:455).
Alternatively, misexpression can be accomplished using a two component system, whereby the first component comprises a transgenic plant comprising a transcriptional activator operatively linked to a promoter and the second component comprises a transgenic plant comprising a sequence of the invention operatively linked to the target binding sequence/region of the transcriptional activator. The two transgenic plants are crossed and the sequence of the invention is expressed in their progeny. In another alternative, the misexpression can be accomplished by transforming the sequences of the two component system into one transgenic plant line.
Any promoter that functions in plants can be used in the first component, such as those discussed above. Suitable transcriptional activator polypeptides include, but are not limited to, those encoding HAP1 and GAL4. The binding sequence recognized and targeted by the selected transcriptional activator protein (e.g. a UAS element) is used in the second component.

Transformation

Nucleotide sequences of the invention are introduced into the genome or the cell of the appropriate host plant by a variety of techniques. These techniques for transforming a wide variety of higher plant species are well known and described in the technical and scientific literature. See, e.g. Weising et al., Ann. Rev. Genet. 22:421 (1988); and Christou, Euphytica, v. 85, n.1-3:13-27, (1995).
Processes for the transformation and regeneration of monocotyledonous and dicotyledonous plants are known to the person skilled in the art. For the introduction of DNA into a plant host cell a variety of techniques is available. These techniques include transformation of plant cells by injection (e.g. Newell, 2000), microinjection (e.g. Griesbach (1987) Plant Sci. 50 69-77), electroporation of DNA (e.g. Fromm et al. (1985) Proc. Natl Acad. Sci. USA 82:5824 and Wan and Lemaux, Plant Physiol. 104 (1994), 37-48), PEG (e.g. Paszkowski et al. (1984) EMBO J. 3:2717), use of biolistics (e.g. Klein et al. (1987) Nature 327:773), fusion of cells or protoplasts (Willmitzer, L., 1993 Transgenic plants. In: Biotechnology, A Multi-Volume Comprehensive Treatise (H. J. Rehm, G. Reed, A. Pühler, P. Stadler, eds., Vol. 2, 627-659, VCH Weinheim-New York-Basel-Cambridge), via T-DNA using Agrobacterium tumefaciens (e.g. Fraley et al. (Crit. Rev. Plant. Sci. 4, 1-46 and Fromm et al., Biotechnology 8 (1990), 833-844) or Agrobacterium rhizogenes (e.g. Cho et al. (2000) Planta 210:195-204) or other bacterial hosts (e.g. Brootghaerts et al. (2005) Nature 433:629-633), as well as further possibilities.
In addition, a number of non-stable transformation methods well known to those skilled in the art may be desirable for the present invention. Such methods include, but are not limited to, transient expression (e.g. Lincoln et al. (1998) Plant Mol. Biol. Rep. 16:1-4) and viral transfection (e.g. Lacomme et al. (2001) In “Genetically Engineered Viruses” (C. J. A. Ring and E. D. Blair, Eds). Pp. 59-99, BIOS Scientific Publishers, Ltd. Oxford, UK).
Seeds are obtained from the transformed plants and used for testing stability and inheritance. Generally, two or more generations are cultivated to ensure that the phenotypic feature is stably maintained and transmitted.
One of skill will recognize that after the expression cassette is stably incorporated in transgenic plants and confirmed to be operable, it can be introduced into other plants by sexual crossing. Any of a number of standard breeding techniques can be used, depending upon the species to be crossed.
The nucleic acids of the invention can be used to confer the trait of increased tolerance to heat and/or low water conditions, without reduction in fertility, on essentially any plant.
The nucleotide sequences according to the invention encode appropriate proteins from any organism, in particular from plants, fungi, bacteria or animals.
The process according to the invention can be applied to any plant, preferably higher plants, pertaining to the classes of Angiospermae and Gymnospermae. Plants of the subclasses of the Dicotylodenae and the Monocotyledonae are particularly suitable. Dicotyledonous plants belong to the orders of the Magniolales, Illiciales, Laurales, Piperales Aristochiales, Nymphaeales, Ranunculales, Papeverales, Sarraceniaceae, Trochodendrales, Hamamelidales, Eucomiales, Leitneriales, Myricales, Fagales, Casuarinales, Caryophyllales, Batales, Polygonales, Plumbaginales, Dilleniales, Theales, Malvales, Urticales, Lecythidales, Violales, Salicales, Capparales, Ericales, Diapensales, Ebenales, Primulales, Rosales, Fabales, Podostemales, Haloragales, Myrtales, Comales, Proteales, Santales, Rafflesiales, Celastrales, Euphorbiales, Rhanmales, Sapindales, Juglandales, Geraniales, Polygalales, Umbellales, Gentianales, Polemoniales, Lamiales, Plantaginales, Scrophulariales, Campanulales, Rubiales, Dipsacales, and Asterales. Monocotyledonous plants belong to the orders of the Alismatales, Hydrocharitales, Najadales, Triuridales, Commelinales, Eriocaulales, Restionales, Poales, Juncales, Cyperales, Typhales, Bromeliales, Zingiberales, Arecales, Cyclanthales, Pandanales, Arales, Lilliales, and Orchidales. Plants belonging to the class of the Gymnospermae are Pinales, Ginkgoales, Cycadales and Gnetales.
The method of the invention is preferably used with plants that are interesting for agriculture, horticulture, biomass for bioconversion and/or forestry. Examples are tobacco, oilseed rape, sugar beet, potato, tomato, cucumber, pepper, bean, pea, citrus fruit, apple, pear, berries, plum, melon, eggplant, cotton, soybean, sunflower, rose, poinsettia, petunia, guayule, cabbage, spinach, alfalfa, artichoke, corn, wheat, rye, barley, grasses such as switch grass or turf grass, millet, hemp, banana, poplar, eucalyptus trees, conifers.

Homologs Encompassed by the Invention

Agents of the invention include proteins comprising at least about a contiguous 10 amino acid region preferably comprising at least about a contiguous 20 amino acid region, even more preferably comprising at least about a contiguous 25, 35, 50, 75 or 100 amino acid region of a protein of the present invention. In another preferred embodiment, the proteins of the present invention include between about 10 and about 25 contiguous amino acid region, more preferably between about 20 and about 50 contiguous amino acid region, and even more preferably between about 40 and about 80 contiguous amino acid region.
Due to the degeneracy of the genetic code, different nucleotide codons may be used to code for a particular amino acid. A host cell often displays a preferred pattern of codon usage. Nucleic acid sequences are preferably constructed to utilize the codon usage pattern of the particular host cell. This generally enhances the expression of the nucleic acid sequence in a transformed host cell. Any of the above described nucleic acid and amino acid sequences may be modified to reflect the preferred codon usage of a host cell or organism in which they are contained. Modification of a nucleic acid sequence for optimal codon usage in plants is described in U.S. Pat. No. 5,689,052. Additional variations in the nucleic acid sequences may encode proteins having equivalent or superior characteristics when compared to the proteins from which they are engineered.
It is understood that certain amino acids may be substituted for other amino acids in a protein or peptide structure (and the nucleic acid sequence that codes for it) without appreciable change or loss of its biological utility or activity. The amino acid changes may be achieved by changing the codons of the nucleic acid sequence.
It is well known in the art that one or more amino acids in a native sequence can be substituted with other amino acid(s), the charge and polarity of which are similar to that of the native amino acid, i.e., a conservative amino acid substitution, resulting in a silent change. Conservative substitutes for an amino acid within the native polypeptide sequence can be selected from other members of the class to which the amino acid belongs (see below). Amino acids can be divided into the following four groups: (1) acidic (negatively charged) amino acids, such as aspartic acid and glutamic acid; (2) basic (positively charged) amino acids, such as arginine, histidine, and lysine; (3) neutral polar amino acids, such as glycine, serine, threonine, cysteine, cystine, tyrosine, asparagine, and glutamine; and (4) neutral nonpolar (hydrophobic) amino acids such as alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine.
In a further aspect of the present invention, nucleic acid molecules of the present invention can comprise sequences that differ from those encoding a protein or fragment thereof selected from the group consisting of those sequences present in the Sequence Listing due to the fact that the different nucleic acid sequence encodes a protein having one or more conservative amino acid changes.
In another aspect, biologically functional equivalents of the proteins or fragments thereof of the present invention can have about 10 or fewer conservative amino acid changes, more preferably about 7 or fewer conservative amino acid changes, and most preferably about 5 or fewer conservative amino acid changes. In a preferred embodiment, the protein has between about 5 and about 500 conservative changes, more preferably between about 10 and about 300 conservative changes, even more preferably between about 25 and about 150 conservative changes, and most preferably between about 5 and about 25 conservative changes or between 1 and about 5 conservative changes.

5. Experiments Confirming the Usefulness of the Polynucleotides and Polypeptides of the Invention

5.1 Procedures
The nucleotide sequences of the invention were identified by use of a variety of screens for pH and/or low phosphate and/or low nitrogen conditions. These screens are recognized by those skilled in the art to be predictive of nucleotide sequences that provide plants with improved tolerance to pH and/or low phosphate and/or low nitrogen conditions because they emulate the different environmental conditions that can result from increased pH and/or low phosphate and/or low nitrogen conditions. These screens generally fall into two categories (1) soil screens and (2) in vitro screens.
Soil screens have the advantage of assaying the response of the entire plant to particular conditions, such as high pH or low phosphorus. On the other hand, in vitro screens have the advantage of relying on defined media and so allow more defined manipulation of growth conditions. Each of the screens used is described in more detail below.
In general, the screens used to identify the polynucleotides and polypeptides of the invention were conducted using superpools of Arabidopsis T₂transformed plants. The T₁plants were transformed with a Ti plasmid containing a particular SEQ ID NO in the sense orientation relative to a constitutive promoter and harboring the plant-selectable marker gene phosphinothricin acetyltansferase (PAT), which confers herbicide resistance to transformed plants. For in vitro screens, seed from multiple superpools (1,200 T₂seeds from each superpool) were usually tested. T₃seed were collected from the resistant plants and retested on one or more in vitro screens. The results of the screens conducted for each SEQ ID NO can be found in the Examples below.
1. High pH
Screens for high pH resistance identify seedlings better able to thrive under nutritional deficiencies (e.g. Phosphate, Manganese, Iron, Boron) imposed by alkaline conditions.
Seeds are sterilized in 50% household bleach for 5 minutes and then washed with double distilled deionized water three times. Sterilized seed is stored in the dark at 4° C. for a minimum of 3 days before use.
High pH media is prepared by mixing 0.5 g/l MES hydrate with 1X MS+0.5% Sucrose. Prior to autoclaving pH is adjusted with 10 N KNH to the following values: pH 5.7 (control), pH 7.03, pH 8.02, pH 9.01 and pH 10.18. The media pH is retested since pH values drop after autoclaving as follows: pH 5.7→pH 5.66; pH 7.03→pH6.50; pH 8.02→pH 7.50; pH 9.01→pH 8.91; pH10.18→pH 9.91. Generally speaking, pH 9.01(pH 8.91) allows germination but no growth beyond 2 to 5 mm and no root growth. Germination does not occur at higher pH (e.g. pH 10.81).
Approximately 1200 seeds are evenly spaced per MS-sucrose plate before incubating in the vertical position at 22° C. for 14 days. Under these conditions, the plates are exposed to 12,030 LUX from above and 3,190 LUX from the bottom.
Seedlings are scored for root and shoot growth after 7 and 14 days. Putative tolerant seedlings are transferred to MS pH 5.7 for recovery for 14 days prior to transplanting in soil. Finale™ spraying is done after plants are moved to soil to remove non-transgenics from the population.
DNA is isolated from each T₂plant and used in PCR reactions using the following cycling conditions: 95° C. for 5 min, 35 cycles of (94° C. for 30 sec, then 59° C. for 30 sec, then 72° C. for 1 min), 72° C. for 8 min and 4° C. hold. Aliquots of the reaction product are analyzed on a 1.0% agarose gel stained with ethidium bromide. The DNA products are sequenced to determine which insert sequences were in each superpool candidate chosen in the screen.
T₃Seed from those plants containing sequenced PCR products are collected and retested on high pH media. In addition, plants are tested on MS media lacking Phosphate and having a pH of 5.7.
2. Zero Phosphate
Screens for zero phosphate tolerance identify seedlings better able to thrive under a phosphate nutritional deficiency.
Seeds are sterilized in 50% household bleach for 5 minutes and then washed with double distilled deionized water three times. Sterilized seed is stored in the dark at 4° C. for a miniumum of 3 days before use.
Zero phosphate media is prepared using commercially available MS media lacking phosphate, pH 5.7.
Approximately 1200 seeds are evenly spaced per MS-P plate before incubating in the vertical position at 22° C. for 14 days. Under these conditions, the plates are exposed to 12,030 LUX from above and 3,190 LUX from the bottom.
Seedlings are scored for root and shoot growth after 7 and 14 days. Putative tolerant seedlings are transferred to MS pH 5.7 for recovery for 14 days prior to transplanting in soil. Finale™ spraying is done after the plants are moved to soil to remove non-transgenics from the population.
DNA is isolated from each T₂plant and used in PCR reactions using the following cycling conditions: 95° C. for 5 min, 35 cycles of (94° C. for 30 sec, then 59° C. for 30 sec, then 72° C. for 1 min), 72° C. for 8 min and 4° C. hold. Aliquots of the reaction product are analyzed on a 1.0% agarose gel stained with ethidium bromide. The DNA products are sequenced to determined which insert sequences were in each superpool candidate chosen in the screen.
T₃Seed from those plants containing the sequenced PCR products are collected and retested.
3. Zero Phosphate, Zero Nitrogen
Screens for zero phosphate, zero nitrogen tolerance identify seedlings better able to thrive under a phosphate nutritional deficiency.
Seeds are sterilized in 50% household bleach for 5 minutes and then washed with double distilled deionized water three times. Sterilized seed is stored in the dark at 4° C. for a miniumum of 3 days before use.
Zero phosphate, zero nitrogen media is prepared using commercially available MS media lacking phosphate, pH 5.7.
Approximately 1200 seeds are evenly spaced per MS-P-N plate before incubating in the vertical position at 22° C. for 14 days. Under these conditions, the plates are exposed to 12,030 LUX from above and 3,190 LUX from the bottom.
Growth and overall greenness are assayed 10 days post-treatment. Seedling recovery is assessed by adding a thin layer (8.3 ml) of complete MS+P+N media, pH 5.7, softened by the addition of 0.02% agar. Media is added to the edge of the plate and slowly rotated until a thin film of +PN media is present on top of the solidified −PN media. Putative tolerant seedlings are greener and have increased growth compared to controls. Finale™ spraying is done after the plants are moved to soil to remove non-transgenics from the population.
DNA is isolated from each T₂plant and used in PCR reactions using the following cycling conditions: 95° C. for 5 min, 35 cycles of (94° C. for 30 sec, then 59° C. for 30 sec, then 72° C. for 1 min), 72° C. for 8 min and 4° C. hold. Aliquots of the reaction product are analyzed on a 1.0% agarose gel stained with ethidium bromide. The DNA products are sequenced to determined which insert sequences were in each superpool candidate chosen in the screen.
T₃Seed from those plants containing the sequenced PCR products are collected and retested.
5.2 Results
The results of the above experiments are set forth below wherein each individual example relates to all of the experimental results for a particular polynucleotide/polypeptide if the invention.

Example 1

Ceres cDNA 12335629

Clone 40781, Ceres cDNA 12335629, encodes a full-length protein with homology to a ferredoxin thioredoxin reductase from Arabidopsis thaliana.
Ectopic expression of Ceres cDNA 12335629 under the control of the CaMV35S promoter induces the following phenotypes:

- Better growth and recovery after exposure to high pH conditions and
- Continued growth under high pH induced phosphate and iron deficiencies.
  Generation and Phenotypic Evaluation of T₁Lines Containing 35S::cDNA 12335629.

Wild-type Arabidopsis Wassilewskija (WS) plants were transformed with a Ti plasmid containing cDNA 12335629 in the sense orientation relative to the 35S constitutive promoter. The T_iplasmid vector used for this construct, CRS338, contains PAT and confers herbicide resistance to transformed plants. Ten independently transformed events were selected and evaluated for their qualitative phenotype in the T_igeneration. No positive or negative phenotypes were observed in the T₁plants.

Screens of Superpools on High pH Media for pH Tolerance.

Seed from superpools of the 35S over-expression lines were evaluated for greenness and size on high pH media as described above. Once cDNA 12335629 was identified in tolerant plants, the five individual T₂events containing this cDNA (ME03527) were screened on high pH media essentially as described above, but where the media pH is 8.5, to identify events with the tolerant phenotype.

Results:

Qualitative Analysis of the Superpool Containing 35S::clone 40781 Plants on high pH
The screen resulted in a decrease in germination and/or growth for both wildtype and superpools as compared to seeds on control media. Only one line survived transplantation to soil. The candidate was greener than controls but overall size was comparable to those of wild-type. There was no delay in flowering time or decrease in seed set in comparison to un-treated wild-type but a faster flowering time and greater seed set was apparent when compared to a recovered pH treated wild-type plant (data not shown). These results are consistent with those of the T₁generation which displayed normal flowering time and fertility.
Qualitative and Quantitative Analysis of T₃-cDNA 12335629 on High pH.
The plants were treated with Finale™ to eliminate any false-positives or any lines where the Finale™ marker was suppressed. All of the Finale™-resistant candidates flowered and set seed. Finale™ segregation was assessed to identify events containing a single insert segregation in a 3:1 (R:S) ratio as calculated by chi-square test. All of the events segregated for a single functional insert (Table 1-1). The transgenic plants were greener and slightly larger than the control under high pH stress.
TABLE 1-1

Observed and expected frequencies assuming a 3:1 ratio for high pH

tolerance of cDNA 12335629 progeny under high pH (pH 8.5).

α of 0.05

Probability

Event Generation Observed Expected χ² of Chi-Test

pH Resistant T₃ 22 29 0.926

pH Sensitive T₃ 14 7 2.778 0.054

N = 36 36 36 3.704

Qualitative and Quantitative Analysis of cDNA 12335629 Progeny on Media Lacking Phosphate
Before testing independent T₂events, plants containing cDNA 12335629 were re-assayed for phosphate starvation tolerance by growth on media containing no phosphate as described above. After seven days only slightly more tolerance compared to controls is observed, but cDNA 12335629 seedlings are a bit larger and slightly greener than those of the control. Because the slight increase in size was particularly difficult to assess, anything lower or equal to the wild-type average of 0.42 cm was assessed to be sensitive and anything higher was assessed as tolerant. Twenty-four resistant and twelve phosphate starved sensitive seedlings were compared to Finale™]frequencies and found to have a Chi-test probability of 0.49, suggesting a positive fit (Table 1-2).
TABLE 1-2

Observed and expected frequencies assuming a 3:1 ratio for phosphate

starvation tolerance among progeny of cDNA 12335629 media lacking

phosphate (-P). α of 0.05

Probability

Event Generation Observed Expected χ² of Chi-Test

-P Resistant T₃ 24 27 0.333

-P Sensitive T₃ 12 9 1.333 0.25

N = 36 36 36 1.666

Qualitative and Quantitative Analysis of Individual T₂Events of cDNA 12335629 on High pH Plate Assay.
Five individual events of cDNA 12335629 (ME03527) were analyzed for a positive phenotype under high pH conditions. All five T₂events had wild-type germination frequencies on MS pH 5.7 plates (data not shown). All T₂lines and recovered T₃lines showed evidence of a single insert as determined by Chi-square analysis (Table 1-3). Seeds from each of the five independent T₂events, were plated on pH 8.5 plates and allowed to germinate and grow for 14 days.
Four of five T₂events of ME03527 (-02,-03,-04, and -05) had a positive high pH tolerance phenotype as defined by growth and greenness. The phenotype of1V1E03527-01 was too weak to assess as positive compared to the controls (Table 1-4). Phenotype strength varied among the four positive independent events, but all showed better growth than controls. The segregation ratios, determined by a Chi-square test, show that the segregation of the transgene is the same as observed for Finale™ (Table 1-4). ME03527-02,-03,-04, and -05 had the strongest and most consistent pH tolerance phenotypes.

TABLE 1-3

Observed and expected frequencies assuming a 3:1 (R:S) ratio for Finale ™
resistance among 35S::clone 40781 T₂and T₃events tested for growth
under high pH conditions. α of 0.05

Event	Generation	Observed	Expected	χ²	Probability of Chi-Test

ME03527-01 Finale ™	T₂	16	18	0.222
Resistant
ME03527-01 Finale ™	T	₂	8	6	0.667	0.35
Sensitive
N = 24		24	24	0.889
ME03527-02 Finale ™	T₂	28	27	0.037
Resistant
ME03527-02 Finale ™	T	₂	8	9	0.111	0.70
Sensitive
N = 36		36	36	0.148
ME03527-03 Finale ™	T₂	17	18	0.056
Resistant
ME03527-03 Finale ™	T	₂	7	6	0.167	0.64
Sensitive
N = 24		24	24	0.223
ME03527-04 Finale ™	T₂	27	27	0
Resistant
ME03527-04 Finale ™	T	₂	9	9	0	1.0
Sensitive
N = 36		36	36	0
ME03527-05 Finale ™	T₂	23	27	0.593
Resistant
ME03527-05 Finale ™	T₂	13	9	1.778	0.12
Sensitive
N = 36		36	36	2.371
cDNA 12335629 Finale ™	T₃	22	27	0.926
Resistant
cDNA 12335629 Finale ™	T₃	14	9	2.778	0.054
Sensitive
N = 36		36	36	3.704

TABLE 1-4

Observed and expected frequencies of high pH tolerance assuming segregation of transgene
is the same as observed in Finale ™ resistance among 35S::clone 40781 T₂and
T₃events that showed increased growth under high pH conditions. α of 0.05

Event	Generation	Observed	Expected	χ²	Probability of Chi-Test

ME03527-01 pH Resistant	T₂	15	25.5	4.324
ME03527-01 pH Sensitive	T₂	19	85.5	2.970	32E−05
N = 36		34	34	7.294
ME03527-02 pH Resistant	T₂	23	24.75	0.124
ME03527-02 pH Sensitive	T₂	10	8.25	0.371	0.48
N = 36		33	33	0.495
ME03527-03 pH Resistant	T₂	23	23.25	0.003	0.92
ME03527-03 pH Sensitive	T	₂	8	7.75	0.008
N = 36		31	31	0.011
ME03527-04 pH Resistant	T₂	24	27	0.333	0.25
ME03527-04 pH Sensitive	T₂	12	9	1.000
N = 36		36	36	1.333
ME03527-05 pH Resistant	T₂	19	27	2.370	0.002
ME03527-05 pH Sensitive	T₂	17	9	7.111
N = 36		36	3	9.481
cDNA 12335629 pH	T₃	19	27	2.370	0.002
Resistant
cDNA 12335629 pH	T₃	17	9	7.111
Sensitive
N = 36		36	36	9.481

Table 1-5 provides the results of the consensus sequence analysis based on Ceres cDNA 13487605.

TABLE 1-5

Example 2

Ceres cDNA 12330185

Clone 34035, Ceres cDNA 12330185, encodes a 128 amino acid protein of unknown function (DUF423) from Arabidopsis thaliana.
Ectopic expression of Ceres cDNA 12330185 under the control of the 32449 promoter induces the following phenotypes:

- Increased size and greenness on nutrient deficiencies incurred by high pH conditions,
- Better soil recovery after exposure to high pH stress, and
- Better recovery after exposure to conditions lacking both phosphate and nitrogen.
  Generation and Phenotypic Evaluation of T₁Lines Containing p32449::cDNA 12330185.

Wild-type Arabidopsis Wassilewskija (WS) plants were transformed with a Ti plasmid containing cDNA 12330185 in the sense orientation relative to the 32449 constitutive promoter. Promoter 32449 has broad expression throughout Arabidopsis, although at much lower expression level than CaMV35S. The T_iplasmid vector used for this construct, CRS311, contains PAT and confers herbicide resistance to transformed plants. Nine independently transformed events were selected and evaluated for their qualitative phenotype in the T₁generation. No positive or negative phenotypes were observed in the T₁plants.

Screens of Superpools on High pH Media for pH Tolerance.

Seed from superpools of the 32449 over-expression lines were evaluated for greenness and size on high pH media as described above. Once cDNA 12330185 was identified in tolerant plants, nine individual T₂events containing this cDNA (ME00077) were screened on high pH media essentially as described above, but where the media pH is 8.5, to identify events with the tolerant phenotype.

Results:

Qualitative Analysis of the Superpool Containing 34449::cDNA 12330185 on High pH
The cDNA 12330185 line displayed a delayed flowering time of ˜8 days and decreased seed set in comparison to the un-treated wild-type. However cDNA 12330185 displayed a faster flowering time (˜15 days) and greater seed set when compared to the high pH grown wild-type plant.
Qualitative and Quantitative Analysis of the T₃32449:: cDNA 12330185 on High pH.
The cDNA 12330185 line was tested for Finale™ resistance and re-assayed for continued pH tolerance. The segregation ratio of T₃seeds from cDNA 12330185 is suggestive of a single insert, as calculated by a Chi-square test (Table 2-1). The cDNA 12330185 line was re-tested on pH 9.0 media as described and found to be tolerant to high pH when compared to controls.
TABLE 2-1

Chi-square analysis of progeny of cDNA 12330185 on

Finale ™ assuming a 3:1 ratio.

Event Observed Expected χ² Probability of Chi-Test

Finale ™ Resistant 27 27 0

Finale ™ Sensitive 9 9 0 1

N = 36 36 36 0

Qualitative and Quantitative Analysis of Phosphate and Nitrate Starvation of T₃(cDNA 12330185) Plants.
To ascertain whether the pH tolerant phenotype is related to better survival under nutrient starvation, T₃seeds were assayed on MS media lacking both phosphate (—P) and nitrate (—N) (pH 5.7) as described above. The cDNA 12330185 line was greener and of equal size compared to wild-type controls. Ten days after the addition of +NP media film, cDNA 12330185 seedlings recovered more quickly than wild type. Twenty-five of 36 seedlings of SP9pH1 had greater growth when compared to wild type. This increased growth frequency is suggestive of a single insert as determined by Chi-square analysis (Table 2-2).

TABLE 2-2

Observed and expected frequencies of no phosphate/nitrate growth
assuming segregation of transgene is 3:1 (R:S) of T₃plants
of cDNA 12330185 that showed increased growth under high pH
conditions. α of 0.05

Event	Observed	Expected	χ²	Probability of Chi-Test

NP Resistant	25	27	0.148	0.441
NP Sensitive	11	9	0.444
N = 36	36	36	0.592

Qualitative and Quantitative Analysis of Individual T₂Events of cDNA 12330185 on High pH.

Seeds from T₂lines representing nine individual events and containing cDNA 12330185 (ME0077-01, 02, 03, 04, 05, 06, 07, 08, 09) were plated on pH media, pH 8.5 as described above. Plates were evaluated at 7 and 12 days post-plating (Table 2-3). All nine T₂events had wild-type germination frequencies except for ME00077-04 (Table 2-4). This germination problem however was not observed when seedlings were plated onto high pH plates.
Six of the nine events showed tolerance to high pH as defined by growth and greenness. The strongest tolerance phenotypes were in ME00077-03 and ME00077-05. ME00077-03 and ME00077-05 both had single inserts as determined by Chi-square analysis (Table 2-3).
The pH tolerant phenotype was strongest in the cDNA 12330185 T₃line recovered from the superpool screen. We did not do a genetic mapping of this line's insert to determine which event it represented. This line's phenotype was so strong that it allowed adjacent wild-type quadrants within same plate to grow normally after 14-days. This is most likely due to acidification of surrounding media by the pH tolerant line. ME00077-03,-05 T₂plants also showed increased recovery during phosphate and nitrogen starvation assays (data not shown). However, the cDNA 12330185 T₃line recovered from the superpool phenotype was stronger than that observed for lines ME00077-03 and -05 under −NP starvation recovery (as noted above).

TABLE 2-3

TABLE 2-4



**Germination reduction in comparison to wild-type control and other ME00077 lines

TABLE 2-5

Observed and expected frequencies of high pH tolerance assuming
segregation of transgene is the same as observed in
Finale ™ segregation among progeny of 32449:: cDNA
12330185 T₂events that showed increased growth under
high pH conditions. α of 0.05

				Probability
Event	Observed	Expected	χ²	of Chi-Test

ME00077-03 pH Resistant	26	25.5	0.009	0.84
ME00077-03 pH Sensitive	8	8.5	0.029
N = 36	34	34	0.038
ME00077-05 pH Resistant	29	26.25	0.288	0.28
ME00077-05 pH Sensitive	6	8.75	0.864
N = 36	35	35	1.152
cDNA 12330185 pH	31	27	0.592	0.124
Resistant
cDNA 12330185 pH	5	9	1.778
Sensitive
N = 36	36	36	2.370

Table 2-6 provides the results of the consensus sequence analysis based on Ceres cDNA 12330185.

TABLE 2-6

Example 3

Ceres cDNA 12482777

Clone 126592, Ceres cDNA 12482777, encodes a full-length protein that has homology to an iron/manganese superoxide dismutase from Arabidopsis thaliana.
Ectopic expression of Ceres cDNA 12482777 under the control of the CaMV35S promoter induces the following phenotypes:

- Increased growth under high pH induced stress
- Better recovery after exposure to pH stress
- Reduced height without a reduction in harvest index.
  Generation and Phenotypic Evaluation of T₁Lines Containing 35S::cDNA 12482777.

Wild-type Arabidopsis Wassilewskija (WS) plants were transformed with a Ti plasmid containing cDNA 12482777 in the sense orientation relative to the 35S constitutive promoter. The T_iplasmid vector used for this construct, CRS338, contains PAT and confers herbicide resistance to transformed plants. Seven independently transformed events were selected and evaluated for their qualitative phenotype in the T₁generation. No negative phenotypes were observed in the T₁plants, although an increase in the number of branches was observed one of the events.

Screens of Superpools on High pH Media for pH Tolerance.

Seed from superpools of the 35S over-expression lines were evaluated for greenness and size on high pH media as described above. T₃seed were also assayed for total seed yield, total tissue dry weight and harvest index as described above.

Results:

Qualitative Analysis of the Superpool Containing 35S:: cDNA 12482777 Plants on High pH
The screen identified a single event that was greener and the overall size was comparable to the controls. There was no delay in flowering time or decrease in seed set compared to un-treated wild-type. After recovery, the plant containing cDNA 12482777 had significantly better seed yield, as determined by seed volume, than controls (FIG. 2).
Qualitative and Quantitative Analysis of T₃-cDNA 12482777 on High pH.
The plants were treated with Finale™ to eliminate any false-positives or any lines where the Finale™ marker was suppressed. All of the Finale™-resistant candidates flowered and set seed. Finale™ resistance segregation in the T₃line suggested a segregation ratio of 1:1 (R:S) as calculated by chi-square test (Table 3-1).
The plants were greener than the pre-pH treated control. There was no tolerant effect found under low phosphate conditions (data not shown), suggesting that the tolerant response is not to the nutrient deficiencies imposed by the high pH but rather to oxidative stress induced by alkalinity.

TABLE 3-1

Observed and expected frequencies assuming ratio for high pH tolerance
among cDNA 12335629 tested for growth under high pH (pH 9.0)
assuming a 3:1 (R:S) segregation ratio. α of 0.05

					Probability
Event	Generation	Observed	Expected	χ²	of Chi-Test

cDNA	T₃	23	27	0.593
12482777
pH
Resistant
cDNA	T₃	13	9	1.778	0.12
12482777
pH
Sensitive
N = 36		36	36	2.371

Qualitative and Quantitative Analysis of Harvest Index, Seed Yield, and Plant Height of T₃Progeny of 35S:: cDNA 12482777.

A segregating population of 17 plants containing cDNA 12482777 was analyzed for harvest index and seed yield compared to wild-type populations. Based upon stem height measurements, the transgenic population of 35S:: cDNA 12482777 (10 plants) was significantly smaller than both internal (6 plants) and external wild-type/control populations. Internal wild-types/controls were those plants segregating from the T₃population of the 35S::cDNA 12482777 line which did not contain the insert (segregating non-transgenics). External wild-types were non-transgenic plants from an outside source which shared no lineage with the line being tested. External wild-types are added to the experiment as a process control to ensure the quality of the growth conditions. Average height for transgenic plants of cDNA 12482777 was 33.44 cm±0.78 versus 44.65 cm±0.70 for the internal wild-type controls. Despite this decrease in plant height, harvest index, as measured by seed weight/total plant weight remained unaffected, i.e., these transgenic plants still produced the same ratio of total seed weight:total plant weight (biomass) as non-transgenic controls. This result means that although the total seed yield is decreased in cDNA 12482777 lines, it still has the same seed proportionally as controls. The cDNA 12482777 plants had a harvest index of 56.96±2.99 compared to the wild-type population's harvest index of 44.92±2.67 (Table 3-2A). This increase in harvest index was significant at a P-value of 0.009 (Table 3-3A).
It is important to note that seed weight of cDNA 12482777 plants with a larger harvest index was 0.30977g±0.025 while the wild-type population had an average seed weight of 0.37155g±0.027 (Table 3-3B). cDNA 12482777 has a slightly smaller seed weight than the wild-type population but not statistically different at a P-value of 0.12 (Table 3-3B), suggesting that the harvest index of 35S:: cDNA 12482777 is comparable to, if not greater than, wild-type plants. This increase in harvest index is not due to an increase in number of branches (data not shown) as observed in the T₁generation. Instead, the internode length between siliques is reduced compared to the internal wild-type control, suggesting that cDNA 12482777 plants have more siliques per stem length.

TABLE 3-2A

Descriptive statistical comparison of Harvest Index between segregating T₄
populations containing cDNA 12482777.

			Internal Wild-
Harvest Index: cDNA	Transgenic	Harvest Index: of	type
12482777 small stature	Population	cDNA 12482777 Wild-type stature	Population

Mean	56.9582619	Mean	44.91972222
Standard Error	2.990040579	Standard Error	2.667294901
Median	56.68809524	Median	45.56319444
Standard Deviation	9.455338527	Standard Deviation	6.533511501
Sample Variance	89.40342666	Sample Variance	42.68677253
Minimum	43.41666667	Minimum	33.9375
Maximum	70.11666667	Maximum	54.36666667
Sum	569.582619	Sum	269.5183333
Count	10	Count	6
Confidence Level	6.763946869	Confidence Level	6.856488619
(95.0%)		(95.0%)

TABLE 3-2B

Descriptive statistical comparison of total seed weight (g) at time of
harvest between segregating T₄populations containing cDNA 12482777.

Total Seed Weight (g)		Total Seed Weight (g)	Internal Wild-
of: cDNA 12482777:	Transgenic	of: cDNA 12482777:	type
Small Stature	Population	Wild-type Stature	Population

Mean	0.30977	Mean	0.37155
Standard Error	0.024799382	Standard Error	0.027304014
Median	0.3017	Median	0.3796
Standard Deviation	0.078422531	Standard Deviation	0.066880902
Sample Variance	0.006150093	Sample Variance	0.004473055
Minimum	0.1956	Minimum	0.2715
Maximum	0.4207	Maximum	0.4621
Sum	3.0977	Sum	2.2293
Count	10	Count	6
Confidence Level	0.056100142	Confidence Level	0.070187087
(95.0%)		(95.0%)

TABLE 3-4A

Statistical comparison of harvest index between
transgenic populations of clone 126592 and internal
wild-type populations using a t-test on two
samples assuming unequal variances. cDNA 1248277
Wt stature (internal wild-type population) and cDNA
12482777 small stature (transgenic population).

	Harvest Index:	Harvest Index
	cDNA 12482777	cDNA 12482777
	Wt stature	small stature

Mean	44.91972222	56.9582619
Variance	42.68677253	89.40342666
Observations	6	10
Hypothesized
Mean
Difference
	0
df	14
t Stat	-3.004493678
P (T <= t) one-tail	0.004733406
t Critical one-tail	1.76130925
P (T <= t) two-tail	0.009466812
t Critical two-tail	2.144788596

TABLE 3-44B

Statistical comparison of seed weight between transgenic population
of clone 126592 and internal wild-type populations using a
t-test on two samples assuming unequal variances. cDNA 12482777
Wt stature (internal wild-type population) and cDNA 12482777
small stature (transgenic population)

	Seed Weight 12482777:	Seed Weight 12482777:
	WT stature	Small Stature

Mean	0.37155	0.30977
Variance	0.004473055	0.006150093
Observations	6	10
Hypothesized Mean	0
Difference
df	12
t Stat	1.674926201
P(T <= t) one-tail	0.059894848
t Critical one-tail	1.782286745
P(T <= t) two-tail	0.119789696
t Critical two-tail	2.178812792

Table 3-5 provides the results of the consensus sequence analysis based on Ceres cDNA 12482777.

TABLE 3-5

Example 4

Ceres cDNA 12333678

Clone 26006, Ceres cDNA 12333678, encodes a full-length glycosyl hydrolase. Ectopic expression of Ceres cDNA 12333678 under the control of the CaMV35S promoter induces the following phenotypes:

- Germination on high concentrations of polyethylene glycol (PEG), mannitol and abscissic acid (ABA).
- Continued growth on high PEG, mannitol and ABA.
  Generation and Phenotypic Evaluation of T₁Lines Containing 35S::cDNA 12333678.

Wild-type Arabidopsis Wassilewskija (WS) plants were transformed with a Ti plasmid containing cDNA 12333678 in the sense orientation relative to the CaMV35S constitutive promoter. The T, plasmid vector used for this construct, CRS338, contains PAT and confers herbicide resistance to transformed plants. Ten independently transformed events were selected and evaluated for their qualitative phenotype in the T₁generation. No positive or negative phenotypes were observed in the T₁plants.

Screens of Superpools on High PEG, Mannitol and ABA as Surrogate Screens for Drought Tolerance.

Seeds from 13 superpools (1,200 T₂seeds from each superpool) from the CaMV35S or 32449 over-expression lines were tested on high pH media as described above. T₃seeds were collected from the tolerant plants and analyzed for tolerance on all additional high pH screens.
Once cDNA 12333678 was identified in tolerant plants, the individual T₂events containing this cDNA (ME01334) were screened on high PEG, mannitol and ABA to identify events with the resistance phenotype.
Superpools (SP) are referred to as SP1, SP2 and so on. The letter following the hyphen refers to the screen (P=PEG, M=mannitol, and A=ABA) and the number following the letter refers to a number assigned to each plant obtained from that screen on that superpool. For example, SP1-M18 is the 18^thplant isolated from a mannitol screen of Superpool 1.

Results:

Qualitative Assessment of MEO1334 on high pH.
Superpool 1 was screened on high pH media as described above. PCR analyses identified ME01334 as one of the ME lines showing high pH resistance. Testing of the second generation confirmed the inheritance of the pH resistance (data not shown).
ME01334 plants that recovered after high pH produced an exceptionally large number of seeds compared to wild-type controls. Additional testing confirmed that these plants statistically produce 30-80% more seeds than either wild-type or transgenic control plants that are recovered from this screen or transferred from regular MS media.
Table 4-1 provides the results of the consensus sequence analysis based on Ceres cDNA 12333678.

TABLE 4-1

The invention being thus described, it will be apparent to one of ordinary skill in the art that various modifications of the materials and methods for practicing the invention can be made. Such modifications are to be considered within the scope of the invention as defined by the following claims.
Each of the references from the patent and periodical literature cited herein is hereby expressly incorporated in its entirety by such citation.

Claims

1. An isolated nucleic acid molecule comprising:

a) a nucleic acid having a nucleotide sequence which encodes an amino acid sequence exhibiting at least 85% sequence identity to any one of those sequences present in the Sequence Listing;

b) a nucleic acid which is a complement of a nucleotide sequence according to paragraph (a);

(c) a nucleic acid which is the reverse of the nucleotide sequence according to subparagraph (a), such that the reverse nucleotide sequence has a sequence order which is the reverse of the sequence order of the nucleotide sequence according to subparagraph (a); or

(d) a nucleic acid capable of hybridizing to a nucleic acid according to any one of paragraphs (a)-(c), under conditions that permit formation of a nucleic acid duplex at a temperature from about 40° C. and 48° C. below the melting temperature of the nucleic acid duplex.

2. The isolated nucleic acid molecule according to claim 1, which has the nucleotide sequence according to any one of those sequences present in the Sequence Listing.

3. The isolated nucleic acid molecule according to claim 1, wherein said amino acid sequence comprises a polypeptide according to any one of the consensus sequences set forth in Tables 1-5, 2-6, 3-5 or 4-1.

4. The isolated nucleic acid molecule according to claim 1, wherein said amino acid sequence has a sequence according to any one of those sequences present in the Sequence Listing.

5. A vector construct comprising:

a) a first nucleic acid having a regulatory sequence capable of causing transcription and/or translation in a plant; and

b) a second nucleic acid having the sequence of the isolated nucleic acid molecule according to claim 1;

wherein said first and second nucleic acids are operably linked and

wherein said second nucleic acid is heterologous to any element in said vector construct.

6. The vector construct according to claim 5, wherein said first nucleic acid is native to said second nucleic acid.

7. The vector construct according to claim 5, wherein said first nucleic acid is heterologous to said second nucleic acid.

8. A host cell comprising an isolated nucleic acid molecule according to claim 1 wherein said nucleic acid molecule is flanked by exogenous sequence.

9. A host cell comprising a vector construct according to claim 5.

10. An isolated polypeptide comprising an amino acid sequence exhibiting at least 85% sequence identity to any of those sequences present in the Sequence Listing.

11. A method of introducing an isolated nucleic acid into a host cell comprising:

a) providing an isolated nucleic acid molecule according to claim 1; and

b) contacting said isolated nucleic acid with said host cell under conditions that permit insertion of said nucleic acid into said host cell.

12. A method of transforming a host cell that comprises contacting a host cell with a vector construct according to claim 5.

13. A method for detecting a nucleic acid in a sample which comprises:

a) providing an isolated nucleic acid molecule according to claim 1;

b) contacting said isolated nucleic acid molecule with a sample under conditions which permit a comparison of the sequence of said isolated nucleic acid molecule with the sequence of DNA in said sample; and

c) analyzing the result of said comparison.

14. A plant, plant cell, plant material or seed of a plant which comprises a nucleic acid molecule according to claim 1 which is exogenous or heterologous to said plant or plant cell.

15. A plant, plant cell, plant material or seed of a plant which comprises a vector construct according to claim 5.

16. A plant that has been regenerated from a plant cell or seed according to claim 14.

17. A plant, plant cell, plant material or seed of a plant which comprises a nucleic acid molecule according to claim 1, wherein said plant has improved pH tolerance or phosphate use efficiency characteristics as compared to a wild-type plant cultivated under the same conditions.

18. A method for increasing pH tolerance or phosphate use efficiency in a plant comprising transforming a plant with a nucleic acid sequence according to claim 1.

19. A transgenic plant having a gene construct comprising a nucleic acid encoding a pH tolerance or phosphate use efficiency component operably linked to a plant promoter so that the pH tolerance or phosphate use efficiency component is ectopically overexpressed in the transgenic plant, and the transgenic plant exhibits:

i) faster rate of growth,

ii) greater fresh or dry weight at maturation,

iii) greater fruit or seed yield,

iv) higher tolerance to pH,

v) higher tolerance to low phosphate concentration, or

vi) higher tolerance to low nitrogen concentration

than a progenitor plant which does not contain the polynucleotide construct, when the transgenic plant and the progenitor plant are cultivated under identical environmental conditions, wherein the pH or phosphate use efficiency component is any one of the polypeptides set forth in the Sequence Listing, or any one of the consensus sequences in claim 3.

20. A method for pH tolerance or phosphate use efficiency in a plant which comprises transforming a plant with a nucleic acid sequence that encodes a polypeptide that comprises at least one of the following:

(a) an amino acid sequence that comprises the residues at positions 29-154 of the consensus sequence of Table 1-5,

(b) an amino acid sequence that comprises the residues at positions 18-128 of the consensus sequence of Table 2-6,

(c) an amino acid sequence that comprises the residues at positions 57-230 of the consensus sequence of Table 3-5,

(d) an amino acid sequence that comprises the residues at positions 234-248 of the consensus sequence of Table 3-5, and

(e) an amino acid sequence that comprises the residues at positions 10-276 of the consensus sequence of Table 4-1.

21. A plant, plant cell, plant material of a plant with improved pH tolerance or phosphate use efficiency characteristics as compared to a wild-type plant cultivated under the same conditions which comprises a nucleic acid sequence that encodes a polypeptide that comprises at least one of the following: