US20140331357A1 - Genes and uses for plant enhancement - Google Patents

Genes and uses for plant enhancement Download PDF

Info

Publication number
US20140331357A1
US20140331357A1 US13/999,850 US201413999850A US2014331357A1 US 20140331357 A1 US20140331357 A1 US 20140331357A1 US 201413999850 A US201413999850 A US 201413999850A US 2014331357 A1 US2014331357 A1 US 2014331357A1
Authority
US
United States
Prior art keywords
dna
binding
enhanced
plants
myb
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Abandoned
Application number
US13/999,850
Inventor
Marie Coffin
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Monsanto Technology LLC
Original Assignee
Monsanto Technology LLC
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Monsanto Technology LLC filed Critical Monsanto Technology LLC
Priority to US13/999,850 priority Critical patent/US20140331357A1/en
Publication of US20140331357A1 publication Critical patent/US20140331357A1/en
Assigned to MONSANTO TECHNOLOGY LLC reassignment MONSANTO TECHNOLOGY LLC ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: COFFIN, MARIE
Priority to US15/211,720 priority patent/US10301642B2/en
Abandoned legal-status Critical Current

Links

Images

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • C12N15/8271—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
    • C12N15/8273—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for drought, cold, salt resistance
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8242—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits
    • C12N15/8243—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits involving biosynthetic or metabolic pathways, i.e. metabolic engineering, e.g. nicotine, caffeine
    • C12N15/8247—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits involving biosynthetic or metabolic pathways, i.e. metabolic engineering, e.g. nicotine, caffeine involving modified lipid metabolism, e.g. seed oil composition
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
    • A01H1/00—Processes for modifying genotypes ; Plants characterised by associated natural traits
    • A01H1/02—Methods or apparatus for hybridisation; Artificial pollination ; Fertility
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8201—Methods for introducing genetic material into plant cells, e.g. DNA, RNA, stable or transient incorporation, tissue culture methods adapted for transformation
    • C12N15/8209—Selection, visualisation of transformants, reporter constructs, e.g. antibiotic resistance markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8242—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits
    • C12N15/8243—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits involving biosynthetic or metabolic pathways, i.e. metabolic engineering, e.g. nicotine, caffeine
    • C12N15/8251—Amino acid content, e.g. synthetic storage proteins, altering amino acid biosynthesis
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • C12N15/8271—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/6895—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for plants, fungi or algae
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/13—Plant traits
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A40/00—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production
    • Y02A40/10—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production in agriculture
    • Y02A40/146—Genetically Modified [GMO] plants, e.g. transgenic plants

Definitions

  • transgenic plant cells, plants and seeds comprising recombinant DNA and methods of making and using such plant cells, plants and seeds.
  • This invention provides plant cell nuclei with recombinant DNA that imparts enhanced agronomic traits in transgenic plants having the nuclei in their cells, e.g. enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced shade tolerance, enhanced high salinity tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein or enhanced seed oil.
  • enhanced water use efficiency e.g. enhanced cold tolerance, enhanced heat tolerance, enhanced shade tolerance, enhanced high salinity tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein or enhanced seed oil.
  • the trait is imparted by producing in the cells a protein that is encoded by recombinant DNA and/or in other cases the trait is imparted by suppressing the production of a protein that is natively produced in the cells.
  • Such recombinant DNA in a plant cell nucleus of this invention is provided in as a construct comprising a promoter that is functional in plant cells and that is operably linked to DNA that encodes a protein or to DNA that results in gene suppression.
  • DNA in the construct is sometimes defined by protein domains of an encoded protein targeted for production or suppression, e.g. a “Pfam domain module” (as defined herein below) from the group of Pfam domain modules identified in Table 17.
  • a Pfam domain module as defined herein below
  • DNA in the construct is defined a consensus amino acid sequence of an encoded protein that is targeted for production or suppression, e.g.
  • transgenic plant cell nuclei e.g. where such a transgenic nucleus is present in a transgenic plant cell, a transgenic plant including plant part(s) such as progeny transgenic seed, and a haploid reproductive derivative of plant cell such as transgenic pollen and transgenic ovule.
  • Such plant cell nuclei and derivatives are advantageously selected from a population of transgenic plants regenerated from plant cells having a nucleus that is transformed with recombinant DNA by screening the transgenic plants or progeny seeds in the population for an enhanced trait as compared to control plants or seed that do not have the recombinant DNA in their nuclei, where the enhanced trait is enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced shade tolerance, enhanced high salinity tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein or enhanced seed oil.
  • One aspect of the present invention includes a plant cell nucleus with stably integrated, recombinant DNA, wherein said recombinant DNA comprises a promoter that is functional in said plant cell and that is operably linked to a protein coding DNA encoding a protein having an amino acid sequence comprising a Pfam domain module selected from the group consisting of WRKY::WRKY, AP2, AUX_IAA, WRKY, WRKY, HLH, Myb_DNA-binding::Linker_histone, zf-B_box::zf-B_box, Ank::Ank::Ank::Chromo, NAM, zf-C2H2, Myb_DNA-binding, bZIP — 1, PHD, Linker_histone::AT_hook::AT_hook::AT_hook::AT_hook, B3::Auxin_resp, HLH, zf-Dof, AT_hook::
  • the plant cell nucleus where said protein coding DNA encodes a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 140 through SEQ ID NO: 6023.
  • the plant cell nucleus can comprising DNA expressing a protein that provides tolerance from exposure to an herbicide, e.g, glyphosate, dicamba, or glufosinate, applied at levels that are lethal to a wild type of said plant cell.
  • Yet in another aspect of the invention includes a plurality of plant cells or planys with the plant cell nucleus described, and the transgenic plant cell or plant are homozygous for said recombinant DNA.
  • these plant cells are transgenic seeds from crops such as a corn, soybean, cotton, canola, alfalfa, wheat or rice plant, or transgenic pollen grain comprising a haploid derivative of a plant cell nucleus.
  • One aspect of the present invention includes a method 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 recombinant DNA in a nucleus described, wherein said method for manufacturing said transgenic seed comprising (a) screening a population of plants for said enhanced trait and said recombinant DNA, wherein individual plants in said population can exhibit said trait at a level less than, essentially the same as or greater than the level that said trait is exhibited in control plants which do not contain the recombinant DNA, wherein said enhanced trait is selected from the group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced high salinity tolerance, enhanced shade tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil, (b) selecting from said population one or more plants that exhibit said trait at a level greater than the level that said trait is exhibited in control plants, and (c) collecting seeds from selected plant selected from step b.
  • the method for manufacturing transgenic seed e.g, corn, soybean, cotton, alfalfa, canola wheat or rice seed, further comprising (a) verifying that said recombinant DNA is stably integrated in said selected plants, and (b) analyzing tissue of said selected plant to determine the expression or suppression of a protein having the function of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO:140-278.
  • Yet another aspect of the present invention includes a method of producing hybrid corn seed comprising (a) acquiring hybrid corn seed from a herbicide tolerant corn plant which also has stably-integrated, recombinant DNA in a nucleus of claim 2 ; (b) 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; (c) selecting corn plants which are homozygous and hemizygous for said recombinant DNA by treating with an herbicide; (d) collecting seed from herbicide-treated-surviving corn plants and planting said seed to produce further progeny corn plants; (e) repeating steps (c) and (d) at least once to produce an inbred corn line; and (f) crossing said inbred corn line with a
  • the transgenic plant comprise recombinant DNA constructs for expressing proteins are characterized by amino acid sequence that have at least 90% identity over at least 90% of the length of a reference sequence selected from the group consisting of SEQ ID NOs: 140-278 when the amino acid sequence is aligned to the reference sequence.
  • the transgenic plant comprise recombinant DNA constructs for expressing proteins are characterized by amino acid sequence that have at least 92.5% identity over at least 92.5% of the length of a reference sequence selected from the group consisting of SEQ ID NOs: 140-278 when the amino acid sequence is aligned to the reference sequence.
  • the transgenic plant comprise recombinant DNA constructs for expressing proteins are characterized by amino acid sequence that have at least 95% identity over at least 95% of the length of a reference sequence selected from the group consisting of SEQ ID NOs: 140-278 when the amino acid sequence is aligned to the reference sequence.
  • the transgenic plant comprise recombinant DNA constructs for expressing proteins are characterized by amino acid sequence that have at least 97% identity over at least 97% of the length of a reference sequence selected from the group consisting of SEQ ID NOs: 140-278 when the amino acid sequence is aligned to the reference sequence.
  • the transgenic plant comprise recombinant DNA constructs for expressing proteins are characterized by amino acid sequence that have at least 98% identity over at least 98% of the length of a reference sequence selected from the group consisting of SEQ ID NOs: 140-278 when the amino acid sequence is aligned to the reference sequence.
  • the transgenic plant comprise recombinant DNA constructs for expressing proteins are characterized by amino acid sequence that have at least 99% identity over at least 99% of the length of a reference sequence selected from the group consisting of SEQ ID NOs: 140-278 when the amino acid sequence is aligned to the reference sequence.
  • the transgenic plant comprise recombinant DNA constructs for expressing proteins are characterized by amino acid sequence that have at least 99.5% identity over at least 99.5% of the length of a reference sequence selected from the group consisting of SEQ ID NOs: 140-278 when the amino acid sequence is aligned to the reference sequence.
  • the nuclei of plant cells and derivative transgenic cells, plants, seeds, pollen and ovules further include recombinant DNA expressing a protein that provides tolerance from exposure to one or more herbicide applied at levels that are lethal to a wild type plant.
  • herbicide tolerance is not only an advantageous trait in such plants but is also useful as a selectable marker in the transformation methods for producing the nuclei and nuclei derivatives of the invention.
  • Such herbicide tolerance includes tolerance to a glyphosate, dicamba, or glufosinate herbicide.
  • transgenic plant cell nuclei which are homozygous for the recombinant DNA.
  • the transgenic plant cell nuclei of the invention and dervitave cells, plants, seed and haploid reproductive derivatives of the invention are advantageously provided in corn, soybean, cotton, canola, alfalfa, wheat, rice plants, or combinations thereof.
  • 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 in the nucleus of the plant cells. More specifically the method includes, but are not limited to, (a) screening a population of plants for an enhanced trait and 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 and (c) collecting seed from a selected plant.
  • Such method can further include the steps of (a) verifying that the recombinant DNA is stably integrated in said selected plants; and (b) analyzing tissue of a selected plant to determine the production of a protein having the function of a protein encoded by a recombinant DNA with a sequence of one of SEQ ID NO: 1-139;
  • the plants in the population can further include DNA expressing a protein that provides tolerance to exposure to an herbicide applied at levels that are lethal to wild type plant cells and where 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 can be used for manufacturing corn, soybean, cotton, canola, alfalfa, wheat and/or rice seed selected as having one of the enhanced traits described above.
  • Another aspect of the invention provides a method of producing hybrid corn seed including the step of acquiring hybrid corn seed from a herbicide tolerant corn plant which also has a nucleus of this invention with stably-integrated, recombinant DNA.
  • the method can further include the steps of producing corn plants from said hybrid corn seed, where 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/or 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.
  • FIGS. 1 , 2 and 3 are pictures illustrating plasmid maps
  • FIGS. 4( a ) and 4 ( b ) illustrate a consensus amino acid sequence of SEQ ID NO: 237 and their homologs.
  • SEQ ID NO: 1-139 are nucleotide sequences of the coding strand of DNA for “genes” used in the recombinant DNA imparting an enhanced trait in plant cells, i.e. each represents a coding sequence for a protein;
  • SEQ ID NO: 140-278 are amino acid sequences of the protein of the “genes” encoding by nucleotide sequence 1-139;
  • SEQ TD NO: 279-6023 homologs are amino acid sequences of homologous proteins;
  • SEQ ID NO: 6024 is a nucleotide sequence of a plasmid base vector useful for corn transformation;
  • SEQ ID NO: 6025 is a DNA sequence of a plasmid base vector useful for soybean transformation
  • SEQ ID NO: 6026 is a DNA sequence of a plasmid base vector useful for cotton transformation.
  • SEQ ID NO: 6027-6034 are consensus sequences.
  • Table 1 lists the protein SEQ ID NOs and their corresponding consensus SEQ ID NOs.
  • the nuclei of this invention are identified by screening transgenic plants for one or more traits including enhanced drought stress tolerance, enhanced heat stress tolerance, enhanced cold stress tolerance, enhanced high salinity stress tolerance, enhanced low nitrogen availability stress tolerance, enhanced shade stress tolerance, enhanced plant growth and development at the stages of seed imbibition through early vegetative phase, and enhanced plant growth and development at the stages of leaf development, flower production and seed maturity.
  • Gene means a chromosomal element for expressing a protein and specifically includes the DNA encoding a protein.
  • the pertinent part of a gene is the DNA encoding the target protein; in cases where suppression of a target is desired, the pertinent part of a gene is that part that is transcribed as mRNA.
  • Recombinant DNA means a polynucleotide having a genetically engineered modification introduced through combination of endogenous and/or exogenous elements in a transcription unit. Recombinant DNA can include DNA segments obtained from different sources, or DNA segments obtained from the same source, but which have been manipulated to join DNA segments which do not naturally exist in the joined form.
  • Trait means a physiological, morphological, biochemical, or physical characteristic of a plant or particular plant material or cell, or any combinations thereor.
  • a “control plant” is a plant without trait-improving recombinant DNA in its nucleus.
  • a control plant is used to measure and compare trait enhancement in a transgenic plant with such trait-improving recombinant DNA.
  • a suitable control plant can be a non-transgenic plant of the parental line used to generate a transgenic plant herein.
  • a control plant can be a transgenic plant having an empty vector or marker gene, but does not contain the recombinant DNA that produces the trait enhancement.
  • a control plant can also be a negative segregant progeny of hemizygous transgenic plant. In certain demonstrations of trait enhancement, the use of a limited number of control plants can cause a wide variation in the control dataset.
  • a “reference” is used.
  • a “reference” is a trimmed mean of all data from both transgenic and control plants grown under the same conditions and at the same developmental stage. The trimmed mean is calculated by eliminating a specific percentage, e.g., 20%, of the smallest and largest observation from the data set and then calculating the average of the remaining observation.
  • Trait enhancement means a detectable and desirable difference in a characteristic in a transgenic plant relative to a control plant or a reference.
  • the trait enhancement can be measured quantitatively.
  • the trait enhancement can entail at least a 2% desirable difference in an observed trait, at least a 5% desirable difference, at least about a 10% desirable difference, at least about a 20% desirable difference, at least about a 30% desirable difference, at least about a 50% desirable difference, at least about a 70% desirable difference, at least about a 80% desirable difference, at least about a 90% desirable difference, at least about a 92.5% desirable difference, at least about a 95% desirable difference, at least about a 98% desirable difference, at least about a 99% desirable difference, at least about a 99.5% desirable difference or at least about a 100% difference, or an even greater desirable difference.
  • the trait enhancement is only measured qualitatively. It is known that there can be a natural variation in a trait. Therefore, the trait enhancement observed entails a change of the normal distribution of the trait in the transgenic plant compared with the trait distribution observed in a control plant or a reference, which is evaluated by statistical methods provided herein.
  • Trait enhancement includes, but is not limited to, yield increase, including increased yield under non-stress conditions and increased yield under environmental stress conditions. Stress conditions can 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, high plant density, or any combinations thereof.
  • agronomic traits can affect “yield”, 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, juvenile traits, or any combinations thereof.
  • Other traits that can affect yield include, 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.
  • transgenic plants that demonstrate desirable phenotypic properties that can confer an increase in overall plant yield. Such properties include enhanced plant morphology, plant physiology or improved components of the mature seed harvested from the transgenic plant.
  • Yield-limiting environment means the condition under which a plant would have the limitation on yield including environmental stress conditions.
  • Stress condition means a condition unfavorable for a plant, which adversely affect plant metabolism, growth and/or development.
  • a plant under the stress condition typically shows reduced germination rate, retarded growth and development, reduced photosynthesis rate, and eventually leading to reduction in yield.
  • water deficit stress used herein refers to the sub-optimal conditions for water and humidity needed for normal growth of natural plants.
  • Relative water content (RWC) can be used as a physiological measure of plant water deficit. It measures the effect of osmotic adjustment in plant water status, when a plant is under stressed conditions. Conditions which can result in water deficit stress include, but are not limited to, heat, drought, high salinity and PEG induced osmotic stress.
  • Cold stress means the exposure of a plant to a temperatures below (two or more degrees Celsius below) those normal for a particular species or particular strain of plant.
  • Nonrogen nutrient means any one or any mix of the nitrate salts commonly used as plant nitrogen fertilizer, including, but not limited to, potassium nitrate, calcium nitrate, sodium nitrate, ammonium nitrate.
  • ammonium as used herein means any one or any mix of the ammonium salts commonly used as plant nitrogen fertilizer, e.g., ammonium nitrate, ammonium chloride, ammonium sulfate, etc.
  • Low nitrogen availability stress means a plant growth condition that does not contain sufficient nitrogen nutrient to maintain a healthy plant growth and/or for a plant to reach its typical yield under a sufficient nitrogen growth condition.
  • a limiting nitrogen condition can refers to a growth condition with 50% or less of the conventional nitrogen inputs.
  • “Sufficient nitrogen growth condition” means a growth condition where the soil or growth medium contains or receives optimal amounts of nitrogen nutrient to sustain a healthy plant growth and/or for a plant to reach its typical yield for a particular plant species or a particular strain.
  • One skilled in the art would recognize what constitute such soil, media and fertilizer inputs for most plant species.
  • Shade stress means a growth condition that has limited light availability that triggers the shade avoidance response in plant. Plants are subject to shade stress when localized at lower part of the canopy, or in close proximity of neighboring vegetation. Shade stress can become exacerbated when the planting density exceeds the average prevailing density for a particular plant species.
  • “Increased yield” of a transgenic plant of the present invention is evidenced and measured in a number of ways, including test weight, seed number per plant, seed weight, seed number per unit area (e.g., seeds, or weight of seeds, per acre), bushels per acre, tons per acre, tons per acre, kilo per hectare.
  • maize yield can be measured as production of shelled corn kernels per unit of production area, e.g., in bushels per acre or metric tons per hectare, often reported on a moisture adjusted basis, e.g., at 15.5% moisture.
  • Increased yield can result from enhanced utilization of key biochemical compounds, such as nitrogen, phosphorous and carbohydrate, or from enhanced tolerance to environmental stresses, such as cold, heat, drought, salt, and attack by pests or pathogens.
  • Trait-improving recombinant DNA can also be used to provide transgenic plants having enhanced 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.
  • a “plant promoter” is a promoter capable of initiating transcription in plant cells whether or not its origin is a plant cell.
  • Exemplary plant promoters include, but are not limited to, those that are obtained from plants, plant viruses, and bacteria which include genes expressed in plant cells such Agrobacterium or Rhizobium .
  • 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 which 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.
  • inducible or “repressible” promoter is a promoter which is under environmental control. Examples of environmental conditions that can 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 refers to the association of two or more nucleic acid elements in a recombinant DNA construct, e.g. as when a promoter is operably linked with DNA that is transcribed to RNA whether for expressing or suppressing a protein.
  • Recombinant DNA constructs can be designed to express a protein which can be an endogenous protein, an exogenous homologue of an endogenous protein or an exogenous protein with no native homologue.
  • recombinant DNA constructs can be designed to suppress the level of an endogenous protein, e.g. by suppression of the native gene.
  • RNAi RNA interference
  • Gene suppression can also be effected by recombinant DNA that comprises anti-sense oriented DNA matched to the gene targeted for suppression.
  • Gene suppression can also be effected by recombinant DNA that comprises DNA that is transcribed to a microRNA matched to the gene targeted for suppression.
  • recombinant DNA for effecting gene suppression that imparts is identified by the term “antisense”. It will be understood by a person of ordinary skill in the art that any of the ways of effecting gene suppression are contemplated and enabled by a showing of one approach to gene suppression.
  • a “consensus amino acid sequence” means an artificial, amino acid sequence indicating conserved amino acids in the sequence of homologous proteins as determined by statistical analyis of an optimal alignment, e.g. CLUSTALW, of amino acid sequence of homolog proteins.
  • the consensus sequences listed in the sequence listing were created by identifying the most frequent amino acid at each position in a set of aligned protein sequences. When there was 100% identity in an alignment the amino acid is indicated by a capital letter. When the occurance of an amino acid is at least about 70% in an alignemnt, the amino acid is indicated by a lower case letter. When there is no amino acid occurance of at least about 70%, e.g. due to diversity or gaps, the amino acid is inidcated by an “x”.
  • a consensus amino acid sequence When used to defined embodiments of the invention, a consensus amino acid sequence will be aligned with a query protein amino acid sequence in an optimal alignment, e.g. CLUSTALW.
  • An embodiment of the invention will have identity to the conserved amino acids indicated in the consensus amino acid sequence.
  • 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.
  • homologs include orthologs, e.g. genes expressed in different species that evolved from a common ancestral genes by speciation and encode proteins retain the same function, but do not include paralogs, e.g., genes that are related by duplication but have evolved to encode proteins with different functions.
  • homologous genes include naturally occurring alleles and artificially-created variants.
  • homolog proteins have typically at least about 60% identity, in some instances at least about 70%, for example about 80% and even at least about 90% identity over the full length of a protein, such as from SEQ ID No. 140-278, identified as being associated with imparting an enhanced trait when expressed in plant cells.
  • homolog proteins have an amino acid sequence that has at least 95%, 98%, 99%, or 99.5% identity to a consensus amino acid sequence of proteins and homologs disclosed herein.
  • Homologs are 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
  • 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 can be identified as an 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 homologs encoded by DNA useful in the transgenic plants of the invention are those proteins that differ from a disclosed protein as the result of deletion or insertion of one or more amino acids in a native sequence.
  • 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. Such optimal alignment is understood to be deemed as local alignment of DNA sequences. For protein alignment, a local alignment of protein sequences should allow introduction of gaps to achieve optimal alignment. Percent identity is calculated over the aligned length not including the gaps introduced by the alignment per se.
  • Homologous genes are genes which encode proteins with the same or similar biological function to the protein encoded by the second gene. Homologous genes can be generated by the event of speciation (see ortholog) or by the event of genetic duplication (see paralog). “Orthologs” refer to a set of homologous genes in different species that evolved from a common ancestral gene by specification. Normally, orthologs retain the same function in the course of evolution; and “paralogs” refer to a set of homologous genes in the same species that have diverged from each other as a consequence of genetic duplication. Thus, homologous genes can be from the same or a different organism. As used herein, “homolog” means a protein that performs the same biological function as a second protein including those identified by sequence identity search.
  • Arabidopsis means plants of Arabidopsis thaliana.
  • Pfam database is a large collection of multiple sequence alignments and hidden Markov models covering many common protein families, e.g. Pfam version 19.0 (December 2005) contains alignments and models for 8183 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. The Pfam database is currently maintained and updated by the 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 protein family 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.
  • profile HMMs Profile hidden Markov models
  • a “Pfam domain module” is a representation of Pfam domains in a protein, in order from N terminus to C terminus. In a Pfam domain module individual Pfam domains are separated by double colons “::”. The order and copy number of the Pfam domains from N to C terminus are attributes of a Pfam domain module. Although the copy number of repetitive domains is important, varying copy number often enables a similar function. Thus, a Pfam domain module with multiple copies of a domain should define an equivalent Pfam domain module with variance in the number of multiple copies.
  • a Pfam domain module is not specific for distance between adjacent domains, but contemplates natural distances and variations in distance that provide equivalent function.
  • the Pfam database contains both narrowly- and broadly-defined domains, leading to identification of overlapping domains on some proteins.
  • a Pfam domain module is characterized by non-overlapping domains. Where there is overlap, the domain having a function that is more closely associated with the function of the protein (based on the E value of the Pfam match) is selected.
  • DNA encoding proteins with the same Pfam domain module are identified by querying the amino acid sequence of protein encoded by candidate DNA against the Hidden Markov Models which characterizes the Pfam domains using HMMER software, a current version of which is provided in the appended computer listing.
  • Candidate proteins meeting the same Pfam domain module are in the protein family and have corresponding 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 with a common Pfam domain module for recombinant DNA in the plant cells of this invention are also included in the appended computer listing.
  • the relevant Pfam modules for use in this invention are WRKY::WRKY, AP2, AUX_IAA, WRKY, WRKY, HLH, Myb_DNA-binding::Linker_histone, zf-B_box::zf-B_box, Ank::Ank::Ank::Chromo, NAM, zf-C2H2, Myb_DNA-binding, bZIP — 1, PHD, Linker_histone::AT_hook::AThook::AT_hook::AT_hook, B3::Auxin_resp, HLH, zf-Dof, AT_hook::DUF296, AT_hook::AT_hook::DUF296, NAM, GATA, NAM, Myb_DNA-binding, zf-B_box::CCT, POX::Homeobox, B3::Auxin_resp::AUX_
  • the invention uses recombinant DNA for imparting one or more enhanced traits to transgenic plant when incorporated into the nucleus of the plant cells.
  • recombinant DNA is a constructcomprising a promoter operatively linked to to DNA for expression or suppression of a target protein in plant cells.
  • Other construct components can include additional regulatory elements, such as 5′ or 3′ untranslated regions (such as polyadenylation sites), intron regions, and transit or signal peptides.
  • Such recombinant DNA constructs can be assembled using methods known to those of ordinary skill in the art.
  • Recombinant constructs prepared in accordance with the present invention also generally include a 3′ untranslated DNA region (UTR) that typically contains a polyadenylation sequence following the polynucleotide coding region.
  • UTR 3′ untranslated DNA region
  • useful 3′ UTRs include those from the nopaline synthase gene of Agrobacterium tumefaciens (nos), a gene encoding the small subunit of a ribulose-1,5-bisphosphate carboxylase-oxygenase (rbcS), and the T7 transcript of Agrobacterium tumefaciens.
  • Constructs and vectors can 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.
  • Table 2 provides a list of genes that provided recombinant DNA that was expressed in a model plant and identified from screening as imparting an enhanced trait.
  • the expression of the gene or a homolog in a crop plant provides the means to identify transgenic events that provide an enhanced trait in the crop plant.
  • the stated orientation is “antisense”
  • the suppression of the native homolog in a crop plant provides the means to identify transgenic events that provide an enhanced trait in the crop plant.
  • the expression/suppression in the model plant exhibited an enhanced trait that corresponds to an enhanced agronomic trait, e.g. cold stress tolerance, water deficit stress tolerance, low nitrogen stress tolerance and the like.
  • the expression/suppression in the model plant exhibited an enhanced trait that is a surrogate to an enhanced agronomic trait, e.g. salinity stress tolerance being a surrogate to drought tolerance or improvement in plant growth and development being a surrogate to enhanced yield.
  • an enhanced trait e.g. salinity stress tolerance being a surrogate to drought tolerance or improvement in plant growth and development being a surrogate to enhanced yield.
  • transgenic plant cell nuclei, cell, plant or seed by making number of transgenic events, typically a very large number, and engaging in screening processes identified in this specification and illustrated in the examples.
  • a screening process includes selecting only those transgenic events with an intact, single copy of the recombinant DNA in a single locus of the host plant genome and further screening for transgenic events that impart a desired trait that is replicatable when the recombinant DNA is introgressed into a variety of germplams without imparting significant adverse traits.
  • NUC SEQ ID NO refers to a SEQ ID NO. for particular DNA sequence in the Sequence Listing.
  • PEP SEQ ID NO refers to a SEQ ID NO. in the Sequence Listing for the amino acid sequence of a protein corresponding to a particular DNA
  • construct_id refers to an arbitrary number used to identify a particular recombinant DNA construct comprising the particular DNA.
  • Gene ID refers to an arbitrary name used to identify the particular DNA.
  • orientation refers to the orientation of the particular DNA in a recombinant DNA construct relative to the promoter.
  • DNA for use in the present invention to improve traits in plants have a nucleotide sequence of SEQ ID NO:1 through SEQ ID NO:139, as well as the homologs of such DNA molecules.
  • a subset of the DNA for gene suppression aspects of the invention includes fragments of the disclosed full polynucleotides consisting of oligonucleotides of 21 or more consecutive nucleotides. Oligonucleotides the larger molecules having a sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 139 are useful as probes and primers for detection of the polynucleotides used in the invention. Also useful in this invention are variants of the DNA.
  • Such variants can be naturally occurring, including DNA from homologous genes from the same or a different species, or can be non-natural variants, for example DNA synthesized using chemical synthesis methods, or generated using recombinant DNA techniques.
  • 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 DNA useful in the present invention can have any base sequence that has been changed from the sequences provided herein by substitution in accordance with degeneracy of the genetic code.
  • DNA is substantially identical to a reference DNA if, when the sequences of the polynucleotides are optimally aligned there is at least about 60% nucleotide equivalence over a comparison window.
  • the DNA can also be about 70% equivalence, about 80% equivalence; about 85% equivalence; about 90%; about 95%; or even about 98%, 98.5%, 99% or 99.5% equivalence over a comparison window.
  • a comparison window is at least about 50-100 nucleotides, and/or is the entire length of the polynucleotide provided herein.
  • Optimal alignment of sequences for aligning a comparison window can be conducted by algorithms or by computerized implementations of these algorithms (for example, the Wisconsin Genetics Software Package Release 7.0-10.0, Genetics Computer Group, 575 Science Dr., Madison, Wis.).
  • the reference polynucleotide can be a full-length molecule or a portion of a longer molecule.
  • the window of comparison for determining polynucleotide identity of protein encoding sequences is the entire coding region.
  • Proteins useful for imparting enhanced traits are entire proteins or at least a sufficient portion of the entire protein to impart the relevant biological activity of the protein. Proteins used for generation of transgenic plants having enhanced traits include the proteins with an amino acid sequence provided herein as SEQ ID NO: 140 through SEQ ID NO: 278, as well as homologs of such proteins.
  • Homologs of the trait-improving proteins provided herein generally demonstrate significant sequence identity.
  • proteins having at least about 50% sequence identity, at least about 70% sequence identity or higher, e.g., at least about 80% sequence identity with an amino acid sequence of SEQ ID NO:140 through SEQ ID NO: 278.
  • Proteins also include those with higher identity, e.g., at least about 100% to at least about 99.5%, at least about 100% to at least about 99%, at least about 100% to at least about 98%, at least about 100% to at least about 97.5%, at least about 100% to at least about 95%, at least about 100% to at least about 92.5%, and at least about 100% to at least about 90%.
  • Identity of protein homologs is determined by aligning the amino acid sequence of a putative protein homolog with a defined amino acid sequence and by calculating the percentage of identical and conservatively substituted amino acids over the window of comparison.
  • the window of comparison for determining identity can be the entire amino acid sequence disclosed herein, e.g., the full sequence of any of SEQ ID NO: 140 through SEQ ID NO: 278.
  • Other functional homolog proteins differ in one or more amino acids from those of a trait-improving protein disclosed herein as the result of one or more of the well-known conservative amino acid substitutions, e.g., valine is a conservative substitute for alanine and threonine is a conservative substitute for serine.
  • Conservative substitutions for an amino acid within the native sequence can be selected from other members of a class to which the naturally occurring amino acid belongs.
  • amino acids within these various classes include, but are not limited to: (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, tyrosine, asparagine, and glutamine; and (4) neutral nonpolar (hydrophobic) amino acids such as alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine.
  • conserveed substitutes for an amino acid within a native amino acid sequence can be selected from other members of the group to which the naturally occurring amino acid belongs.
  • a group of amino acids having aliphatic side chains is glycine, alanine, valine, leucine, and isoleucine
  • a group of amino acids having aliphatic-hydroxyl side chains is serine and threonine
  • a group of amino acids having amide-containing side chains is asparagine and glutamine
  • a group of amino acids having aromatic side chains is phenylalanine, tyrosine, and tryptophan
  • a group of amino acids having basic side chains is lysine, arginine, and histidine
  • a group of amino acids having sulfur-containing side chains is cysteine and methionine.
  • Naturally conservative amino acids substitution groups are: valine-leucine, valine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, aspartic acid-glutamic acid, and asparagine-glutamine.
  • a further aspect of the invention includes proteins that differ in one or more amino acids from those of a described protein sequence as the result of deletion or insertion of one or more amino acids in a native sequence.
  • Protein homologs include proteins with an amino acid sequence that has at least 90% identity to such a consensus amino acid sequence sequences.
  • 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 or Figwort mosaic virus promoters.
  • NOS nopaline synthase
  • OCS octopine synthase
  • caulimovirus promoters such as the cauliflower mosaic virus or Figwort mosaic virus promoters.
  • CaMV35S cauliflower mosaic virus
  • the promoters can include multiple “enhancer sequences” to assist in elevating gene expression.
  • enhancers are known in the art.
  • the expression of the selected protein can 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 in the forward or reverse orientation 5′ or 3′ to the coding sequence.
  • these 5′ enhancing elements are introns. Deemed to be particularly useful as enhancers are the 5′ introns of the rice actin 1 and rice actin 2 genes.
  • enhancers examples include elements from the CaMV 35S promoter, octopine synthase genes, the maize alcohol dehydrogenase gene, the maize shrunken 1 gene and promoters from non-plant eukaryotes.
  • the promoter element in the DNA construct can be capable of causing sufficient expression to result in the production of an effective amount of a polypeptide in water deficit conditions.
  • Such promoters can be identified and isolated from the regulatory region of plant genes that are over expressed in water deficit conditions.
  • Specific water-deficit-inducible promoters for use in this invention are derived from the 5′ regulatory region of genes identified as a heat shock protein 17.5 gene (HSP17.5), an HVA22 gene (HVA22), a Rab17 gene and a cinnamic acid 4-hydroxylase (CA4H) gene (CA4H) of Zea maize .
  • HSP17.5 heat shock protein 17.5 gene
  • HVA22 HVA22
  • Rab17 a cinnamic acid 4-hydroxylase
  • CA4H cinnamic acid 4-hydroxylase
  • 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 (Peri) (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
  • Promoters of interest for such uses include those from genes such as SSU (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).
  • Gene suppression includes any of the well-known methods for suppressing transcription of a gene or the accumulation of the mRNA corresponding to that gene thereby preventing translation of the transcript into protein.
  • Posttranscriptional gene suppression is mediated by transcription of RNA that forms double-stranded RNA (dsRNA) having homology to a gene targeted for suppression.
  • dsRNA double-stranded RNA
  • Suppression can also be achieved by insertion mutations created by transposable elements can also prevent gene function.
  • transformation with the T-DNA of Agrobacterium can be readily achieved and large numbers of transformants can be rapidly obtained.
  • some species have lines with active transposable elements that can efficiently be used for the generation of large numbers of insertion mutations, while some other species lack such options.
  • Mutant plants produced by Agrobacterium or transposon mutagenesis and having altered expression of a polypeptide of interest can be identified using the polynucleotides of the present invention. For example, a large population of mutated plants can be screened with polynucleotides encoding the polypeptide of interest to detect mutated plants having an insertion in the gene encoding the polypeptide of interest.
  • the present invention also contemplates that the trait-improving recombinant DNA provided herein can be used in combination with other recombinant DNA to create plants with multiple desired traits or a further enhanced trait.
  • the combinations generated can include multiple copies of any one or more of the recombinant DNA constructs. These stacked combinations can be created by any method, including but not limited to cross breeding of transgenic plants, or multiple genetic transformation.
  • Transformation of plant material is practiced in tissue culture on a nutrient media, i.e. a mixture of nutrients that will allow cells to grow in vitro.
  • Recipient cell targets include, but are not limited to, meristem cells, hypocotyls, calli, immature embryos and gametic cells such as microspores, pollen, sperm and egg cells.
  • Callus may be initiated from tissue sources including, but not limited to, immature embryos, hypocotyls, seedling apical meristems, microspores and the like. Cells containing a transgenic nucleus are grown into transgenic plants.
  • heterologous DNA randomly, e.g., at a non-specific location, in the genome of a target plant line.
  • target heterologous DNA insertion in order to achieve site-specific integration, e.g., to replace an existing gene in the genome, to use an existing promoter in the plant genome, or to insert a recombinant polynucleotide at a predetermined site known to be active for gene expression.
  • site specific recombination systems exist which are known to function in plants including cre-lox as disclosed in U.S. Pat. No. 4,959,317 and FLP-FRT as disclosed in U.S. Pat. No. 5,527,695, both incorporated herein by reference.
  • Transformation methods of this invention can be 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, calli, hypocotyles, immature embryos and gametic cells such as microspores, pollen, sperm and egg cells. It is contemplated that any cell from which a fertile plant can be regenerated is useful as a recipient cell. Callus can 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.
  • Practical transformation methods and materials for making transgenic plants of this invention, e.g., various media and recipient target cells, transformation of immature embryos and subsequent regeneration of fertile transgenic plants are disclosed in U.S. Pat. Nos. 6,194,636 and 6,232,526 and U.S. patent application Ser. No. 09/757,089, 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 a 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 sonic 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.
  • DNA is introduced into only a small percentage of target cell nuclei.
  • Marker genes are used to provide an efficient system for identification of those cells with nuclei that are stably transformed by receiving and integrating a recombinant DNA molecule into their genomes.
  • Some marker genes provide selective markers that confer resistance to a selective agent, such as an antibiotic or herbicide.
  • Potentially transformed cells with a nucleus of the invention are exposed to the selective agent. In the population of surviving cells will be those cells where, generally, the resistance-conferring gene has been integrated and expressed at sufficient levels to permit cell survival. Cells can be tested further to confirm stable integration of the exogenous DNA in the nucleus.
  • Useful selective marker genes include those conferring resistance to antibiotics such as kanamycin (nptII), hygromycin B (aph IV), spectinomycin (aadA) and gentamycin (aac3 and aacC4) or resistance to herbicides such as glufosinate (bar or pat), dicamba (DMO) and glyphosate (EPSPS). Examples of such selectable markers 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.
  • Screenable markers which provide an ability to visually identify transformants can also be employed, e.g., 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. It is also contemplated that combinations of screenable and selectable markers will be useful for identification of transformed cells. See PCT publication WO 99/61129 (herein incorporated by reference) which discloses use of a gene fusion between a selectable marker gene and a screenable marker gene, e.g., an NPTII gene and a GFP gene.
  • a gene fusion between a selectable marker gene and a screenable marker gene e.g., an NPTII gene and a GFP gene.
  • Plant cells that survive exposure to the selective agent, or cells that have been scored positive in a screening assay can be cultured in regeneration media and allowed to mature into plants.
  • Developing plantlets can be transferred to soil less plant growth mix, and hardened off, e.g., 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 matured either in a growth chamber or greenhouse. Plants are regenerated from about 6 weeks to 10 months after a transformant is identified, depending on the initial tissue. During regeneration, cells are grown to plants on solid media at about 19 to 28° C. After regenerating plants have reached the stage of shoot and root development, they can be transferred to a greenhouse for further growth and testing. Plants can be pollinated using conventional plant breeding methods known to those of skill in the art and seed produced.
  • Progeny can be recovered from transformed plants and tested for expression of the exogenous recombinant polynucleotide.
  • useful assays include, for example, “molecular biological” assays, such as Southern and Northern blotting and PCR; “biochemical” assays, such as detecting the presence of RNA, e.g., double stranded RNA, or a protein product, e.g., by immunological means (ELISAs and Western blots) or by enzymatic function; plant part assays, such as leaf or root assays; and also, by analyzing the phenotype of the whole regenerated plant.
  • “molecular biological” assays such as Southern and Northern blotting and PCR
  • biochemical assays, such as detecting the presence of RNA, e.g., double stranded RNA, or a protein product, e.g., by immunological means (ELISAs and Western blots) or by enzymatic function
  • Arabidopsis thaliana was transformed with a candidate recombinant DNA construct and screened for an enhanced trait.
  • Arabidopsis thaliana is used a model for genetics and metabolism in plants.
  • a two-step to screening process was employed which included two passes of trait characterization to ensure that the trait modification was dependent on expression of the recombinant DNA, but not due to the chromosomal location of the integration of the transgene. Twelve independent transgenic lines for each recombinant DNA construct were established and assayed for the transgene expression levels. Five transgenic lines with high transgene expression levels were used in the first pass screen to evaluate the transgene's function in T2 transgenic plants. Subsequently, three transgenic events, which had been shown to have one or more enhanced traits, were further evaluated in the second pass screen to confirm the transgene's ability to impart an enhanced trait.
  • Table 3 summarizes the enhanced traits that have been confirmed as provided by a recombinant DNA construct.
  • PEP SEQ ID which is the amino acid sequence of the protein corresponding to the DNA in the recombinant DNA construct corresponding to a protein sequence of a SEQ ID NO. in the Sequence Listing.
  • construct_id is an arbitrary name for the recombinant DNA describe more particularly in Table 1.
  • “annotation” refers to a description of the top hit protein obtained from an amino acid sequence query of each PEP SEQ ID NO to GenBank database of the National Center for Biotechnology Information (ncbi). More particularly, “gi” is the GenBank ID number for the top BLAST hit.
  • “description” refers to the description of the top BLAST hit.
  • e-value provides the expectation value for the BLAST hit.
  • % id refers to the percentage of identically matched amino acid residues along the length of the portion of the sequences which is aligned by BLAST between the sequence of interest provided herein and the hit sequence in GenBank.
  • “traits” identify by two letter codes the confirmed enhancement in a transgenic plant provided by the recombinant DNA.
  • the codes for enhanced traits are:
  • CS cold tolerance enhancement identified by a cold germination tolerance screen
  • DS drought tolerance enhancement identified by a soil drought stress tolerance screen
  • PEG which indicates osmotic stress tolerance enhancement identified by a PEG induced osmotic stress tolerance screen
  • PP which indicates enhanced growth and development at early stages identified by an early plant growth and development screen
  • SP which indicates enhanced growth and development at late stages identified by a late plant growth and development screen provided herein.
  • Drought or water deficit conditions impose mainly osmotic stress on plants. Plants are particularly vulnerable to drought during the flowering stage.
  • the drought condition in the screening process disclosed in Example 1B started from the flowering time and was sustained to the end of harvesting.
  • the present invention provides recombinant DNA that can improve the plant survival rate under such sustained drought condition. Exemplary recombinant DNA for conferring such drought tolerance are identified as such in Table 3. Such recombinant DNA can be used in generating transgenic plants that are tolerant to the drought condition imposed during flowering time and in other stages of the plant life cycle.
  • transgenic plants with trait-improving recombinant DNA grown under such sustained drought condition can also have increased total seed weight per plant in addition to the increased survival rate within a transgenic population, providing a higher yield potential as compared to control plants.
  • Various drought levels can be artificially induced by using various concentrations of polyethylene glycol (PEG) to produce different osmotic potentials (Pilon-Smits e.g., (1995) Plant Physiol. 107:125-130).
  • PEG polyethylene glycol
  • Several physiological characteristics have been reported as being reliable indications for selection of plants possessing drought tolerance. These characteristics include the rate of seed germination and seedling growth. The traits can be assayed relatively easily by measuring the growth rate of seedling in PEG solution.
  • a PEG-induced osmotic stress tolerance screen is a useful surrogate for drought tolerance screen.
  • embodiments of transgenic plants with trait-improving recombinant DNA identified in the PEG-induced osmotic stress tolerance screen can survive better drought conditions providing a higher yield potential as compared to control plants.
  • the present invention provides genes that help plants maintain biomass, root growth, and/or plant development in high salinity conditions, which are identified as such in Table 3. Since osmotic effect is one of the major components of salt stress, which is common to the drought stress, trait-improving recombinant DNA identified in a high salinity stress tolerance screen can also provide transgenic crops with enhanced drought tolerance. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a high salinity stress tolerance screen can survive better drought conditions and/or high salinity conditions providing a higher yield potential as compared to control plants.
  • Heat and drought stress often occur simultaneously, limiting plant growth. Heat stress can cause the reduction in photosynthesis rate, inhibition of leaf growth and osmotic potential in plants.
  • genes identified by the present invention as heat stress tolerance conferring genes can also impart enhanced thought tolerance to plants.
  • embodiments of transgenic plants with trait-improving recombinant DNA identified in a heat stress tolerance screen can survive better heat stress conditions and/or drought conditions providing a higher yield potential as compared to control plants.
  • cold shock tolerance screen CK
  • cold germination tolerance screen the transgenic Arabidopsis plants were exposed to a constant temperature of 8° C. from planting until day 28 post plating.
  • the trait-improving recombinant DNA identified by such screen are particular useful for the production of transgenic plant that can germinate more robustly in a cold temperature as compared to the wild type plants.
  • cold shock tolerance screen the transgenic plants were first grown under the normal growth temperature of 22° C.
  • transgenic plants with trait-improving recombinant DNA identified in a cold shock stress tolerance screen and/or a cold germination stress tolerance screen can survive better cold conditions providing a higher yield potential as compared to control plants.
  • PEP SEQ ID NO:172 can be used to enhance both cold chock tolerance and heat stress tolerance in plants.
  • plants transformed with PEP SEQ ID NO: 235 can resist salt and osmotic stress.
  • Plants transformed with PEP SEQ ID NO: 243 can also improve growth in early stage and under heat stress.
  • the stress tolerance conferring genes provided by the present invention may be used in combinations to generate transgenic plants that can resist multiple stress conditions.
  • the present invention provides genes that are useful to produce transgenic plants that have advantages in one or more processes including, but not limited to, germination, seedling vigor, root growth and root morphology under non-stressed conditions.
  • the transgenic plants starting from a more robust seedling are less susceptible to the fungal and bacterial pathogens that attach germinating seeds and seedling.
  • seedlings with advantage in root growth are more resistant to drought stress due to extensive and deeper root architecture. Therefore, it can be recognized by those skilled in the art that genes conferring the growth advantage in early stages to plants can also be used to generate transgenic plants that are more resistant to various stress conditions due to enhanced early plant development.
  • the present invention provides such exemplary recombinant DNA that confer both the stress tolerance and growth advantages to plants, identified as such in Table 3, e.g., PEP SEQ ID NO: 173 which can improve the plant early growth and development, and impart salt tolerance to plants.
  • PEP SEQ ID NO: 173 which can improve the plant early growth and development, and impart salt tolerance to plants.
  • embodiments of transgenic plants with trait-improving recombinant DNA identified in the early plant development screen can grow better under non-stress conditions and/or stress conditions providing a higher yield potential as compared to control plants.
  • “Late growth and development” used herein encompasses the stages of leaf development, flower production, and seed maturity.
  • transgenic plants produced using genes that confer growth advantages to plants provided by the present invention, identified as such in Table 3 exhibit at least one phenotypic characteristics including, but not limited to, increased rosette radius, increased rosette dry weight, seed dry weight, silique dry weight, and silique length.
  • the rosette radius and rosette dry weight are used as the indexes of photosynthesis capacity, and thereby plant source strength and yield potential of a plant.
  • the seed dry weight, silique dry weight and silique length are used as the indexes for plant sink strength, which are considered as the direct determinants of yield.
  • embodiments of transgenic plants with trait-improving recombinant DNA identified in the late development screen can grow better and/or have enhanced development during leaf development and seed maturation providing a higher yield potential as compared to control plants.
  • a plant seeding develops according to a characteristic photomorphogenic pattern, in which plants have open and expanded cotyledons and short hypocotyls. Then the plant's energy is devoted to cotyledon and leaf development while longitudinal extension growth is minimized.
  • a seedling displays a shade-avoidance pattern, in which the seedling displays a reduced cotyledon expansion, and hypocotyls extension is greatly increased.
  • the present invention provides recombinant DNA that enable plants to have an attenuated shade avoidance response so that the source of plant can be contributed to reproductive growth efficiently, resulting higher yield as compared to the wild type plants.
  • embodiments of transgenic plants with trait-improving recombinant DNA identified in a shade stress tolerance screen can have attenuated shade response under shade conditions providing a higher yield potential as compared to control plants.
  • the transgenic plants generated by the present invention can be suitable for a higher density planting, thereby resulting increased yield per unit area.
  • the metabolism, growth and development of plants are profoundly affected by their nitrogen supply. Restricted nitrogen supply alters shoot to root ratio, root development, activity of enzymes of primary metabolism and the rate of senescence (death) of older leaves.
  • All field crops have a fundamental dependence on inorganic nitrogenous fertilizer. Since fertilizer is rapidly depleted from most soil types, it must be supplied to growing crops two or three times during the growing season. Enhanced nitrogen use efficiency by plants should enable crops cultivated under low nitrogen availability stress condition resulted from low fertilizer input or poor soil quality.
  • the transgenic plants provided by the present invention with enhanced nitrogen use efficiency can also have altered amino acid or protein compositions, increased yield and/or better seed quality.
  • the transgenic plants of the present invention can be productively cultivated under low nitrogen growth conditions, e.g., nitrogen-poor soils and low nitrogen fertilizer inputs, which would cause the growth of wild type plants to cease or to be so diminished as to make the wild type plants practically useless.
  • the transgenic plants also can be advantageously used to achieve earlier maturing, faster growing, and/or higher yielding crops and/or produce more nutritious foods and animal feedstocks when cultivated using nitrogen non-limiting growth conditions.
  • the present invention also encompasses transgenic plants with stacked engineered traits, e.g., a crop having an enhanced phenotype resulting from expression of a trait-improving recombinant DNA, 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, for example a RoundUp Ready® trait, 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 resistance is useful in a plant include glyphosate herbicides, phosphinothricin herbicides, oxynil herbicides, imidazolinone herbicides, dinitroaniline herbicides, pyridine herbicides, sulfonylurea herbicides, bialaphos herbicides, sulfonamide herbicides and gluphosinate herbicides.
  • glyphosate herbicides glyphosate herbicides, phosphinothricin herbicides, oxynil herbicides, imidazolinone herbicides, dinitroaniline herbicides, pyridine herbicides, sulfonylurea herbicides, bialaphos herbicides, sulfonamide herbicides and gluphosinate herbicides.
  • the invention provides methods for identifying a homologous gene with a DNA sequence homologous to any of SEQ ID NO: 1 through SEQ ID NO: 139, or a homologous protein with an amino acid sequence homologous to any of SEQ ID NO: 140 through SEQ ID NO: 278.
  • the present invention provides the protein sequences of identified homologs for a sequence listed as SEQ ID NO: 279 through SEQ ID NO: 6023.
  • the present invention also includes linking or associating one or more desired traits, or gene function with a homolog sequence provided herein.
  • the trait-improving recombinant DNA and methods of using such trait-improving recombinant DNA for generating transgenic plants with enhanced traits provided by the present invention are not limited to any particular plant species.
  • the plants according to the present invention can be of any plant species, e.g., can be monocotyledonous or dicotyledonous. In one embodiment, they will be agricultural useful plants, e.g., plants cultivated by man for purposes of food production or technical, particularly industrial applications.
  • Of particular interest in the present invention are corn and soybean plants.
  • the recombinant DNA constructs optimized for soybean transformation and recombinant DNA constructs optimized for corn transformation are provided by the present invention.
  • Other plants of interest in the present invention for production of transgenic plants having enhanced traits include, without limitation, cotton, canola, wheat, sunflower, sorghum, alfalfa, barley, millet, rice, tobacco, fruit and vegetable crops, and turfgrass.
  • the present invention contemplates to use an orthologous gene in generating the transgenic plants with similarly enhanced traits as the transgenic Arabidopsis counterpart.
  • Enhanced physiological properties in transgenic plants of the present invention can be confirmed in responses to stress conditions, for example in assays using imposed stress conditions to detect enhanced responses to drought stress, nitrogen deficiency, cold growing conditions, or alternatively, under naturally present stress conditions, for example under field conditions.
  • Biomass measures can be made on greenhouse or field grown plants and can include such measurements as plant height, stem diameter, root and shoot dry weights, and, for corn plants, ear length and diameter.
  • Trait data on morphological changes can be collected by visual observation during the process of plant regeneration as well as in regenerated plants transferred to soil.
  • Such trait data includes characteristics such as normal plants, bushy plants, taller plants, thicker stalks, narrow leaves, striped leaves, knotted phenotype, chlorosis, albino, anthocyanin production, or altered tassels, ears or roots.
  • Other enhanced traits can be identified by measurements taken under field conditions, such as 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.
  • trait characteristics of harvested grain can be confirmed, 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.
  • hybrid yield in transgenic corn plants expressing genes of the present invention it can be desirable to test hybrids over multiple years at multiple locations in a geographical location where maize is conventionally grown, e.g., in Iowa, Illinois or other locations in the midwestern United States, under “normal” field conditions as well as under stress conditions, e.g., under drought or population density stress.
  • Transgenic plants can be used to provide plant parts according to the invention for regeneration or tissue culture of cells or tissues containing the constructs described herein.
  • Plant parts for these purposes can include leaves, stems, roots, flowers, tissues, epicotyl, meristems, hypocotyls, cotyledons, pollen, ovaries, cells and protoplasts, or any other portion of the plant which can be used to regenerate additional transgenic plants, cells, protoplasts or tissue culture.
  • Seeds of transgenic plants are provided by this invention can be used to propagate more plants containing the trait-improving recombinant DNA constructs of this invention. These descendants are intended to be included in the scope of this invention if they contain a trait-improving recombinant DNA construct of this invention, whether or not these plants are selfed or crossed with different varieties of plants.
  • Transformation vectors were prepared to constitutively transcribe DNA in either sense orientation (for enhanced protein expression) or anti-sense orientation (for endogenous gene suppression) under the control of an enhanced Cauliflower Mosaic Virus 35S promoter (U.S. Pat. No. 5,359,142) directly or indirectly (Moore, e.g., PNAS 95:376-381, 1998; Guyer, e.g., Genetics 149: 633-639, 1998; International patent application NO. PCT/EP98/07577).
  • the transformation vectors also contain a bar gene as a selectable marker for resistance to glufosinate herbicide.
  • This example describes a soil drought tolerance screen to identify Arabidopsis plants transformed with recombinant DNA that wilt less rapidly and/or produce higher seed yield when grown in soil under drought conditions
  • T2 seeds were sown in flats filled with Metro/Mix® 200 (The Scotts® Company, USA).
  • Humidity domes were added to each flat and flats were assigned locations and placed in climate-controlled growth chambers. Plants were grown under a temperature regime of 22° C. at day and 20° C. at night, with a photoperiod of 16 hours and average light intensity of 170 ⁇ mol/m 2 /s. After the first true leaves appeared, humidity domes were removed. The plants were sprayed with glufosinate herbicide and put back in the growth chamber for 3 additional days. Flats were watered for 1 hour the week following the herbicide treatment. Watering was continued every seven days until the flower bud primordia became apparent, at which time plants were watered for the last time.
  • plants were evaluated for wilting response and seed yield. Beginning ten days after the last watering, plants were examined daily until 4 plants/line had wilted. In the next six days, plants were monitored for wilting response. Five drought scores were assigned according to the visual inspection of the phenotypes: 1 for healthy, 2 for dark green, 3 for wilting, 4 severe wilting, and 5 for dead. A score of 3 or higher was considered as wilted.
  • seed yield measured as seed weight per plant under the drought condition was characterized for the transgcnic plants and their controls and analyzed as a quantitative response according to example 1M.
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 160, 161, 184, 239, 240 or 268 showed enhanced drought tolerance by the second criteria as illustrated in Example 1 L.
  • This example sets forth the heat stress tolerance screen to identify Arabidopsis plants transformed with the gene of interest that are more resistant to heat stress based on primarily their seedling weight and root growth under high temperature.
  • T2 seeds were plated on 1 ⁇ 2 ⁇ MS salts, 1/% phytagel, with 10 ⁇ g/ml BASTA (7 per plate with 2 control seeds; 9 seeds total per plate). Plates were placed at 4° C. for 3 days to stratify seeds. Plates were then incubated at room temperature for 3 hours and then held vertically for 11 additional days at temperature of 34° C. at day and 20° C. at night. Photoperiod was 16 h. Average light intensity was ⁇ 140 ⁇ mol/m 2 /s. After 14 days of growth, plants were scored for glufosinate resistance, root length, final growth stage, visual color, and seedling fresh weight. A photograph of the whole plate was taken on day 14.
  • the seedling weight and root length were analyzed as quantitative responses according to example 1M.
  • the final grow stage at day 14 was scored as success if 50% of the plants had reached 3 rosette leaves and size of leaves are greater than 1 mm (Boyer, el al. (2001) The Plant Cell 13, 1499-1510).
  • the growth stage data was analyzed as a qualitative response according to example 1L.
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 179, 222 or 243 showed enhanced heat stress tolerance by the second criteria as illustrated in Example 1 L and 1M.
  • This example sets forth the high salinity stress screen to identify Arabidopsis plants transformed with the gene of interest that are tolerant to high levels of salt based on their rate of development, root growth and chlorophyll accumulation under high salt conditions.
  • T2 seeds were plated on glufosinate selection plates containing 90 mM NaCl and grown under standard light and temperature conditions. All seedlings used in the embodiments were grown at a temperature of 22° C. at day and 20° C. at night, a 16-hour photoperiod, an average light intensity of approximately 120 umol/m 2 . On day 11, plants were measured for primary root length. After 3 more days of growth (day 14), plants were scored for transgenic status, primary root length, growth stage, visual color, and the seedlings were pooled for fresh weight measurement. A photograph of the whole plate was also taken on day 14.
  • the seedling weight and root length were analyzed as quantitative responses according to example 1M.
  • the final growth stage at day 14 was scored as success if 50% of the plants reached 3 rosette leaves and size of leaves are greater than 1 mm (Boyes, D. C., et al., (2001), The Plant Cell 13, 1499/1510).
  • the growth stage data was analyzed as a qualitative response according to example 1 L.
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 143, 144, 146, 150, 163, 165, 166, 174, 183, 199, 235, 264 or 273 showed enhanced salt stress tolerance by the second criteria as illustrated in Example 1L and 1M.
  • T2 seeds were plated on BASTA selection plates containing 3% PEG and grown under standard light and temperature conditions. Seeds were plated on each plate containing 3% PEG, 1 ⁇ 2 ⁇ MS salts, 1% phytagel, and 10 ⁇ g/ml glufosinatc. Plates were placed at 4° C. for 3 days to stratify seeds. On day 11, plants were measured for primary root length. After 3 more days of growth, i.e., at day 14, plants were scored for transgenic status, primary root length, growth stage, visual color, and the seedlings were pooled for fresh weight measurement. A photograph of the whole plate was taken on day 14.
  • Seedling weight and root length were analyzed as quantitative responses according to example 1M.
  • the final growth stage at day 14 was scored as success or failure based on whether the plants reached 3 rosette leaves and size of leaves are greater than 1 mm.
  • the growth stage data was analyzed as a qualitative response according to example 1 L.
  • Table 7 A list of recombinant DNA constructs that improve osmotic stress tolerance in transgenic plants illustrated in Table 7.
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 147, 157, 198, 202, 207, 211, 252, 253, 266 or 272 showed enhanced PEG osmotic stress tolerance by the second criteria as illustrated in Example 1L and 1M.
  • This example set forth a screen to identify Arabidopsis plants transformed with the genes of interest that are more tolerant to cold stress subjected during day 8 to day 28 after seed planting. During these crucial early stages, seedling growth and leaf area increase were measured to assess tolerance when Arabidopsis seedlings were exposed to low temperatures. Using this screen, genetic alterations can be found that enable plants to germinate and grow better than wild type plants under sudden exposure to low temperatures.
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in PEP SEQ ID NO. 265 or 270 showed enhanced cold stress tolerance by the second criterial as illustrated in Example 1L and 1M.
  • This example sets forth a screen to identify Arabidopsis plants transformed with the genes of interests are resistant to cold stress based on their rate of development, root growth and chlorophyll accumulation under low temperature conditions.
  • T2 seeds were plated and all seedlings used in the embodiments were grown at 8° C. Seeds were first surface disinfested using chlorine gas and then seeded on assay plates containing an aqueous solution of 1 ⁇ 2 ⁇ Gamborg's B/5 Basal Salt Mixture (Sigma/Aldrich Corp., St. Louis, Mo., USA G/5788), 1% PhytagelTM (Sigma-Aldrich, P-8169), and 10 ug/ml glufosinate with the final pH adjusted to 5.8 using KOH. Test plates were held vertically for 28 days at a constant temperature of 8° C., a photoperiod of 16 hr, and average light intensity of approximately 100 umol/m 2 /s. At 28 days post plating, root length was measured, growth stage was observed, the visual color was assessed, and a whole plate photograph was taken.
  • 1 ⁇ 2 ⁇ Gamborg's B/5 Basal Salt Mixture Sigma/Aldrich Corp., St. Louis, Mo., USA
  • the root length at day 28 was analyzed as a quantitative response according to example 1M.
  • the growth stage at day 7 was analyzed as a qualitative response according to example 1L.
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 173, 204, 207, 208, 209, 213, 228 or 251 showed enhanced cold stress tolerance by the second criterial as illustrated in Example 1L and 1M.
  • This protocol describes a screen to look for Arabidopsis plants that show an attenuated shade avoidance response and/or grow better than control plants under low light intensity. Of particular interest, we were looking for plants that didn't extend their petiole length, had an increase in seedling weight relative to the reference and had leaves that were more close to parallel with the plate surface.
  • T2 seeds were plated on glufosinate selection plates with 1 ⁇ 2 MS medium. Seeds were sown on 1 ⁇ 2 ⁇ MS salts, 1% Phytagel, 10 ug/ml BASTA. Plants were grown on vertical plates at a temperature of 22° C. at day, 20° C. at night and under low light (approximately 30 uE/m 2 /s, far/red ratio (655/665/725/735) ⁇ 0.35 using PLAQ lights with GAM color filter #680). Twenty-three days after seedlings were sown, measurements were recorded including seedling status, number of rosette leaves, status of flower bud, petiole leaf angle, petiole length, and pooled fresh weights. A digital image of the whole plate was taken on the measurement day. Seedling weight and petiole length were analyzed as quantitative responses according to example 1M. The number of rosette leaves, flowering bud formation and leaf angel were analyzed as qualitative responses according to example 1L.
  • seeding weight if p ⁇ 0.05 and delta or risk score mean>0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p ⁇ 0.2 and delta or risk score mean>0, the transgenic plants showed a trend of trait enhancement as compared to the reference with p ⁇ 0.2.
  • transgenic plants For “petiole length”, if p ⁇ 0.05 and delta ⁇ 0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p ⁇ 0.2 and delta ⁇ 0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 160, 184, 197, 225, 233, 234, 236, 237, 241, 242, 255, 258, 259, 260, 263, 267 or 276 showed enhanced tolerance to shade or low light condition by the second criterial as illustrated in Example 1L and 1M.
  • This example sets forth a plate based phenotypic analysis platform for the rapid detection of phenotypes that are evident during the first two weeks of growth.
  • the transgenic plants with advantages in seedling growth and development were determined by the seedling weight and root length at day 14 after seed planting.
  • T2 seeds were plated on glufosinate selection plates and grown under standard conditions ( ⁇ 100 uE/m 2 /s, 16 h photoperiod, 22° C. at day, 20° C. at night). Seeds were stratified for 3 days at 4° C. Seedlings were grown vertically (at a temperature of 22° C. at day 20° C. at night). Observations were taken on day 10 and day 14. Both seedling weight and root length at day 14 were analyzed as quantitative responses according to example 1M.
  • Transgenic plants comprising recombinant DNA expressing a protein as set forth in SEQ ID NO: 149, 155, 165, 173, 174, 186, 218 or 243 showed enhanced tolerance to shade or low light condition by the second criterial as illustrated in Example 1L and 1M.
  • This example sets forth a soil based phenotypic platform to identify genes that confer advantages in the processes of leaf development, flowering production and seed maturity to plants.
  • Arabidopsis plants were grown on a commercial potting mixture (Metro Mix 360, Scotts Co., Marysville, Ohio) consisting of 30-40% medium grade horticultural vermiculite, 35-55% sphagnum peat moss, 10-20% processed bark ash, 1-15% pine bark and a starter nutrient charge. Soil was supplemented with Osmocote time-release fertilizer at a rate of 30 mg/ft 3 . T2 seeds were imbibed in 1% agarose solution for 3 days at 4° C. and then sown at a density of ⁇ 5 per 21 ⁇ 2′′ pot. Thirty-two pots were ordered in a 4 by 8 grid in standard greenhouse flat.
  • Plants were grown in environmentally controlled rooms under a 16 h day length with an average light intensity of ⁇ 200 ⁇ moles/m 2 /s. Day and night temperature set points were 22° C. and 20° C., respectively. Humidity was maintained at 65%. Plants were watered by sub-irrigation every two days on average until mid-flowering, at which point the plants were watered daily until flowering was complete.
  • glufosinate was performed to select T2 individuals containing the target transgene. A single application of glufosinate was applied when the first true leaves were visible. Each pot was thinned to leave a single glufosinate-resistant seedling ⁇ 3 days after the selection was applied.
  • the rosette radius was measured at day 25.
  • the silique length was measured at day 40.
  • the plant parts were harvested at day 49 for dry weight measurements if flowering production was stopped. Otherwise, the dry weights of rosette and silique were carried out at day 53.
  • the seeds were harvested at day 58. All measurements were analyzed as quantitative responses according to example 1M.
  • transgenic plants showed statistically significant trait enhancement as compared to the reference. If p ⁇ 0.2 and delta or risk score mean>0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 245 showed enhanced tolerance to shade or low light condition by the second criterial as illustrated in Example 1L and 1M.
  • Arabidopsis seedlings become chlorotic and have less biomass.
  • This example sets forth the limited nitrogen tolerance screen to identify Arabidopsis plants transformed with the gene of interest that are altered in their ability to accumulate biomass and/or retain chlorophyll under low nitrogen condition.
  • T2 seeds were plated on glufosinate selection plates containing 0.5 ⁇ N-Free Hoagland's T 0.1 mM NH 4 NO 3 T 0.1% sucrose T 1% phytagel media and grown under standard light and temperature conditions. At 12 days of growth, plants were scored for seedling status (i.e., viable or non-viable) and root length. After 21 days of growth, plants were scored for BASTA resistance, visual color, seedling weight, number of green leaves, number of rosette leaves, root length and formation of flowering buds. A photograph of each plant was also taken at this time point.
  • the seedling weight and root length were analyzed as quantitative responses according to example 1M.
  • the number green leaves, the number of rosette leaves and the flowerbud formation were analyzed as qualitative responses according to example 1 L.
  • the leaf color raw data were collected on each plant as the percentages of five color elements (Green, DarkGreen, LightGreen, RedPurple, YellowChlorotic) using a computer imaging system.
  • a statistical logistic regression model was developed to predict an overall value based on five colors for each plant.
  • the transgenic plants For rosette weight, if p ⁇ 0.05 and delta or risk score mean>0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p ⁇ 0.2 and delta or risk score mean>0, the transgenic plants showed a trend of trait enhancement as compared to the reference with p ⁇ 0.2. For root length, if p ⁇ 0.05, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p ⁇ 0.2, the transgenic plants showed a trend of trait enhancement as compared to the reference.
  • Transgenic plants comprising recombinant DNA expressing a protein as set forth in SED ID NO: 151, 152, 188, 195, 206, 254, 256, 261, 264, or 274 showed enhanced tolerance to shade or low light condition by the second criterial as illustrated in Example 1L and 1M.
  • the risk scores from multiple events of the transgene of interest were evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS institute Inc., Cary, N.C., USA).
  • SAS 9 SAS/STAT User's Guide, SAS institute Inc., Cary, N.C., USA.
  • RS with a value greater than 0 indicates that the transgenic plants perform better than the reference.
  • RS with a value less than 0 indicates that the transgenic plants perform worse than the reference.
  • the RS with a value equal to 0 indicates that the performance of the transgenic plants and the reference don't show any difference. If p ⁇ 0.05 and risk score mean>0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p ⁇ 0.2 and risk score mean>0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
  • the RS from each event was evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA).
  • SAS 9 SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA.
  • the RS with a value greater than 0 indicates that the transgenic plants from this event performs better than the reference.
  • the RS with a value less than 0 indicates that the transgenic plants from this event perform worse than the reference.
  • the RS with a value equal to 0 indicates that the performance of the transgenic plants from this event and the reference don't show any difference.
  • p ⁇ 0.05 and risk score mean>0 the transgenic plants from this event showed statistically significant trait enhancement as compared to the reference.
  • p ⁇ 0.2 and risk score mean>0 the transgenic plants showed a trend of trait enhancement as compared to the reference. If two or more events of the transgene of interest showed improvement in the same response, the transgene was deemed
  • the measurements (M) of each plant were transformed by log, calculation.
  • the Delta was calculated as log 2 M(transgenic) ⁇ log 2M(reference).
  • Two criteria were used to determine trait enhancement. A transgene of interest could show trait enhancement according to either or both of the two criteria.
  • the measurements (M) of each plant were transformed by log 2 calculation.
  • the Delta was calculated as log 2M(transgenic) ⁇ log 2M(reference). If the measured response was Petiole Length for the Low Light assay, Delta was subsequently multiplied by ⁇ 1, to account for the fact that a shorter petiole length is considered an indication of trait enhancement.
  • the Deltas from multiple events of the transgene of interest were evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA).
  • Delta with a value greater than 0 indicates that the transgenic plants perform better than the reference.
  • Delta with a value less than 0 indicates that the transgenic plants perform worse than the reference.
  • the Delta with a value equal to 0 indicates that the performance of the transgenic plants and the reference don't show any difference. If p ⁇ 0.05 and risk score mean>0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p ⁇ 0.2 and risk score mean>0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
  • the delta from each event was evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc., Cary, N.C., USA).
  • SAS 9 SAS/STAT User's Guide, SAS Institute Inc., Cary, N.C., USA.
  • the Delta with a value greater than 0 indicates that the transgenic plants from this event performs better than the reference.
  • the Delta with a value less than 0 indicates that the transgenic plants from this event perform worse than the reference.
  • the Delta with a value equal to 0 indicates that the performance of the transgenic plants from this event and the reference don't show any difference.
  • p ⁇ 0.05 and delta mean>0 the transgenic plants from this event showed statistically significant trait improvement as compared to the reference.
  • p ⁇ 0.2 and delta mean>0 the transgenic plants showed a trend of trait enhancement as compared to the reference. If two or more events of the transgene of interest showed enhancement in the same response, the transgene was deemed to show trait improvement
  • a BLAST searchable “All Protein Database” is 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 DNA sequence provided herein was obtained, an “Organism Protein Database” is constructed of known protein sequences of the organism; the Organism Protein Database 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 is queried using amino acid sequence of protein for gene DNA used in trait-improving recombinant DNA, e.g., sequences of SEQ ID NO: 140 through SEQ ID NO: 278 using “blastp” with E-value cutoff of 1e ⁇ 8 .
  • Up to 1000 top hits were kept, and separated by organism names.
  • a list is 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, 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 is queried using amino acid sequences of SEQ ID NO: 140 through SEQ ID NO: 278 using “blastp” with E-value cutoff of 1e ⁇ 4 . Up to 1000 top hits are kept. A BLAST searchable database is constructed based on these hits, and is referred to as “SubDB”. SubDB was queried with each sequence in the Hit List using “blastp” with E-value cutoff of 1e ⁇ 8 . The hit with the best E-value is 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.
  • ClustalW program is selected for multiple sequence alignments of an amino acid sequence of SEQ ID NO: 140 and its homologs, through SEQ ID NO: 278 and its homologs.
  • Three major factors affecting the sequence alignments dramatically are (1) protein weight matrices; (2) gap open penalty; (3) gap extension penalty.
  • Protein weight matrices available for ClustalW program include Blosum, Pam and Gonnet series. Those parameters with gap open penalty and gap extension penalty were extensively tested. On the basis of the test results, Blosum weight matrix, gap open penalty of 10 and gap extension penalty of 1 were chosen for multiple sequence alignment.
  • the consensus sequence of SEQ ID NO: 237 and its 9 homologs were derived according to the procedure described above and is displayed in FIGS. 4( a ) and 4 ( b ).
  • FIG. 4( b ) is a continuation of FIG. 4( a ).
  • SEQ ID NO: 6033 is the consensus sequence built.
  • This example illustrates the identification of domain and domain module by Pfam analysis.
  • 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 domain modules and individual protein domain for the proteins of SEQ ID NO: 140 through 278 are shown in Table 17 and Table 18 respectively.
  • 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 corresponding 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.
  • the protein with amino acids of SEQ ID NO: 180 is characterized by two Pfam domains, e.g. “Homeobox” and “HALZ”. See also the protein with amino acids of to SEQ ID NO: 248 which is characterized by two copies of the Pfam domain “Ank”.
  • SEQ ID NO: 248 which is characterized by two copies of the Pfam domain “Ank”.
  • Score is the gathering score for the Hidden Markov Model of the domain which exceeds the gathering cutoff reported in Table 19.
  • This example illustrates the construction of plasmids for transferring recombinant DNA into the nucleus of a plant cell which can be regenerated into a transgenic crop plant of this invention.
  • Primers for PCR amplification of protein coding nucleotides of recombinant DNA 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.
  • DNA of interest e.g., each DNA identified in Table 2 and the DNA for the identified homologous genes, are cloned and amplified by PCR prior to insertion into the insertion site the base vector.
  • OR-Ec.oriV-RK2 The vegetative origin of 6696-7092 in E. coli replication from plasmid RK2.
  • OR-Ec.ori-ColE1 The minimal origin of 9220-9808 replication from the E. coli plasmid ColE1.
  • Plasmids for use in transformation of soybean are also prepared. Elements of an exemplary common expression vector plasmid pMON82053 are shown in Table 21 below.
  • This exemplary soybean transformation base vector illustrated in FIG. 2 is assembled using the technology known in the art. DNA of interest, e.g., each DNA identified in Table 2 and the DNA for the identified homologous genes, is cloned and amplified by PCR prior to insertion into the insertion site the base vector at the insertion site between the enhanced 35S CaMV promoter and the termination sequence of cotton E6 gene.
  • T-AGRtu.nos A 3′ non-translated region of the 9466-9718 nopaline synthase gene of Agrobacterium tumefaciens Ti plasmid which functions to direct polyadenylation of the mRNA.
  • Gene of interest P-CaMV.35S-enh Promoter for 35S RNA from CaMV 1-613 expression containing a duplication of the ⁇ 90 to cassette ⁇ 350 region.
  • T-Gb.E6-3b 3′ untranslated region from the fiber 688-1002 protein E6 gene of sea-island cotton; Agrobaterium B-AGRtu.right Agro right border sequence, essential for 1033-1389 T-DNA transfer border transfer of T-DNA.
  • OR-Ec.oriV-RK2 The vegetative origin of replication from 5661-6057 E. coli plasmid RK2.
  • OR-Ec.ori-ColE1 The minimal origin of replication from 2945-3533 the E. coli plasmid ColE1.
  • Plasmids for use in transformation of cotton are also prepared. Elements of an exemplary common expression vector plasmid pMON99053 are shown in Table 22 below and FIG. 3 . Primers for PCR amplification of protein coding nucleotides of recombinant DNA 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. Each recombinant DNA coding for a protein identified in Table 2 is amplified by PCR prior to insertion into the insertion site within the gene of interest expression cassette of one of the base.
  • OR-Ec.oriV-RK2 The vegetative origin of 3837-4233 E. coli replication from plasmid RK2.
  • OR-Ec.ori-Co1E1 The minimal origin of replication 6361-6949 from the E. coli plasmid ColE1.
  • transgenic corn cells are prepared with recombinant DNA expressing each of the protein encoding DNAs listed in Table 2 by Agrobacterium -mediated transformation using the corn transformation constructs as disclosed in Example 5.
  • Corn transformation is effected using methods disclosed in U.S. Patent Application Publication 2004/0344075 A1 where corn embryos are inoculated and co-cultured with the Agrobacterium tumefaciens strain ABI and the corn transformation vector.
  • To regenerate transgenic corn plants the transgenic callus 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 followed by a mist bench before transplanting to pots where plants are grown to maturity.
  • the plants are self fertilized and seed is harvested for screening as seed, seedlings or progeny R2 plants or hybrids, e.g., for yield trials in the screens indicated above.
  • transgenic plants and seeds having the transgenic cells of this invention which have recombinant DNA imparting the enhanced agronomic traits are identified by screening for nitrogen use efficiency, yield, water use efficiency, cold tolerance and enhanced seed composition.
  • transgenic soybean cells are prepared with recombinant DNA expressing each of the protein encoding DNAs listed in Table 1 by Agrobacterium -mediated transformation using the soybean transformation constructs disclosed in Example 5. Soybean transformation is effected using methods disclosed in U.S. Pat. No. 6,384,301 where soybean meristem explants are wounded then inoculated and co-cultured with the soybean transformation vector, then transferred to selection media for 6-8 weeks to allow selection and growth of transgenic shoots.
  • an enhanced agronomic trait e.g., enhanced nitrogen use efficiency, increased yield, enhanced water use efficiency, enhanced tolerance to cold and/or enhanced seed compositions as compared to control plants.
  • Transgenic shoots producing roots are transferred to the greenhouse and potted in soil. Many transgenic events which survive to fertile transgenic plants that produce seeds and progeny plants do not exhibit an enhanced agronomic trait.
  • the transgenic plants and seeds having the transgenic cells of this invention which have recombinant DNA imparting the enhanced agronomic traits are identified by screening for nitrogen use efficiency, yield, water use efficiency, cold tolerance and enhanced seed composition.
  • This example illustrates identification of nuclei of the invention by screening derived plants and seeds for an enhanced trait identified below.
  • transgenic seed and plants prepared in Examples 6 and 7 are screened to identify those transgenic events providing transgenic plant cells with a nucleus having recombinant DNA imparting an enhanced trait.
  • Each population is screened for enhanced nitrogen use efficiency, increased yield, enhanced water use efficiency, enhanced tolerance to cold and heat, increased level of oil and protein in seed using assays described below.
  • Plant cell nuclei having recombinant DNA with each of the genes identified in Table 2 and the identified homologs are identified in plants and seeds with at least one of the enhanced traits.
  • Transgenic corn plants with nuclei of the invention are planted in fields with three levels of nitrogen (N) fertilizer being applied, i.e. low level (0 pounds per acre N), medium level (80 pounds per acre N) and high level (180 pounds per acre N). 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 in the low level treatment, the soil should still be disturbed in the same fashion as the treated area.
  • Transgenic plants and control plants can be grouped by genotype and construct with controls arranged randomly within genotype blocks. For improved statistical analysis each type of transgenic plant can be tested by 3 replications and across 4 locations.
  • Nitrogen levels in the fields are analyzed before planting by collecting 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 corn plants prepared in Example 6 and which exhibit a 2 to 5% yield increase as compared to control plants when grown in the high nitrogen field are selected as having nuclei of the invention.
  • Transgenic corn plants which have at least the same or higher yield as compared to control plants when grown in the medium nitrogen field are selected as having nuclei of the invention.
  • Transgenic corn plants having a nucleus with DNA identified in Table 3 as imparting nitrogen use efficiency (LN) and homologous DNA are selected from a nitrogen use efficiency screen as having a nucleus of this invention.
  • transgenic plants of this invention exhibit increased yield as compared to a control plant.
  • Increased yield can result from enhanced seed sink potential, e.g., the number and size of endosperm cells or kernels and/or enhanced sink strength, e.g., 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 increased 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 can be applied in multiple and diverse geographic locations, for example up to 16 or more locations, over one or more planting seasons, for example at least two planting seasons to statistically distinguish yield improvement from natural environmental effects.
  • Each of the transgenic corn plants and soybean plants with a nucleus of the invention prepared in Examples 6 and 7 are screened for yield enhancement. At least one event from each of the corn plants is selected as having at least between 3 and 5% increase in yield as compared to a control plant as having a nucleus of this invention.
  • the following is a high-throughput method for screening for water use efficiency in a greenhouse to identify the transgenic corn plants with a nucleus of this invention.
  • 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 5th 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 heights 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 corn plants and soybean plants prepared in Examples 6 and 7 are screened for water use efficiency.
  • Transgenic plants having at least a 1% increase in RGR and RWC as compared to control plants are identified as having enhanced water used efficiency and are selected as having a nucleus of this invention.
  • Transgenic corn and soybean plants having in their nucleus DNA identified in Table 3 as imparting drought tolerance enhancement (DS, HS, SS, and PEG) and homologous DNA are identified as showing increased water use efficiency as compared to control plants and are selected as having a nucleus of this invention.
  • Cold germination assay Three sets of seeds are used for the assay.
  • the first set consists of positive transgenic events (F1 hybrid) where the genes of the present invention are expressed in the seed.
  • the second seed set is nontransgenic, wild-type negative control made from the same genotype as the transgenic events.
  • the third set consisted of two cold tolerant and one cold sensitive commercial check lines of corn. All seeds are treated with a fungicide “Captan” (MAESTRO® 80 DF Fungicide, Arvesta Corporation, San Francisco, Calif., USA). 0.43 mL Captan is applied per 45 g of corn seeds by mixing it well and drying the fungicide prior to the demonstation.
  • Captan MAESTRO® 80 DF Fungicide
  • 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 PGV36, Controlled Environments, Winnipeg, Canada). Two hundred and fifty millilters of deionized water are added to each germination tray.
  • Convrion® growth chamber Convrion® growth chamber
  • Germination counts are taken 10th, 11th, 12th, 13th, 14th, 17th, 19th, 21st, and 24th day after start date of the demonstration. Seeds are considered germinated if the emerged radicle size is 1 cm. From the germination counts germination index is calculated.
  • the germination index is calculated as per:
  • Germination index ( ⁇ ([T+1 ⁇ n i ]*[P i ⁇ P i-1 ]))/T where T is the total number of days for which the germination assay is performed. The number of days after planting is defined by n. 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.
  • Transgenic corn plants and soybean plants prepared in Examples 6 and 7 are screened for water use efficiency.
  • Transgenic plants having at least a 5% increase in germination index as compared to control plants are identified as having enhanced cold stress tolerance and are selected as having a nucleus of this invention.
  • Transgenic corn and soybean plants having in their nucleus DNA identified in Table 3 as imparting cold tolerance enhancement (CK or CS) and homologous DNA are identified as showing increased cold stress tolerance as compared to control plants and are selected as having a nucleus of this invention.
  • the following is a high-throughput selection method 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 analyzer 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. Calculations are performed 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 com and soybean seeds
  • Analytical time to run Less than 0.75 min per sample method Total elapsed time per 1.5 minute per sample run: Typical and minimum Com typical: 50 cc; minimum 30 cc sample size: Soybean typical: 50 cc; minimum 5 cc
  • Typical analytical range Determined in part by the specific calibration. Com—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%.
  • Transgenic corn plants and soybean plants prepared in Examples 6 and 7 are screened for increased protein and oil in seed.
  • Transgenic inbred corn and soybean plants having an increase of at least 1 percentage point in the total percent seed protein or at least 0.3 percentage point in total seed oil and transgenic hybrid corn plants having an increase of at least 0.4 percentage point in the total percent seed protein as compared to control plants are identified as having enhanced seed protein or enhanced seed oil and are selected as having a nucleus of this invention.
  • Transgenic cotton plants containing each of the recombinant DNA having a sequence of SEQ ID NO: 1 through SEQ ID NO: 139 are obtained by transforming with recombinant DNA from each of the genes identified in Table 1.
  • Progeny transgenic plants are selected from a population of transgenic cotton events under specified growing conditions and are compared with control cotton plants.
  • Control cotton plants are substantially the same cotton genotype but without the recombinant DNA, for example, either a parental cotton plant of the same genotype that was not transformed with the identical recombinant DNA or a negative isoline of the transformed plant.
  • a commercial cotton cultivar adapted to the geographical region and cultivation conditions i.e. cotton variety ST474, cotton variety FM 958, and cotton variety Siokra L-23, are used to compare the relative performance of the transgenic cotton plants containing the recombinant DNA.
  • the specified culture conditions are growing a first set of transgenic and control plants under “wet” conditions, e.g., irrigated in the range of 85 to 100 percent of evapotranspiration to provide leaf water potential of ⁇ 14 to ⁇ 18 bars, and growing a second set of transgenic and control plants under “dry” conditions, e.g., irrigated in the range of 40 to 60 percent of evapotranspiration to provide a leaf water potential of ⁇ 21 to ⁇ 25 bars.
  • Pest control such as weed and insect control is applied equally to both wet and dry treatments as needed.
  • Data gathered during the trial includes weather records throughout the growing season including detailed records of rainfall; soil characterization information; any herbicide or insecticide applications; any gross agronomic differences observed such as leaf morphology, branching habit, leaf color, time to flowering, and fruiting pattern; plant height at various points during the trial; stand density; node and fruit number including node above white flower and node above crack boll measurements; and visual wilt scoring.
  • Cotton boll samples are taken and analyzed for lint fraction and fiber quality. The cotton is harvested at the normal harvest timeframe for the trial area. Enhanced water use efficiency is indicated by increased yield, improved relative water content, enhanced leaf water potential, increased biomass, enhanced leaf extension rates, and improved fiber parameters.
  • transgenic cotton plants of this invention are identified from among the transgenic cotton plants by agronomic trait screening as having increased yield and enhanced water use efficiency.
  • This example illustrates plant transformation useful in producing the transgenic canola plants of this invention and the production and identification of transgenic seed for transgenic canola having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • Tissues from in vitro grown canola seedlings are prepared and inoculated with a suspension of overnight grown Agrobacterium containing plasmid DNA with the gene of interest cassette and a plant selectable marker cassette. Following co-cultivation with Agrobacterium , the infected tissues are allowed to grow on selection to promote growth of transgenic shoots, followed by growth of roots from the transgenic shoots. The selected plantlets are then transferred to the greenhouse and potted in soil. Molecular characterizations are performed to confirm the presence of the gene of interest, and its expression in transgenic plants and progenies. Progeny transgenic plants are selected from a population of transgenic canola events under specified growing conditions and are compared with control canola plants.
  • Control canola plants are substantially the same canola genotype but without the recombinant DNA, for example, either a parental canola plant of the same genotype that is not transformed with the identical recombinant DNA or a negative isoline of the transformed plant
  • Transgenic canola plant cells are transformed with recombinant DNA from each of the genes identified in Table 2.
  • Transgenic progeny plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • This example illustrates monocot and dicot plant transformation to produce nuclei of this invention in cells of a transgenic plant by transformation where the recombinant DNA suppresses the expression of an endogenous protein identified in Table 24.
  • Corn, soybean, cotton, or canola tissue are transformed as describe in Examples 6, 7, 9 or 10 using recombinant DNA in the nucleus with DNA that transcribes to RNA that forms double-stranded RNA targeted to an endogenous gene with DNA encoding the protein.
  • the genes for which the double-stranded RNAs are targeted are the native gene in corn and soybean that are homolog of the genes encoding the protein of Arabidopsis thaliana as identified in table 24.

Abstract

The present invention discloses transgenic seeds for crops with enhanced agronomic traits are provided by trait-improving recombinant DNA in the nucleus of cells of the seed where plants grown from such transgenic seed exhibit one or more enhanced traits as compared to a control plant. Of particular interest are transgenic plants that have increased yield. The present invention also provides recombinant DNA molecules for expression of a protein, and recombinant DNA molecules for suppression of a protein.

Description

    CROSS REFERENCE TO RELATED APPLICATIONS
  • This application is a continuation of U.S. application Ser. No. 13/140,920, filed Jun. 21, 2011, which is a national stage application under 35 U.S.C. §371 of PCT/US2009/068351, filed Dec. 17, 2009, and published as WO 2010/075143 on Jul. 1, 2010, which claims the benefit of U.S. provisional application Ser. No. 61/203,529, filed Dec. 22, 2008, which applications and publication are incorporated by reference as if reproduced herein and made a part hereof in their entirety, and the benefit of priority of each of which is claimed herein, along with sequence listings and computer program listings.
    • INCORPORATION OF SEQUENCE LISTING
  • Two copies of the sequence listing (Copy #1 and Copy #2) and a computer readable form (CRF) copy of the sequence listing, all on CD-Rs, each containing the text file name “31 26.024US2.TXT”, which is 17,264,640 bytes (measured in MS-WINDOWS) created on Mar. 26, 2014, are incorporated herein by reference.
    • FIELD OF THE INVENTION
  • Disclosed herein are transgenic plant cells, plants and seeds comprising recombinant DNA and methods of making and using such plant cells, plants and seeds.
    • SUMMARY OF THE INVENTION
  • This invention provides plant cell nuclei with recombinant DNA that imparts enhanced agronomic traits in transgenic plants having the nuclei in their cells, e.g. enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced shade tolerance, enhanced high salinity tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein or enhanced seed oil. In certain cases the trait is imparted by producing in the cells a protein that is encoded by recombinant DNA and/or in other cases the trait is imparted by suppressing the production of a protein that is natively produced in the cells.
  • Such recombinant DNA in a plant cell nucleus of this invention is provided in as a construct comprising a promoter that is functional in plant cells and that is operably linked to DNA that encodes a protein or to DNA that results in gene suppression. Such DNA in the construct is sometimes defined by protein domains of an encoded protein targeted for production or suppression, e.g. a “Pfam domain module” (as defined herein below) from the group of Pfam domain modules identified in Table 17. Alternatively, e.g. where a Pfam domain module is not available, such DNA in the construct is defined a consensus amino acid sequence of an encoded protein that is targeted for production or suppression, e.g. a protein having amino acid sequence with at least 90%, with at least 95%, with at least 98%, and with at least 99%, or 99.5% identity to a consensus amino acid sequence in the group of SEQ ID NO: 6027 through SEQ ID NO: 6034, or their corresponding nucleic acid sequences.
  • Other aspects of the invention are directed to specific derivative physical forms of the transgenic plant cell nuclei, e.g. where such a transgenic nucleus is present in a transgenic plant cell, a transgenic plant including plant part(s) such as progeny transgenic seed, and a haploid reproductive derivative of plant cell such as transgenic pollen and transgenic ovule. Such plant cell nuclei and derivatives are advantageously selected from a population of transgenic plants regenerated from plant cells having a nucleus that is transformed with recombinant DNA by screening the transgenic plants or progeny seeds in the population for an enhanced trait as compared to control plants or seed that do not have the recombinant DNA in their nuclei, where the enhanced trait is enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced shade tolerance, enhanced high salinity tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein or enhanced seed oil.
  • One aspect of the present invention includes a plant cell nucleus with stably integrated, recombinant DNA, wherein said recombinant DNA comprises a promoter that is functional in said plant cell and that is operably linked to a protein coding DNA encoding a protein having an amino acid sequence comprising a Pfam domain module selected from the group consisting of WRKY::WRKY, AP2, AUX_IAA, WRKY, WRKY, HLH, Myb_DNA-binding::Linker_histone, zf-B_box::zf-B_box, Ank::Ank::Ank::Chromo, NAM, zf-C2H2, Myb_DNA-binding, bZIP —1, PHD, Linker_histone::AT_hook::AT_hook::AT_hook::AT_hook, B3::Auxin_resp, HLH, zf-Dof, AT_hook::DUF296, AT_hook::AT_hook::DUF296, NAM, GATA, NAM, Myb_DNA-binding, zf-B_box::CCT, POX::Homeobox, B3::Auxin_resp::AUX_IAA, Myb_DNA-binding::Myb_DNA-binding, Myb_DNA-binding::Myb_DNA-binding, zf-C2H2, zf-C2H2, Myb_DNA-binding::Myb_DNA-binding, Myb_DNA-binding::Myb_DNA-binding, TCP, KNOX1::KNOX2, zf-ZPR1::zf-ZPR1, Myb_DNA-binding::Myb_DNA-binding, DUF630::DUF632, WRKY, Myb_DNA-binding, zf-C2H2, HLH, AP2, AT_hook::DUF296, Ank::Ank::Ank::Ank::Ank, WRKY, zf-C2H2, NAM, AP2, NAM, Myb_DNA-binding::Myb_DNA-binding::Myb_DNA-binding, NAM, HLH, Myb_DNA-binding::Myb_DNA-binding, Myb_DNA-binding, HLH, bZIP—2, bZTP—2, BAH::PHD, HLH, NAM, GATA, SSrecog::Rtt106::HMG_box, DUF573, zf-B_box::CCT, HLH, RWP-RK, AP2::B3, AUX_IAA, SRF-TF, AP2, AP2, HSF_DNA-bind, AP2, SRF-TF::K-box, Myb_DNA-binding, zf-LSD1::zf-LSD1::zf-LSD1, KNOX1::KNOX2::ELK, zf-C3HC4, MFMR::bZIP —1, DUF573, Myb_DNA-binding, HLH, NAM, Myb_DNA-binding::Myb_DNA-binding, SRF-TF::K-box, zf-C3HC4, zf-B_box, WRKY, zf-B_box::CCT, EIN3, HSF_DNA-bind, AUX_IAA, TCP, Myb_DNA-binding::Myb_DNA-binding, AP2, KNOX1::KNOX2::ELK::Homeobox, HSF_DNA-bind, HSF_DNA-bind, AP2::B3, NAM, SBP, AP2, zf-C2H2, SRF-TF::K-box, zf-C2H2, GRAS, AP2, Myb_DNA-binding, AP2, AP2::AP2, HLH, CXC::CXC, AP2, NAM, zf-C3HC4, Myb_DNA-binding::Myb_DNA-binding, GRAS, Homeobox::HALZ, Myb_DNA-binding, NAM, WRKY, zf-C2H2, zf-C2H2, NAM, zf-C2H2, AP2::AP2, zf-C3HC4, RWP-RK::PB1, SRF-TF::K-box, and zf-B_box; said recombinant DNA comprises a promoter that is functional in said plant cell and that is operably linked to a protein coding DNA encoding a protein comprising an amino acid sequence with at least 90% identity to a consensus amino acid sequence selected from the group consisting of SEQ ID NO: 6027 through 6034; or said recombinant DNA suppresses comprises a promoter that is functional in said plant cell and operably linked to DNA that transcribe into RNA that suppresses the level of an endogenous protein wherein said endogenous protein has an amino acid sequence comprising a pfam domain module selected from the group consisting of RWP-RK, AUX_IAA, SRF-TF, zf-C3HC4, Myb_DNA-binding, CCT, PHD, EIN3, and AP2; and wherein said plant cell nucleus is selected by screening a population of transgenic plants that have said recombinant DNA and an enhanced trait as compared to control plants that do not have said recombinant DNA in their nuclei; and wherein said enhanced trait is selected from group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced resistance to salt exposure, enhanced shade tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • In another aspect of the present invention, the plant cell nucleus where said protein coding DNA encodes a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 140 through SEQ ID NO: 6023. In addition, the plant cell nucleus can comprising DNA expressing a protein that provides tolerance from exposure to an herbicide, e.g, glyphosate, dicamba, or glufosinate, applied at levels that are lethal to a wild type of said plant cell.
  • Yet in another aspect of the invention includes a plurality of plant cells or planys with the plant cell nucleus described, and the transgenic plant cell or plant are homozygous for said recombinant DNA. In addition, these plant cells are transgenic seeds from crops such as a corn, soybean, cotton, canola, alfalfa, wheat or rice plant, or transgenic pollen grain comprising a haploid derivative of a plant cell nucleus.
  • One aspect of the present invention includes a method 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 recombinant DNA in a nucleus described, wherein said method for manufacturing said transgenic seed comprising (a) screening a population of plants for said enhanced trait and said recombinant DNA, wherein individual plants in said population can exhibit said trait at a level less than, essentially the same as or greater than the level that said trait is exhibited in control plants which do not contain the recombinant DNA, wherein said enhanced trait is selected from the group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced high salinity tolerance, enhanced shade tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil, (b) selecting from said population one or more plants that exhibit said trait at a level greater than the level that said trait is exhibited in control plants, and (c) collecting seeds from selected plant selected from step b.
  • In another aspect, the method for manufacturing transgenic seed, e.g, corn, soybean, cotton, alfalfa, canola wheat or rice seed, further comprising (a) verifying that said recombinant DNA is stably integrated in said selected plants, and (b) analyzing tissue of said selected plant to determine the expression or suppression of a protein having the function of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO:140-278.
  • Yet another aspect of the present invention includes a method of producing hybrid corn seed comprising (a) acquiring hybrid corn seed from a herbicide tolerant corn plant which also has stably-integrated, recombinant DNA in a nucleus of claim 2; (b) 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; (c) selecting corn plants which are homozygous and hemizygous for said recombinant DNA by treating with an herbicide; (d) collecting seed from herbicide-treated-surviving corn plants and planting said seed to produce further progeny corn plants; (e) repeating steps (c) and (d) at least once to produce an inbred corn line; and (f) crossing said inbred corn line with a second corn line to produce hybrid seed.
  • In one aspect of the invention, the transgenic plant comprise recombinant DNA constructs for expressing proteins are characterized by amino acid sequence that have at least 90% identity over at least 90% of the length of a reference sequence selected from the group consisting of SEQ ID NOs: 140-278 when the amino acid sequence is aligned to the reference sequence.
  • In one aspect of the invention, the transgenic plant comprise recombinant DNA constructs for expressing proteins are characterized by amino acid sequence that have at least 92.5% identity over at least 92.5% of the length of a reference sequence selected from the group consisting of SEQ ID NOs: 140-278 when the amino acid sequence is aligned to the reference sequence.
  • In one aspect of the invention, the transgenic plant comprise recombinant DNA constructs for expressing proteins are characterized by amino acid sequence that have at least 95% identity over at least 95% of the length of a reference sequence selected from the group consisting of SEQ ID NOs: 140-278 when the amino acid sequence is aligned to the reference sequence.
  • In one aspect of the invention, the transgenic plant comprise recombinant DNA constructs for expressing proteins are characterized by amino acid sequence that have at least 97% identity over at least 97% of the length of a reference sequence selected from the group consisting of SEQ ID NOs: 140-278 when the amino acid sequence is aligned to the reference sequence.
  • In one aspect of the invention, the transgenic plant comprise recombinant DNA constructs for expressing proteins are characterized by amino acid sequence that have at least 98% identity over at least 98% of the length of a reference sequence selected from the group consisting of SEQ ID NOs: 140-278 when the amino acid sequence is aligned to the reference sequence.
  • In one aspect of the invention, the transgenic plant comprise recombinant DNA constructs for expressing proteins are characterized by amino acid sequence that have at least 99% identity over at least 99% of the length of a reference sequence selected from the group consisting of SEQ ID NOs: 140-278 when the amino acid sequence is aligned to the reference sequence.
  • In one aspect of the invention, the transgenic plant comprise recombinant DNA constructs for expressing proteins are characterized by amino acid sequence that have at least 99.5% identity over at least 99.5% of the length of a reference sequence selected from the group consisting of SEQ ID NOs: 140-278 when the amino acid sequence is aligned to the reference sequence.
  • In other aspects of the invention the nuclei of plant cells and derivative transgenic cells, plants, seeds, pollen and ovules further include recombinant DNA expressing a protein that provides tolerance from exposure to one or more herbicide applied at levels that are lethal to a wild type plant. Such herbicide tolerance is not only an advantageous trait in such plants but is also useful as a selectable marker in the transformation methods for producing the nuclei and nuclei derivatives of the invention. Such herbicide tolerance includes tolerance to a glyphosate, dicamba, or glufosinate herbicide.
  • Yet other aspects of the invention provide transgenic plant cell nuclei which are homozygous for the recombinant DNA. The transgenic plant cell nuclei of the invention and dervitave cells, plants, seed and haploid reproductive derivatives of the invention are advantageously provided in corn, soybean, cotton, canola, alfalfa, wheat, rice plants, or combinations thereof.
  • 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 in the nucleus of the plant cells. More specifically the method includes, but are not limited to, (a) screening a population of plants for an enhanced trait and 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 and (c) collecting seed from a selected plant. Such method can further include the steps of (a) verifying that the recombinant DNA is stably integrated in said selected plants; and (b) analyzing tissue of a selected plant to determine the production of a protein having the function of a protein encoded by a recombinant DNA with a sequence of one of SEQ ID NO: 1-139; In one aspect of the invention the plants in the population can further include DNA expressing a protein that provides tolerance to exposure to an herbicide applied at levels that are lethal to wild type plant cells and where the selecting is effected by treating the population with the herbicide, e.g. a glyphosate, dicamba, or glufosinate compound. In another aspect of the invention, the plants are selected by identifying plants with the enhanced trait. The methods can be used for manufacturing corn, soybean, cotton, canola, alfalfa, wheat and/or rice seed selected as having one of the enhanced traits described above.
  • Another aspect of the invention provides a method of producing hybrid corn seed including the step of acquiring hybrid corn seed from a herbicide tolerant corn plant which also has a nucleus of this invention with stably-integrated, recombinant DNA. The method can further include the steps of producing corn plants from said hybrid corn seed, where 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/or 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.
    • BRIEF DESCRIPTION OF THE DRAWINGS
  • FIGS. 1, 2 and 3 are pictures illustrating plasmid maps; and
  • FIGS. 4( a) and 4(b) illustrate a consensus amino acid sequence of SEQ ID NO: 237 and their homologs.
    •  DETAILED DESCRIPTION OF THE INVENTION
  • In the attached sequence listing:
  • SEQ ID NO: 1-139 are nucleotide sequences of the coding strand of DNA for “genes” used in the recombinant DNA imparting an enhanced trait in plant cells, i.e. each represents a coding sequence for a protein;
  • SEQ ID NO: 140-278 are amino acid sequences of the protein of the “genes” encoding by nucleotide sequence 1-139;
  • SEQ TD NO: 279-6023 homologs are amino acid sequences of homologous proteins; SEQ ID NO: 6024 is a nucleotide sequence of a plasmid base vector useful for corn transformation;
  • SEQ ID NO: 6025 is a DNA sequence of a plasmid base vector useful for soybean transformation;
  • SEQ ID NO: 6026 is a DNA sequence of a plasmid base vector useful for cotton transformation; and
  • SEQ ID NO: 6027-6034 are consensus sequences.
  • Table 1 lists the protein SEQ ID NOs and their corresponding consensus SEQ ID NOs.
  • TABLE 1
    NUC PEP CONSENSUS
    SEQ ID NO SEQ ID NO GENE ID SEQ ID NO
     4 143 CGPG2053 6027
     21 160 CGPG2704 6028
     23 162 CGPG2735 6029
     50 189 CGPG3347 6030
     52 191 CGPG3449 6031
     95 234 CGPG4537 6032
     98 237 CGPG4632 6033
    139 278 CGPG8726 6034
  • The nuclei of this invention are identified by screening transgenic plants for one or more traits including enhanced drought stress tolerance, enhanced heat stress tolerance, enhanced cold stress tolerance, enhanced high salinity stress tolerance, enhanced low nitrogen availability stress tolerance, enhanced shade stress tolerance, enhanced plant growth and development at the stages of seed imbibition through early vegetative phase, and enhanced plant growth and development at the stages of leaf development, flower production and seed maturity.
  • “Gene” means a chromosomal element for expressing a protein and specifically includes the DNA encoding a protein. In cases where expression of a target protein is desired, the pertinent part of a gene is the DNA encoding the target protein; in cases where suppression of a target is desired, the pertinent part of a gene is that part that is transcribed as mRNA. “Recombinant DNA” means a polynucleotide having a genetically engineered modification introduced through combination of endogenous and/or exogenous elements in a transcription unit. Recombinant DNA can include DNA segments obtained from different sources, or DNA segments obtained from the same source, but which have been manipulated to join DNA segments which do not naturally exist in the joined form.
  • “Trait” means a physiological, morphological, biochemical, or physical characteristic of a plant or particular plant material or cell, or any combinations thereor.
  • A “control plant” is a plant without trait-improving recombinant DNA in its nucleus. A control plant is used to measure and compare trait enhancement in a transgenic plant with such trait-improving recombinant DNA. A suitable control plant can be a non-transgenic plant of the parental line used to generate a transgenic plant herein. Alternatively, a control plant can be a transgenic plant having an empty vector or marker gene, but does not contain the recombinant DNA that produces the trait enhancement. A control plant can also be a negative segregant progeny of hemizygous transgenic plant. In certain demonstrations of trait enhancement, the use of a limited number of control plants can cause a wide variation in the control dataset. To minimize the effect of the variation within the control dataset, a “reference” is used. As use herein a “reference” is a trimmed mean of all data from both transgenic and control plants grown under the same conditions and at the same developmental stage. The trimmed mean is calculated by eliminating a specific percentage, e.g., 20%, of the smallest and largest observation from the data set and then calculating the average of the remaining observation.
  • “Trait enhancement” means a detectable and desirable difference in a characteristic in a transgenic plant relative to a control plant or a reference. In some cases, the trait enhancement can be measured quantitatively. For example, the trait enhancement can entail at least a 2% desirable difference in an observed trait, at least a 5% desirable difference, at least about a 10% desirable difference, at least about a 20% desirable difference, at least about a 30% desirable difference, at least about a 50% desirable difference, at least about a 70% desirable difference, at least about a 80% desirable difference, at least about a 90% desirable difference, at least about a 92.5% desirable difference, at least about a 95% desirable difference, at least about a 98% desirable difference, at least about a 99% desirable difference, at least about a 99.5% desirable difference or at least about a 100% difference, or an even greater desirable difference. In other cases, the trait enhancement is only measured qualitatively. It is known that there can be a natural variation in a trait. Therefore, the trait enhancement observed entails a change of the normal distribution of the trait in the transgenic plant compared with the trait distribution observed in a control plant or a reference, which is evaluated by statistical methods provided herein. Trait enhancement includes, but is not limited to, yield increase, including increased yield under non-stress conditions and increased yield under environmental stress conditions. Stress conditions can 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, high plant density, or any combinations thereof.
  • Many agronomic traits can affect “yield”, 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, juvenile traits, or any combinations thereof. Other traits that can affect yield include, 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. Also of interest is the generation of transgenic plants that demonstrate desirable phenotypic properties that can confer an increase in overall plant yield. Such properties include enhanced plant morphology, plant physiology or improved components of the mature seed harvested from the transgenic plant.
  • “Yield-limiting environment” means the condition under which a plant would have the limitation on yield including environmental stress conditions.
  • “Stress condition” means a condition unfavorable for a plant, which adversely affect plant metabolism, growth and/or development. A plant under the stress condition typically shows reduced germination rate, retarded growth and development, reduced photosynthesis rate, and eventually leading to reduction in yield. Specifically, “water deficit stress” used herein refers to the sub-optimal conditions for water and humidity needed for normal growth of natural plants. Relative water content (RWC) can be used as a physiological measure of plant water deficit. It measures the effect of osmotic adjustment in plant water status, when a plant is under stressed conditions. Conditions which can result in water deficit stress include, but are not limited to, heat, drought, high salinity and PEG induced osmotic stress.
  • “Cold stress” means the exposure of a plant to a temperatures below (two or more degrees Celsius below) those normal for a particular species or particular strain of plant.
  • “Nitrogen nutrient” means any one or any mix of the nitrate salts commonly used as plant nitrogen fertilizer, including, but not limited to, potassium nitrate, calcium nitrate, sodium nitrate, ammonium nitrate. The term ammonium as used herein means any one or any mix of the ammonium salts commonly used as plant nitrogen fertilizer, e.g., ammonium nitrate, ammonium chloride, ammonium sulfate, etc.
  • “Low nitrogen availability stress” means a plant growth condition that does not contain sufficient nitrogen nutrient to maintain a healthy plant growth and/or for a plant to reach its typical yield under a sufficient nitrogen growth condition. For example, a limiting nitrogen condition can refers to a growth condition with 50% or less of the conventional nitrogen inputs. “Sufficient nitrogen growth condition” means a growth condition where the soil or growth medium contains or receives optimal amounts of nitrogen nutrient to sustain a healthy plant growth and/or for a plant to reach its typical yield for a particular plant species or a particular strain. One skilled in the art would recognize what constitute such soil, media and fertilizer inputs for most plant species.
  • “Shade stress” means a growth condition that has limited light availability that triggers the shade avoidance response in plant. Plants are subject to shade stress when localized at lower part of the canopy, or in close proximity of neighboring vegetation. Shade stress can become exacerbated when the planting density exceeds the average prevailing density for a particular plant species.
  • “Increased yield” of a transgenic plant of the present invention is evidenced and measured in a number of ways, including test weight, seed number per plant, seed weight, seed number per unit area (e.g., seeds, or weight of seeds, per acre), bushels per acre, tons per acre, tons per acre, kilo per hectare. For example, maize yield can be measured as production of shelled corn kernels per unit of production area, e.g., in bushels per acre or metric tons per hectare, often reported on a moisture adjusted basis, e.g., at 15.5% moisture. Increased yield can result from enhanced utilization of key biochemical compounds, such as nitrogen, phosphorous and carbohydrate, or from enhanced tolerance to environmental stresses, such as cold, heat, drought, salt, and attack by pests or pathogens. Trait-improving recombinant DNA can also be used to provide transgenic plants having enhanced 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.
  • A “plant promoter” is a promoter capable of initiating transcription in plant cells whether or not its origin is a plant cell. Exemplary plant promoters include, but are not limited to, those that are obtained from plants, plant viruses, and bacteria which include genes expressed in plant cells such Agrobacterium or Rhizobium. 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 which 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 can 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.
  • As used herein, “operably linked” refers to the association of two or more nucleic acid elements in a recombinant DNA construct, e.g. as when a promoter is operably linked with DNA that is transcribed to RNA whether for expressing or suppressing a protein. Recombinant DNA constructs can be designed to express a protein which can be an endogenous protein, an exogenous homologue of an endogenous protein or an exogenous protein with no native homologue. Alternatively, recombinant DNA constructs can be designed to suppress the level of an endogenous protein, e.g. by suppression of the native gene. Such gene suppression can be effectively employed through a native RNA interference (RNAi) mechanism in which recombinant DNA comprises both sense and anti-sense oriented DNA matched to the gene targeted for suppression where the recombinant DNA is transcribed into RNA that can form a double-strand to initiate an RNAi mechanism. Gene suppression can also be effected by recombinant DNA that comprises anti-sense oriented DNA matched to the gene targeted for suppression. Gene suppression can also be effected by recombinant DNA that comprises DNA that is transcribed to a microRNA matched to the gene targeted for suppression. In the examples illustrating the invention recombinant DNA for effecting gene suppression that imparts is identified by the term “antisense”. It will be understood by a person of ordinary skill in the art that any of the ways of effecting gene suppression are contemplated and enabled by a showing of one approach to gene suppression.
  • A “consensus amino acid sequence” means an artificial, amino acid sequence indicating conserved amino acids in the sequence of homologous proteins as determined by statistical analyis of an optimal alignment, e.g. CLUSTALW, of amino acid sequence of homolog proteins. The consensus sequences listed in the sequence listing were created by identifying the most frequent amino acid at each position in a set of aligned protein sequences. When there was 100% identity in an alignment the amino acid is indicated by a capital letter. When the occurance of an amino acid is at least about 70% in an alignemnt, the amino acid is indicated by a lower case letter. When there is no amino acid occurance of at least about 70%, e.g. due to diversity or gaps, the amino acid is inidcated by an “x”. When used to defined embodiments of the invention, a consensus amino acid sequence will be aligned with a query protein amino acid sequence in an optimal alignment, e.g. CLUSTALW. An embodiment of the invention will have identity to the conserved amino acids indicated in the consensus amino acid sequence.
  • As used herein a “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. With reference to homologous genes, homologs include orthologs, e.g. genes expressed in different species that evolved from a common ancestral genes by speciation and encode proteins retain the same function, but do not include paralogs, e.g., genes that are related by duplication but have evolved to encode proteins with different functions. 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. When optimally aligned, homolog proteins have typically at least about 60% identity, in some instances at least about 70%, for example about 80% and even at least about 90% identity over the full length of a protein, such as from SEQ ID No. 140-278, identified as being associated with imparting an enhanced trait when expressed in plant cells. In one aspect of the invention homolog proteins have an amino acid sequence that has at least 95%, 98%, 99%, or 99.5% identity to a consensus amino acid sequence of proteins and homologs disclosed herein.
  • Homologs are 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, 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. Because a protein hit with the best E-value for a particular organism may not necessarily be an ortholog, i.e. have the same function, or be the only ortholog, a reciprocal query is used 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 can be identified as an 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 homologs encoded by DNA useful in the transgenic plants of the invention are those proteins that differ from a disclosed protein as the result of deletion or insertion of one or more amino acids in a native sequence.
  • As used herein, “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. Such optimal alignment is understood to be deemed as local alignment of DNA sequences. For protein alignment, a local alignment of protein sequences should allow introduction of gaps to achieve optimal alignment. Percent identity is calculated over the aligned length not including the gaps introduced by the alignment per se.
  • Homologous genes are genes which encode proteins with the same or similar biological function to the protein encoded by the second gene. Homologous genes can be generated by the event of speciation (see ortholog) or by the event of genetic duplication (see paralog). “Orthologs” refer to a set of homologous genes in different species that evolved from a common ancestral gene by specification. Normally, orthologs retain the same function in the course of evolution; and “paralogs” refer to a set of homologous genes in the same species that have diverged from each other as a consequence of genetic duplication. Thus, homologous genes can be from the same or a different organism. As used herein, “homolog” means a protein that performs the same biological function as a second protein including those identified by sequence identity search.
  • “Arabidopsis” means plants of Arabidopsis thaliana.
  • “Pfam” database is a large collection of multiple sequence alignments and hidden Markov models covering many common protein families, e.g. Pfam version 19.0 (December 2005) contains alignments and models for 8183 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. The Pfam database is currently maintained and updated by the 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 protein family 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.
  • A “Pfam domain module” is a representation of Pfam domains in a protein, in order from N terminus to C terminus. In a Pfam domain module individual Pfam domains are separated by double colons “::”. The order and copy number of the Pfam domains from N to C terminus are attributes of a Pfam domain module. Although the copy number of repetitive domains is important, varying copy number often enables a similar function. Thus, a Pfam domain module with multiple copies of a domain should define an equivalent Pfam domain module with variance in the number of multiple copies. A Pfam domain module is not specific for distance between adjacent domains, but contemplates natural distances and variations in distance that provide equivalent function. The Pfam database contains both narrowly- and broadly-defined domains, leading to identification of overlapping domains on some proteins. A Pfam domain module is characterized by non-overlapping domains. Where there is overlap, the domain having a function that is more closely associated with the function of the protein (based on the E value of the Pfam match) is selected.
  • Once one DNA is identified as encoding a protein which imparts an enhanced trait when expressed in transgenic plants, other DNA encoding proteins with the same Pfam domain module are identified by querying the amino acid sequence of protein encoded by candidate DNA against the Hidden Markov Models which characterizes the Pfam domains using HMMER software, a current version of which is provided in the appended computer listing. Candidate proteins meeting the same Pfam domain module are in the protein family and have corresponding 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 with a common Pfam domain module for recombinant DNA in the plant cells of this invention are also included in the appended computer listing.
  • Version 19.0 of the HMMER software and Pfam databases were used to identify known domains in the proteins corresponding to amino acid sequence of SEQ ID NO: 140 through SEQ ID NO:278. All DNA encoding proteins that have scores higher than the gathering cutoff disclosed in Table 19 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 Pfam modules for use in this invention, as more specifically disclosed below, are WRKY::WRKY, AP2, AUX_IAA, WRKY, WRKY, HLH, Myb_DNA-binding::Linker_histone, zf-B_box::zf-B_box, Ank::Ank::Ank::Chromo, NAM, zf-C2H2, Myb_DNA-binding, bZIP—1, PHD, Linker_histone::AT_hook::AThook::AT_hook::AT_hook, B3::Auxin_resp, HLH, zf-Dof, AT_hook::DUF296, AT_hook::AT_hook::DUF296, NAM, GATA, NAM, Myb_DNA-binding, zf-B_box::CCT, POX::Homeobox, B3::Auxin_resp::AUX_IAA, Myb_DNA-binding::Myb_DNA-binding, Myb_DNA-binding::Myb_DNA-binding, zf-C2H2, zf-C2H2, Myb_DNA-binding::Myb_DNA-binding, Myb_DNA-binding::Myb_DNA-binding, TCP, KNOX1::KNOX2, zf-ZPR1::zf-ZPR1, Myb_DNA-binding::Myb_DNA-binding, DUF630::DUF632, WRKY, Myb_DNA-binding, zf-C2H2, HLH, AP2, AT_hook::DUF296, Ank::Ank::Ank::Ank::Ank, WRKY, zf-C2H2, NAM, AP2, NAM, Myb_DNA-binding::Myb_DNA-binding::Myb_DNA-binding, NAM, HLH, Myb_DNA-binding::Myb_DNA-binding, Myb_DNA-binding, HLH, bZIP—2, bZIP—2, BAH::PHD, HLH, NAM, GATA, SSrecog::Rtt106::HMG_box, DUF573, zf-B_box::CCT, HLH, RWP-RK, AP2::B3, AUX_IAA, SRF-TF, AP2, AP2, HSF_DNA-bind, AP2, SRF-TF::K-box, Myb_DNA-binding, zf-LSD1::zf-LSD1::zf-LSD1, KNOX1::KNOX2::ELK, zf-C3HC4, MFMR::bZIP—1, DUF573, Myb_DNA-binding, HLH, NAM, Myb_DNA-binding::Myb_DNA-binding, SRF-TF::K-box, zf-C3HC4, zf-B_box, WRKY, zf-B_box::CCT, EIN3, HSF_DNA-bind, AUX_IAA, TCP, Myb_DNA-binding::Myb_DNA-binding, AP2, KNOX1::KNOX2::ELK::Homeobox, HSF_DNA-bind, HSF_DNA-bind, AP2::B3, NAM, SBP, AP2, zf-C2H2, SRF-TF::K-box, zf-C2H2, GRAS, AP2, Myb_DNA-binding, AP2, AP2::AP2, HLH, CXC::CXC, AP2, NAM, zf-C3HC4, Myb_DNA-binding::Myb_DNA-binding, GRAS, Homeobox::HALZ, Myb_DNA-binding, NAM, WRKY, zf-C2H2, zf-C2H2, NAM, zf-C2H2, AP2::AP2, zf-C3HC4, RWP-RK::PB1, SRF-TF::K-box, and zf-B_box.
    • Recombinant DNA Constructs
  • The invention uses recombinant DNA for imparting one or more enhanced traits to transgenic plant when incorporated into the nucleus of the plant cells. Such recombinant DNA is a constructcomprising a promoter operatively linked to to DNA for expression or suppression of a target protein in plant cells. Other construct components can include additional regulatory elements, such as 5′ or 3′ untranslated regions (such as polyadenylation sites), intron regions, and transit or signal peptides. Such recombinant DNA constructs can be assembled using methods known to those of ordinary skill in the art.
  • Recombinant constructs prepared in accordance with the present invention also generally include a 3′ untranslated DNA region (UTR) that typically contains a polyadenylation sequence following the polynucleotide coding region. Examples of useful 3′ UTRs include those from the nopaline synthase gene of Agrobacterium tumefaciens (nos), a gene encoding the small subunit of a ribulose-1,5-bisphosphate carboxylase-oxygenase (rbcS), and the T7 transcript of Agrobacterium tumefaciens.
  • Constructs and vectors can also include a transit peptide for targeting of a gene target to a plant organelle, particularly to a chloroplast, leucoplast or other plastid organelle. For descriptions of the use of chloroplast transit peptides, see U.S. Pat. No. 5,188,642 and U.S. Pat. No. 5,728,925, incorporated herein by reference.
  • Table 2 provides a list of genes that provided recombinant DNA that was expressed in a model plant and identified from screening as imparting an enhanced trait. When the stated orientation is “sense”, the expression of the gene or a homolog in a crop plant provides the means to identify transgenic events that provide an enhanced trait in the crop plant. When the stated orientation is “antisense”, the suppression of the native homolog in a crop plant provides the means to identify transgenic events that provide an enhanced trait in the crop plant. In some cases the expression/suppression in the model plant exhibited an enhanced trait that corresponds to an enhanced agronomic trait, e.g. cold stress tolerance, water deficit stress tolerance, low nitrogen stress tolerance and the like. In other cases the expression/suppression in the model plant exhibited an enhanced trait that is a surrogate to an enhanced agronomic trait, e.g. salinity stress tolerance being a surrogate to drought tolerance or improvement in plant growth and development being a surrogate to enhanced yield. Even when expression of a transgene or suppression of a native gene imparts an enhanced trait in a model plant, not every crop plant expressing the same transgene or suppressing the same native gene will necessarily demonstrate an indicated enhanced agronomic trait. For instance, it is well known that multiple transgenic events are required to identify a transgenic plant that can exhibit an enhanced agronomic trait. A skilled artisan can identify a transgenic plant cell nuclei, cell, plant or seed by making number of transgenic events, typically a very large number, and engaging in screening processes identified in this specification and illustrated in the examples. For example, a screening process includes selecting only those transgenic events with an intact, single copy of the recombinant DNA in a single locus of the host plant genome and further screening for transgenic events that impart a desired trait that is replicatable when the recombinant DNA is introgressed into a variety of germplams without imparting significant adverse traits.
  • An understanding of Table 2 is facilitated by the following description of the headings:
  • “NUC SEQ ID NO” refers to a SEQ ID NO. for particular DNA sequence in the Sequence Listing.
  • “PEP SEQ ID NO” refers to a SEQ ID NO. in the Sequence Listing for the amino acid sequence of a protein corresponding to a particular DNA
  • “construct_id” refers to an arbitrary number used to identify a particular recombinant DNA construct comprising the particular DNA.
  • “Gene ID” refers to an arbitrary name used to identify the particular DNA.
  • “orientation” refers to the orientation of the particular DNA in a recombinant DNA construct relative to the promoter.
  • TABLE 2
    NUC
    SEQ PEP
    ID SEQ ID Construct
    NO Gene id NO id Orientation
    1 CGPG113 140 12796 SENSE
    2 CGPG1754 141 18301 SENSE
    3 CGPG1809 142 70733 ANTI-
    SENSE
    4 CGPG2053 143 17013 SENSE
    5 CGPG2164 144 15707 ANTI-
    SENSE
    6 CGPG2551 145 17507 SENSE
    7 CGPG2578 146 17518 SENSE
    8 CGPG2583 147 17521 SENSE
    9 CGPG2586 148 17523 SENSE
    10 CGPG2593 149 17629 SENSE
    11 CGPG2594 150 70734 SENSE
    12 CGPG26 151 10106 ANTI-
    SENSE
    13 CGPG2604 152 72053 SENSE
    14 CGPG2615 153 76106 SENSE
    15 CGPG2639 154 17491 SENSE
    16 CGPG2644 155 19152 SENSE
    17 CGPG2657 156 17907 SENSE
    18 CGPG2664 157 17526 SENSE
    19 CGPG2678 158 70736 SENSE
    20 CGPG2699 159 76073 SENSE
    21 CGPG2704 160 76239 SENSE
    22 CGPG2711 161 18215 SENSE
    23 CGPG2735 162 72674 SENSE
    24 CGPG2752 163 17909 SENSE
    25 CGPG2757 164 17911 SENSE
    26 CGPG2767 165 17914 SENSE
    27 CGPG2778 166 74311 SENSE
    28 CGPG2797 167 78468 SENSE
    29 CGPG2805 168 19640 SENSE
    30 CGPG2811 169 71530 SENSE
    31 CGPG2907 170 17832 SENSE
    32 CGPG2935 171 18504 SENSE
    33 CGPG2943 172 18547 SENSE
    34 CGPG2948 173 18548 SENSE
    35 CGPG2961 174 18387 SENSE
    36 CGPG2975 175 18542 SENSE
    37 CGPG2985 176 74056 SENSE
    38 CGPG3107 177 73821 SENSE
    39 CGPG3169 178 18549 SENSE
    40 CGPG3171 179 18517 SENSE
    41 CGPG3175 180 19644 SENSE
    42 CGPG3287 181 18836 SENSE
    43 CGPG3289 182 18240 SENSE
    44 CGPG3296 183 71309 SENSE
    45 CGPG3298 184 19184 SENSE
    46 CGPG3309 185 19186 SENSE
    47 CGPG3312 186 70336 SENSE
    48 CGPG3327 187 18325 SENSE
    49 CGPG3341 188 18333 SENSE
    50 CGPG3347 189 18248 SENSE
    51 CGPG3369 190 18843 SENSE
    52 CGPG3449 191 77332 SENSE
    53 CGPG3451 192 19650 SENSE
    54 CGPG3463 193 18436 SENSE
    55 CGPG3468 194 19634 SENSE
    56 CGPG3476 195 18509 SENSE
    57 CGPG3505 196 18610 SENSE
    58 CGPG359 197 10456 ANTI-
    SENSE
    59 CGPG367 198 11115 ANTI-
    SENSE
    60 CGPG3750 199 70449 SENSE
    61 CGPG3761 200 70461 SENSE
    62 CGPG3793 201 70470 SENSE
    63 CGPG3795 202 70452 SENSE
    64 CGPG3804 203 70473 SENSE
    65 CGPG3810 204 70455 SENSE
    66 CGPG3813 205 70542 SENSE
    67 CGPG382 206 10362 ANTI-
    SENSE
    68 CGPG3825 207 70479 SENSE
    69 CGPG3828 208 70546 SENSE
    70 CGPG3837 209 70481 SENSE
    71 CGPG3841 210 78318 SENSE
    72 CGPG3843 211 72907 SENSE
    73 CGPG3857 212 70485 SENSE
    74 CGPG3858 213 70486 SENSE
    75 CGPG3865 214 70483 SENSE
    76 CGPG3868 215 70625 SENSE
    77 CGPG3869 216 70489 SENSE
    78 CGPG3875 217 74202 SENSE
    79 CGPG3879 218 71971 SENSE
    80 CGPG3947 219 19880 SENSE
    81 CGPG3987 220 19972 SENSE
    82 CGPG4004 221 19920 SENSE
    83 CGPG4013 222 19995 SENSE
    84 CGPG4015 223 19896 SENSE
    85 CGPG4061 224 19957 SENSE
    86 CGPG4066 225 19826 SENSE
    87 CGPG4082 226 19748 SENSE
    88 CGPG4106 227 70930 SENSE
    89 CGPG4112 228 70983 SENSE
    90 CGPG4133 229 19796 SENSE
    91 CGPG4166 230 19869 SENSE
    92 CGPG4195 231 19924 SENSE
    93 CGPG4525 232 71822 SENSE
    94 CGPG4527 233 70758 SENSE
    95 CGPG4537 234 70760 SENSE
    96 CGPG4591 235 75032 SENSE
    97 CGPG4612 236 72943 SENSE
    98 CGPG4632 237 70773 SENSE
    99 CGPG490 238 70215 SENSE
    100 CGPG5130 239 73675 SENSE
    101 CGPG5278 240 72057 SENSE
    102 CGPG5280 241 72093 SENSE
    103 CGPG5292 242 72047 SENSE
    104 CGPG5306 243 72106 SENSE
    105 CGPG5316 244 72117 SENSE
    106 CGPG5324 245 72118 SENSE
    107 CGPG5330 246 72109 SENSE
    108 CGPG5334 247 72129 SENSE
    109 CGPG5422 248 74307 SENSE
    110 CGPG5599 249 72926 SENSE
    111 CGPG690 250 12179 ANTI-
    SENSE
    112 CGPG7354 251 74844 SENSE
    113 CGPG7367 252 74810 SENSE
    114 CGPG7369 253 74834 SENSE
    115 CGPG7373 254 74882 SENSE
    116 CGPG7374 255 74894 SENSE
    117 CGPG7376 256 74823 SENSE
    118 CGPG7378 257 77801 SENSE
    119 CGPG7641 258 75494 SENSE
    120 CGPG7655 259 75472 SENSE
    121 CGPG7678 260 75574 SENSE
    122 CGPG7697 261 75517 SENSE
    123 CGPG7709 262 75566 SENSE
    124 CGPG7714 263 75531 SENSE
    125 CGPG7743 264 75594 SENSE
    126 CGPG7748 265 75559 SENSE
    127 CGPG7757 266 75572 SENSE
    128 CGPG7759 267 75596 SENSE
    129 CGPG7822 268 75680 SENSE
    130 CGPG7840 269 75611 SENSE
    131 CGPG7876 270 75751 SENSE
    132 CGPG858 271 73934 SENSE
    133 CGPG2562 272 74555 SENSE
    134 CGPG31 273 10114 ANTI-
    SENSE
    135 CGPG4213 274 78654 SENSE
    136 CGPG477 275 10804 ANTI-
    SENSE
    137 CGPG6312 276 77507 SENSE
    138 CGPG7188 277 78989 SENSE
    139 CGPG8726 278 78560 SENSE
    • Recombinant DNA
  • DNA for use in the present invention to improve traits in plants have a nucleotide sequence of SEQ ID NO:1 through SEQ ID NO:139, as well as the homologs of such DNA molecules. A subset of the DNA for gene suppression aspects of the invention includes fragments of the disclosed full polynucleotides consisting of oligonucleotides of 21 or more consecutive nucleotides. Oligonucleotides the larger molecules having a sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 139 are useful as probes and primers for detection of the polynucleotides used in the invention. Also useful in this invention are variants of the DNA. Such variants can be naturally occurring, including DNA from homologous genes from the same or a different species, or can be non-natural variants, for example DNA synthesized using chemical synthesis methods, or generated using recombinant DNA techniques. 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. Hence, a DNA useful in the present invention can have any base sequence that has been changed from the sequences provided herein by substitution in accordance with degeneracy of the genetic code.
  • Homologs of the genes providing DNA demonstrated as useful in improving traits in model plants disclosed herein will generally have significant identity with the DNA disclosed herein. DNA is substantially identical to a reference DNA if, when the sequences of the polynucleotides are optimally aligned there is at least about 60% nucleotide equivalence over a comparison window. The DNA can also be about 70% equivalence, about 80% equivalence; about 85% equivalence; about 90%; about 95%; or even about 98%, 98.5%, 99% or 99.5% equivalence over a comparison window. A comparison window is at least about 50-100 nucleotides, and/or is the entire length of the polynucleotide provided herein. Optimal alignment of sequences for aligning a comparison window can be conducted by algorithms or by computerized implementations of these algorithms (for example, the Wisconsin Genetics Software Package Release 7.0-10.0, Genetics Computer Group, 575 Science Dr., Madison, Wis.). The reference polynucleotide can be a full-length molecule or a portion of a longer molecule. In one embodiment, the window of comparison for determining polynucleotide identity of protein encoding sequences is the entire coding region.
  • Proteins useful for imparting enhanced traits are entire proteins or at least a sufficient portion of the entire protein to impart the relevant biological activity of the protein. Proteins used for generation of transgenic plants having enhanced traits include the proteins with an amino acid sequence provided herein as SEQ ID NO: 140 through SEQ ID NO: 278, as well as homologs of such proteins.
  • Homologs of the trait-improving proteins provided herein generally demonstrate significant sequence identity. Of particular interest are proteins having at least about 50% sequence identity, at least about 70% sequence identity or higher, e.g., at least about 80% sequence identity with an amino acid sequence of SEQ ID NO:140 through SEQ ID NO: 278. Proteins also include those with higher identity, e.g., at least about 100% to at least about 99.5%, at least about 100% to at least about 99%, at least about 100% to at least about 98%, at least about 100% to at least about 97.5%, at least about 100% to at least about 95%, at least about 100% to at least about 92.5%, and at least about 100% to at least about 90%. Identity of protein homologs is determined by aligning the amino acid sequence of a putative protein homolog with a defined amino acid sequence and by calculating the percentage of identical and conservatively substituted amino acids over the window of comparison. The window of comparison for determining identity can be the entire amino acid sequence disclosed herein, e.g., the full sequence of any of SEQ ID NO: 140 through SEQ ID NO: 278.
  • The relationship of homologs with amino acid sequences of SEQ ID NO: 279 to SEQ ID NO: 6023 to the proteins with amino acid sequences of SEQ ID NO: to 140 to SEQ ID NO: 278 are found in the listing of Table 16.
  • Other functional homolog proteins differ in one or more amino acids from those of a trait-improving protein disclosed herein as the result of one or more of the well-known conservative amino acid substitutions, e.g., valine is a conservative substitute for alanine and threonine is a conservative substitute for serine. Conservative substitutions for an amino acid within the native sequence can be selected from other members of a class to which the naturally occurring amino acid belongs. Representative amino acids within these various classes include, but are not limited to: (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, tyrosine, asparagine, and glutamine; and (4) neutral nonpolar (hydrophobic) amino acids such as alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine. Conserved substitutes for an amino acid within a native amino acid sequence can be selected from other members of the group to which the naturally occurring amino acid belongs. For example, a group of amino acids having aliphatic side chains is glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains is serine and threonine; a group of amino acids having amide-containing side chains is asparagine and glutamine; a group of amino acids having aromatic side chains is phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains is lysine, arginine, and histidine; and a group of amino acids having sulfur-containing side chains is cysteine and methionine. Naturally conservative amino acids substitution groups are: valine-leucine, valine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, aspartic acid-glutamic acid, and asparagine-glutamine. A further aspect of the invention includes proteins that differ in one or more amino acids from those of a described protein sequence as the result of deletion or insertion of one or more amino acids in a native sequence.
  • Genes that are homologous to each other can be grouped into families and included in multiple sequence alignments. Then a consensus sequence for each group can be derived. This analysis enables the derivation of conserved and class-(family) specific residues or motifs that are functionally important. These conserved residues and motifs can be further validated with 3D protein structure if available. The consensus sequence can be used to define the full scope of the invention, e.g., to identify proteins with a homolog relationship. Thus, the present invention contemplates that protein homologs include proteins with an amino acid sequence that has at least 90% identity to such a consensus amino acid sequence sequences.
    • Promoters
  • Numerous 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 or Figwort mosaic virus promoters. For instance, see U.S. Pat. Nos. 5,858,742 and 5,322,938 which disclose versions of the constitutive promoter derived from cauliflower mosaic virus (CaMV35S), U.S. Pat. No. 5,378,619 which discloses a Figwort Mosaic Virus (FMV) 35S promoter, U.S. Pat. No. 6,437,217 which discloses a maize RS81 promoter, U.S. Pat. No. 5,641,876 which discloses a rice actin promoter, U.S. Pat. No. 6,426,446 which discloses a maize RS324 promoter, U.S. Pat. No. 6,429,362 which discloses a maize PR-1 promoter, U.S. Pat. No. 6,232,526 which discloses a maize A3 promoter, U.S. Pat. No. 6,177,611 which discloses constitutive maize promoters, U.S. Pat. No. 6,433,252 which discloses a maize L3 oleosin promoter, U.S. Pat. No. 6,429,357 which discloses a rice actin 2 promoter and intron, U.S. Pat. No. 5,837,848 which discloses a root specific promoter, U.S. Pat. No. 6,084,089 which discloses cold inducible promoters, U.S. Pat. No. 6,294,714 which discloses light inducible promoters, U.S. Pat. No. 6,140,078 which discloses salt inducible promoters, U.S. Pat. No. 6,252,138 which discloses pathogen inducible promoters, U.S. Pat. No. 6,175,060 which discloses phosphorus deficiency inducible promoters, 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. 09/078,972 which discloses a coixin promoter, U.S. patent application Ser. No. 09/757,089 which discloses a maize chloroplast aldolase promoter, and U.S. patent application Ser. No. 10/739,565 which discloses water-deficit inducible promoters, 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.
  • Furthermore, the promoters can include multiple “enhancer sequences” to assist in elevating gene expression. Such enhancers are known in the art. By including an enhancer sequence with such constructs, the expression of the selected protein can 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 in the forward or reverse orientation 5′ or 3′ to the coding sequence. In some instances, these 5′ enhancing elements are introns. Deemed to be particularly useful as enhancers are the 5′ introns of the rice actin 1 and rice actin 2 genes. Examples of other enhancers that can be used in accordance with the invention include elements from the CaMV 35S promoter, octopine synthase genes, the maize alcohol dehydrogenase gene, the maize shrunken 1 gene and promoters from non-plant eukaryotes.
  • In some aspects of the invention, the promoter element in the DNA construct can be capable of causing sufficient expression to result in the production of an effective amount of a polypeptide in water deficit conditions. Such promoters can be identified and isolated from the regulatory region of plant genes that are over expressed in water deficit conditions. Specific water-deficit-inducible promoters for use in this invention are derived from the 5′ regulatory region of genes identified as a heat shock protein 17.5 gene (HSP17.5), an HVA22 gene (HVA22), a Rab17 gene and a cinnamic acid 4-hydroxylase (CA4H) gene (CA4H) of Zea maize. Such water-deficit-inducible promoters are disclosed in U.S. application Ser. No. 10/739,565, incorporated herein by reference.
  • In some aspects of the invention, sufficient expression in plant seed tissues is desired to effect improvements in seed composition. Exemplary 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 (Peri) (Stacy et al., (1996) Plant Mol Biol. 31(6):1205-1216).
  • In some aspects of the invention, expression in plant green tissues is desired. Promoters of interest for such uses include those from genes such as SSU (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).
  • Gene suppression includes any of the well-known methods for suppressing transcription of a gene or the accumulation of the mRNA corresponding to that gene thereby preventing translation of the transcript into protein. Posttranscriptional gene suppression is mediated by transcription of RNA that forms double-stranded RNA (dsRNA) having homology to a gene targeted for suppression. Suppression can also be achieved by insertion mutations created by transposable elements can also prevent gene function. For example, in many dicot plants, transformation with the T-DNA of Agrobacterium can be readily achieved and large numbers of transformants can be rapidly obtained. Also, some species have lines with active transposable elements that can efficiently be used for the generation of large numbers of insertion mutations, while some other species lack such options. Mutant plants produced by Agrobacterium or transposon mutagenesis and having altered expression of a polypeptide of interest can be identified using the polynucleotides of the present invention. For example, a large population of mutated plants can be screened with polynucleotides encoding the polypeptide of interest to detect mutated plants having an insertion in the gene encoding the polypeptide of interest.
    • Gene Stacking
  • The present invention also contemplates that the trait-improving recombinant DNA provided herein can be used in combination with other recombinant DNA to create plants with multiple desired traits or a further enhanced trait. The combinations generated can include multiple copies of any one or more of the recombinant DNA constructs. These stacked combinations can be created by any method, including but not limited to cross breeding of transgenic plants, or multiple genetic transformation.
    • Transformation Methods
  • Numerous methods for producing plant cell nuclei with recombinant DNA are known in the art and can be used in the present invention. Two commonly used methods for plant transformation are Agrobacterium-mediated transformation and microprojectile bombardment. Microprojectile bombardment methods are illustrated in U.S. Pat. No. 5,015,580 (soybean); U.S. Pat. No. 5,550,318 (corn); 5,538,880 (corn); U.S. Pat. No. 5,914,451 (soybean); 6,160,208 (corn); U.S. Pat. No. 6,399,861 (corn) and U.S. Pat. No. 6,153,812 (wheat) and Agrobacterium-mediated transformation is described in U.S. Pat. No. 5,159,135 (cotton); U.S. Pat. No. 5,824,877 (soybean); 5,463,174 (canola), U.S. Pat. No. 5,591,616 (corn); and U.S. Pat. No. 6,384,301 (soybean), all of which are incorporated herein by reference. For Agrobacterium tumefaciens based plant transformation system, additional elements present on transformation constructs will include T-DNA left and right border sequences to facilitate incorporation of the recombinant polynucleotide into the plant genome.
  • Numerous methods for transforming chromosomes in a plant cell nucleus with recombinant DNA are known in the art and are used in methods of preparing a transgenic plant cell nucleus cell, and plant. Two effective methods for such transformation are Agrobacterium-mediated transformation and microprojectile bombardment. Microprojectile bombardment methods are illustrated in U.S. Pat. No. 5,015,580 (soybean); U.S. Pat. No. 5,550,318 (corn); 5,538,880 (corn); U.S. Pat. No. 5,914,451 (soybean); 6,160,208 (corn); U.S. Pat. No. 6,399,861 (corn); 6,153,812 (wheat) and U.S. Pat. No. 6,365,807 (rice) and Agrobacterium-mediated transformation is described in U.S. Pat. No. 5,159,135 (cotton); U.S. Pat. No. 5,824,877 (soybean); U.S. Pat. No. 5,463,174 (canola, also known as rapeseed); U.S. Pat. No. 5,591,616 (corn); U.S. Pat. No. 6,384,301 (soybean), U.S. Pat. No. 7,026,528 (wheat) and U.S. Pat. No. 6,329,571 (rice), all of which are incorporated herein by reference for enabling the production of transgenic plants. Transformation of plant material is practiced in tissue culture on a nutrient media, i.e. a mixture of nutrients that will allow cells to grow in vitro. Recipient cell targets include, but are not limited to, meristem cells, hypocotyls, calli, immature embryos and gametic cells such as microspores, pollen, sperm and egg cells. Callus may be initiated from tissue sources including, but not limited to, immature embryos, hypocotyls, seedling apical meristems, microspores and the like. Cells containing a transgenic nucleus are grown into transgenic plants.
  • In general it is useful to introduce heterologous DNA randomly, e.g., at a non-specific location, in the genome of a target plant line. In special cases it can be useful to target heterologous DNA insertion in order to achieve site-specific integration, e.g., to replace an existing gene in the genome, to use an existing promoter in the plant genome, or to insert a recombinant polynucleotide at a predetermined site known to be active for gene expression. Several site specific recombination systems exist which are known to function in plants including cre-lox as disclosed in U.S. Pat. No. 4,959,317 and FLP-FRT as disclosed in U.S. Pat. No. 5,527,695, both incorporated herein by reference.
  • Transformation methods of this invention can be 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, calli, hypocotyles, immature embryos and gametic cells such as microspores, pollen, sperm and egg cells. It is contemplated that any cell from which a fertile plant can be regenerated is useful as a recipient cell. Callus can 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. Practical transformation methods and materials for making transgenic plants of this invention, e.g., various media and recipient target cells, transformation of immature embryos and subsequent regeneration of fertile transgenic plants are disclosed in U.S. Pat. Nos. 6,194,636 and 6,232,526 and U.S. patent application Ser. No. 09/757,089, which are incorporated herein by reference.
  • The seeds of 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. In addition to direct transformation of a plant with a recombinant DNA, transgenic plants can be prepared by crossing a first plant having a recombinant DNA with a second plant lacking the DNA. For example, recombinant DNA can be introduced into a 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. enhanced yield, can be crossed with transgenic plant line having other recombinant DNA that confers another trait, for example herbicide resistance or pest resistance, to produce 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 sonic 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.
  • In practice, DNA is introduced into only a small percentage of target cell nuclei. Marker genes are used to provide an efficient system for identification of those cells with nuclei that are stably transformed by receiving and integrating a recombinant DNA molecule into their genomes. Some marker genes provide selective markers that confer resistance to a selective agent, such as an antibiotic or herbicide. Potentially transformed cells with a nucleus of the invention are exposed to the selective agent. In the population of surviving cells will be those cells where, generally, the resistance-conferring gene has been integrated and expressed at sufficient levels to permit cell survival. Cells can be tested further to confirm stable integration of the exogenous DNA in the nucleus. Useful selective marker genes include those conferring resistance to antibiotics such as kanamycin (nptII), hygromycin B (aph IV), spectinomycin (aadA) and gentamycin (aac3 and aacC4) or resistance to herbicides such as glufosinate (bar or pat), dicamba (DMO) and glyphosate (EPSPS). Examples of such selectable markers 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. Screenable markers which provide an ability to visually identify transformants can also be employed, e.g., 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. It is also contemplated that combinations of screenable and selectable markers will be useful for identification of transformed cells. See PCT publication WO 99/61129 (herein incorporated by reference) which discloses use of a gene fusion between a selectable marker gene and a screenable marker gene, e.g., an NPTII gene and a GFP gene.
  • Plant cells that survive exposure to the selective agent, or cells that have been scored positive in a screening assay, can be cultured in regeneration media and allowed to mature into plants. Developing plantlets can be transferred to soil less plant growth mix, and hardened off, e.g., in an environmentally controlled chamber at about 85% relative humidity, 600 ppm CO2, and 25-250 microeinsteins m−2 s−1 of light, prior to transfer to a greenhouse or growth chamber for maturation. Plants are matured either in a growth chamber or greenhouse. Plants are regenerated from about 6 weeks to 10 months after a transformant is identified, depending on the initial tissue. During regeneration, cells are grown to plants on solid media at about 19 to 28° C. After regenerating plants have reached the stage of shoot and root development, they can be transferred to a greenhouse for further growth and testing. Plants can be pollinated using conventional plant breeding methods known to those of skill in the art and seed produced.
  • Progeny can be recovered from transformed plants and tested for expression of the exogenous recombinant polynucleotide. Useful assays include, for example, “molecular biological” assays, such as Southern and Northern blotting and PCR; “biochemical” assays, such as detecting the presence of RNA, e.g., double stranded RNA, or a protein product, e.g., by immunological means (ELISAs and Western blots) or by enzymatic function; plant part assays, such as leaf or root assays; and also, by analyzing the phenotype of the whole regenerated plant.
    • Discovery of Trait-improving Recombinant DNA
  • To identify nuclei with recombinant DNA that confer enhanced traits to plants, Arabidopsis thaliana was transformed with a candidate recombinant DNA construct and screened for an enhanced trait.
  • Arabidopsis thaliana is used a model for genetics and metabolism in plants. A two-step to screening process was employed which included two passes of trait characterization to ensure that the trait modification was dependent on expression of the recombinant DNA, but not due to the chromosomal location of the integration of the transgene. Twelve independent transgenic lines for each recombinant DNA construct were established and assayed for the transgene expression levels. Five transgenic lines with high transgene expression levels were used in the first pass screen to evaluate the transgene's function in T2 transgenic plants. Subsequently, three transgenic events, which had been shown to have one or more enhanced traits, were further evaluated in the second pass screen to confirm the transgene's ability to impart an enhanced trait. The following Table 3 summarizes the enhanced traits that have been confirmed as provided by a recombinant DNA construct.
  • In particular, Table 3 reports:
  • “PEP SEQ ID” which is the amino acid sequence of the protein corresponding to the DNA in the recombinant DNA construct corresponding to a protein sequence of a SEQ ID NO. in the Sequence Listing.
  • “construct_id” is an arbitrary name for the recombinant DNA describe more particularly in Table 1.
  • “annotation” refers to a description of the top hit protein obtained from an amino acid sequence query of each PEP SEQ ID NO to GenBank database of the National Center for Biotechnology Information (ncbi). More particularly, “gi” is the GenBank ID number for the top BLAST hit.
  • “description” refers to the description of the top BLAST hit.
  • “e-value” provides the expectation value for the BLAST hit.
  • “% id” refers to the percentage of identically matched amino acid residues along the length of the portion of the sequences which is aligned by BLAST between the sequence of interest provided herein and the hit sequence in GenBank.
  • “traits” identify by two letter codes the confirmed enhancement in a transgenic plant provided by the recombinant DNA. The codes for enhanced traits are:
  • “CK” which indicates cold tolerance enhancement identified under a cold shock tolerance screen;
  • “CS” which indicates cold tolerance enhancement identified by a cold germination tolerance screen; to “DS” which indicates drought tolerance enhancement identified by a soil drought stress tolerance screen;
  • “PEG” which indicates osmotic stress tolerance enhancement identified by a PEG induced osmotic stress tolerance screen;
  • “HS” which indicates heat stress tolerance enhancement identified by a heat stress tolerance screen;
  • “SS” which indicates high salinity stress tolerance enhancement identified by a salt stress tolerance screen;
  • “LN” which indicates nitrogen use efficiency enhancement identified by a limited nitrogen tolerance screen;
  • “LL” which indicates attenuated shade avoidance response identified by a shade tolerance screen under a low light condition;
  • “PP” which indicates enhanced growth and development at early stages identified by an early plant growth and development screen;
  • “SP” which indicates enhanced growth and development at late stages identified by a late plant growth and development screen provided herein.
  • TABLE 3
    PEP
    Seq
    NUC ID Annotation
    Seq ID No. Gene ID No. E-value % id Description Traits
    1 CGPG113 140 0 90 gb|AAA86281.1|CKC HS
    2 CGPG1754 141 1.00E−156 78 ref|NP_564784.1|DNA-binding storekeeper protein-related PP
    [Arabidopsis thaliana]
    3 CGPG1809 142 1.00E−105 76 ref|NP_200116.1|RWP-RK domain-containing protein [Arabidopsis SP
    thaliana]
    4 CGPG2053 143 1.00E−124 82 gb|AAD22130.2|expressed protein [Arabidopsis thaliana] SS
    5 CGPG2164 144 0 93 gb|AAG53999.1|AF336918_1ARF2 [Arabidopsis thaliana] SS
    6 CGPG2551 145 3.00E−92 81 ref|NP_172518.1|ZFP5 (ZINC FINGER PROTEIN 5); nucleic acid LL
    binding/transcription factor/zinc ion binding [Arabidopsis thaliana]
    7 CGPG2578 146 1.00E−139 95 ref|NP_187963.1|ATMYB5 (myb domain protein 5); DNA binding/ SS
    transcription factor [Arabidopsis thaliana]
    8 CGPG2583 147 1.00E−112 100 pir||H84613probable MADS-box protein [imported] - Arabidopsis PP PEG
    thaliana
    9 CGPG2586 148 1.00E−107 79 ref|NP_177524.2|BEE3 (BR ENHANCED EXPRESSION 3); DNA PEG
    binding/transcription factor [Arabidopsis thaliana]
    10 CGPG2593 149 1.00E−147 84 ref|NP_188962.2|basic helix-loop-helix (bHLH) family protein PP
    [Arabidopsis thaliana]
    11 CGPG2594 150 0 83 sp|Q9LEZ3|BIM1_ARATHTranscription factor BIM1 (BES1-interacting SS
    Myc-like protein 1) (Transcription factor EN 126) (Basic helix-loop-
    helix protein 46)
    12 CGPG26 151 1.00E−134 94 ref|NP_177074.1|AP1 (APETALA1); DNA binding/transcription factor LN
    [Arabidopsis thaliana]
    13 CGPG2604 152 1.00E−151 100 ref|NP_187737.1|myb family transcription factor [Arabidopsis thaliana] LN
    14 CGPG2615 153 1.00E−178 92 ref|NP_177338.1|VND7 (VASCULAR RELATED NAC-DOMAIN HS
    PROTEIN 7); transcription factor [Arabidopsis thaliana]
    15 CGPG2639 154 5.00E−91 60 ref|NP_566232.1|DNA-binding protein-related [Arabidopsis thaliana] DS
    16 CGPG2644 155 1.00E−174 88 ref|NP_189199.1|basic helix-loop-helix (bHLH) family protein HS
    [Arabidopsis thaliana]
    17 CGPG2657 156 1.00E−102 77 ref|NP_188666.1|ERF7 (ETHYLINE RESPONSE FACTOR7); DNA PP SP
    binding/protein binding/transcription factor/transcriptional repressor
    [Arabidopsis thaliana]
    18 CGPG2664 157 2.00E−69 100 ref|NP_188827.1|zinc finger (B-box type) family protein [Arabidopsis PEG PP
    thaliana]
    19 CGPG2678 158 1.00E−110 94 ref|NP_564263.1|zinc finger (C3HC4-type RING finger) family protein CK
    [Arabidopsis thaliana]
    20 CGPG2699 159 0 91 ref|NP_200853.1|ARF4 (AUXIN RESPONSE FACTOR 4); CK
    transcription factor [Arabidopsis thaliana]
    21 CGPG2704 160 0 100 ref|NP_001030821.1|TRFL1 (TRF-LIKE 1); DNA binding [Arabidopsis DS LL
    thaliana]
    22 CGPG2711 161 0 94 ref|NP_191351.1|squamosa promoter-binding protein, putative DS
    [Arabidopsis thaliana]
    23 CGPG2735 162 1.00E−102 100 ref|NP_191211.1|no apical meristem (NAM) family protein HS
    [Arabidopsis thaliana]
    24 CGPG2752 163 1.00E−176 100 ref|NP_172279.1|zinc finger (GATA type) family protein [Arabidopsis SS
    thaliana]
    25 CGPG2757 164 0 96 ref|NP_171609.1|ANAC001 (Arabidopsis NAC domain containing PP
    protein 1); transcription factor [Arabidopsis thaliana]
    26 CGPG2767 165 0 65 ref|NP_175412.1|zinc finger (C2H2 type) family protein [Arabidopsis PP SS
    thaliana]
    27 CGPG2778 166 0 100 ref|NP_197640.1|zinc finger (ZPR1-type) family protein [Arabidopsis SS
    thaliana]
    28 CGPG2797 167 0 92 dbj|BAF62149.1|C2—H2 zinc finger protein [Arabidopsis thaliana] PP
    29 CGPG2805 168 1.00E−167 100 ref|NP_564230.1|MYB116 (myb domain protein 116); DNA binding/ DS HS
    transcription factor [Arabidopsis thaliana]
    30 CGPG2811 169 1.00E−158 79 gb|AAG50818.1|AC079281_20hypothetical protein [Arabidopsis DS HS
    thaliana]
    31 CGPG2907 170 0 86 gb|AAF99784.1|AC012463_1T2E6.3 [Arabidopsis thaliana] HS
    32 CGPG2935 171 1.00E−57 100 ref|NP_200132.2|TRY (TRIPTYCHON); DNA binding/transcription DS
    factor [Arabidopsis thaliana]
    33 CGPG2943 172 0 95 gb|AAF25987.1|AC013354_6F15H18.16 [Arabidopsis thaliana] CK HS
    34 CGPG2948 173 1.00E−167 94 ref|NP_198065.2|MADS-box family protein [Arabidopsis thaliana] CS HS PP
    35 CGPG2961 174 1.00E−146 80 ref|NP_189218.1|AP2 domain-containing transcription factor, putative PP SS
    [Arabidopsis thaliana]
    36 CGPG2975 175 2.00E−97 91 ref|NP_850951.2|KNAT6 (Knotted-like Arabidopsis thaliana 6); DNA CK
    binding/transcription factor s
    37 CGPG2985 176 1.00E−127 79 ref|NP_201559.1|ATTRB2/TRB2 (TELOMERE REPEAT BINDING HS
    FACTOR 2); DNA binding/transcription factor [Arabidopsis thaliana]
    38 CGPG3107 177 0 97 ref|NP_566442.1|myb family transcription factor [Arabidopsis thaliana] HS
    39 CGPG3169 178 1.00E−118 100 ref|NP_196979.1|WER (WEREWOLF 1); DNA binding/transcription HS
    factor [Arabidopsis thaliana]
    40 CGPG3171 179 1.00E−128 95 ref|NP_197898.1|ZFP3 (ZINC FINGER PROTEIN 3); nucleic acid HS
    binding/transcription factor/zinc ion binding [Arabidopsis thaliana]
    41 CGPG3175 180 1.00E−116 81 ref|NP_182191.1|ATHB-7 (ARABIDOPSIS THALIANA HOMEOBOX HS
    7); transcription factor [Arabidopsis thaliana]
    42 CGPG3287 181 1.00E−180 86 ref|NP_566101.1|CAO (CHAOS); chromatin binding [Arabidopsis PP
    thaliana]
    43 CGPG3289 182 1.00E−65 86 ref|NP_566290.1|zinc finger (GATA type) family protein [Arabidopsis CS HS
    thaliana
    44 CGPG3296 183 0 77 ref|NP_564359.1|WRKY14 (WRKY DNA-binding protein 14); SS
    transcription factor [Arabidopsis thaliana]
    45 CGPG3298 184 1.00E−172 92 ref|NP_564486.1|VIP1 (VIRE2-INTERACTING PROTEIN 1); DS LL
    transcription factor [Arabidopsis thaliana]
    46 CGPG3309 185 1.00E−118 94 ref|NP_178188.1|ZFP1 (ARABIDOPSIS THALIANA INC-FINGER HS
    PROTEIN 1); nucleic acid binding/transcription factor/zinc ion
    binding [Arabidopsis thaliana]
    47 CGPG3312 186 1.00E−174 86 ref|NP_181594.1|bZIP transcription factor family protein [Arabidopsis PP
    thaliana]
    48 CGPG3327 187 2.00E−87 88 ref|NP_172872.1|zinc finger (C3HC4-type RING finger) family protein HS
    [Arabidopsis thaliana]
    49 CGPG3341 188 0 85 ref|NP_195410.1|AP2 (APETALA 2); transcription factor [Arabidopsis LN
    thaliana]
    50 CGPG3347 189 5.00E−82 74 ref|NP_566567.1|transcription factor [Arabidopsis thaliana] PP
    51 CGPG3369 190 0 91 ref|NP_175475.2|SCL5; transcription factor [Arabidopsis thaliana] CK HS
    52 CGPG3449 191 1.00E−122 62 ref|NP_193820.1|ethylene-responsive nuclear protein/ethylene- SS
    regulated nuclear protein (ERT2) [Arabidopsis thaliana]
    53 CGPG3451 192 1.00E−113 94 ref|NP_194271.1|basix helix-loop-helix (bHLH) family protein HS
    [Arabidopsis thaliana]
    54 CGPG3463 193 0 87 ref|NP_200855.1|zinc finger (C2H2 type) family protein [Arabidopsis HS
    thaliana]
    55 CGPG3468 194 1.00E−176 95 ref|NP_001031160.1|zinc ion binding [Arabidopsis thaliana] LN
    56 CGPG3476 195 4.00E−92 72 ref|NP_177887.1|AP2 domain-containing transcription factor, putative LN
    [Arabidopsis thaliana]
    57 CGPG3505 196 0 100 gb|AAF05867.1|AC011698_18transfactor-like [Arabidopsis thaliana] CS HS
    58 CGPG359 197 4.00E−95 100 ref|NP_176569.1|zinc finger (C3HC4-type RING finger) family protein LL
    [Arabidopsis thaliana]
    59 CGPG367 198 1.00E−132 86 ref|NP_177583.1|MYB95 (myb domain protein 95); DNA binding/ PEG
    transcription factor [Arabidopsis thaliana]
    60 CGPG3750 199 0 83 ref|NP_172690.1|VND4 (VASCULAR RELATED NAC-DOMAIN SS
    PROTEIN 4); transcription factor [Arabidopsis thaliana]
    61 CGPG3761 200 0 98 ref|NP_190564.1|scarecrow transcription factor family protein HS SP
    [Arabidopsis thaliana]
    62 CGPG3793 201 1.00E−164 93 ref|NP_199078.1|zinc finger (C2H2 type) family protein [Arabidopsis HS
    thaliana]
    63 CGPG3795 202 0 92 ref|NP_173950.1|basic helix-loop-helix (bHLH) family protein HS PEG
    [Arabidopsis thaliana]
    64 CGPG3804 203 1.00E−147 90 ref|NP_174279.1|WRKY71 (WRKY DNA-binding protein 71); HS
    transcription factor [Arabidopsis thaliana]
    65 CGPG3810 204 1.00E−166 83 ref|NP_174494.2|bZIP transcription factor family protein [Arabidopsis CS HS
    thaliana]
    66 CGPG3813 205 0 100 ref|NP_174554.1|ANAC012/NST3/SND1 (ARABIDOPSIS NAC HS
    DOMAIN CONTAINING PROTEIN 12, NAC SECONDARY WALL
    THICKENING PROMOTING 3); transcription factor/transcriptional
    activator [Arabidopsis thaliana]
    67 CGPG382 206 0 90 gb|AAG52391.1|AC011915_5putative B-box zinc finger protein; LN
    52092-50677 [Arabidopsis thaliana]
    68 CGPG3825 207 1.00E−144 100 ref|NP_176829.1|WRKY64 (WRKY DNA-binding protein 64); CS PEG
    transcription factor [Arabidopsis thaliana]
    69 CGPG3828 208 1.00E−151 74 ref|NP_177346.1|TCP family transcription factor, putative [Arabidopsis CS HS
    thaliana]
    70 CGPG3837 209 1.00E−177 92 ref|NP_179176.1|zinc finger (C2H2 type) family protein [Arabidopsis HS
    thaliana]
    71 CGPG3841 210 0 85 ref|NP_180679.2|basic helix-loop-helix (bHLH) family protein HS
    [Arabidopsis thaliana]
    72 CGPG3843 211 0 89 ref|NP_181555.1|myb family transcription factor [Arabidopsis thaliana] HS PEG
    73 CGPG3857 212 1.00E−133 89 ref|NP_001077812.1|ethylene-responsive element-binding protein, CS HS
    putative [Arabidopsis thaliana]]
    74 CGPG3858 213 1.00E−112 75 ref|NP_177090.1|WRKY57 (WRKY DNA-binding protein 57); CS
    transcription factor [Arabidopsis thaliana]
    75 CGPG3865 214 2.00E−96 83 ref|NP_195806.1|zinc finger (C2H2 type) family protein [Arabidopsis HS
    thaliana
    76 CGPG3868 215 9.00E−78 86 ref|NP_199895.3|ANAC097 (Arabidopsis NAC domain containing HS
    protein 97); transcription factor [Arabidopsis thaliana]
    77 CGPG3869 216 1.00E−139 95 ref|NP_188400.1|ANAC057 (Arabidopsis NAC domain containing CK
    protein 57); transcription factor [Arabidopsis thaliana]
    78 CGPG3875 217 0 82 gb|AAF26166.1|AC008261_23putative DNA-binding protein PP
    [Arabidopsis thaliana]
    79 CGPG3879 218 0 80 ref|NP_027544.1|myb family transcription factor [Arabidopsis thaliana] LN PP
    80 CGPG3947 219 2.00E−92 74 gb|AAX13296.1|MADS box protein AP1a [Lotus corniculatus var. PP
    japonicus]
    81 CGPG3987 220 2.00E−75 99 gb|ABH02834.1|MYB transcription factor MYB178 [Glycine max] HS
    82 CGPG4004 221 1.00E−104 56 emb|CAO43809.1|unnamed protein product [Vitis vinifera] HS
    83 CGPG4013 222 1.00E−126 74 gb|AAQ57226.1|DREB2 [Glycine max] HS
    84 CGPG4015 223 1.00E−136 87 dbj|BAA81733.2|GmMYB29A2 [Glycine max] HS LL
    85 CGPG4061 224 1.00E−113 59 emb|CAN68564.1|hypothetical protein [Vitis vinifera] PP
    86 CGPG4066 225 1.00E−134 75 gb|AAK84889.1|AF402608_1TGA-type basic leucine zipper protein LL
    TGA2.1 [Phaseolus vulgaris]
    87 CGPG4082 226 3.00E−88 56 emb|CAO17657.1|unnamed protein product [Vitis vinifera] HS
    88 CGPG4106 227 1.00E−103 67 ref|NP_171677.1|ATAF1 (Arabidopsis NAC domain containing protein HS
    2); transcription factor [Arabidopsis thaliana]
    89 CGPG4112 228 2.00E−87 64 emb|CAO67297.1|unnamed protein product [Vitis vinifera] CS
    90 CGPG4133 229 1.00E−132 85 emb|CAA87077.1|heat shock transcription factor 34 [Glycine max] CK PP
    91 CGPG4166 230 1.00E−122 66 emb|CAO43957.1|unnamed protein product [Vitis vinifera] DS
    92 CGPG4195 231 1.00E−143 85 gb|ABK92551.1|unknown [Populus trichocarpa] HS
    93 CGPG4525 232 0 91 ref|NP_180366.1|BLH8 (BEL1-LIKE HOMEODOMAIN 8); DNA HS
    binding/transcription factor [Arabidopsis thaliana]
    94 CGPG4527 233 1.00E−138 79 emb|CAL64011.1|BRANCHED2 [Arabidopsis thaliana] LL
    95 CGPG4537 234 1.00E−175 78 ref|NP_176237.1|apical meristem formation protein-related LL
    [Arabidopsis thaliana
    96 CGPG4591 235 1.00E−98 80 ref|NP_188752.1|zinc finger (B-box type) family protein [Arabidopsis SS PEG
    thaliana]
    97 CGPG4612 236 1.00E−157 93 ref|NP_174529.2|ANAC011 (Arabidopsis NAC domain containing LL
    protein 11); transcription factor [Arabidopsis thaliana]
    98 CGPG4632 237 5.00E−58 89 ref|NP_194270.1|basix helix-loop-helix (bHLH) family protein CS LL
    [Arabidopsis thaliana]
    99 CGPG490 238 1.00E−127 68 gb|AAZ66389.1|RAV-like DNA-binding protein [Glycine max] LL
    100 CGPG5130 239 1.00E−173 82 ref|NP_176536.2|DNA-binding family protein [Arabidopsis thaliana] CK DS
    101 CGPG5278 240 2.00E−98 55 emb|CAO15010.1|unnamed protein product [Vitis vinifera] DS
    102 CGPG5280 241 1.00E−110 83 ref|NP_001031695.1|DNA binding [Arabidopsis thaliana] LL
    103 CGPG5292 242 1.00E−104 69 gb|ABH02859.1|MYB transcription factor MYB138 [Glycine max] LL
    104 CGPG5306 243 3.00E−68 55 emb|CAA67968.1|MADS4 protein [Betula pendula] HS PP LN
    105 CGPG5316 244 0 60 emb|CAO15649.1|unnamed protein product [Vitis vinifera] LN
    106 CGPG5324 245 3.00E−47 60 sp|Q00423|HMGYA_SOYBNHMG-Y-related protein A (Protein LN SP
    SB16A)
    107 CGPG5330 246 2.00E−44 50 gb|ABD64947.1|ethylene responsive element binding factor, putative HS
    [Brassica oleracea]
    108 CGPG5334 247 1.00E−174 88 gb|ABH02830.1|MYB transcription factor MYB62 [Glycine max] HS
    109 CGPG5422 248 0 89 ref|NP_172900.2|protein binding [Arabidopsis thaliana] DS
    110 CGPG5599 249 0 95 ref|NP_179306.2|RWP-RK domain-containing protein [Arabidopsis PP
    thaliana]
    111 CGPG690 250 1.00E−113 80 ref|NP_189865.1|PHD finger family protein [Arabidopsis thaliana] CK
    112 CGPG7354 251 2.00E−93 68 gb|ABY84652.1|transcription factor [Glycine max] CS
    113 CGPG7367 252 1.00E−131 67 emb|CAC84706.1|aux/IAA protein [Populus tremula × Populus PEG
    tremuloides]
    114 CGPG7369 253 1.00E−154 89 gb|ABI16022.1|Dof21 [Glycine max] PEG
    115 CGPG7373 254 1.00E−68 47 emb|CAN72162.1|hypothetical protein [Vitis vinifera] LN
    116 CGPG7374 255 1.00E−107 53 gb|ABK20308.1|Myb transcription factor [Malus x domestica] LL
    117 CGPG7376 256 1.00E−130 90 gb|ABS18444.1|WRKY48 [Glycine max] LN
    118 CGPG7378 257 2.00E−86 57 emb|CAO23794.1|unnamed protein product [Vitis vinifera] DS
    119 CGPG7641 258 1.00E−111 65 emb|CAN62363.1|hypothetical protein [Vitis vinifera] LL
    120 CGPG7655 259 4.00E−50 48 emb|CAO61053.1|unnamed protein product [Vitis vinifera] LL
    121 CGPG7678 260 1.00E−125 86 gb|ABH02860.1|MYB transcription factor MYB139 [Glycine max] LL
    122 CGPG7697 261 0 96 gb|AAX85980.1|NAC3 protein [Glycine max] LN
    123 CGPG7709 262 2.00E−65 68 emb|CAO46779.1|unnamed protein product [Vitis vinifera] SP
    124 CGPG7714 263 1.00E−94 92 sp|P13088|AUX22_SOYBNAuxin-induced protein AUX22 CS LL
    125 CGPG7743 264 6.00E−37 45 ref|NP_201280.1|ABR1 (ABA REPRESSOR1); DNA binding/ SS LN
    transcription factor [Arabidopsis thaliana]
    126 CGPG7748 265 0 70 emb|CAO68379.1|unnamed protein product [Vitis vinifera] CK
    127 CGPG7757 266 0 81 sp|O04235|SSRP1_VICFAFACT complex subunit SSRP1 (Facilitates CS PEG
    chromatin transcription complex subunit SSRP1) (Recombination
    signal sequence recognition protein 1)
    128 CGPG7759 267 9.00E−64 73 emb|CAO44022.1|unnamed protein product [Vitis vinifera] LL
    129 CGPG7822 268 9.00E−99 70 emb|CAN77695.1|hypothetical protein [Vitis vinifera] DS
    130 CGPG7840 269 6.00E−75 40 ref|NP_188826.1|zinc finger (B-box type) family protein [Arabidopsis DS
    thaliana]
    131 CGPG7876 270 1.00E−45 46 gb|AAD09248.1|EREBP-3 homolog [Stylosanthes hamata] CK
    132 CGPG858 271 0 91 ref|NP_566718.2|TSO1 (CHINESE FOR ‘UGLY’); transcription factor HS
    [Arabidopsis thaliana] dbj|BAB01253.1|DNA binding protein-like
    [Arabidopsis thaliana]
    133 CGPG2562 272 0 88 ref|NP_176964.1|AT-HSFA8 (Arabidopsis thalianaheat shock PEG
    transcription factor A8); DNA binding/transcription factor
    134 CGPG31 273 0 88 ref|NP_188713.1|EIN3 (ETHYLENE-INSENSITIVE3); transcription SS
    factor [Arabidopsis thaliana]
    135 CGPG4213 274 1.00E−113 85 ref|NP_181549.1|basic helix-loop-helix (bHLH) family protein LN
    [Arabidopsis thaliana]
    136 CGPG477 275 5.00E−56 71 ref|NP_196837.1|RAP2.6L (related to AP2 6L); DNA binding/ LN
    transcription factor [Arabidopsis thaliana]
    137 CGPG6312 276 0 76 ref|NP_190697.1|proline-rich family protein [Arabidopsis thaliana] LL
    138 CGPG7188 277 1.00E−121 79 ref|NP_564491.1|transcription regulator [Arabidopsis thaliana] HS
    139 CGPG8726 278 1.00E−124 94 gb|AAY78741.1|DNA-binding protein-related [Arabidopsis thaliana] HS
    • Trait Enhancement Screens
  • DS-Enhancement of Drought Tolerance Identified by a Soil Drought Stress Tolerance Screen:
  • Drought or water deficit conditions impose mainly osmotic stress on plants. Plants are particularly vulnerable to drought during the flowering stage. The drought condition in the screening process disclosed in Example 1B started from the flowering time and was sustained to the end of harvesting. The present invention provides recombinant DNA that can improve the plant survival rate under such sustained drought condition. Exemplary recombinant DNA for conferring such drought tolerance are identified as such in Table 3. Such recombinant DNA can be used in generating transgenic plants that are tolerant to the drought condition imposed during flowering time and in other stages of the plant life cycle. As demonstrated from the model plant screen, in some embodiments of transgenic plants with trait-improving recombinant DNA grown under such sustained drought condition can also have increased total seed weight per plant in addition to the increased survival rate within a transgenic population, providing a higher yield potential as compared to control plants.
  • PEG-Enhancement of Drought Tolerance Identified by PEG Induced Osmotic Stress Tolerance Screen:
  • Various drought levels can be artificially induced by using various concentrations of polyethylene glycol (PEG) to produce different osmotic potentials (Pilon-Smits e.g., (1995) Plant Physiol. 107:125-130). Several physiological characteristics have been reported as being reliable indications for selection of plants possessing drought tolerance. These characteristics include the rate of seed germination and seedling growth. The traits can be assayed relatively easily by measuring the growth rate of seedling in PEG solution. Thus, a PEG-induced osmotic stress tolerance screen is a useful surrogate for drought tolerance screen. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in the PEG-induced osmotic stress tolerance screen can survive better drought conditions providing a higher yield potential as compared to control plants.
  • SS-Enhancement of Drought Tolerance Identified by High Salinity Stress Tolerance Screen:
  • Three different factors are responsible for salt damages: (1) osmotic effects, (2) disturbances in the mineralization process, and (3) toxic effects caused by the salt ions, e.g., inactivation of enzymes. While the first factor of salt stress results in the wilting of the plants that is similar to drought effect, the ionic aspect of salt stress is clearly distinct from drought. The present invention provides genes that help plants maintain biomass, root growth, and/or plant development in high salinity conditions, which are identified as such in Table 3. Since osmotic effect is one of the major components of salt stress, which is common to the drought stress, trait-improving recombinant DNA identified in a high salinity stress tolerance screen can also provide transgenic crops with enhanced drought tolerance. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a high salinity stress tolerance screen can survive better drought conditions and/or high salinity conditions providing a higher yield potential as compared to control plants.
  • HS-Enhancement of Drought Tolerance Identified by Heat Stress Tolerance Screen:
  • Heat and drought stress often occur simultaneously, limiting plant growth. Heat stress can cause the reduction in photosynthesis rate, inhibition of leaf growth and osmotic potential in plants. Thus, genes identified by the present invention as heat stress tolerance conferring genes can also impart enhanced thought tolerance to plants. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a heat stress tolerance screen can survive better heat stress conditions and/or drought conditions providing a higher yield potential as compared to control plants.
  • CK and CS-Enhancement of Tolerance to Cold Stress:
  • Low temperature can immediately result in mechanical constraints, changes in activities of macromolecules, and reduced osmotic potential. In the present invention, two screening conditions, e.g., cold shock tolerance screen (CK) and cold germination tolerance screen (CS), were set up to look for transgenic plants that display visual growth advantage at lower temperature. In cold germination tolerance screen, the transgenic Arabidopsis plants were exposed to a constant temperature of 8° C. from planting until day 28 post plating. The trait-improving recombinant DNA identified by such screen are particular useful for the production of transgenic plant that can germinate more robustly in a cold temperature as compared to the wild type plants. In cold shock tolerance screen, the transgenic plants were first grown under the normal growth temperature of 22° C. until day 8 post plating, and subsequently were placed under 8° C. until day 28 post plating. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a cold shock stress tolerance screen and/or a cold germination stress tolerance screen can survive better cold conditions providing a higher yield potential as compared to control plants.
  • Enhancement of Tolerance to Multiple Stresses:
  • Different kinds of stresses often lead to identical or similar reaction in the plants. Genes that are activated or inactivated as a reaction to stress can either act directly in a way the genetic product reduces a specific stress, or they can act indirectly by activating other specific stress genes. By manipulating the activity of such regulatory genes, e.g., multiple stress tolerance genes, the plant can be enabled to react to different kinds of stresses. For examples, PEP SEQ ID NO:172 can be used to enhance both cold chock tolerance and heat stress tolerance in plants. Of particular interest, plants transformed with PEP SEQ ID NO: 235 can resist salt and osmotic stress. Plants transformed with PEP SEQ ID NO: 243 can also improve growth in early stage and under heat stress. In addition to these multiple stress tolerance genes, the stress tolerance conferring genes provided by the present invention may be used in combinations to generate transgenic plants that can resist multiple stress conditions.
  • PP-Enhancement of Early Plant Growth and Development:
  • It has been known in the art that to minimize the impact of disease on crop profitability, it is important to start the season with healthy and vigorous plants. This means avoiding seed and seedling diseases, leading to increased nutrient uptake and increased yield potential. Traditionally early planting and applying fertilizer are the methods used for promoting early seedling vigor. In early development stage, plant embryos establish only the basic root-shoot axis, a cotyledon storage organ(s), and stem cell populations, called the root and shoot apical meristems that continuously generate new organs throughout post-embryonic development. “Early growth and development” used herein encompasses the stages of seed imbibition through the early vegetative phase. The present invention provides genes that are useful to produce transgenic plants that have advantages in one or more processes including, but not limited to, germination, seedling vigor, root growth and root morphology under non-stressed conditions. The transgenic plants starting from a more robust seedling are less susceptible to the fungal and bacterial pathogens that attach germinating seeds and seedling. Furthermore, seedlings with advantage in root growth are more resistant to drought stress due to extensive and deeper root architecture. Therefore, it can be recognized by those skilled in the art that genes conferring the growth advantage in early stages to plants can also be used to generate transgenic plants that are more resistant to various stress conditions due to enhanced early plant development. The present invention provides such exemplary recombinant DNA that confer both the stress tolerance and growth advantages to plants, identified as such in Table 3, e.g., PEP SEQ ID NO: 173 which can improve the plant early growth and development, and impart salt tolerance to plants. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in the early plant development screen can grow better under non-stress conditions and/or stress conditions providing a higher yield potential as compared to control plants.
  • SP-Enhancement of Late Plant Growth and Development:
  • “Late growth and development” used herein encompasses the stages of leaf development, flower production, and seed maturity. In certain embodiments, transgenic plants produced using genes that confer growth advantages to plants provided by the present invention, identified as such in Table 3, exhibit at least one phenotypic characteristics including, but not limited to, increased rosette radius, increased rosette dry weight, seed dry weight, silique dry weight, and silique length. On one hand, the rosette radius and rosette dry weight are used as the indexes of photosynthesis capacity, and thereby plant source strength and yield potential of a plant. On the other hand, the seed dry weight, silique dry weight and silique length are used as the indexes for plant sink strength, which are considered as the direct determinants of yield. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in the late development screen can grow better and/or have enhanced development during leaf development and seed maturation providing a higher yield potential as compared to control plants.
  • LL-Enhancement of Tolerance to Shade Stress Identified in a Low Light Screen:
  • The effects of light on plant development are especially prominent at the seedling stage. Under normal light conditions with unobstructed direct light, a plant seeding develops according to a characteristic photomorphogenic pattern, in which plants have open and expanded cotyledons and short hypocotyls. Then the plant's energy is devoted to cotyledon and leaf development while longitudinal extension growth is minimized. Under low light condition where light quality and intensity are reduced by shading, obstruction or high population density, a seedling displays a shade-avoidance pattern, in which the seedling displays a reduced cotyledon expansion, and hypocotyls extension is greatly increased. As the result, a plant under low light condition increases significantly its stem length at the expanse of leaf, seed or fruit and storage organ development, thereby adversely affecting of yield. The present invention provides recombinant DNA that enable plants to have an attenuated shade avoidance response so that the source of plant can be contributed to reproductive growth efficiently, resulting higher yield as compared to the wild type plants. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a shade stress tolerance screen can have attenuated shade response under shade conditions providing a higher yield potential as compared to control plants. The transgenic plants generated by the present invention can be suitable for a higher density planting, thereby resulting increased yield per unit area.
  • LN-Enhancement of Tolerance to Low Nitrogen Availability Stress
  • Nitrogen is a key factor in plant growth and crop yield. The metabolism, growth and development of plants are profoundly affected by their nitrogen supply. Restricted nitrogen supply alters shoot to root ratio, root development, activity of enzymes of primary metabolism and the rate of senescence (death) of older leaves. All field crops have a fundamental dependence on inorganic nitrogenous fertilizer. Since fertilizer is rapidly depleted from most soil types, it must be supplied to growing crops two or three times during the growing season. Enhanced nitrogen use efficiency by plants should enable crops cultivated under low nitrogen availability stress condition resulted from low fertilizer input or poor soil quality.
  • This invention demonstrates that the transgenic plants generated using the recombinant nucleotides, which confer enhanced nitrogen use efficiency, identified as such in Table 3, exhibit one or more desirable traits including, but not limited to, increased seedling weight, greener leaves, increased number of rosette leaves, increased or decreased root length. One skilled in the art can recognize that the transgenic plants provided by the present invention with enhanced nitrogen use efficiency can also have altered amino acid or protein compositions, increased yield and/or better seed quality. The transgenic plants of the present invention can be productively cultivated under low nitrogen growth conditions, e.g., nitrogen-poor soils and low nitrogen fertilizer inputs, which would cause the growth of wild type plants to cease or to be so diminished as to make the wild type plants practically useless. The transgenic plants also can be advantageously used to achieve earlier maturing, faster growing, and/or higher yielding crops and/or produce more nutritious foods and animal feedstocks when cultivated using nitrogen non-limiting growth conditions.
  • Stacked Traits: The present invention also encompasses transgenic plants with stacked engineered traits, e.g., a crop having an enhanced phenotype resulting from expression of a trait-improving recombinant DNA, in combination with herbicide and/or pest resistance traits. For example, genes of the current invention can be stacked with other traits of agronomic interest, such as a trait providing herbicide resistance, for example a RoundUp Ready® trait, 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 resistance is useful in a plant include glyphosate herbicides, phosphinothricin herbicides, oxynil herbicides, imidazolinone herbicides, dinitroaniline herbicides, pyridine herbicides, sulfonylurea herbicides, bialaphos herbicides, sulfonamide herbicides and gluphosinate herbicides. To illustrate that the production of transgenic plants with herbicide resistance is a capability of those of ordinary skill in the art, reference is made to U.S. patent application publications 2003/0106096A1 and 2002/0112260A1 and U.S. Pat. Nos. 5,034,322; 5,776,760, 6,107,549 and 6,376,754, all of which are incorporated herein by reference. To illustrate that the production of transgenic plants with pest resistance is a capability of those of ordinary skill in the art, reference is made to U.S. Pat. Nos. 5,250,515 and 5,880,275 which disclose plants expressing an endotoxin of Bacillus thuringiensis bacteria, to U.S. Pat. No. 6,506,599 which discloses control of invertebrates which feed on transgenic plants which express dsRNA for suppressing a target gene in the invertebrate, to U.S. Pat. No. 5,986,175 which discloses the control of viral pests by transgenic plants which express viral replicase, and to U.S. Patent Application Publication 2003/0150017 A1 which discloses control of pests by a transgenic plant which express a dsRNA targeted to suppressing a gene in the pest, all of which are incorporated herein by reference.
  • Once one recombinant DNA has been identified as conferring an enhanced trait of interest in transgenic Arabidopsis plants, several methods are available for using the sequence of that recombinant DNA and knowledge about the protein it encodes to identify homologs of that sequence from the same plant or different plant species or other organisms, e.g., bacteria and yeast. Thus, in one aspect, the invention provides methods for identifying a homologous gene with a DNA sequence homologous to any of SEQ ID NO: 1 through SEQ ID NO: 139, or a homologous protein with an amino acid sequence homologous to any of SEQ ID NO: 140 through SEQ ID NO: 278. In another aspect, the present invention provides the protein sequences of identified homologs for a sequence listed as SEQ ID NO: 279 through SEQ ID NO: 6023. In yet another aspect, the present invention also includes linking or associating one or more desired traits, or gene function with a homolog sequence provided herein.
  • The trait-improving recombinant DNA and methods of using such trait-improving recombinant DNA for generating transgenic plants with enhanced traits provided by the present invention are not limited to any particular plant species. Indeed, the plants according to the present invention can be of any plant species, e.g., can be monocotyledonous or dicotyledonous. In one embodiment, they will be agricultural useful plants, e.g., plants cultivated by man for purposes of food production or technical, particularly industrial applications. Of particular interest in the present invention are corn and soybean plants. The recombinant DNA constructs optimized for soybean transformation and recombinant DNA constructs optimized for corn transformation are provided by the present invention. Other plants of interest in the present invention for production of transgenic plants having enhanced traits include, without limitation, cotton, canola, wheat, sunflower, sorghum, alfalfa, barley, millet, rice, tobacco, fruit and vegetable crops, and turfgrass.
  • In certain embodiments, the present invention contemplates to use an orthologous gene in generating the transgenic plants with similarly enhanced traits as the transgenic Arabidopsis counterpart. Enhanced physiological properties in transgenic plants of the present invention can be confirmed in responses to stress conditions, for example in assays using imposed stress conditions to detect enhanced responses to drought stress, nitrogen deficiency, cold growing conditions, or alternatively, under naturally present stress conditions, for example under field conditions. Biomass measures can be made on greenhouse or field grown plants and can include such measurements as plant height, stem diameter, root and shoot dry weights, and, for corn plants, ear length and diameter.
  • Trait data on morphological changes can be collected by visual observation during the process of plant regeneration as well as in regenerated plants transferred to soil. Such trait data includes characteristics such as normal plants, bushy plants, taller plants, thicker stalks, narrow leaves, striped leaves, knotted phenotype, chlorosis, albino, anthocyanin production, or altered tassels, ears or roots. Other enhanced traits can be identified by measurements taken under field conditions, such as 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. In addition, trait characteristics of harvested grain can be confirmed, 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.
  • To confirm hybrid yield in transgenic corn plants expressing genes of the present invention, it can be desirable to test hybrids over multiple years at multiple locations in a geographical location where maize is conventionally grown, e.g., in Iowa, Illinois or other locations in the midwestern United States, under “normal” field conditions as well as under stress conditions, e.g., under drought or population density stress.
  • Transgenic plants can be used to provide plant parts according to the invention for regeneration or tissue culture of cells or tissues containing the constructs described herein. Plant parts for these purposes can include leaves, stems, roots, flowers, tissues, epicotyl, meristems, hypocotyls, cotyledons, pollen, ovaries, cells and protoplasts, or any other portion of the plant which can be used to regenerate additional transgenic plants, cells, protoplasts or tissue culture. Seeds of transgenic plants are provided by this invention can be used to propagate more plants containing the trait-improving recombinant DNA constructs of this invention. These descendants are intended to be included in the scope of this invention if they contain a trait-improving recombinant DNA construct of this invention, whether or not these plants are selfed or crossed with different varieties of plants.
  • The various aspects of the invention are illustrated by means of the following examples which are in no way intended to limit the full breath and scope of claims.
    • Examples Example 1 Identification of Recombinant DNA that Confers Enhanced Trait(s) to Plants A. Plant Expression Constructs for Arabidopsis Transformation
  • Each gene of interest was amplified from a genomic or cDNA library using primers specific to sequences upstream and downstream of the coding region. Transformation vectors were prepared to constitutively transcribe DNA in either sense orientation (for enhanced protein expression) or anti-sense orientation (for endogenous gene suppression) under the control of an enhanced Cauliflower Mosaic Virus 35S promoter (U.S. Pat. No. 5,359,142) directly or indirectly (Moore, e.g., PNAS 95:376-381, 1998; Guyer, e.g., Genetics 149: 633-639, 1998; International patent application NO. PCT/EP98/07577). The transformation vectors also contain a bar gene as a selectable marker for resistance to glufosinate herbicide. The transformation of Arabidopsis plants was carried out using the vacuum infiltration method known in the art (Bethtold, e.g., Methods Mol. Biol. 82:259-66, 1998). Seeds harvested from the plants, named as T1 seeds, were subsequently grown in a glufosinate-containing selective medium to select for plants which were actually transformed and which produced T2 transgcnic seed.
    • B. Soil Drought Tolerance Screen
  • This example describes a soil drought tolerance screen to identify Arabidopsis plants transformed with recombinant DNA that wilt less rapidly and/or produce higher seed yield when grown in soil under drought conditions
  • T2 seeds were sown in flats filled with Metro/Mix® 200 (The Scotts® Company, USA). Humidity domes were added to each flat and flats were assigned locations and placed in climate-controlled growth chambers. Plants were grown under a temperature regime of 22° C. at day and 20° C. at night, with a photoperiod of 16 hours and average light intensity of 170 μmol/m2/s. After the first true leaves appeared, humidity domes were removed. The plants were sprayed with glufosinate herbicide and put back in the growth chamber for 3 additional days. Flats were watered for 1 hour the week following the herbicide treatment. Watering was continued every seven days until the flower bud primordia became apparent, at which time plants were watered for the last time.
  • To identify drought tolerant plants, plants were evaluated for wilting response and seed yield. Beginning ten days after the last watering, plants were examined daily until 4 plants/line had wilted. In the next six days, plants were monitored for wilting response. Five drought scores were assigned according to the visual inspection of the phenotypes: 1 for healthy, 2 for dark green, 3 for wilting, 4 severe wilting, and 5 for dead. A score of 3 or higher was considered as wilted.
  • At the end of this assay, seed yield measured as seed weight per plant under the drought condition was characterized for the transgcnic plants and their controls and analyzed as a quantitative response according to example 1M.
  • Two approaches were used for statistical analysis on the wilting response. First, the risk score was analyzed for wilting phenotype and treated as a qualitative response according to the example 1L. Alternatively, the survival analysis was carried out in which the proportions of wilted and non-wilted transgenic and control plants were compared over each of the six days under scoring and an overall log rank test was performed to compare the two survival curves using S-PLUS statistical software (S-PLUS 6, Guide to statistics, Insightful, Seattle, Wash., USA). A list of recombinant DNA constructs which improve drought tolerance in transgenic plants is illustrated in Table 4
  • TABLE 4
    NUC PEP Drought score Seed yield
    SEQ SEQ Construct Nomination Delta Delta
    ID ID ID ID Orientation mean P-value mean P-value
    15 154 17491 CGPG2639 SENSE 0.437 0.006 −1.429 0.021
    32 171 18504 CGPG2935 SENSE 0.150 0.233 −0.598 0.013
    29 168 19640 CGPG2805 SENSE −0.282 0.027 0.287 0.019
    91 230 19869 CGPG4166 SENSE −0.076 0.292 −0.489 0.023
    30 169 71530 CGPG2811 SENSE 0.000 0.242 −0.574 0.008
    109 248 74307 CGPG5422 SENSE 0.276 0.027 −1.258 0.015
    130 269 75611 CGPG7840 SENSE 0.330 0.030 −1.029 0.070
    118 257 77801 CGPG7378 SENSE 0.032 0.361 −0.912 0.021
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 160, 161, 184, 239, 240 or 268 showed enhanced drought tolerance by the second criteria as illustrated in Example 1 L.
    • C. Heat Stress Tolerance Screen
  • Under high temperatures, Arabidopsis seedlings become chlorotic and root growth is inhibited. This example sets forth the heat stress tolerance screen to identify Arabidopsis plants transformed with the gene of interest that are more resistant to heat stress based on primarily their seedling weight and root growth under high temperature.
  • T2 seeds were plated on ½× MS salts, 1/% phytagel, with 10 μg/ml BASTA (7 per plate with 2 control seeds; 9 seeds total per plate). Plates were placed at 4° C. for 3 days to stratify seeds. Plates were then incubated at room temperature for 3 hours and then held vertically for 11 additional days at temperature of 34° C. at day and 20° C. at night. Photoperiod was 16 h. Average light intensity was ˜140 μmol/m2/s. After 14 days of growth, plants were scored for glufosinate resistance, root length, final growth stage, visual color, and seedling fresh weight. A photograph of the whole plate was taken on day 14.
  • The seedling weight and root length were analyzed as quantitative responses according to example 1M. The final grow stage at day 14 was scored as success if 50% of the plants had reached 3 rosette leaves and size of leaves are greater than 1 mm (Boyer, el al. (2001) The Plant Cell 13, 1499-1510). The growth stage data was analyzed as a qualitative response according to example 1L. A list of recombinant DNA constructs that improve heat tolerance in transgenic plants illustrated in Table 5.
  • TABLE 5
    Growth stage
    Root length at day 14 Seedling
    NUC PEP Con- day 14 Risk weight
    Seq SEQ struct Delta P- score P- Delta P-
    ID ID ID mean value mean value mean value
    1 140 12796 0.029 0.808 −0.137 0.383 0.783 0.007
    31 170 17832 0.311 0.157 0.385 0.235 1.029 0.013
    43 182 18240 0.098 0.585 0.095 0.795 0.856 0.021
    48 187 18325 −0.001 0.993 0.691 0.085 0.724 0.017
    54 193 18436 0.208 0.016 0.548 0.364 1.091 0.009
    33 172 18547 0.249 0.230 −0.004 0.918 0.024
    34 173 18548 −0.017 0.305 0.525 0.014 0.670 0.038
    39 178 18549 0.127 0.441 0.601 0.202 0.912 0.016
    57 196 18610 0.093 0.762 0.034 0.586 0.977 0.015
    51 190 18843 0.147 0.087 0.603 0.042 0.641 0.006
    16 155 19152 0.218 0.183 0.000 0.935 0.004
    46 185 19186 0.081 0.586 −0.055 0.645 0.020
    29 168 19640 0.070 0.518 0.043 0.762 0.815 0.014
    41 180 19644 0.226 0.139 1.126 0.086 1.244 0.003
    53 192 19650 −0.182 0.011 −0.062 0.714 0.606 0.008
    87 226 19748 0.612 0.016 0.795 0.254 1.149 0.003
    84 223 19896 0.172 0.057 0.136 0.269 0.969 0.002
    82 221 19920 0.189 0.414 0.993 0.152 1.023 0.017
    92 231 19924 0.032 0.455 0.110 0.323 0.877 0.002
    81 220 19972 0.136 0.079 1.169 0.001 0.970 0.012
    63 202 70452 −0.043 0.557 0.326 0.372 0.735 0.002
    65 204 70455 −0.012 0.920 −0.023 0.772 0.506 0.003
    61 200 70461 0.295 0.014 1.656 0.121 1.139 0.000
    62 201 70470 −0.122 0.507 0.125 0.663 0.783 0.003
    64 203 70473 −0.085 0.499 −0.022 0.613 0.676 0.015
    70 209 70481 0.179 0.299 −0.018 1.124 0.026
    75 214 70483 0.014 0.842 0.914 0.312 0.843 0.018
    73 212 70485 0.226 0.314 1.242 0.220 1.339 0.024
    66 205 70542 0.139 0.018 0.639 0.527 0.887 0.030
    69 208 70546 −0.065 0.712 0.579 0.591 0.780 0.023
    76 215 70625 −0.104 0.274 0.466 0.244 0.682 0.004
    88 227 70930 0.147 0.322 1.129 0.130 1.044 0.025
    30 169 71530 0.100 0.445 −0.107 0.058 0.690 0.021
    93 232 71822 0.111 0.458 1.305 0.204 1.139 0.002
    107 246 72109 0.101 0.637 −0.007 0.901 1.006 0.012
    108 247 72129 0.204 0.202 0.234 0.410 1.189 0.022
    23 162 72674 0.145 0.103 0.196 0.693 0.956 0.006
    72 211 72907 0.345 0.069 0.901 0.228 1.374 0.005
    38 177 73821 −0.078 0.622 −0.151 0.467 0.000
    132 271 73934 0.109 0.337 0.239 0.491 1.150 0.012
    37 176 74056 0.136 0.335 −0.012 0.816 0.012
    14 153 76106 0.221 0.291 0.934 0.218 0.994 0.019
    71 210 78318 0.079 0.438 −0.012 0.949 0.905 0.002
    139 278 78560 0.204 0.033 0.590 0.260 0.903 0.041
    138 277 78989 0.102 0.417 0.308 0.303 0.625 0.014
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 179, 222 or 243 showed enhanced heat stress tolerance by the second criteria as illustrated in Example 1 L and 1M.
    • D. Salt Stress Tolerance Screen
  • This example sets forth the high salinity stress screen to identify Arabidopsis plants transformed with the gene of interest that are tolerant to high levels of salt based on their rate of development, root growth and chlorophyll accumulation under high salt conditions.
  • T2 seeds were plated on glufosinate selection plates containing 90 mM NaCl and grown under standard light and temperature conditions. All seedlings used in the embodiments were grown at a temperature of 22° C. at day and 20° C. at night, a 16-hour photoperiod, an average light intensity of approximately 120 umol/m2. On day 11, plants were measured for primary root length. After 3 more days of growth (day 14), plants were scored for transgenic status, primary root length, growth stage, visual color, and the seedlings were pooled for fresh weight measurement. A photograph of the whole plate was also taken on day 14.
  • The seedling weight and root length were analyzed as quantitative responses according to example 1M. The final growth stage at day 14 was scored as success if 50% of the plants reached 3 rosette leaves and size of leaves are greater than 1 mm (Boyes, D. C., et al., (2001), The Plant Cell 13, 1499/1510). The growth stage data was analyzed as a qualitative response according to example 1 L. A list of recombinant DNA constructs that improve high salinity tolerance in transgenic plants illustrated in Table 6.
  • TABLE 6
    Seedling
    NUC Root length Root length Growth stage weight
    Seq PEP at day 11 at day 14 at day 14 at day 14
    ID SEQ Delta P- Delta P- Delta P- Delta P-
    No. ID mean value mean value mean value mean value
    52 191 0.351 0.028 0.370 0.014 0.883 0.272 0.878 0.020
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 143, 144, 146, 150, 163, 165, 166, 174, 183, 199, 235, 264 or 273 showed enhanced salt stress tolerance by the second criteria as illustrated in Example 1L and 1M.
    • E. Polyethylene Glycol (PEG) Induced Osmotic Stress Tolerance Screen
  • There are numerous factors, which can influence seed germination and subsequent seedling growth, one being the availability of water. Genes, which can directly affect the success rate of germination and early seedling growth, are potentially useful agronomic traits for improving the germination and growth of crop plants under drought stress. In this assay, PEG was used to induce osmotic stress on germinating transgenic lines of Arabidopsis thaliana seeds in order to screen for osmotically resistant seed lines.
  • T2 seeds were plated on BASTA selection plates containing 3% PEG and grown under standard light and temperature conditions. Seeds were plated on each plate containing 3% PEG, ½× MS salts, 1% phytagel, and 10 μg/ml glufosinatc. Plates were placed at 4° C. for 3 days to stratify seeds. On day 11, plants were measured for primary root length. After 3 more days of growth, i.e., at day 14, plants were scored for transgenic status, primary root length, growth stage, visual color, and the seedlings were pooled for fresh weight measurement. A photograph of the whole plate was taken on day 14.
  • Seedling weight and root length were analyzed as quantitative responses according to example 1M. The final growth stage at day 14 was scored as success or failure based on whether the plants reached 3 rosette leaves and size of leaves are greater than 1 mm. The growth stage data was analyzed as a qualitative response according to example 1 L. A list of recombinant DNA constructs that improve osmotic stress tolerance in transgenic plants illustrated in Table 7.
  • TABLE 7
    Root length Root length Growth stage Seedling weight
    Nuc PEP Con- at day 11 at day 14 at day 14 at day 14
    SEQ SEQ struct Delta P- Delta P- Delta P- Delta P-
    ID ID ID mean value mean value mean value mean value
    9 148 17523 0.342 0.005 0.283 0.045 2.877 0.124 0.405 0.119
    96 235 75032 0.449 0.031 0.545 0.042 1.022 0.581 0.327 0.118
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 147, 157, 198, 202, 207, 211, 252, 253, 266 or 272 showed enhanced PEG osmotic stress tolerance by the second criteria as illustrated in Example 1L and 1M.
    • F. Cold Shock Tolerance Screen
  • This example set forth a screen to identify Arabidopsis plants transformed with the genes of interest that are more tolerant to cold stress subjected during day 8 to day 28 after seed planting. During these crucial early stages, seedling growth and leaf area increase were measured to assess tolerance when Arabidopsis seedlings were exposed to low temperatures. Using this screen, genetic alterations can be found that enable plants to germinate and grow better than wild type plants under sudden exposure to low temperatures.
  • Eleven seedlings from T2 seeds of each transgenic line plus one control line were plated together on a plate containing ½× Gamborg Salts with 0.8 Phytagel™, 1% Phytagel, and 0.3% Sucrose. Plates were then oriented horizontally and stratified for three days at 4° C. At day three, plates were removed from stratification and exposed to standard conditions (16 hr photoperiod, 22° C. at day and 20° C. at night) until day 8. At day eight, plates were removed from standard conditions and exposed to cold shock conditions (24 hr photoperiod, 8° C. at both day and night) until the final day of the assay, i.e., day 28. Rosette areas were measured at day 8 and day 28, which were analyzed as quantitative responses according to example 1M. A list of recombinant nucleotides that improve cold shock stress tolerance in plants is illustrated in Table 8.
  • TABLE 8
    Rosette area
    NUC Rosette area at day 28 Rosette area
    Seq PEP Con- at day 8 Risk difference
    ID SEQ struct Delta P- score P- Delta P-
    No. ID ID mean value mean value mean value
    111 250 12179 −0.611 0.0161 0.0353 0.666 0.862 0.007
    36 175 18542 0.583 0.184 0.094 0.019 0.078 0.006
    33 172 18547 −0.162 0.531 0.521 0.059 0.622 0.020
    51 190 18843 0.114 0.495 0.728 0.009 0.667 0.007
    90 229 19796 0.157 0.0886 0.438 0.005 0.382 0.0164
    77 216 70489 0.488 0.081 0.312 0.010 0.220 0.311
    19 158 70736 −0.213 0.549 0.389 0.013 0.226 0.344
    100 239 73675 0.088 0.832 0.586 0.041 0.720 0.032
    131 270 75751 0.199 0.251 0.987 0.033 1.093 0.033
    20 159 76073 0.510 0.329 0.515 0.020 0.566 0.067
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in PEP SEQ ID NO. 265 or 270 showed enhanced cold stress tolerance by the second criterial as illustrated in Example 1L and 1M.
    • G. Cold Germination Tolerance Screen
  • This example sets forth a screen to identify Arabidopsis plants transformed with the genes of interests are resistant to cold stress based on their rate of development, root growth and chlorophyll accumulation under low temperature conditions.
  • T2 seeds were plated and all seedlings used in the embodiments were grown at 8° C. Seeds were first surface disinfested using chlorine gas and then seeded on assay plates containing an aqueous solution of ½× Gamborg's B/5 Basal Salt Mixture (Sigma/Aldrich Corp., St. Louis, Mo., USA G/5788), 1% Phytagel™ (Sigma-Aldrich, P-8169), and 10 ug/ml glufosinate with the final pH adjusted to 5.8 using KOH. Test plates were held vertically for 28 days at a constant temperature of 8° C., a photoperiod of 16 hr, and average light intensity of approximately 100 umol/m2/s. At 28 days post plating, root length was measured, growth stage was observed, the visual color was assessed, and a whole plate photograph was taken.
  • The root length at day 28 was analyzed as a quantitative response according to example 1M. The growth stage at day 7 was analyzed as a qualitative response according to example 1L. A list of recombinant DNA constructs that improve cold stress tolerance in transgenic plants illustrated in Table 9.
  • TABLE 9
    NUC Root length Growth stage
    Seq PEP Con- at day 28 at day 28
    ID SEQ struct Nomination Delta P- Delta P-
    No. ID ID ID Orientation mean value mean value
    43 182 18240 CGPG3289 SENSE 0.289 0.020 0.325 0.029
    57 196 18610 CGPG3505 SENSE 0.642 0.059 0.983 0.006
    65 204 70455 CGPG3810 SENSE 4.000
    73 212 70485 CGPG3857 SENSE 0.213 0.102 0.959 0.010
    74 213 70486 CGPG3858 SENSE 0.383 0.223 1.682 0.049
    98 237 70773 CGPG4632 SENSE 0.134 0.186 1.455 0.005
    89 228 70983 CGPG4112 SENSE 0.362 0.015 2.033 0.059
    124 263 75531 CGPG7714 SENSE 0.035 0.778 1.717 0.001
    127 266 75572 CGPG7757 SENSE 0.278 0.025 2.252 0.002
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 173, 204, 207, 208, 209, 213, 228 or 251 showed enhanced cold stress tolerance by the second criterial as illustrated in Example 1L and 1M.
    • H. Shade Tolerance Screen
  • Plants undergo a characteristic morphological response in shade that includes the elongation of the petiole, a change in the leaf angle, and a reduction in chlorophyll content. While these changes can confer a competitive advantage to individuals, in a monoculture the shade avoidance response is thought to reduce the overall biomass of the population. Thus, genetic alterations that prevent the shade avoidance response can be associated with higher yields. Genes that favor growth under low light conditions can also promote yield, as inadequate light levels frequently limit yield. This protocol describes a screen to look for Arabidopsis plants that show an attenuated shade avoidance response and/or grow better than control plants under low light intensity. Of particular interest, we were looking for plants that didn't extend their petiole length, had an increase in seedling weight relative to the reference and had leaves that were more close to parallel with the plate surface.
  • T2 seeds were plated on glufosinate selection plates with ½ MS medium. Seeds were sown on ½× MS salts, 1% Phytagel, 10 ug/ml BASTA. Plants were grown on vertical plates at a temperature of 22° C. at day, 20° C. at night and under low light (approximately 30 uE/m2/s, far/red ratio (655/665/725/735) ˜0.35 using PLAQ lights with GAM color filter #680). Twenty-three days after seedlings were sown, measurements were recorded including seedling status, number of rosette leaves, status of flower bud, petiole leaf angle, petiole length, and pooled fresh weights. A digital image of the whole plate was taken on the measurement day. Seedling weight and petiole length were analyzed as quantitative responses according to example 1M. The number of rosette leaves, flowering bud formation and leaf angel were analyzed as qualitative responses according to example 1L.
  • A list of recombinant DNA constructs that improve shade tolerance in plants illustrated in Table 10.
  • TABLE 10
    Seedling weight Petiole length
    NUC PEP Con- at day 23 at day 23
    Seq SEQ struct Nomination Delta P- Delta P-
    ID ID ID ID Orientation mean value mean value
    6 145 17507 CGPG2551 SENSE 0.467 0.025 0.312 0.067
    84 223 19896 CGPG4015 SENSE 0.360 0.035 0.262 0.060
    99 238 70215 CGPG490 SENSE −0.080 0.133 −0.088 0.050
  • For “seeding weight”, if p<0.05 and delta or risk score mean>0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2 and delta or risk score mean>0, the transgenic plants showed a trend of trait enhancement as compared to the reference with p<0.2.
  • For “petiole length”, if p<0.05 and delta <0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2 and delta <0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 160, 184, 197, 225, 233, 234, 236, 237, 241, 242, 255, 258, 259, 260, 263, 267 or 276 showed enhanced tolerance to shade or low light condition by the second criterial as illustrated in Example 1L and 1M.
    • I. Early Plant Growth and Development Screen
  • This example sets forth a plate based phenotypic analysis platform for the rapid detection of phenotypes that are evident during the first two weeks of growth. In this screen, we were looking for genes that confer advantages in the processes of germination, seedling vigor, root growth and root morphology under non-stressed growth conditions to plants. The transgenic plants with advantages in seedling growth and development were determined by the seedling weight and root length at day 14 after seed planting.
  • T2 seeds were plated on glufosinate selection plates and grown under standard conditions (˜100 uE/m2/s, 16 h photoperiod, 22° C. at day, 20° C. at night). Seeds were stratified for 3 days at 4° C. Seedlings were grown vertically (at a temperature of 22° C. at day 20° C. at night). Observations were taken on day 10 and day 14. Both seedling weight and root length at day 14 were analyzed as quantitative responses according to example 1M.
  • A list recombinant DNA constructs that improve early plant growth and development illustrated in Table 11.
  • TABLE 11
    Root length Root length Seedling weight
    Nuc PEP Con- at day 10 at day 14 at day 14
    SEQ SEQ struct Delta P- Delta P- Delta P-
    ID ID ID mean value mean value mean value
    8 147 17521 0.508 0.003 0.385 0.003 0.164 0.222
    17 156 17907 0.588 0.021
    25 164 17911 0.272 0.049 0.107 0.295 0.254 0.091
    50 189 18248 0.477 0.014 0.301 0.004 0.592 0.048
    2 141 18301 0.200 0.173 0.157 0.048 0.299 0.001
    42 181 18836 0.081 0.426 0.144 0.037 0.066 0.734
    80 219 19880 0.405 0.010 0.239 0.003 0.459 0.024
    85 224 19957 0.234 0.052 0.240 0.035 0.332 0.027
    110 249 72926 0.244 0.024 0.119 0.304 0.235 0.033
    78 217 74202 0.094 0.044 0.080 0.056 0.025 0.587
    28 167 78468 0.194 0.050 0.087 0.039 0.309 0.039
    90 229 19796 0.274 0.004 0.221 0.022 0.561 0.0002
  • Transgenic plants comprising recombinant DNA expressing a protein as set forth in SEQ ID NO: 149, 155, 165, 173, 174, 186, 218 or 243 showed enhanced tolerance to shade or low light condition by the second criterial as illustrated in Example 1L and 1M.
    • J. Late Plant Growth and Development Screen
  • This example sets forth a soil based phenotypic platform to identify genes that confer advantages in the processes of leaf development, flowering production and seed maturity to plants.
  • Arabidopsis plants were grown on a commercial potting mixture (Metro Mix 360, Scotts Co., Marysville, Ohio) consisting of 30-40% medium grade horticultural vermiculite, 35-55% sphagnum peat moss, 10-20% processed bark ash, 1-15% pine bark and a starter nutrient charge. Soil was supplemented with Osmocote time-release fertilizer at a rate of 30 mg/ft3. T2 seeds were imbibed in 1% agarose solution for 3 days at 4° C. and then sown at a density of ˜5 per 2½″ pot. Thirty-two pots were ordered in a 4 by 8 grid in standard greenhouse flat. Plants were grown in environmentally controlled rooms under a 16 h day length with an average light intensity of ˜200 μmoles/m2/s. Day and night temperature set points were 22° C. and 20° C., respectively. Humidity was maintained at 65%. Plants were watered by sub-irrigation every two days on average until mid-flowering, at which point the plants were watered daily until flowering was complete.
  • Application of the herbicide glufosinate was performed to select T2 individuals containing the target transgene. A single application of glufosinate was applied when the first true leaves were visible. Each pot was thinned to leave a single glufosinate-resistant seedling ˜3 days after the selection was applied.
  • The rosette radius was measured at day 25. The silique length was measured at day 40. The plant parts were harvested at day 49 for dry weight measurements if flowering production was stopped. Otherwise, the dry weights of rosette and silique were carried out at day 53. The seeds were harvested at day 58. All measurements were analyzed as quantitative responses according to example 1M.
  • A list of recombinant DNA constructs that improve late plant growth and development illustrated in Table 12.
  • TABLE 12
    Rosette Rosette Seed net Silique Silique
    dry weight radius dry weight dry weight length
    NUC PEP at day 53 at day 25 at day 62 at day 53 at day 40
    SEQ SEQ Delta P- Delta P- Delta P- Delta P- Delta P-
    ID ID mean value mean value mean value mean value mean value
    17 156 −0.333 0.026 0.000 1.000 1.401 0.017 0.419 0.040 0.020 0.635
    61 200 −0.354 0.147 −0.120 0.139 1.079 0.006 0.009 0.819
    3 142 −0.234 0.138 −0.024 0.756 1.618 0.000 −0.192 0.476 0.025 0.100
    123 262 −0.057 0.586 0.042 0.480 0.985 0.014 −0.085 0.537 −0.068 0.363
  • If p<0.05 and delta or risk score mean>0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2 and delta or risk score mean>0, the transgenic plants showed a trend of trait enhancement as compared to the reference. Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 245 showed enhanced tolerance to shade or low light condition by the second criterial as illustrated in Example 1L and 1M.
    • K. Limited Nitrogen Tolerance Screen
  • Under low nitrogen conditions, Arabidopsis seedlings become chlorotic and have less biomass. This example sets forth the limited nitrogen tolerance screen to identify Arabidopsis plants transformed with the gene of interest that are altered in their ability to accumulate biomass and/or retain chlorophyll under low nitrogen condition.
  • T2 seeds were plated on glufosinate selection plates containing 0.5× N-Free Hoagland's T 0.1 mM NH4NO3 T 0.1% sucrose T 1% phytagel media and grown under standard light and temperature conditions. At 12 days of growth, plants were scored for seedling status (i.e., viable or non-viable) and root length. After 21 days of growth, plants were scored for BASTA resistance, visual color, seedling weight, number of green leaves, number of rosette leaves, root length and formation of flowering buds. A photograph of each plant was also taken at this time point.
  • The seedling weight and root length were analyzed as quantitative responses according to example 1M. The number green leaves, the number of rosette leaves and the flowerbud formation were analyzed as qualitative responses according to example 1 L. The leaf color raw data were collected on each plant as the percentages of five color elements (Green, DarkGreen, LightGreen, RedPurple, YellowChlorotic) using a computer imaging system. A statistical logistic regression model was developed to predict an overall value based on five colors for each plant.
  • A list of recombinant DNA constructs that improve low nitrogen availability tolerance in plants illustrated in Table 13.
  • TABLE 13
    Leaf color
    at day 21 Rosette weight
    NUC PEP Con- Risk at day 21
    SEQ SEQ struct Nomination score P- Delta P-
    ID ID ID ID Orientation mean value mean value
    136 275 10804 CGPG477 ANTI- 3.281 0.015 −0.118 0.063
    SENSE
    55 194 19634 CGPG3468 SENSE 1.332 0.025 −0.008 0.933
    79 218 71971 CGPG3879 SENSE 1.566 0.539 0.182 0.011
    105 244 72117 CGPG5316 SENSE −1.264 0.178 0.060 0.048
    106 245 72118 CGPG5324 SENSE 2.897 0.130 0.093 0.018
    104 243 72106 CGPG5306 SENSE −1.867 0.048 0.117 0.018
    125 264 75594 CGPG7743 SENSE −4.165 0.0009 −0.216 0.344
  • For rosette weight, if p<0.05 and delta or risk score mean>0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2 and delta or risk score mean>0, the transgenic plants showed a trend of trait enhancement as compared to the reference with p<0.2. For root length, if p<0.05, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2, the transgenic plants showed a trend of trait enhancement as compared to the reference.
  • Transgenic plants comprising recombinant DNA expressing a protein as set forth in SED ID NO: 151, 152, 188, 195, 206, 254, 256, 261, 264, or 274 showed enhanced tolerance to shade or low light condition by the second criterial as illustrated in Example 1L and 1M.
    • L. Statistic Analysis for Qualitative Responses
  • A list of responses that were analyzed as qualitative responses illustrated in Table 14.
  • TABLE 14
    categories
    response Screen (success vs. failure)
    Wilting response Soil drought tolerance non-wilted vs. wilted
    Risk Score screen
    growth stage at heat stress tolerance 50% of plants reach
    day 14 screen stage 1.03 vs. not
    growth stage at salt stress tolerance 50% of plants reach
    day 14 screen stage 1.03 vs. not
    growth stage at PEG induced osmotic 50% of plants reach
    day 14 stress tolerance screen stage 1.03 vs. not
    growth stage at cold germination 50% of plants reach
    day 7 tolerance screen stage 0.5 vs. not
    number of rosette Shade tolerance screen 5 leaves appeared
    leaves at day 23 vs. not
    Flower bud Shade tolerance screen flower buds appear
    formation at day 23 vs. not
    leaf angle at day 23 Shade tolerance screen >60 degree vs.
    <60 degree
    number of green limited nitrogen 6 or 7 leaves
    leaves at day 21 tolerance screen appeared vs. not
    number of rosette limited nitrogen 6 or 7 leaves
    leaves at day 21 tolerance screen appeared vs. not
    Flower bud limited nitrogen flower buds
    formation at day 21 tolerance screen appear vs. not
  • Plants were grouped into transgenic and reference groups and were scored as success or failure according to Table 14. First, the risk (R) was calculated, which is the proportion of plants that were scored as of failure plants within the group. Then the relative risk (RR) was calculated as the ratio of R (transgenic) to R (reference). Risk score (RS) was calculated as −log2 RR. Two criteria were used to determine a transgenic with enhanced trait(s). Transgenic plants comprising recombinant DNA disclosed herein showed trait enhancement according to either or both of the two criteria.
  • For the first criteria, the risk scores from multiple events of the transgene of interest were evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS institute Inc., Cary, N.C., USA). RS with a value greater than 0 indicates that the transgenic plants perform better than the reference. RS with a value less than 0 indicates that the transgenic plants perform worse than the reference. The RS with a value equal to 0 indicates that the performance of the transgenic plants and the reference don't show any difference. If p<0.05 and risk score mean>0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2 and risk score mean>0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
  • For the second criteria, the RS from each event was evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA). The RS with a value greater than 0 indicates that the transgenic plants from this event performs better than the reference. The RS with a value less than 0 indicates that the transgenic plants from this event perform worse than the reference. The RS with a value equal to 0 indicates that the performance of the transgenic plants from this event and the reference don't show any difference. If p<0.05 and risk score mean>0, the transgenic plants from this event showed statistically significant trait enhancement as compared to the reference. If p<0.2 and risk score mean>0, the transgenic plants showed a trend of trait enhancement as compared to the reference. If two or more events of the transgene of interest showed improvement in the same response, the transgene was deemed to show trait enhancement.
    • M. Statistic Analysis for Quantitative Responses
  • A list of responses that were analyzed as quantitative responses illustrated in Table 15.
  • TABLE 15
    response screen
    seed yield Soil drought stress tolerance screen
    seedling weight at day 14 heat stress tolerance screen
    root length at day 14 heat stress tolerance screen
    seedling weight at day 14 salt stress tolerance screen
    root length at day 14 salt stress tolerance screen
    root length at day 11 salt stress tolerance screen
    seedling weight at day 14 PEG induced osmotic stress tolerance
    screen
    root length at day 11 PEG induced osmotic stress tolerance
    screen
    root length at day 14 PEG induced osmotic stress tolerance
    screen
    rosette area at day 8 cold shock tolerance screen
    rosette area at day 28 cold shock tolerance screen
    difference in rosette area cold shock tolerance screen
    from day 8 to day 28
    root length at day 28 cold germination tolerance screen
    seedling weight at day 23 Shade tolerance screen
    petiole length at day 23 Shade tolerance screen
    root length at day 14 Early plant growth and development screen
    Seedling weight at day 14 Early plant growth and development screen
    Rosette dry weight at day 53 Late plant growth and development screen
    rosette radius at day 25 Late plant growth and development screen
    seed dry weight at day 58 Late plant growth and development screen
    silique dry weight at day 53 Late plant growth and development screen
    silique length at day 40 Late plant growth and development screen
    Seedling weight at day 21 Limited nitrogen tolerance screen
    Root length at day 21 Limited nitrogen tolerance screen
  • The measurements (M) of each plant were transformed by log, calculation. The Delta was calculated as log2M(transgenic)−log 2M(reference). Two criteria were used to determine trait enhancement. A transgene of interest could show trait enhancement according to either or both of the two criteria. The measurements (M) of each plant were transformed by log2 calculation. The Delta was calculated as log 2M(transgenic)−log 2M(reference). If the measured response was Petiole Length for the Low Light assay, Delta was subsequently multiplied by −1, to account for the fact that a shorter petiole length is considered an indication of trait enhancement.
  • For the first criteria, the Deltas from multiple events of the transgene of interest were evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA). Delta with a value greater than 0 indicates that the transgenic plants perform better than the reference. Delta with a value less than 0 indicates that the transgenic plants perform worse than the reference. The Delta with a value equal to 0 indicates that the performance of the transgenic plants and the reference don't show any difference. If p<0.05 and risk score mean>0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2 and risk score mean>0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
  • For the second criteria, the delta from each event was evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc., Cary, N.C., USA). The Delta with a value greater than 0 indicates that the transgenic plants from this event performs better than the reference. The Delta with a value less than 0 indicates that the transgenic plants from this event perform worse than the reference. The Delta with a value equal to 0 indicates that the performance of the transgenic plants from this event and the reference don't show any difference. If p<0.05 and delta mean>0, the transgenic plants from this event showed statistically significant trait improvement as compared to the reference. If p<0.2 and delta mean>0, the transgenic plants showed a trend of trait enhancement as compared to the reference. If two or more events of the transgene of interest showed enhancement in the same response, the transgene was deemed to show trait improvement.
    • Example 2 Identification of Homologs
  • A BLAST searchable “All Protein Database” is 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 DNA sequence provided herein was obtained, an “Organism Protein Database” is constructed of known protein sequences of the organism; the Organism Protein Database is a subset of the All Protein Database based on the NCBI taxonomy ID for the organism.
  • The All Protein Database is queried using amino acid sequence of protein for gene DNA used in trait-improving recombinant DNA, e.g., sequences of SEQ ID NO: 140 through SEQ ID NO: 278 using “blastp” 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 is 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, 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 is queried using amino acid sequences of SEQ ID NO: 140 through SEQ ID NO: 278 using “blastp” with E-value cutoff of 1e−4. Up to 1000 top hits are kept. A BLAST searchable database is constructed based on these hits, and is referred to as “SubDB”. SubDB was queried with each sequence in the Hit List using “blastp” with E-value cutoff of 1e−8. The hit with the best E-value is 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. Likely orthologs from a large number of distinct organisms were identified and are reported by amino acid sequences of SEQ ID NO: 279 to SEQ ID NO: 6023. These orthologs are reported in Tables 16 as homologs to the proteins corresponding to genes used in trait-improving recombinant DNA.
  • TABLE 16
    SEQ ID NO: homolog SEQ ID NOs
    140: 706 583 749 1086 889 4107 4890 5430 5612 5594 5975 5992
    3470 3467 4873 5969 2008 1250 2884 2958 5903 2565 2070 1078
    773 2235 4335 3214 4415 4455 3698 2745 2621 5012 3281 5559
    5099 4670 5882 4112 292 2139 2117 574 3241 5646 765
    141: 5572 480 2492 5574 3604 3508 1313 4894 2962 1986 980 1872
    2159 5857 2531 4416 2195 5995 3011 1037 1829 1932 332
    142: 1425 4267 1156 1158 3175 3370 5813 5349 323 1183 3689 3801
    5576 909 3422
    143: 1940 1119 2138 1862 5052 5472 868 572 1040 4058. 676 5951
    1286 4676 5427 5999 6004
    144: 4034 1262 5043 4488 3122 382 2293 4246 5255 3244 265 2807
    2929 5984 4993 1551 4627 1294 1566 1459 458 4519 2776 1652
    2082 2649 5796 2283 2023 4293 4315 1293 4100 3901 3311 4688
    4068 820 1612 1221 4055 3085 1996 4893 3751 5025 2729 845
    2135 3195 3814 4466 5641 5108 5763 2640 586 4810 5694 4552
    496 1055 1714 4402 1493 3104
    145: 4559 4904 5098 4982 1325 2232 4706 2837
    146: 4044 4599 4596 4123 4126 4927 3191 3185 3187 1517 523 421
    469 474 3181 3946 3466 1289 684 2433 4760 554 5051 1173
    1177 4119 4157 4154 4153 1653 1623 4318 3119 1096 1895 1538
    686 1291 3891 370 4991 5005 4396 2493 386 3794 1257 5775
    2919 1934 5213 4973 1838 3945 5344 5304 2122 4587 646 5819
    2977 2759 3349 2817 2736 5208 526 1147 525 551 550 548
    547 1144 2160 2158 2163 1561 1801 1804 608 626 4158 2547
    1771 1137 1923 751 299 5783 690 1295 5690 3430 833 992
    1100 4289 1726 5130 3169 3149 582 3850
    147: 2968 1281 3943 3942 2774 2848 2846 3813 1113 1696 1881 1858
    5614 1426 1427 1900 1902 1879 1876 1057 3093 2526 2530 2522
    1823 1821 4989 2826 2824 2026 2027 4260 5513 5078 2002 4849
    3096 3094 1850 1848 2532 1851 1056 1700 1633 2879 1017 3441
    3443 3884 2057 2054 2024 2000 1997 1781 2494 1110 2855 1115
    5275 2020 402 4915 2190 1957 931 2654 4159 4332 5767 1062
    1061 1085 1083 2489 1087 1673 1698 3188 1815 1713 3439 4122
    3541 5209 2025 1386 1363 1391 3739 3815 4065 5795 1865 4640
    4278 2787 2984 2735 5981 1990 1972 1974 1646 2858 1600 1596
    2225 2204 2211 1595 2208 2227 2199 2223 2224 2202 1114 1116
    738 367 5838 4568 647 450 5010 2251 5512 2691 1129 2798
    641 659 4698 1165 1089 1716 4731 2721 2306 2324 1754 1907
    1760 4220 4238 2121 1373 3967 5220 4005 4022 3832 3835 3852
    2175 1521 4240 405 1395 4268 1569 516 1752 2019 2073 2074
    1689 654 2092 4857 2046 3575 5183 2042 3831 2593 705 3763
    3296 5917 5625 2641 5890 2658 1108 4250 3736 2327 3342 374
    5119 1079 3170 1813 3859 2820 2080 1039 2497 2500 5121 3783
    3803 4103 3382 3385 1976 3336 2313 1311 353 2646 3954 2071
    1971 4404 609 1675 1694 3840 4456 1530 4622 1202 3539 2203
    148: 4182 2778 4726 3323 4652 2981 322 390 3479 1263 2331 1241
    1956 5803 3120 4500 4418 732 4740 2645
    149: 3953 1949 1651 4276 5811 2557 5727 4517 2978 4020 3215 4950
    3135
    150: 2990 2566 3100 4734 3825 756 4214 5757 3851 2321 4679 5525
    3354 3855 3941 5018 3517 4172 3250 5399 873
    151: 2968 2970 4423 3943 3942 1859 5233 1155 3627 3653 4236 4254
    3680 4989 3816 2771 3935 5513 5138 3009 5832 5266 3963 3964
    3707 3711 2002 4790 5326 5331 5192 3940 3921 3687 305 2329
    5540 5724 5235 3556 5395 1633 3784 4113 1017 3884 2024 2057
    2000 1997 2923 2855 3489 3490 5198 2186 4613 5382 5392 5387
    5887 2051 2020 2021 452 455 2628 476 5122 4332 803 4118
    5139 3739 1945 1941 3128 2596 2614 4690 932 910 929 3105
    3101 3080 5069 3010 3026 3013 3012 3815 546 5153 2342 2936
    2924 5254 5251 3672 4241 4453 3675 4640 5652 1952 1774 2735
    1882 3728 3702 3704 591 5231 1990 1972 1974 1646 5408 2612
    2642 2699 4985 4841 5637 4876 1114 1116 219 5072 5101 4785
    4225 4752 4753 5415 5352 3660 6003 5114 541 5054 5132 3914
    3919 3916 1548 3402 902 2721 2718 3334 5965 1543 3087 4523
    5088 4134 806 1338 1340 3967 3966 4244 2053 3992 5602 4005
    4003 3944 5355 5358 5363 4249 3807 979 981 4497 2877 1581
    2340 2050 908 1926 1584 2872 4266 5369 5453 5449 5421 5423
    2098 3930 4102 2942 563 2667 2623 1368 4475 4399 911 2345
    1964 5889 4704 4192 4008 2686 4811 2806 2939 3636 681 3639
    2946 2948 4713 4831 4830 2644 1857 4103 2529 1908 3385 2799
    1740 1861 6023 2943 2941 3033 3049 1311 3074 3077 3030 3028
    3962 3108 3123 336 353 2646 4716 3908 2179 3808 2134 1971
    1993 4781 5732 5102 922 1570 4031 4084 4036 4082 4039
    152: 5416 883 5152 2568 5743 1968 2983 3159 4213 5015 2469 3190
    2028 515 2432 2739 2741 2018 4146 5137 4751 4953 2987 3255
    1704 2044 1245 1192 1773 1292 3528
    153: 2405 5876 2401 1562 2187 3269 1611 5721 1822 1816 3058 3232
    3795 5928 880 3889 2299 5638 721 3362 3121 3699 4832 5124
    1690 5173 4966 1819 1810 786 633 509 4205 4092 5880 4436
    154: 819 4425 5257 4363 642 5501 1511 5785 5942 2716 1841 5443
    3600 4353 2428 3445 3444 5473 2410 2184 5526 2013 2918 5569
    371 2032 3873 5203 5161 578
    155: 1721 1093 2228 4171 2514 2318 1917 804 3460 459 2578 341
    4880 4511 1090 6021 1868 1824 5028 4480 1013 4255 4612
    156: 3014 1344 2750 2332 1438 5692 3595 2508 1587 1572 5265 5262
    5713 1374 2443 602 2045 2510 5219 4408 4037 2274 2289 3348
    3431 1350 680 3247 1226 1663 3469 479 3084 5286 4921 4557
    5008 2576 1402 533 361 357 1767 279 5630 5936 5961 1994
    3838 3124 359 449 2351 2724 2316 5250 3114 4494 5238 5827
    3261 368 2993 3777 2803 5597 4526 876
    157: 5202 4554 5544 1467 3645 5899 735 4111 3024 1002 4992 3589
    3905 3715 5971 4300 3290 1222 3628
    158: 2474 5667 561 5836 1953 3107 2481 2238 1342 5800 1664 2499
    792 5755 2191 1502 1370
    159: 1494 464 5709 2152 2279 3994 4034 5789 2738 5600 3122 4398
    382 4030 1938 2293 4246 3601 853 5636 2582 4316 4313 4310
    5446 2426 4367 5694
    160: 2374 1010 5914 1710 712 2261 5977 4454 2033 4256 4756 770
    3703 1200 5588 5082 5524 2996 1574 4380 1939 4668 4602 4348
    1556 5940 2065 3932 4351 3156 5024 5738 2146 1191 713 5128
    4759 5040 4089 4416 905 3678 1942 3138 3607 2209 962 898
    1212 388 2119 2952 5810 2384 2367 3878
    161: 1680 4990 4400 5120 1549 1008 3563 912 4945 2252 3585 4631
    5821 5229 4996 4540 1833 4207 2049 2650 1607 5658 3847 1510
    788 1573 1343 4639 590 3078 628 3194 3192 3371 4403 407
    3098 3086 5498 577 4501 387 385 383 365 346 343 339
    337 4168 4330 4626
    162: 3724 5809 4846 3166
    163: 3366 5222 5300 3266 447 3614 632 285 4094 3785 2294 4482
    4678 604 3616 5846 4285 767 2624 5056 5632 1776 3868 5285
    378 3092 4924
    164: 1654 2695 3293 4355 2088 1611 1365 1943 4070 1816 1822 2055
    5693 317 4606 5124 1690 1810 1819 786 3223 509 4205 4092
    5100 2606 349 5880 998 2341 5514 3648 5623 4979 1980 1274
    2344 2302 4135 5451 2130 5545 5237 4301 4529 797 3242 4262
    165: 4371 5585 2976 4302 1393 2287 857 1167 3936 4011 5870 1697
    1720 4625 5097 1954 2600 852 1211 5206 4892 821 1239 2501
    3780 2655 2626 1478 5657 2571 4955 2643 1505 3482
    166: 5373 1616 5059 4534 2772 5175 2483 5884 3243 4618 2938 2613
    2856 3110 3168 2189 1006 5414 2780 1028 4142 4971 2567 4314
    4515 1583 1430 1431 514 2193 660 2256 4634 3619 4574 1929
    4527 1749 5146 769 2505 3072 1890 3357 5123 2857 1302 1436
    5357 848 4889 1560 2218 2889 456 596 5994 2165 3845 3846
    4389 1787 4032 1593 414 335 4661 5178 3789
    167: 5845 1878 567 1423 4601 2722 2391 4729 3634 2698 771 3501
    2078 4021 3126 4095 5650 5607 1755 2271 1464 1328 1359 761
    2476 4373 2603 3363 1909 5816 2177 4464 3484 1190 3856 1683
    3221 2609 1648 886 338 664 381 999 986 3265 5665
    168: 4044 1836 2399 1517 418 421 469 472 474 4685 4660 4662
    3466 684 1289 4655 2982 320 395 3043 3054 4396 3794 1257
    1280 2919 4973 4378 1912 5519 2107 737 5662 1845 543 675
    1204 4896 2104 2116 2122 2120 1801 1804 4158 4328 5403 4617
    1276 5438 1466 5783 5690 3430 404 4289 403 5130 582 3850
    2131 3224 5941
    169: 1277 2372 1925 5947 4545 2136 921 1594 429 620 2947 1251
    3038 1709 5556 1435 471 5067 1094 4877 5182 2730 4705 4096
    4843 174 1632
    170: 4908 1888 5020 5021 5036 5405 5913 5522 3125 2634 4681 2182
    1620 4516 2355 435 4869 2387 4434 3657 1396 4271 3139 4919
    2933 2300 1259 1487 2141 4385 2304 1134 1649 5035
    171: 5601 2178 1509 1817 2260 512 527 3478 6017 1358 3551 347
    1074 1347 2011 4975 3975
    172: 4150 3450 2563 5837 937 5062 3696 3827 5946 1958 892 3810
    5017 651 3925 3321 4621 3369 4326 5401 4009 2058 4356 5306
    3822 2455 5551 3416 1421 3414 1418 1415 5770 5766 3411 3393
    3392 3320 3312 2715 5756 3387 3288 2746 2744 1417 3316 3289
    3388 3361 3358 3390 3350 3295 3355 3353 2749 2748 2713 3446
    3447 3452 3510 3480 1434 1433 3598 3593 3542 3509 3483 3473
    3453 3423 3544 3502 3591 3513 3548 3587 3424 3582 3504 4166
    3449 4176 1585 1568 5535 4771 5496 3679 4208 5716 1258 319
    4686 3364 4762 3203 5243 3070 4115 1513 1488 1483 3655 1157
    5026 3758 759
    173: 4447 4541 1214 534 2512 5290 5242 2315 1800 433 3950 5619
    3958 4350 2217 5505 4433 2168 3610 1580 1482 334 3673 4724
    2743
    174: 5568 1277 2372 1925 5947 4930 429 620 2947 1251 1709 5556
    3038 2311 1435 471 4189 5067 4877 4076 2396
    175: 5343 4666 1525 1526 2766 4329 1869 2897 1225 1224 2867 2728
    2813 2836 2883 2833 2832 2881 2830 2827 2814 2859 2693 2090
    2811 1634 1300 1927 1930 2692 2732 1831 4062 4438 4413 4409
    4410 1324 1319 1962 3263 4317 4467 3580 5215 3020 2108 5799
    915 997 995 1685 291 3088 3036 2997 2994 2991 3019 1446
    2210 1579 1474 1428 5729 5773 5706 636 4926 3246 3227 3270
    1357 585 540 4845 4818 5604 4887 5629 298 4229 4006 881
    5748 5745 6011 4180 4352 5931 5217 4247 3623 3476 6007 5136
    5798 5096 4426 3674 2885 2840 2140 2111 4558 6002 2094 3208
    290 6008 6005 5986 2448 5293 1273 3474 3496 3498 3497 1501
    4345 503 502 3481 1499 1066 2397 2047 2660 2659 311 1853
    5167 5168 1565 2673 1029 268 3767 4934 1670 970 5296 5295
    4739 5381 5307 5379 5410 4361 1306 4463 1576 1559 4656 4462
    822 3769 3701 1629 3924 3918 5339 5733 3637 4598 1318 1916
    4594 380 3524 930 2385 2386 2388 3245 3248 3426 3432 2132
    519 1883 4564 3913 4595 2253 3708 2591 3915 4728 1249 1254
    4732 4735 2037 2012 4725 5742 5354 901 3903 4987 5071 3590
    1628 4486 3057 4072 5368 4667 384 5842 891 4590 1711 3111
    325 5853 1528 983 5726 1496 1904 1899 3907 837 838 649
    5507 4045 2995 1766 2444 4530 3834 4303 5277
    176: 1586 4775 3515 1476 4682 2688 2109 2291 3164 3890 568 1837
    1264 4577 286 3286 1031 1208 3690 4963 4965 5508 5939 1535
    560 3090 2040 5159 1285 2056 1486 1092 946 345 1232 1217
    177: 4555 5998 1792 2093 4556 961 5561 4547 4390 2657 4520 2999
    3968 1712 3391 682 2523 5211 882 5105 2206 5877 3526 3791
    879 614 3849 5888 4743 6015 3182
    178: 4044 4599 4596 4123 3805 1284 1836 3185 3191 3187 2399 1517
    418 469 474 3181 2666 3466 3946 715 4961 3097 4177 3154
    1176 3297 489 1173 4119 4157 1623 4153 1653 4156 1627 3781
    1895 1096 4318 3119 4575 3043 1538 3440 3054 370 4991 5005
    3681 795 3651 2349 454 2765 3794 4288 1131 5344 646 2977
    2759 2736 2817 3349 4638 4948 1804 4158 2547 4617 720 717
    5690 4289 701 4290 1726 5317 5316 3169 3149 582
    179: 4334 1320 2950 3218 1541 627 4235 3260 5826 3239 1105 495
    3989 3308 4362 5991 3865 5083 2369 1658 1278 2412 3271 1808
    1406 3695 5070 1537 3743 4280 5073
    180: 1966 2015 2267 5147 4138 5312 1782 5270 1515 5715 3576 5029
    4657 1863 890 549 3732 3931 2845 3377 3032 5590 619 2147
    1027 579 2325 4460 4860 2328 4077 3155 5391 2086 5047 3298
    1979 4311 5164 5162 5190 5165 5193 5187 4702 878 4050 5278
    1707
    181: 5679 5907 2200 3826 5471 3605 4284 4379 4320 985 4148 4357
    3866 3196 5675 2231 5090 3400 2371 934 2172
    182: 743 1279 2456 5589 3183 4450 2648 5298 3471 5860 4492 3830
    2669 2870 3543 5350 1270 5444 1261 674 4179 1577
    183: 1795 1794 5504 3837 1046 2389 5668 3979 4922 3798 4518 4647
    501 4768 4782 2222 1275 3500 4607 5542 5549 3180 5843 1744
    5660 2917 3514 1780 4769 1656 5454 2197 4098 5595 5527 508
    4397 5972 4412 5484 3978 2229 1601 2269 2248 5440 760 375
    1770 5417 914 2518 559
    184: 5993 3521 2513 3291 3017 4699 3222 4505 5944 5541 4972 1470
    754 2262 4736 314 1458 5615 1197 344 1122 1591 3406 3824
    4188 4491 569 4614 1255 5489 3252 2268
    185: 5378 3046 1687 4334 2950 4235 627 3417 4143 2326 5826 3239
    3260 4197 1424 836 1170 3753 1105 5083 1808 1406 3695 5070
    1537
    186: 4370 2960 3521 3741 1518 4699 5560 1073 1504 4223 314 1458
    392 1445 1650 4294 3682 2171 936 4524
    187: 624 5667 561 5836 1175 831 2212 2499 5755 5402 1502 4169
    1169
    188: 706 753 3969 1086 889 1733 5370 3806 4324 4890 5430 5973
    5978 3467 3470 4873 1181 1182 5968 2008 5703 704 5205 2565
    4521 2174 4988 1351 3546 1961 597 5474 2804 4913 4916 2462
    2463 5374 5475 1297 3165 5371 4658 4419 1719 1532 5515 1025
    420 4393 3770 4604 2117 2139 2166 507 574 2926 3241 1172
    2022 5646 3373
    189: 2290 1706 3332 4422 1329 2914 3643 863 4802 1234 4014 5216
    3717 2398 3016 4259 5823 5345 4974 1870 5095
    190: 1180 282 5348 1818 2036 307 352 393 4805 1152 1194 5801
    348 1196 5718 1070 1067 1041 4834 4836 1353 1404 4833 5741
    4531 4506 1331 1243 1148 1045 1049 5413 424 5879 351 5089
    4231 5840 1272 4354 658 1362 4066 4088 4064 4042 4018 4136
    4870 4202 4804 4902 4900 4931 4942 4994 4962 4935 4905 5620
    4928 5016 5013 4741 4744 4871 4897 4750 4809 4808 4776 4623
    4211 4322 4321 4319 4298 431 960 2406 4591 1547 1023 1452
    3836 846 2851 3881 1507 3961 5533 1268 1298 4206 4777 4868
    4865 4779 4803 4838 4842 4747 4749 4874 4903 4901 4774 5867
    5851 1014 2234 1610 2507 1178 1198 844
    191: 963 3161 2708 4263 5794 372 945 3965 593 4895 3748 1437
    2216 5060 1199
    192: 1193 3937 5922 3970 398 893 3378 5847 492 4954 4087 4636
    193: 4551 2254 3050 2988 1423 1400 2391 564 3634 4152 1328 1359
    761 3564 3557 6018 2854 1739 1308 5199
    194: 416 417 4815 442 1052 3389 621 4110 5133 5320 4431 444
    1983 5688 3116 5009 2866 5653 4325 2916 517 1588 4025 4691
    1485 5932 3550 5771 4999 3737
    195: 2001 1995 1992 4043 3381 6016 3375 1814 3376 3335 3337 2096
    2892 1635 2077 580 2170 3306 3574 1797 2980 1405 3137 3130
    3299 1856 5186 4863 4761 3742 2672 1267 1360 3823 5829 3172
    521 5812 5023 2690 835 5308 2215 5156 3511 4866 4835 379
    2538 613 5683 5708 3755 4248 3885 5447 5145 3345 3305 2631
    3343 2128 5661 3457 2760 1555
    196: 4555 3235 1533 3060 3912 2622 2480 3056 4556 4847 961 5561
    5432 775 566 4390 5547 3117 2986 4799 1352 667 4956 304
    5919 2661 2517 4116 426 2188 2689 4366 4457 1449 5987 2007
    2664 1238 614 3849 5888 4743 1873 4498 5905 4162 2679 631
    5327 766
    197: 4619 1614 1668 4958 1643 3771 2742 3947 1398 3731 4694 2611
    4695 1875 4199 1495 1791 3583 1082 1937 1567 897 1477
    198: 4044 4123 4128 4959 3191 3185 5855 421 469 3181 3946 2651
    1539 3887 370 4396 2525 386 1257 5532 2919 5213 1934 4973
    4381 5344 5764 5958 1145 5252 5493 2104 4587 4638 1801 1804
    2246 4158 432 2547 5428 5424 5455 5486 1827 2992 4562 5491
    4617 364 5690 3430 3327 5130 3169 3149 582 4807
    199: 1654 2401 5876 3237 3568 427 1121 4355 4070 5721 1816 1822
    1762 5638 826 1408 5693 5104 3121 3699 4424 1564 2411 4566
    783 5124 1690 5173 1810 1819 786 2546 3267 3861 576 5004
    4205 4092 349 5880 4436 5689 3875 400 2585 3141
    200: 1180 282 1012 3612 5874 1790 307 352 393 4805 1152 1194
    5801 348 1196 1070 1067 1041 4834 1353 4833 3972 2181 4687
    1016 1015 5085 1148 1049 1045 5413 424 5170 4287 887 2284
    5006 1717 5356 2148 4231 1272 4360 2873 4042 4064 4018 4136
    4088 4202 4066 4804 4870 4741 4744 4871 4750 4897 4808 4809
    4776 4211 4322 4321 4319 4298 573 1730 431 625 4674 4692
    4206 4777 4868 4865 4779 4803 4842 4838 4749 4747 4874 4903
    4774 4901 5851 5867 1014 1610 2133 1178 1918 2702
    201: 1098 1060 5786 5523 4091 5297 209 2647 2620 5039 3842 1914
    3140 4507 3160
    202: 2844 3179 5027 4726 2778 4093 5396 4178 2435 2581 2447 2752
    5878 2424 1409 4024 5710 2331 1241 4151 1956 1420 3472 4976
    3864 2439 616 5579 4500 401 3442 4237 3549 3230 4054 5746
    732 5951 4740 4858 1154 3061 4977 1731
    203: 4789 1795 1794 5924 2482 5225 3572 4495 5648 1419 1844 4139
    3418 1380 750 5129 5328 1151 2714 5091 2602 2558 3220 4201
    3837 1125 1622 1631 2286 2103 3979 1933 1931 1896 5336 1928
    5635 3902 5461 4518 1248 4647 501 4672 3790 1128 2754 2153
    5660 2917 1247 752 3730 4821 1682 3109 5985 4010 830 1536
    1778 2434 4769 2115 2949 2805 2550 373 1462 2541 2764 4485
    3978 5626 2229 1601 2269 2248 389 412 1189 3503 5384 1271
    411 3178 789 3922
    204: 2064 2537 5112 4071 1746 5669 993 1950 5337 4382 2365 2333
    1678 3799 4624 5543 5722 5719 2429 2381 5329 1722 1718 1307
    5779 862 1332 5144 800 2633 1529 306 4855 2336 2696 1312
    1399 707 5116 5768 1138 685 662 5322 3313 5019 694 5720
    3983 522 312 3274 2066 2275 2573 463
    205: 2401 5876 3237 4867 3700 3568 5557 1562 2187 4421 3795 4125
    3351 3641 3699 3745 4569 5124 1690 1810 1819 786 2528 1758
    3142 4439 509 349 4436
    206: 861 3389 1052 2373 4608 5063 621 4502 5478 2464 4251 4711
    2438 3987 5126 4839 4795 468 5133 5320 3116 5009 1983 4325
    2916 5653 1588 4693 517 3277 2129 5909 2944 5771 4999 1485
    5055 1799 2060 834 4675 1705 3386 2907
    207: 1844 1109 1631 5668 5400 5360 2769 5635 3463 5195 5626 5440
    2488 2521 1644 5087 5323
    208: 5204 1132 5728 1500 1924 1638 399 645 1265 5731 3876 3397
    3204 1982 1826
    209: 1098 1060 5786 5523 1914 4091 5297 201 1326 2620 5039 3842
    4507
    210: 1489 843 958 2339 5714 3468 5380 4813 5881 3599 2676 1508
    4375 2777 5258 1702 758 1349 1847 5948 3257 2314 4386 2599
    558 4757 1323 545
    211: 4555 4307 5534 1387 4556 5561 5432 5774 4390 1874 1195 623
    2317 2999 859 1737 1582 4279 928 2477 817 2149 3776 2740
    2307 4209 535 460 3340 5539 4200 4780 2761 1840 1141 2945
    2378 2890 2998 3849 824
    212: 1985 3595 989 5125 1374 1797 2484 2789 4037 2289 2274 3348
    394 4391 1640 3228 1951 1026 5936 3838 3151 3860 1450 2316
    1348 4344 1765 3683 1266 4048 1102 2993 2803 3777 876 2361
    213: 4789 1795 1794 5924 4495 4139 5648 1419 2482 728 1125 1622
    1631 2286 3979 5336 1931 1928 1933 1896 2769 5635 5461 4518
    3980 629 5804 4567 2801 951 3730 752 1247 2920 2912 3109
    5985 830 1536 1778 2434 4769 2115 2949 4722 3649 2545 2420
    2770 2124 4019 2616 2350 1613 3978 2229 1601 2269 2248 2570
    1271 411 789
    214: 3417 4947
    215: 2405 1562 2187 2695 656 2734 2839 3232 2055 2052 2266 2588
    5584 3121 3699 509 4205 4092 349 598 2221
    216: 3951 1562 2784 4355 1822 1816 3494 2055 5226 5230 3408 1408
    3699 3505 3307 5124 1690 1975 3558 1819 1810 1789 5880
    217: 3888 920 5833 3892 3894 5834 923 5850 5299 948 5856 5301
    950 5873 5321 969 5324 973 5908 5325 5910 5346 5347 988
    5915 1003 5351 5934 5375 1004 5670 5924 3870 919 5831 3843
    3220 4201 3837 1125 1626 3979 4049 1931 1896 2769 3143 1935
    4920 4327 870 4518 5131 3676 4647 501 4532 6000 3176 1454
    5660 2917 752 1247 3730 4737 2243 1522 4659 2470 1536 2434
    2115 2949 5744 1315 3309 1339 4576 5155 4184 2370 3978 2229
    1601 2269 2248 1271 3178 789 3867 903 3152 1520 3259
    213: 2967 1403 5318 4078 5871 3622 5561 2899 965 2276 4358 5656
    1383 1051 2810 2661 2014 4395 2589 2689 391 1228 4149 4186
    614 3849
    219: 2968 4423 3942 3943 5233 4236 4254 2595 4161 1426 1427 5663
    3680 2771 3935 2027 2026 5513 5138 3009 5469 5832 5271 3963
    3964 5078 5079 3707 2002 5192 3940 3921 3687 305 2329 5540
    2878 5724 5235 3556 1633 3784 4113 1017 2024 2057 2000 1997
    2923 3489 3490 5198 2186 4613 5887 2020 2051 2021 452 4938
    5747 1598 5777 4332 4118 803 5139 1941 1945 3128 2596 2614
    932 910 929 3105 3101 3080 5069 3010 3815 4264 546 5795
    5153 5135 5701 1317 2936 2924 5254 5251 3672 4241 4640 1570
    151 3955 922 5102 4035 4082 4031 4036 4084 4039 4059 2358
    3419 2712 5652 1952 1774 2735 3728 3702 3704 591 5231 1990
    1972 1974 1646 5408 5376 2642 2699 2612 4985 1116 1114 738
    4225 4752 3660 6003 5114 3055 5132 5054 3914 3919 3916 1548
    902 2721 3334 2718 5864 5088 4134 2121 806 1338 4244 2053
    3992 5602 3944 4249 3807 979 981 982 4497 2877 2340 1926
    2050 908 1581 1584 2872 3998 2282 4181 4266 2098 2345 1964
    2686 5889 4704 4008 4192 5830 3193 1305 1361 1042 5442 4811
    2806 2939 3639 2946 5064 4713 5929 4451 5956 5933 2644 1857
    3783 3803 3786 3788 4103 2414 2529 3385 2799 2943 2941 3033
    3049 1311 3074 3077 3030 3028 3962 3108 3123 3102 3103 353
    336 2646 4716 3908 3808 2134 1971 609 611 2747 3840 1993
    5196 1530 4781 5732 5101
    220: 4596 4599 724 699 3898 731 3181 2520 4414 4417 4441 4440
    668 696 689 1805 4664 3234 3031 3346 438 2955 3554 2700
    2535 925 4124 1662 4127 4129 1659 1655 3043 1542 693 3887
    386 1969 2542 5364 441 1024 718 3596 3910 3225 5366 5080
    4553 4510 5918 4427 2322 895 3809 4376 2496 5651 653 672
    5696 2630 3189 665 366 4484 1750 5448 4800 410 2491 4638
    4943 4944 1804 2757 1988 3719 3775 799 5938 2335 330 4615
    1864 594 1832 4772 3877 2639 2515 1314 1283 4286 4493 4144
    3425 4689 1076 4578 2862 700 4642 280 1469 5783 5687 5817
    716 698 726 719 4218 1786 423 2758 2423 5566 1807 1619
    221: 1948 2237 2487 5068 3207 4549 1018 2430 4461 4584 5598 3276
    5166 1072 5111 5127 5697 747 1369 4898 634 1558 2922 2240
    1811 477 1091 4435 3559 2265 1050 943 3211 2392 1048 2383
    2971 3333 2207 2619 3883 4306 3981 2802 5188 5792 5896 5180
    4274 4270 1397 814 3686 3948 1523 2005 413 5772 1734 5749
    1906 1973 1889 4499 1866 3620 2241 3911 2258 5627 1498 358
    3492 3762 1171 5433 5419 5621 3760 1681 3367 991
    222: 1330 4043 297 2653 5081 4629 5479 1438 1590 1589 2590 520
    4120 1686 3858 2656 3407 2310 3409 1107 2577 1903 2652 802
    1174 4283 2838 4742 4190 5900 1095 4173 2733 2403 5236 811
    1201 4079 5084 2323 2888 491 2337 1065 2731 818 5185 289
    1001 809 5686 4797 531 2473 3722 3720 5333 606 5769 3615
    2800 3212 5570 5758 4257 1645 6009 1453 6012 6013 5163 5528
    5592 4745 2039 3200 5828 288 1724 3518 2849 2869 3485 3456
    5176 2150 3404 5886 5536 2684 4611 5456 847 669 2144 3339
    1102 927 3777 4654 3303 2852 3264 3630
    223: 4044 4599 4596 1118 4927 3191 3187 3185 421 469 474 3181
    2668 1984 4163 395 4258 4156 3043 686 370 386 1257 5781
    2059 2919 1934 5213 4997 2496 3945 5344 4719 3379 2180 3001
    1647 5516 5435 5493 5448 1835 3349 2759 2736 2817 4638 5642
    1801 1804 3854 436 2808 2246 4158 2547 5428 5424 5455 5486
    2169 4384 3352 2296 4075 3213 5491 4617 4281 4573 4277 4117
    4875 3403 5273 1390 1127 2143 3254 3812 5633 2213 3045 1571
    3662 1812 2816 4720 5673 3063 4816 4879 2506 5704 4183 5783
    690 1295 5690 3327 3430 833 992 1726 4807 3066 3025 1020
    3048 3923
    224: 3068 1379 2590 3405 745 2292 2818 3258 2928 957 956 5634
    238 340 4140 3986 3144 4899 4198 1321 2081 918 2347 536
    900 2594 5643 4909 1728 1679 1860 1209 1944 683 3084 3042
    1981 1978 2004 5260 570 2409 3486 3714 1413 4610 5340 1999
    505 3412 1346 3151 5148 1783 2415 5739 3879 3718 1796 4703
    1701 3008 3537 4080 5862 1133 2123 4041 1855 542 3697
    225: 1164 1166 3451 2194 3300 2694 2554 422 5912 4444 3394 5044
    4673 2911 2360 1019 2790 4023 5680 3817 3752 2860 4981 1385
    2717 5303 4368 5970 4216 5409 4442 1684 376 1337 3744 362
    1081 363 947 791 1237 1497
    226: 5699 2102 2835 1407 679 3506 5587 589 3186 5723 3002 2781
    643 1213 1461 4561 3197 396 3095 4548 2303 2812 537 1099
    4765 2106 4282 3249 2062 2574 1367 5902 3059 793 1150 5482
    926 4337 6020
    227: 1654 2404 2402 1562 2295 5031 5177 3106 1611 1414 1822 1816
    842 5104 3746 3721 3047 3699 1690 1819 1810 688 714 692
    349 5880 4436 301 1185
    228: 624 4536 5667 561 5836 1605 1175 1953 831 3839 3107 2219
    610 5894 581 2167 1946 5824 666 3018 3301 2214 2499 530
    4910 1244 2675 2380 5429 3820 1288 630 3173 2309 3201 5240
    1674 2255 3787 3792 3285 4826 779 1735 4056 2569 2601 2587
    1531 1316 4428 2091 2319 3231 2285 1502 3712 2707 397 2564
    5578 5735
    229: 1948 2237 2487 5068 3207 4549 1018 2430 4584 4461 5166 3276
    5598 1072 5111 5127 5697 747 1886 4420 1369 4898 634 1558
    1618 2922 3578 477 2240 1811 1091 4435 3559 2265 1050 943
    3211 1048 2392 2383 4000 2971 3333 2207 2619 3883 4306 2802
    3981 5188 5792 5896 5180 4274 4270 3499 1599 3948 5943 1523
    5700 3384 1389 406 1898 5749 1906 1889 1973 4499 1866 4411
    5897 984 5707 865 4265 4028 5608 2258 5627 1498 358 3492
    3762 1171 5419 5433 4490 5621 3760 1681 3367 3199 991 5691
    230: 1654 1562 2695 2880 655 4394 1611 5197 5721 1822 1816 2069
    3853 1296 2458 4683 3699 1159 5124 1690 4210 1819 1810 786
    2084 1378 4205 4092 688 714 692 349 5880
    231: 5343 1525 1526 2766 4432 5952 3051 1603 808 1831 4465 2072
    4062 5011 2843 3725 1688 2876 3040 5404 3294 5367 1345 3314
    5436 3208 1479 1480 839 5465 2932 3982 3292 3310 3317 2448
    2446 670 3498 2930 1472 350 1468 4342 303 4936 4643 3523
    5835 2453 5168 5167 5295 4739 5388 746 4253 1364 3209 755
    5341 2298 3793 930 2386 2388 3432 1913 1911 5822 587 618
    5841 677 710 4732 5825 4735 4725 5338 3035 832 1384 5885
    2618 513 2264 3669 1621 2842 1624 4637 777 1528 994 1033
    2418 1692 983 2610 976 1465 1554 840 649 5507 5037 3545
    4864
    232: 1411 2629 4051 5110 2437 2843 5160 5759 3410 2662 2875 2617
    2687 3638 437 2017 2579 2533 2954 443 466 467 462 1699
    4160 313 4017 486 470 369 4708 5953 4957 5586 2281 4164
    1592
    233: 764 3328 3330 1053 1075 2723 2725 1030 1088 2680 5450 5452
    5818 5791 5494 5470 5497 5227 4850 4844 4848 2683 3427 1104
    2682 2061 1038 3322 3325 4401 488 5282 5362 5359 5365 5274
    3779 3713 3663 3569 3635 3661 3560 3633 3666 3565 661 4338
    2527 2782 1035 2751 2755 2753 3368 2638 3372 1084 3374 3395
    5288 5287 5289 4717 5802 3428 5805 5790 5788 5310 5311 5313
    5949 5891 5901 5920 5959 5923 5974 5926 5980 5925 3650 3654
    5210 4814 4817 4822 4820 5503 5517 5520 5500 5499 5518 5521
    5332 5334 5335 5393 5389 5269 5309 5305 5426 5422 5462 5466
    5458 5490 5485 5492 2703 2706 2524 3464 3527 2756 1036 4881
    4878 4854 4851 592 4155 3778 3709 3764 2270 4508 4721 4718
    5459 5467 5464 4917 4914 5468 4911 529 553 2592 2348 1448
    2198 2956 1463 2957 2979 1444 652 4925 1849 4233 1825 5418
    5420 3561 4336 3566 3461 5283 4763 4755 4758 4888 4884 4886
    3547 2727 3640 3692 5041 4487 3608 4620 3304 4131 3044 4052
    3534 3667 3611 3688 3609 4794 4792 4791 4796 4812 4767 4787
    5765 4026 3434 4230 4786 4783 4232 4960 2636 1054 2516 3459
    3493 3462 4333 955 5034 924 2417 711 885 884 2442 3495
    1871 1854 487 506 5563 5593 5582 5510 5538 2959 1077 1106
    2436 2422 3491 2472 5053 5750 949 953 3530 3535 5174 2701
    5950 5895 5476 5480 1442 1447 3691 3694 3629 3631 3331 1058
    2779 2580 2584 1034 2719 3454 1111 2720 3613 3734 3757 3632
    3759 3665 4215 4588 4616 4929 4980 4933 2894 2895 5904 5957
    4828 5927 5982 3804 3671 867 3062 730
    234: 2552 2110 3754 2029 5207 3021 1130 3000 2063 1471 2598 3819
    235: 5202 1642 2809 1617 4111 3024 1002 3715 5955 3589 5971 1575
    4300 3290 1893 3628 4308 2162 1222 3761
    236: 2402 2466 3951 3064 1757 4355 1414 1365 4070 1822 1816 3995
    5865 3699 3262 1690 1975 1810 1819 2910 539 866 3882
    237: 3937 5922 1193 3378 2697 4085 2953 5407
    238: 3068 1379 2332 745 2292 2818 3258 5265 1374 1209 1944 683
    224 2927 2003 1473 430 394 5286 3042 1981 1978 2004 5260
    570 2409 3486 3714 2407 1413 4610 5340 5148 1783 2415 5739
    3879 3718 4703 1796 1701 3008 2549 1133 5862 4080 2123 3537
    4041 1855 542 3697 796 4407
    239: 819 5267 2716 3929 615 1920 5618 3555 2428 3445 3444 5330
    5967 4793 3685 4937 3928 3359 1602 1775
    240: 1654 4696 1322 5737 1216 1987 2695 3106 655 4394 2792 1334
    3153 5294 5107 1769 2368 5386 708 3991 2763 637 5506 5721
    1822 1816 5445 2305 5705 2458 4683 3118 3853 1296 2266 3774
    939 2099 2097 3699 3716 2413 3993 3065 328 781 2394 5124
    1690 2364 584 4040 2379 5778 5564 1819 1810 786 509 688
    714 692 349 5880
    241: 5681 3973 2791 4701 2239 4033 1412 5740 3592 1963 1253 2031
    1960 1299 2677 1695 3477 3081 4194 4754 2902 3727 1661 4669
    5030 3869 1798 4560 1615 2075 1456 1236 5434 3205 2126 294
    1742 4939 5751 5154 296 2793 3553 888 5793 499 2509 638
    2898 3863 5276 2242 2544 2572 4746 1809 3796 5575 4222 4593
    4932 5412 5149 2125 5264 3433 4446 3594 996 829
    242: 5416 2359 5038 4784 5152 2568 498 2441 1246 1192 1773 4074
    1292 3562 2356 2465 2586
    243: 4406 4254 4236 1426 1427 3680 4989 2771 2829 5138 3009 5832
    5271 5078 5079 5192 3940 3921 3687 305 3278 3275 2329 5540
    2878 5724 1839 3556 3784 4113 3884 1997 5736 5666 1781 1779
    2923 2821 3489 3490 4613 2186 5275 5887 3488 4388 805 803
    5139 3739 1941 1945 3128 3133 3129 910 929 3105 3101 3080
    3010 3013 3026 3012 1301 4264 546 5795 5153 1327 1317 2936
    2924 4640 1563 2735 1990 1972 1974 5376 4876 4872 738 4261
    4225 4752 5142 4243 5114 3055 5054 5132 3919 3914 3916 1548
    3402 3076 902 5893 2985 5864 1543 2121 4244 2053 3992 3944
    3710 4249 3807 979 981 982 2877 4497 1581 2340 1926 2050
    908 1584 3998 2282 2872 4181 1546 4266 5369 2098 2345 1964
    2686 5442 2320 4811 2806 2939 871 3859 2948 2946 5064 4713
    5929 4451 5956 4831 4830 2644 293 3783 3803 3786 3788 4103
    2414 2529 1908 2799 1976 2943 2941 4193 3033 3049 1311 3074
    3077 3030 3028 3108 3123 3102 3103 2646 4716 2134 1971 609
    2747 611 3840 1993 5196 1530 4781 4245 5732 5158
    244: 4044 4513 308 3533 2607 974 1836 1071 1069 418 421 3996
    2786 3083 3684 5875 4441 4440 4417 4414 2583 2540 2273 3236
    3747 5609 3750 2338 4512 316 1662 4124 4129 2651 1542 3887
    5685 5684 1257 1443 3735 2635 1665 4452 640 5477 860 2966
    2451 5628 896 2762 5171 5654 1715 4504 3475 2427 3132 5263
    4097 3939 2975 5546 4369 4234 5213 1934 4372 653 672 1131
    3167 2503 2475 2445 3005 5553 1777 5672 3206 1609 3652 4145
    5976 1691 4677 6014 2951 3091 4081 3145 3756 1260 3448 2257
    4800 1227 1229 1231 4943 4944 3854 436 2868 2808 2246 432
    4331 5457 5861 782 784 5113 2815 1919 785 938 511 1120
    1524 5022 2016 2335 3985 4027 4459 5806 3399 3283 2874 757
    3706 5687 3430 3327 3053 3874 2366 582 5817 5782
    245: 697 5617 4680 4007 671 942 4312 3383 954 1220 1219 5232
    4978 2105 687 2137 1806 3067 3318 3347 695 2400 2421 2705
    1240 1242 4645 4650 3997 1235 5212 2118 5531 4185 5001 3957
    5046 5048 1768
    246: 4304 2904 917 1059 2089 5647 318 874 736 855 3356 858
    3595 2151 3150 5061 494 2310 3990 3988 1371 300 1374 1797
    5169 3977 1210 1998 2390 5562 5558 4086 415 3740 3577 3617
    4387 2789 1142 2289 2274 3348 3084 2937 2825 3507 5286 4391
    2278 2280 571 331 1381 1022 3722 2473 1793 1772 1703 2145
    3833 5935 5118 4949 3838 2961 3151 5674 5189 5567 3625 4473
    3099 4458 972 3800 4509 1011 3069 1187 622 673 1102 2548
    368 2993 2901 2852 2863 4526 3264 2230 2010
    247: 2359 5038 4644 1759 5989 644 3904 3906 648 3956 1484 3159
    1834 5076 801 4542 565 5007 2459 2101 2425 4305 5049 5150
    3573 5015 703 4635 3329 5734 5937 2989 5537 4546 1192 1773
    4074 3562 5645 1788 2861
    248: 2450 409 5292 3436 1514 3766 3765 913 617 5279 1184 2244
    4773 1491 4219 1970 3659 5385 4347 5411 326 5086
    249: 722 2797 484 3115 4998 1669 1392 869 5103 3437 650 4748
    5092 5815 2067 907 5194 600 5962 5253 815 1512 691 2095
    1553 1557 1550 1552 4296 4099 4343 4217 2511 2796 4550 4191
    1936 377 327 2259 1506 4528 3782 4061 5314 2183 4292 5157
    823 5571 4469 603 2921 2969 321 1416
    250: 324 4801 2498 1000 457 987 3532 780 5616 3540 1894 3642
    1481 1429 4970 5820 4952 899 3136 5762 5439 4946 4405 5509
    552 3512 4837 3862 2393 875 3268 663 2671 2233 1676 1179
    251: 2353 5695 1795 1794 5504 3843 3220 3837 1335 1723 1046 1933
    2769 4922 1290 4340 3798 4518 4647 501 2440 4628 4782 4738
    4768 2222 5141 4912 4563 4607 3500 5542 2605 453 2773 1744
    5549 3180 3974 4570 5843 2377 5660 2917 3729 4648 3514 3109
    1534 4769 2115 2949 1636 798 3041 1656 4707 4098 2974 2197
    5454 4840 5595 1743 4700 1666 3174 3536 4412 284 2965 2847
    5058 5954 5972 1064 508 5596 2468 5484 2205 4397 3978 5626
    2229 1601 2269 2248 5384 5440
    252: 1727 1725 2767 3365 4273 1103 3421 4764 5964 3273 3341 3338
    3949 4586 3089 1101 5094 5892 355 2460 451 2085 2560 2556
    3401 3396 1309 1880 2887 3003 3857 1207 5906 5872 5248 2408
    2562 4585 3113 3210 2711 1660 2785 425 5599 4187 333 4479
    1140 1143 1126 3624 1519 2485 4038 964 3829 2247
    253: 5244 5284 5184 4859 2375 4221 2154 556 4067 4449 3146 2357
    990 4923 3429 5460 2553 5249 2156 5606 2674 3147 1333 5730
    5990 4481 1785 5247 5268 2906 2828 2637 5397 1828 5191 3134
    3668 2449 2164 5966 5611 2079 2263 1063 2490 1188 1282 2362
    741 3251 2250 1802 1223
    254: 1948 2237 2487 5068 3207 4549 1018 2430 4584 4461 5166 5598
    3276 1072 5111 5127 5697 747 4898 1369 634 1558 2922 2240
    1811 477 1091 4435 3559 2265 1050 943 3211 1048 2392 2971
    3333 2619 3883 4306 2802 3981 5188 5792 5896 5180 4274 4270
    5394 814 3686 3948 2272 1523 5700 588 309 2597 2841 413
    1734 5749 2909 4228 2905 2908 2903 2891 1889 1973 1455 2940
    4499 1866 5898 4001 5707 5580 2142 2882 5488 5678 2258 5627
    1498 358 3492 2236 3762 1171 5433 5419 5621 3760 1681 3367
    991 4339
    255: 4044 4513 5002 967 418 3181 4392 3554 2955 2700 2535 316
    370 386 1257 2185 1032 1667 1376 2536 2322 2900 5651 5342
    2608 5319 4800 410 1804 432 1153 2335 3158 4852 5783 833
    992 4503 5817
    256: 2353 5695 1795 1794 5504 5045 774 3979 5400 5360 2769 4922
    475 4299 1375 3798 4518 4647 501 2555 1732 1852 5660 2917
    3729 4648 3514 3516 3522 3487 3519 3581 2434 4769 5221 916
    5315 5143 5000 490 5605 5134 5302 4885 2176 5201 448 4114
    2245 2201 2083 3978 2229 1601 2269 2248 5384 1271 411 3178
    5440 977 1230 3773
    257: 2466 1843 1846 4582 1562 4137 4141 4133 4108 3552 1756 4377
    1822 1816 5065 2055 2964 864 2627 2794 842 317 3699 2030
    3603 1921 5124 1690 812 1819 1810 786 440 3171 4539 2823
    1887 509 5100 2606 688 714 692 349 5880 4436
    258: 819 5267 5093 4671 4474 2454 2710 2100 1897 3602 5942 2716
    3897 1336 5997 4940 3929 5849 2925 2157 1955 5214 2428 3444
    3445 3841 5241 3071 2249 2013 5330 1168 1741 5760 5406 5911
    4633
    259: 1608 2783 1763 5218 1135 790 483 4630 4544 3163 1136 2834
    3723 1457 5610 2114 1693 3465 5677 851 4132 2972 1139 4583
    739 2009 4710 2288 4204 2795 2575 1490 1440 3202 1820
    260: 4044 1836 1517 469 472 4685 4660 1965 395 3794 850 2334
    4383 3952 4470 4581 1356 445 2919 4973 4378 1131 5342 4632
    841 2308 5502 4374 3027 2775 5398 5493 4587 2246 4158 5428
    5424 5486 3738 2871 3326 1388 1186 4617 4665 2173 1977 3520
    5383 740 944 5256 3999 5377 2893 3670 5050 635 2452 5361
    1124 404 3850 1729 5353 2467 510 4730 2006
    261: 1654 2402 2404 2041 5228 3420 763 2695 3413 4603 655 4394
    1611 1414 657 2615 3893 816 1527 4641 3162 4477 5712 3618
    1080 1146 3802 1822 1816 5065 2055 842 1408 317 5584 3699
    5124 1690 1819 1810 509 4205 4092 349 5880 3818 4853 2461
    5441 3933 3821
    262: 1708 3917 500 4609 1947 2663 1047 4297 4121 1377 5581 4788
    5495 1672 2519 1432 5702 5869 1215 2346 3226 4964 2277 287
    3315 5682 3279 3256 482 4073 354 3034 5033 5814 3705 952
    1905 4496 2226
    263: 1747 1745 3398 2767 3365 4273 3896 3341 3338 4589 3089 5094
    5892 356 355 2457 451 1341 1877 4239 1044 5390 3079 1097
    4806 3075 810 1422 3844 5246 4083 4187 1143 1140 3656 1519
    5245
    264: 3886 3014 1021 3644 2625 461 729 4941 2332 3595 2486 494
    5265 302 1374 1797 3348 3084 4391 975 1910 6022 505 3151
    3693 2685 4309 2155 622 1102 2548 368 5858 2993 2803 3777
    2852 4526 876 3264 3280 1112 5664
    265: 5789 1262 5043 4489 3122 4398 382 4030 1938 1714 4552 1055
    496 2038 4246 1294 1566 1459 458 1652 2082 2776 4519 2023
    2649 2283 5796 4293 5140 4313 4310 3901 4068 3311 4688 1612
    4100 1293 820 1996 845 3195 2135 4466 3814 5996 4810 3244
    266: 4046 4476 5754 1751 959 1475 3927 2035 2665 532 2678 3029
    4883 465 5979 5725 2504 2382 4891 1149 1606 1410 3588 3976
    4572 3006 3435 1492 5622 1355 2788 1630 709 3934 4252 2220
    538 1123 5613 2192 807 3646 4684 1252 4224 5644 5057 4543
    605 575 3971 1959 4016 4723 4862 5437 3872 5463 3037 5761
    4995 4646 3272 518 4472 1269 5780 1441 5945 1677 4798 4825
    5200 849 1892 6019 595 1256 813 734 5753 497 2431
    267: 1394 3886 6016 3375 1814 3376 3335 3438 504 2865 4535 2048
    4349 485 971 3571 3677 3253 478 4443 4437 5075 4715 3287
    6010 4629 2096 1635 2892 3023 5125 3567 3570 3574 1657 5172
    3959 295 4714 4712 4709 787 4227 854 3137 3130 5866 1991
    493 5084 5676 2363 5808 872 3004 5787 5807 835 4969 4967
    3284 1401 2495 4203 3131 5156 1545 5176 4212 2376 4882 2973
    2161 1597 6006 5106 2416 4226 4533 555 1639 4170 3339 5145
    3345 927 1451 2993 5181 3303 3343 2128 3217 894
    268: 5343 2766 4329 1869 3051 2897 1225 1224 2836 2833 2867 2813
    2832 2728 2883 2693 2090 2811 1603 1634 808 1300 1930 1927
    2692 2732 2681 1831 4465 2072 4062 4438 4413 4410 4409 1324
    1319 1962 5215 2108 1688 915 5799 3040 3314 5404 3294 5367
    5436 1345 3208 3292 3310 3982 3317 2448 5293 670 1273 3498
    2930 1472 1501 4345 1468 3481 1499 5698 2397 2047 2660 2659
    1853 5167 5168 5296 5295 4739 2831 4600 776 778 825 3768
    4295 4733 4291 822 3769 3701 1738 702 1748 4951 4597 2034
    3880 3899 5988 3240 2709 5280 2068 4471 725 723 4364 4861
    4829 4823 4824 1218 4727 3984 1203 1287 3924 755 3918 5733
    3637 2298 1318 1916 930 2297 519 1883 1885 1884 5822 587
    4564 3913 4595 2591 3708 2253 5841 677 710 3915 4728 4732
    5825 4735 2037 2012 4725 5071 1711 4590 3590 5842 384 5368
    4486 325 4072 5853 1033 1692 2610 976 1465 1554 1496 1904
    1899 3907 768 837 838 970 1670 3767
    269: 4242 4060 4063 4012 4015 4002 4057 439 5425 1604 3233 2419
    5784
    270: 3014 2332 1438 2590 3405 2127 5639 2310 5262 3871 302 1374
    1797 5839 1503 2395 2471 4175 3647 3900 4986 5115 4323 3909
    2886 4037 2289 2274 3586 5930 5281 533 361 357 1026 2473
    1767 2113 279 5630 5936 1989 5117 3838 3124 3151 359 449
    2343 4907 2316 5555 5554 5552 5573 1625 5550 5548 5529 2896
    5261 4778 3664 4478 5109 733 4906 2479 3772 772 3626 607
    5655 4605 4592 1540 4130 941 3529 4004 622 2539 2993 876
    315
    271: 2850 4029 5797 5717 1761 434 1922 5077 4565 5577 4359 5151
    4819 1967 4653 3015 1439 4537 3238 678 4272 5223 5671 5844
    4090 1007 5624 3157 5003 2853 1005 4053 428 3216 978 2534
    5372 966 3415 2768 935 5179 3749 3198 1206 4918 4468 1736
    2543 3797 1641 4571 4663 446 5511 4196 310 5481 748 329
    4827 524
    272: 1948 2237 3052 2561 4697 5960 2487 5068 3207 4549 1018 2430
    4584 4461 5598 3276 5166 1072 5111 5127 5697 747 1369 634
    4898 1558 2922 2240 477 1811 1091 4435 3559 2265 1050 943
    3211 1048 2392 2383 2971 3333 2207 2619 3883 4306 2802 3981
    5896 5188 5792 5180 4274 4270 5583 814 3948 4275 1523 5700
    588 940 1906 5530 1889 1973 5272 4047 4147 3022 5042 3177
    4499 1866 5898 3911 5707 4346 3184 968 5752 2258 5627 1498
    358 3492 419 3762 1171 5433 5621 3760 1681 3367 991
    273: 1163 2076 1830 1303 4069 544 562 4165 4167 4174 2963 1304
    5852 5848 5854 4109 4448 3733 3579 3584 828 4429 4430 5631
    1784 4483 2330 3073 1205 481 2301 2915 5859 3148 1460 4538
    4580 3127 3938 4770 1354 1382 281 283 5921 1161 1160 5603
    1162 601 4104 4105 3811 4649 4651 4106 1544 5916 933 599
    473 1637 3112 3621 2312 3039 1915 5487 5066 5776 2737 612
    1366 904 794 5868 3606 5565
    274: 3538 5649 2228 2704 3658 459 3828 727 5028 2087
    275: 3886 4043 3014 3644 2625 4941 1021 461 729 1438 2590 3405
    4525 360 3595 2486 2310 302 1797 5169 5483 2289 2274 3348
    1901 3344 3084 3586 4269 3926 2604 762 5591 342 3722 2473
    975 1999 3151 3282 3848 2819 4984 3302 3219 1867 1102 368
    3777 2852 2863 876 3264
    276: 1043 1753 5074 408 2632 2112 4101 5032 5640 2502 3007 3380
    4968 1009 5983 5963 4522 2551 557 2043 4579 4365 5224 3960
    1372 5863 2864 1891 3597 5259 5234 6001 3319 5239 2822 2670
    4341 3920 2352 2354 4445 2478 2934 742 1516 827 1671 1117
    1842 5291 5883 3458 5711 5659 2931 4013
    277: 4766 1313 3531 980 2159 2935 906 4416 1068 3895 2559
    278: 4983 639 5014 5431 2860 3082 3324 1578 4195 2196 4856 2717
    3229 3455 2726 3726 376 4514 528 1337 362 3744 363 1081
    2913 877 1764 3360 1803 3525 856 1310 1237 1233 744
    • Example 3 Consensus Sequence Build
  • ClustalW program is selected for multiple sequence alignments of an amino acid sequence of SEQ ID NO: 140 and its homologs, through SEQ ID NO: 278 and its homologs. Three major factors affecting the sequence alignments dramatically are (1) protein weight matrices; (2) gap open penalty; (3) gap extension penalty. Protein weight matrices available for ClustalW program include Blosum, Pam and Gonnet series. Those parameters with gap open penalty and gap extension penalty were extensively tested. On the basis of the test results, Blosum weight matrix, gap open penalty of 10 and gap extension penalty of 1 were chosen for multiple sequence alignment. The consensus sequence of SEQ ID NO: 237 and its 9 homologs were derived according to the procedure described above and is displayed in FIGS. 4( a) and 4(b). FIG. 4( b) is a continuation of FIG. 4( a). SEQ ID NO: 6033 is the consensus sequence built.
    • Example 4 Pfam Module Annoation
  • This example illustrates the identification of domain and domain module by Pfam analysis.
  • 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 domain modules and individual protein domain for the proteins of SEQ ID NO: 140 through 278 are shown in Table 17 and Table 18 respectively. 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 corresponding 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: 180 is characterized by two Pfam domains, e.g. “Homeobox” and “HALZ”. See also the protein with amino acids of to SEQ ID NO: 248 which is characterized by two copies of the Pfam domain “Ank”. In Table 18 “score” is the gathering score for the Hidden Markov Model of the domain which exceeds the gathering cutoff reported in Table 19.
  • TABLE 17
    PEP Seq
    ID No. Construct ID Pfam module Position
    217 CGPG3875.pep WRKY::WRKY 204-262::343-402
    169 CGPG2811.pep AP2 206-257
    252 CGPG7367.pep AUX_IAA 66-359
    207 CGPG3825.pep WRKY 102-164
    213 CGPG3858.pep WRKY 146-205
    192 CGPG3451.pep HLH 43-95
    176 CGPG2985.pep Myb_DNA-binding::Linker_histone 5-57::123-189
    259 CGPG7655.pep zf-B_box::zf-B_box 1-47::53-100
    181 CGPG3287.pep Ank::Ank::Ank::Chromo 127-158::159-191::
    193-225::320-368
    236 CGPG4612.pep NAM 6-141
    185 CGPG3309.pep zf-C2H2 68-90
    171 CGPG2935.pep Myb_DNA-binding 30-75
    186 CGPG3312.pep bZIP_1 146-209
    250 CGPG690.pep PHD 196-246
    245 CGPG5324.pep Linker_histone::AT_hook::AT_hook:: 11-78::84-96::
    AT_hook::AT hook 106-118::132-144::
    156-168
    159 CGPG2699.pep B3::Auxin_resp 176-281::302-384
    150 CGPG2594.pep HLH 277-327
    253 CGPG7369.pep zf-Dof 38-100
    258 CGPG7641.pep AT_hook::DUF296 70-82::142-262
    239 CGPG5130.pep AT_hook::AT_hook::DUF296 105-117::147-159::
    177-296
    164 CGPG2757.pep NAM 3-139
    182 CGPG3289.pep GATA 43-78
    205 CGPG3813.pep NAM 16-145
    218 CGPG3879.pep Myb_DNA-binding 235-286
    269 CGPG7840.pep zf-B_box::CCT 1-47::367-411
    232 CGPG4525.pep POX::Homeobox 261 -385::426-484
    265 CGPG7748.pep B3::Auxin_resp::AUX_IAA 141-246::268-
    350::640-805
    220 CGPG3987.pep Myb_DNA-binding::Myb_DNA-binding 13-59::65-110
    255 CGPG7374.pep Myb_DNA-binding::Myb_DNA-binding 38-84::90-135
    214 CGPG3865.pep zf-C2H2 67-89
    201 CGPG3793.pep zf-C2H2 243-265
    152 CGPG2604.pep Myb_DNA-binding::Myb_DNA-binding 30-79::126-173
    178 CGPG3169.pep Myb_DNA-binding::Myb_DNA-binding 18-65::71-116
    233 CGPG4527.pep TCP 96-305
    175 CGPG2975.pep KNOX1::KNOX2 83-127::134- 185
    166 CGPG2778.pep zf-ZPR1 ::zf-ZPR1 32-193::283-444
    260 CGPG7678.pep Myb_DNA-binding::Myb_DNA-binding 8-55::61-106
    276 CGPG6312.pep DUF630::DUF632 1-60::186-502
    256 CGPG7376.pep WRKY 84-144
    242 CGPG5292.pep Myb_DNA-binding 88-135
    145 CGPG2551.pep zf-C2H2 60-82
    202 CGPG3795.pep HLH 230-280
    174 CGPG2961.pep AP2 129-180
    154 CGPG2639.pep AT_hook::DUF296 80-92:107-232
    248 CGPG5422.pep Ank::Ank::Ank::Ank::Ank 36-68::70-102::
    104-137::138-170::
    184-226
    183 CGPG3296.pep WRKY 216-276
    167 CGPG2797.pep zf-C2H2 206-228
    261 CGPG7697.pep NAM 14-140
    195 CGPG3476.pep AP2 41-92
    257 CGPG7378.pep NAM 25-156
    244 CGPG5316.pep Myb_DNA-binding::Myb_DNA- 60-106::112-
    binding::Myb_DNA-binding 158::164-209
    216 CGPG3869.pep NAM 6-134
    148 CGPG2586.pep HLH 154-204
    168 CGPG2805.pep Myb_DNA-binding::Myb_DNA-binding 20-67::73-118
    177 CGPG3107.pep Myb_DNA-binding 243-294
    274 CGPG4213.pep HLH 63-112
    225 CGPG4066.pep bZIP_2 69-119
    184 CGPG3298.pep bZIP_2 192-246
    241 CGPG5280.pep BAH::PHD 21-136::140-189
    155 CGPG2644.pep HLH 132-181
    199 CGPG3750.pep NAM 7-136
    163 CGPG2752.pep GATA 222-257
    266 CGPG7757.pep SSrecog::Rtt106::HMG box 219-434::359-
    500::556-624
    141 CGPG1754.pep DUF573 153-246
    206 CGPG382.pep zf-B_box::CCT 11-59::357-401
    210 CGPG3841.pep HLH 211-260
    142 CGPG1809.pep RWP-RK 144-195
    238 CGPG490.pep AP2::B3 81-130::209-330
    144 CGPG2164.pep AUX_IAA 266-436
    173 CGPG2948.pep SRF-TF 20-73
    264 CGPG7743.pep AP2 164-215
    212 CGPG3857.pep AP2 74-125
    221 CGPG4004.pep HSF_DNA-bind 42-212
    267 CGPG7759.pep AP2 27-78
    151 CGPG26.pep SRF-TF::K-box 9-59::75-174
    196 CGPG3505.pep Myb_DNA-binding 47-98
    262 CGPG7709.pep zf-LSD1::zf-LSD1::zf-LSD1 7-31::46-70::
    82-106
    231 CGPG4195.pep KNOX1::KNOX2:: ELK 18-62::73-128::
    184-205
    228 CGPG4112.pep zf-C3HC4 202-242
    204 CGPG3810.pep MFMR::bZIP_1 1-205::293-356
    277 CGPG7188.pep DUF573 120-211
    211 CGPG3843.pep Myb_DNA-binding 84-135
    149 CGPG2593.pep HLH 163-214
    153 CGPG2615.pep NAM 9-138
    198 CGPG367.pep Myb_DNA-binding::Myb_DNA-binding 14-61::67-112
    243 CGPG5306.pep SRF-TF::K-box 9-59::76-173
    187 CGPG3327.pep zf-C3HC4 109-149
    235 CGPG4591.pep zf-B_box 1-46
    251 CGPG7354.pep WRKY 159-219
    194 CGPG3468.pep zf-B_box::CCT 10-57::265-309
    273 CGPG31.pep EIN3 31-422
    272 CGPG2562.pep HSF_DNA-bind 18-188
    263 CGPG7714.pep AUX_IAA 6-173
    208 CGPG3828.pep TCP 44-253
    146 CGPG2578.pep Myb_DNA-binding::Myb_DNA-binding 25-72::78-123
    275 CGPG477.pep AP2 37-88
    268 CGPG7822.pep KNOX 1::KNOX2::ELK::Homeobox 32-76::79-130::
    178-199::201-260
    254 CGPG7373.pep HSF_DNA-bind 14-194
    229 CGPG4133.pep HSF_DNA-bind 8-206
    224 CGPG4061.pep AP2::B3 75-124::204-318
    230 CGPG4166.pep NAM 11-139
    161 CGPG2711.pep SBP 58-136
    246 CGPG5330.pep AP2 128-180
    179 CGPG3171.pep zf-C2H2 61-83
    147 CGPG2583.pep SRF-TF::K-box 9-59::79-173
    170 CGPG2907.pep zf-C2H2 177-200
    200 CGPG3761.pep GRAS 1-320
    222 CGPG4013.pep AP2 119-170
    172 CGPG2943.pep Myb_DNA-binding 65-110
    270 CGPG7876.pep AP2 21-72
    140 CGPG113.pep AP2::AP2 282-342::384-436
    226 CGPG4082.pep HLH 127-178
    271 CGPG858.pep CXC::CXC 398-439::484-525
    156 CGPG2657.pep AP2 25-76
    215 CGPG3868.pep NAM 17-139
    197 CGPG359.pep zf-C3HC4 89-132
    223 CGPG4015.pep Myb_DNA-binding::Myb_DNA-binding 14-61::67-112
    190 CGPG3369.pep GRAS 130-436
    180 CGPG3175.pep Homeobox::HALZ 30-86::87-131
    247 CGPG5334.pep Myb_DNA-binding 109-156
    227 CGPG4106.pep NAM 9-134
    203 CGPG3804.pep WRKY 135-194
    209 CGPG3837.pep zf-C2H2 244-266
    193 CGPG3463.pep zf-C2H2 6-28
    240 CGPG5278.pep NAM 20-146
    165 CGPG2767.pep zf-C2H2 193-215
    188 CGPG3341.pep AP2::AP2 130-180::222-273
    158 CGPG2678.pep zf-C3HC4 113-153
    249 CGPG5599.pep RWP-RK::PB1 605-656::811-894
    219 CGPG3947.pep SRF-TF::K-box 9-59::75-174
    157 CGPG2664.pep zf-B_box 26-72
  • TABLE 18
    PEP Seq
    ID No. Construct ID Pfam domain name Begin Stop score E-value
    140 CGPG113.pep AP2 282 342 60.7 4.90E−15
    140 CGPG113.pep AP2 384 436 64.2 4.50E−16
    141 CGPG1754.pep DUF573 153 246 225.4 1.30E−64
    142 CGPG1809.pep RWP-RK 144 195 76 1.20E−19
    144 CGPG2164.pep AUX_IAA 266 436 −74.9 0.00043
    145 CGPG2551.pep zf-C2H2 60 82 24.2 0.00048
    146 CGPG2578.pep Myb_DNA-binding 25 72 47.2 5.90E−11
    146 CGPG2578.pep Myb_DNA-binding 78 123 46.4 9.80E−11
    147 CGPG2583.pep SRF-TF 9 59 107.5 4.10E−29
    147 CGPG2583.pep K-box 79 173 44.6 3.50E−10
    148 CGPG2586.pep HLH 154 204 27.2 5.90E−05
    149 CGPG2593.pep HLH 163 214 43.8 6.00E−10
    150 CGPG2594.pep HLH 277 327 66.3 1.00E−16
    151 CGPG26.pep SRF-TF 9 59 119.5 1.00E−32
    151 CGPG26.pep K-box 75 174 166.3 8.30E−47
    152 CGPG2604.pep Myb_DNA-binding 30 79 31 4.30E−06
    152 CGPG2604.pep Myb_DNA-binding 126 173 45 2.70E−10
    153 CGPG2615.pep NAM 9 138 293.9 3.10E−85
    154 CGPG2639.pep AT_hook 80 92 7.5 1.2
    154 CGPG2639.pep DUF296 107 232 209.5 8.00E−60
    155 CGPG2644.pep HLH 132 181 51 4.10E−12
    156 CGPG2657.pep AP2 25 76 78.3 2.60E−20
    157 CGPG2664.pep zf-B_box 26 72 43.1 1.00E−09
    158 CGPG2678.pep zF-C3HC4 113 153 44.5 3.70E−10
    159 CGPG2699.pep B3 176 281 104.7 2.80E−28
    159 CGPG2699.pep Auxin_resp 302 384 204.5 2.50E−58
    161 CGPG2711.pep SBP 58 136 173.4 6.00E−49
    163 CGPG2752.pep GATA 222 257 75.4 1.90E−19
    164 CGPG2757.pep NAM 3 139 145.1 2.00E−40
    165 CGPG2767.pep zf-C2H2 193 215 21.8 0.0025
    166 CGPG2778.pep zf-ZPR1 32 193 253 6.50E−73
    166 CGPG2778.pep zf-ZPR1 283 444 207.6 3.00E−59
    167 CGPG2797.pep zf-C2H2 206 228 30.5 6.00E−06
    168 CGPG2805.pep Myb_DNA-binding 20 67 42.7 1.30E−09
    168 CGPG2805.pep Myb_DNA-binding 73 118 50.8 4.80E−12
    169 CGPG2811.pep AP2 206 257 32.1 2.00E−06
    170 CGPG2907.pep zf-C2H2 177 200 24.1 0.00052
    171 CGPG2935.pep Myb_DNA-binding 30 75 32.3 1.80E−06
    172 CGPG2943.pep Myb_DNA-binding 65 110 57.6 4.40E−14
    173 CGPG2948.pep SRF-TF 20 73 27.1 6.40E−05
    174 CGPG2961.pep AP2 129 180 65 2.50E−16
    175 CGPG2975.pep KNOX1 83 127 94.4 3.50E−25
    175 CGPG2975.pep KNOX2 134 185 114.1 4.10E−31
    176 CGPG2985.pep Myb_DNA-binding 5 57 34.7 3.30E−07
    176 CGPG2985.pep Linker histone 123 189 0.3 0.00099
    177 CGPG3107.pep Myb_DNA-binding 243 294 44.6 3.60E−10
    178 CGPG3169.pep Myb_DNA-binding 18 65 53.4 7.80E−13
    178 CGPG3169.pep Myb_DNA-binding 71 116 59 1.60E−14
    179 CGPG3171.pep zf-C2H2 61 83 21.8 0.0026
    180 CGPG3175.pep Homeobox 30 86 66.5 8.90E−17
    180 CGPG3175.pep HALZ 87 131 37.6 4.30E−08
    181 CGPG3287.pep Ank 127 158 6.6 3.7
    181 CGPG3287.pep Ank 159 191 24.8 0.00033
    181 CGPG3287.pep Ank 193 225 30.7 5.50E−06
    181 CGPG3287.pep Chromo 320 368 45.7 1.60E−10
    182 CGPG3289.pep GATA 43 78 65.8 1.50E−16
    183 CGPG3296.pep WRKY 216 276 141 3.30E−39
    184 CGPG3298.pep bZIP_2 192 246 31 4.30E−06
    184 CGPG3298.pep bZIP_1 194 255 26.8 8.00E−05
    185 CGPG3309.pep zf-C2H2 68 90 20.4 0.0066
    186 CGPG3312.pep bZIP_1 146 209 34.3 4.50E−07
    186 CGPG3312.pep bZIP_2 146 200 28.6 2.40E−05
    187 CGPG3327.pep zf-C3HC4 109 149 49 1.60E−11
    188 CGPG3341.pep AP2 130 180 62.3 1.60E−15
    188 CGPG3341.pep AP2 222 273 58.2 2.90E−14
    190 CGPG3369.pep GRAS 130 436 532.9  3.50E−157
    192 CGPG3451.pep HLH 43 95 33.5 7.80E−07
    193 CGPG3463.pep zf-C2H2 6 28 24.2 0.00047
    194 CGPG3468.pep zf-B_box 10 57 39.9 9.30E−09
    194 CGPG3468.pep CCT 265 309 86.2 1.00E−22
    195 CGPG3476.pep AP2 41 92 73.1 9.10E−19
    196 CGPG3505.pep Myb_DNA-binding 47 98 43.1 1.00E−09
    197 CGPG359.pep zf-C3HC4 89 132 35.3 2.30E−07
    198 CGPG367.pep Myb_DNA-binding 14 61 46.6 8.70E−11
    198 CGPG367.pep Myb_DNA-binding 67 112 53.8 6.00E−13
    199 CGPG3750.pep NAM 7 136 307.5 2.50E−89
    200 CGPG3761.pep GRAS 1 320 391.8  1.00E−114
    201 CGPG3793.pep zf-C2H2 243 265 22.2 0.002
    202 CGPG3795.pep HLH 230 280 33.3 8.80E−07
    203 CGPG3804.pep WRKY 135 194 153.9 4.40E−43
    204 CGPG3810.pep MFMR 1 205 368.8  9.00E−108
    204 CGPG3810.pep bZIP_1 293 356 91.5 2.60E−24
    204 CGPG3810.pep bZIP_2 293 347 29.2 1.50E−05
    205 CGPG3813.pep NAM 16 145 295.2 1.20E−85
    206 CGPG382.pep zf-B_box 11 59 38 3.40E−08
    206 CGPG382.pep CCT 357 401 85.6 1.60E−22
    207 CGPG3825.pep WRKY 102 164 94.6 3.10E−25
    208 CGPG3828.pep TCP 44 253 149.4 1.00E−41
    209 CGPG3837.pep zf-C2H2 244 266 24.8 0.00032
    210 CGPG3841.pep HLH 211 260 44.6 3.50E−10
    211 CGPG3843.pep Myb_DNA-binding 84 135 47.7 4.00E−11
    212 CGPG3857.pep AP2 74 125 83.2 8.60E−22
    213 CGPG3858.pep WRKY 146 205 144.2 3.80E−40
    214 CGPG3865.pep zf-C2H2 67 89 22.1 0.0021
    215 CGPG3868.pep NAM 17 139 58.4 2.50E−14
    216 CGPG3869.pep NAM 6 134 304.9 1.50E−88
    217 CGPG3875.pep WRKY 204 262 141.3 2.70E−39
    217 CGPG3875.pep WRKY 343 402 151.5 2.30E−42
    218 CGPG3879.pep Myb_DNA-binding 235 286 35.8 1.60E−07
    219 CGPG3947.pep SRF-TF 9 59 118.6 1.90E−32
    219 CGPG3947.pep K-box 75 174 165.8 1.20E−46
    220 CGPG3987.pep Myb_DNA-binding 13 59 59.2 1.40E−14
    220 CGPG3987.pep Myb_DNA-binding 65 110 50.8 4.90E−12
    221 CGPG4004.pep HSF_DNA-bind 42 212 267.1 3.60E−77
    222 CGPG4013.pep AP2 119 170 87.4 4.70E−23
    223 CGPG4015.pep Myb_DNA-binding 14 61 46.6 8.80E−11
    223 CGPG4015.pep Myb_DNA-binding 67 112 40.9 4.40E−09
    224 CGPG4061.pep AP2 75 124 50.7 5.30E−12
    224 CGPG4061.pep B3 204 318 116.1 1.00E−31
    225 CGPG4066.pep bZIP_2 69 119 24.4 0.00043
    226 CGPG4082.pep HLH 127 178 59.2 1.40E−14
    227 CGPG4106.pep NAM 9 134 300.7 2.80E−87
    228 CGPG4112.pep zf-C3HC4 202 242 39.7 1.00E−08
    229 CGPG4133.pep HSF_DNA-bind 8 206 179.6 7.80E−51
    230 CGPG4166.pep NAM 11 139 316.4 5.10E−92
    231 CGPG4195.pep KNOX1 18 62 72.1 1.90E−18
    231 CGPG4195.pep KNOX2 73 128 86.8 7.00E−23
    231 CGPG4195.pep ELK 184 205 25.4 0.0002
    232 CGPG4525.pep POX 261 385 200.7 3.60E−57
    232 CGPG4525.pep Homeobox 426 484 6.6 0.0024
    233 CGPG4527.pep TCP 96 305 303.9 3.10E−88
    235 CGPG4591.pep zf-B_box 1 46 22.6 0.00055
    236 CGPG4612.pep NAM 6 141 278.3 1.60E−80
    238 CGPG490.pep AP2 81 130 55.4 1.90E−13
    238 CGPG490.pep B3 209 330 110.8 4.00E−30
    239 CGPG5130.pep AT_hook 105 117 19 0.013
    239 CGPG5130.pep AT_hook 147 159 6.3 1.9
    239 CGPG5130.pep DUF296 177 296 206.6 6.00E−59
    240 CGPG5278.pep NAM 20 146 307.2 3.00E−89
    241 CGPG5280.pep BAH 21 136 139.8 7.60E−39
    241 CGPG5280.pep PHD 140 189 56.9 6.90E−14
    242 CGPG5292.pep Myb_DNA-binding 88 135 49 1.70E−11
    243 CGPG5306.pep SRF-TF 9 59 98.7 1.90E−26
    243 CGPG5306.pep K-box 76 173 133.1 8.00E−37
    244 CGPG5316.pep Myb_DNA-binding 60 106 51.8 2.40E−12
    244 CGPG5316.pep Myb_DNA-binding 112 158 59.9 8.70E−15
    244 CGPG5316.pep Myb_DNA-binding 164 209 45.4 2.00E−10
    245 CGPG5324.pep Linker_histone 11 78 93.2 8.30E−25
    245 CGPG5324.pep AT_hook 84 96 9.3 0.6
    245 CGPG5324.pep AT_hook 106 118 16.7 0.031
    245 CGPG5324.pep AT_hook 132 144 11.7 0.23
    245 CGPG5324.pep AT_hook 156 168 13.4 0.12
    246 CGPG5330.pep AP2 128 180 85.5 1.70E−22
    247 CGPG5334.pep Myb_DNA-binding 109 156 48.1 3.10E−11
    248 CGPG5422.pep Ank 36 68 3.5 10
    248 CGPG5422.pep Ank 70 102 9.1 1.6
    248 CGPG5422.pep Ank 104 137 11 0.85
    248 CGPG5422.pep Ank 138 170 8.5 2
    248 CGPG5422.pep Ank 184 226 13.3 0.39
    249 CGPG5599.pep RWP-RK 605 656 106.1 1.10E−28
    249 CGPG5599.pep PB1 811 894 87.3 5.00E−23
    250 CGPG690.pep PHD 196 246 53.8 5.80E−13
    251 CGPG7354.pep WRKY 159 219 139.2 1.20E−38
    252 CGPG7367.pep AUX_IAA 66 359 448.6  8.70E−132
    253 CGPG7369.pep zf-Dof 38 100 138.6 1.80E−38
    254 CGPG7373.pep HSF_DNA-bind 14 194 189.2 1.00E−53
    255 CGPG7374.pep Myb_DNA-binding 38 84 57.8 3.80E−14
    255 CGPG7374.pep Myb_DNA-binding 90 135 58.8 1.80E−14
    256 CGPG7376.pep WRKY 84 144 130.5 4.70E−36
    257 CGPG7378.pep NAM 25 156 247.7 2.50E−71
    258 CGPG7641.pep AT_hook 70 82 19.1 0.012
    258 CGPG7641.pep DUF296 142 262 232.7 8.20E−67
    259 CGPG7655.pep zf-B_box 1 47 41.2 3.60E−09
    259 CGPG7655.pep zf-B_box 53 100 54.5 3.80E−13
    260 CGPG7678.pep Myb_DNA-binding 8 55 50.2 7.30E−12
    260 CGPG7678.pep Myb_DNA-binding 61 106 57.2 5.50E−14
    261 CGPG7697.pep NAM 14 140 299.2 7.80E−87
    262 CGPG7709.pep zf-LSD1 7 31 38.1 3.20E−08
    262 CGPG7709.pep zf-LSD1 46 70 52 2.10E−12
    262 CGPG7709.pep zf-LSD1 82 106 46.7 8.20E−11
    263 CGPG7714.pep AUX_IAA 6 173 339.7 5.10E−99
    264 CGPG7743.pep AP2 164 215 80.1 7.30E−21
    265 CGPG7748.pep B3 141 246 110.7 4.50E−30
    265 CGPG7748.pep Auxin_resp 268 350 198.6 1.50E−56
    265 CGPG7748.pep AUX IAA 640 805 −72.2 0.00028
    266 CGPG7757.pep SSrecog 219 434 495.1 8.70E−146
    266 CGPG7757.pep Rtt106 359 500 179.1 1.20E−50
    266 CGPG7757.pep HMG box 556 624 110.2 6.50E−30
    267 CGPG7759.pep AP2 27 78 79.5 1.10E−20
    268 CGPG7822.pep KNOX1 32 76 81.2 3.30E−21
    268 CGPG7822.pep KNOX2 79 130 92.5 1.30E−24
    268 CGPG7822.pep ELK 178 199 30 8.50E−06
    268 CGPG7822.pep Homeobox 201 260 0.4 0.0098
    269 CGPG7840.pep zf-B_box 1 47 23.5 0.00044
    269 CGPG7840.pep CCT 367 411 80.2 6.50E−21
    270 CGPG7876.pep AP2 21 72 82.5 1.40E−21
    271 CGPG858.pep CXC 398 439 89.7 9.20E−24
    271 CGPG858.pep CXC 484 525 82.7 1.10E−21
    272 CGPG2562.pep HSF_DNA-bind 18 188 213.9 3.70E−61
    273 CGPG31.pep EIN3 31 422 1032.5 0
    274 CGPG4213.pep HLH 63 112 44.3 4.40E−10
    275 CGPG477.pep AP2 37 88 79.6 9.90E−21
    276 CGPG6312.pep DUF630 1 60 123.9 4.80E−34
    276 CGPG6312.pep DUF632 186 502 465.8  5.80E−137
    277 CGPG7188.pep DUF573 120 211 191.2 2.60E−54
  • TABLE 19
    Pfam domain gathering
    name Accession # cutoff domain description
    AT_hook PF02178.10 3.6 AT hook motif
    AUX_IAA PF02309.7 −83 AUX/IAA family
    Ank PF00023.21 0 Ankyrin repeat
    Auxin_resp PF06507.4 25 Auxin response factor
    B3 PF02362.12 26.5 B3 DNA binding domain
    BAH PF01426.9 7 BAH domain
    CCT PF06203.5 25 CCT motif
    CXC PF03638.6 25 Tesmin/TSO1 -like CXC domain
    Chromo PF00385.15 27.5 ′chromo′ (CHRromatin
    Organisation MOdifier) domain
    DUF296 PF03479.6 −11 Domain of unknown function
    (DUF296)
    DUF573 PF04504.5 25 Protein of unknown function,
    DUF573
    DUF630 PF04783.3 25 Protein of unknown function
    (DUF630)
    DUF632 PF04782.3 25 Protein of unknown function
    (DUF632)
    EIN3 PF04873.4 −137.6 Ethylene insensitive 3
    ELK PF03789.4 25 ELK domain
    GATA PF00320.18 28.5 GATA zinc finger
    GRAS PF03514.5 −78 GRAS family transcription factor
    HALZ PF02183.9 18.1 Homeobox associated leucine
    zipper
    HLH PF00010.17 8.3 Helix-loop-helix DNA-binding
    domain
    HMG_box PF00505.10 4.1 HMG (high mobility group) box
    HSF_DNA- PF00447.8 −70 HSF-type DNA-binding
    bind
    Homeobox PF00046.20 −4.1 Homeobox domain
    K-box PF01486.8 0 K-box region
    KNOX1 PF03790.4 25 KNOX1 domain
    KNOX2 PF03791.4 25 KNOX2 domain
    Linker_ PF00538.10 −8 linker histone H1 and H5 family
    histone
    MFMR PF07777.2 −46.7 G-box binding protein MFMR
    Myb_DNA- PF00249.22 14 Myb-like DNA-binding domain
    binding
    NAM PF02365.6 −19 No apical meristem (NAM)
    protein
    PB1 PF00564.15 12.3 PB1 domain
    PHD PF00628.20 26.2 PHD-finger
    POX PF07526.2 −39.4 Associated with HOX
    RWP-RK PF02042.6 25 RWP-RK domain
    Rtt106 PF08512.3 10.1 Histone chaperone Rttp106-like
    SBP PF03110.5 25 SBP domain
    SRF-TF PF00319.9 11 SRF-type transcription factor
    (DNA-binding and dimerisation
    domain)
    SSrecog PF03531.5 −73.6 Structure-specific recognition
    protein (SSRP1)
    TCP PF03634.4 −38 TCP family transcription factor
    WRKY PF03106.6 −6.7 WRKY DNA-binding domain
    bZIP_1 PF00170.12 24.8 bZIP_transcription factor
    bZIP_2 PF07716.6 15 Basic region leucine zipper
    zf-B_box PF00643.15 15.3 B-box zinc finger
    zf-C2H2 PF00096.17 17.7 Zinc finger, C2H2 type
    zf-C3HC4 PF00097.16 16 Zinc finger, C3HC4 type
    (RING finger)
    zf-Dof PF02701.6 25 Dof domain, zinc finger
    zf-LSD1 PF06943.3 25 LSD1 zinc finger
    z f-ZPR1 PF03367.4 25 ZPR1 zinc-finger domain
    • Example 5 Plasmid Contruction for Transferring Recombinant DNA
  • This example illustrates the construction of plasmids for transferring recombinant DNA into the nucleus of a plant cell which can be regenerated into a transgenic crop plant of this invention. Primers for PCR amplification of protein coding nucleotides of recombinant DNA 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. DNA of interest, e.g., each DNA identified in Table 2 and the DNA for the identified homologous genes, are cloned and amplified by PCR prior to insertion into the insertion site the base vector.
  • A. Plant Expression Constructs for Corn Transformation
  • Elements of an exemplary common expression vector, pMON93039 are illustrated in Table 20. The exemplary base vector which is especially useful for corn transformation is illustrated in FIG. 2 and assembled using technology known in the art.
  • TABLE 20
    pMON93039
    Coordinates of
    function name annotation SEQ ID NO: 6024
    Agrobacterium B-AGRtu.right border Agro right border 11364-11720
    T-DNA sequence, essential for
    trabsfer transfer of T-DNA.
    Gene of E-Os.Act1 upstream promoter region  19-775
    interest of the rice actin 1 gene
    expression E-CaMV.35S.2xA1-B3 duplicated35S A1-B3  788-1120
    cassette domain without TATA box
    P-Os.Act1 promoter region of the rice 1125-1204
    actin 1 gene
    L-Ta.Lhcb1 5′ untranslated leader of 1210-1270
    wheat major chlorophyll
    a/b binding protein
    I-Os.Act1 first intron and flanking 1287-1766
    UTR exon sequences from
    the rice actin 1 gene
    T-St.Pis4 3′ non-translated region of 1838-2780
    the potato proteinase
    inhibitor II gene which
    functions to direct
    polyadenylation of the
    mRNA
    Plant P-Os.Act1 Promoter from the rice 2830-3670
    selectable actin 1 gene
    marker L-Os.Act1 first exon of the rice actin 3671-3750
    expression 1 gene
    cassette I-Os.Act1 first intron and flanking 3751-4228
    UTR exon sequences from
    the rice actin 1 gene
    TS-At.ShkG-CTP2 Transit peptide region of 4238-4465
    Arabidopsis EPSPS
    CR-AGRtu.aroA-CP4.nat coding region for bacterial 4466-5833
    strain CP4 native arogA
    gene
    T-AGRtu.nos A 3′ non-translated region 5849-6101
    of the nopaline synthase
    gene of Agrobacterium
    tumefaciens Ti plasmid
    which functions to direct
    polyadenylation of the
    mRNA.
    Agrobacterium B-AGRtu.left border Agro left border sequence, 6168-6609
    T-DNA essential for transfer of T-
    transfer DNA.
    Maintenance OR-Ec.oriV-RK2 The vegetative origin of 6696-7092
    in E. coli replication from plasmid
    RK2.
    CR-Ec.rop Coding region for 8601-8792
    repressor of primer from
    the ColE1 plasmid.
    Expression of this gene
    product interferes with
    primer binding at the
    origin of replication,
    keeping plasmid copy
    number low.
    OR-Ec.ori-ColE1 The minimal origin of 9220-9808
    replication from the E. coli
    plasmid ColE1.
    P-Ec.aadA-SPC/STR romoter for Tn7 10339-10380
    adenylyltransferase
    (AAD(3″))
    CR-Ec.aadA-SPC/STR Coding region for Tn7 10381-11169
    adenylyltransferase
    (AAD(3″)) conferring
    spectinomycin and
    streptomycin resistance.
    T-Ec.aadA-SPC/STR 3′ UTR from the Tn7 11170-11227
    adenylyltransferase
    (AAD(3″)) gene of E. coli.
  • B. Plant Expression Constructs for Soybean or Canola Transformation
  • Plasmids for use in transformation of soybean are also prepared. Elements of an exemplary common expression vector plasmid pMON82053 are shown in Table 21 below. This exemplary soybean transformation base vector illustrated in FIG. 2 is assembled using the technology known in the art. DNA of interest, e.g., each DNA identified in Table 2 and the DNA for the identified homologous genes, is cloned and amplified by PCR prior to insertion into the insertion site the base vector at the insertion site between the enhanced 35S CaMV promoter and the termination sequence of cotton E6 gene.
  • TABLE 21
    pMON82053
    Coordinates of
    function name annotation SEQ ID NO: 6025
    Agrobacterium B-AGRtu.left Agro left border sequence, essential 6144-6585
    T-DNA transfer border for transfer of T-DNA.
    Plant selectable P-At.Act7 Promoter from the arabidopsis actin 7 6624-7861
    marker gene
    expression L-At.Act7 5′UTR of Arabidopsis Act7 gene
    cassette I-At.Act7 Intron from the Arabidopsis actin7 gene
    TS-At.ShkG-CTP2 Transit peptide region of Arabidopsis 7864-8091
    EPSPS
    CR-AGRtu.aroA- Synthetic CP4 coding region with dicot 8092-9459
    CP4.nno_At preferred codon usage.
    T-AGRtu.nos A 3′ non-translated region of the 9466-9718
    nopaline synthase gene of
    Agrobacterium tumefaciens Ti plasmid
    which functions to direct
    polyadenylation of the mRNA.
    Gene of interest P-CaMV.35S-enh Promoter for 35S RNA from CaMV  1-613
    expression containing a duplication of the −90 to
    cassette −350 region.
    T-Gb.E6-3b 3′ untranslated region from the fiber  688-1002
    protein E6 gene of sea-island cotton;
    Agrobaterium B-AGRtu.right Agro right border sequence, essential for 1033-1389
    T-DNA transfer border transfer of T-DNA.
    Maintenance in OR-Ec.oriV-RK2 The vegetative origin of replication from 5661-6057
    E. coli plasmid RK2.
    CR-Ec.rop Coding region for repressor of primer 3961-4152
    from the ColE1 plasmid. Expression of
    this gene product interferes with primer
    binding at the origin of replication,
    keeping plasmid copy number low.
    OR-Ec.ori-ColE1 The minimal origin of replication from 2945-3533
    the E. coli plasmid ColE1.
    P-Ec.aadA- romoter for Tn7 adenylyltransferase 2373-2414
    SPC/STR (AAD(3″))
    CR-Ec.aadA- Coding region for Tn7 1584-2372
    SPC/STR adenylyltransferase (AAD(3″))
    conferring spectinomycin and
    streptomycin resistance.
    T-Ec.aadA- 3′ UTR from the Tn7 1526-1583
    SPC/STR adenylyltransferase (AAD(3″)) gene of
    E. coli.
  • C. Plant Expression Constructs for Cotton Transformation
  • Plasmids for use in transformation of cotton are also prepared. Elements of an exemplary common expression vector plasmid pMON99053 are shown in Table 22 below and FIG. 3. Primers for PCR amplification of protein coding nucleotides of recombinant DNA 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. Each recombinant DNA coding for a protein identified in Table 2 is amplified by PCR prior to insertion into the insertion site within the gene of interest expression cassette of one of the base.
  • TABLE 22
    pMON99053
    Coordinates of
    function name annotation SEQ ID NO: 6026
    Agrobacterium B-AGRtu.right Agro right border sequence,  1-357
    T-DNA transfer border essential for transfer of T-DNA.
    Gene of interest Exp-CaMV.35S- Enhanced version of the 35S  388-1091
    expression enh+ph.DnaK RNA promoter from CaMV plus
    cassette the petunia hsp70 5′ untranslated
    region
    T-Ps.RbcS2-E9 The 3′ non-translated region of 1165-1797
    the pea RbcS2 gene which
    functions to direct
    polyadenylation of the mRNA.
    Plant selectable Exp-CaMV.35S Promoter and 5′ untranslated 1828-2151
    marker region of the 35S RNA from
    expression CaMV
    cassette CR-Ec.nptil-Tn5 Neomycin Phosphotransferase II 2185-2979
    gene that confers resistance to
    neomycin and kanamycin
    T-AGRtu.nos A 3′ non-translated region of the 3011-3263
    nopaline synthase gene of
    Agrobacterium tumefaciens Ti
    plasmid which functions to direct
    polyadenylation of the mRNA.
    Agrobacterium B-AGRtu.left Agro left border sequence, 3309-3750
    T-DNA transfer border essential for transfer of T-DNA.
    Maintenance in OR-Ec.oriV-RK2 The vegetative origin of 3837-4233
    E. coli replication from plasmid RK2.
    CR-Ec.rop Coding region for repressor of 5742-5933
    primer from the ColE1 plasmid.
    Expression of this gene product
    interferes with primer binding at
    the origin of replication, keeping
    plasmid copy number low.
    OR-Ec.ori-Co1E1 The minimal origin of replication 6361-6949
    from the E. coli plasmid ColE1.
    P-Ec.aadA- romoter for Tn7 7480-7521
    SPC/STR adenylyltransferase (AAD(3″))
    CR-Ec.aadA- Coding region for Tn7 7522-8310
    SPC/STR adenylyltransferase (AAD(3″))
    conferring spectinomycin and
    streptomycin resistance.
    T-Ec.aadA- 3′ UTR from the Tn7 8311-8368
    SPC/STR adenylyltransferase (AAD(3″))
    gene of E. coli.
    • Example 6 Corn Plant Tranformation
  • This example illustrates the production and identification of transgenic corn cells in seed of transgenic corn plants having an enhanced agronomic trait, e.g., enhanced nitrogen use efficiency, increased yield, enhanced water use efficiency, enhanced tolerance to cold and/or enhanced seed compositions as compared to control plants. Transgenic corn cells are prepared with recombinant DNA expressing each of the protein encoding DNAs listed in Table 2 by Agrobacterium-mediated transformation using the corn transformation constructs as disclosed in Example 5.
  • Corn transformation is effected using methods disclosed in U.S. Patent Application Publication 2004/0344075 A1 where corn embryos are inoculated and co-cultured with the Agrobacterium tumefaciens strain ABI and the corn transformation vector. To regenerate transgenic corn plants the transgenic callus 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 followed by a mist bench before transplanting to pots where plants are grown to maturity. The plants are self fertilized and seed is harvested for screening as seed, seedlings or progeny R2 plants or hybrids, e.g., for yield trials in the screens indicated above.
  • Many transgenic events which survive to fertile transgenic plants that produce seeds and progeny plants do not exhibit an enhanced agronomic trait. The transgenic plants and seeds having the transgenic cells of this invention which have recombinant DNA imparting the enhanced agronomic traits are identified by screening for nitrogen use efficiency, yield, water use efficiency, cold tolerance and enhanced seed composition.
    • Example 7 Soybean Plant Transformation
  • This example illustrates the production and identification of transgenic soybean cells in seed of transgenic soybean plants having an enhanced agronomic trait, e.g., enhanced nitrogen use efficiency, increased yield, enhanced water use efficiency, enhanced tolerance to cold and/or enhanced seed compositions as compared to control plants. Transgenic soybean cells are prepared with recombinant DNA expressing each of the protein encoding DNAs listed in Table 1 by Agrobacterium-mediated transformation using the soybean transformation constructs disclosed in Example 5. Soybean transformation is effected using methods disclosed in U.S. Pat. No. 6,384,301 where soybean meristem explants are wounded then inoculated and co-cultured with the soybean transformation vector, then transferred to selection media for 6-8 weeks to allow selection and growth of transgenic shoots.
  • The transformation is repeated for each of the protein encoding DNAs identified in Table 2.
  • Transgenic shoots producing roots are transferred to the greenhouse and potted in soil. Many transgenic events which survive to fertile transgenic plants that produce seeds and progeny plants do not exhibit an enhanced agronomic trait. The transgenic plants and seeds having the transgenic cells of this invention which have recombinant DNA imparting the enhanced agronomic traits are identified by screening for nitrogen use efficiency, yield, water use efficiency, cold tolerance and enhanced seed composition.
    • Example 8 Selection of Transgenic Plants with Enhanced Agronomic Trait(s)
  • This example illustrates identification of nuclei of the invention by screening derived plants and seeds for an enhanced trait identified below.
  • Many transgenic events which survive to fertile transgenic plants that produce seeds and progeny plants will not exhibit an enhanced agronomic trait. Populations of transgenic seed and plants prepared in Examples 6 and 7 are screened to identify those transgenic events providing transgenic plant cells with a nucleus having recombinant DNA imparting an enhanced trait. Each population is screened for enhanced nitrogen use efficiency, increased yield, enhanced water use efficiency, enhanced tolerance to cold and heat, increased level of oil and protein in seed using assays described below. Plant cell nuclei having recombinant DNA with each of the genes identified in Table 2 and the identified homologs are identified in plants and seeds with at least one of the enhanced traits.
  • a. Selection for Enhanced Nitrogen Use Efficiency
  • Transgenic corn plants with nuclei of the invention are planted in fields with three levels of nitrogen (N) fertilizer being applied, i.e. low level (0 pounds per acre N), medium level (80 pounds per acre N) and high level (180 pounds per acre N). 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 in the low level treatment, the soil should still be disturbed in the same fashion as the treated area. Transgenic plants and control plants can be grouped by genotype and construct with controls arranged randomly within genotype blocks. For improved statistical analysis each type of transgenic plant can be tested by 3 replications and across 4 locations. Nitrogen levels in the fields are analyzed before planting by collecting 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 corn plants prepared in Example 6 and which exhibit a 2 to 5% yield increase as compared to control plants when grown in the high nitrogen field are selected as having nuclei of the invention. Transgenic corn plants which have at least the same or higher yield as compared to control plants when grown in the medium nitrogen field are selected as having nuclei of the invention. Transgenic corn plants having a nucleus with DNA identified in Table 3 as imparting nitrogen use efficiency (LN) and homologous DNA are selected from a nitrogen use efficiency screen as having a nucleus of this invention.
    • B. Selection for Increased Yield
  • Many transgenic plants of this invention exhibit increased yield as compared to a control plant. Increased yield can result from enhanced seed sink potential, e.g., the number and size of endosperm cells or kernels and/or enhanced sink strength, e.g., 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.
  • Much of the increase in corn yield of the past several decades has resulted from an increase in planting density. During that period, corn yield has been increasing at a rate of 2.1 bushels/acre/year, but the planting density has increased at a rate of 250 plants/acre/year. A characteristic of modern hybrid corn is the ability of these varieties to be planted at high density. Many studies have shown that a higher than current planting density should result in more biomass production, but current germplasm does not perform well at these higher densities. One approach to increasing yield is to increase harvest index (HI), the proportion of biomass that is allocated to the kernel compared to total biomass, in high density plantings.
  • 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 increased 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 can be applied in multiple and diverse geographic locations, for example up to 16 or more locations, over one or more planting seasons, for example at least two planting seasons to statistically distinguish yield improvement from natural environmental effects. Each of the transgenic corn plants and soybean plants with a nucleus of the invention prepared in Examples 6 and 7 are screened for yield enhancement. At least one event from each of the corn plants is selected as having at least between 3 and 5% increase in yield as compared to a control plant as having a nucleus of this invention.
    • C. Selection for Enhanced Water Use Efficiency (WUE)
  • The following is a high-throughput method for screening for water use efficiency in a greenhouse to identify the transgenic corn plants with a nucleus of this invention. 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 5th 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 heights are measured at three time points. The first is taken just prior to the onset drought when the plant is 11 days old, which is the shoot initial height (SIH). The plant height is also measured halfway throughout the drought/re-water regimen, on day 18 after planting, to give rise to the shoot mid-drought height (SMH). Upon the completion of the final drought cycle on day 26 after planting, the shoot portion of the plant is harvested and measured for a final height, which is the shoot wilt height (SWH) and also measured for shoot wilted biomass (SWM). The shoot is placed in water at 40 degree Celsius in the dark. Three days later, the shoot is weighted to give rise to the shoot turgid weight (STM). After drying in an oven for four days, the shoots are weighted for shoot dry biomass (SDM). The shoot average height (SAH) is the mean plant height across the 3 height measurements. The procedure described above can be adjusted for +/−˜one day for each step given the situation.
  • To correct for slight differences between plants, a size corrected growth value is derived from SIH and SWH. This is the Relative Growth Rate (RGR). Relative Growth Rate (RGR) is calculated for each shoot using the formula [RGR %=(SWH−SIH)/((SWH+SIH)/2)×100]. Relative water content (RWC) is a measurement of how much (%) of the plant was water at harvest. Water Content (RWC) is calculated for each shoot using the formula [RWC %=(SWM-SDM)/(STM-SDM)×100]. Fully watered corn plants of this age run around 98% RWC.
  • Transgenic corn plants and soybean plants prepared in Examples 6 and 7 are screened for water use efficiency. Transgenic plants having at least a 1% increase in RGR and RWC as compared to control plants are identified as having enhanced water used efficiency and are selected as having a nucleus of this invention. Transgenic corn and soybean plants having in their nucleus DNA identified in Table 3 as imparting drought tolerance enhancement (DS, HS, SS, and PEG) and homologous DNA are identified as showing increased water use efficiency as compared to control plants and are selected as having a nucleus of this invention.
    • D. Selection for Growth Under Cold Stress
  • Cold germination assay—Three sets of seeds are used for the assay. The first set consists of positive transgenic events (F1 hybrid) where the genes of the present invention are expressed in the seed. The second seed set is nontransgenic, wild-type negative control made from the same genotype as the transgenic events. The third set consisted of two cold tolerant and one cold sensitive commercial check lines of corn. All seeds are treated with a fungicide “Captan” (MAESTRO® 80 DF Fungicide, Arvesta Corporation, San Francisco, Calif., USA). 0.43 mL Captan is applied per 45 g of corn seeds by mixing it well and drying the fungicide prior to the demonstation.
  • 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 PGV36, Controlled Environments, Winnipeg, Canada). Two hundred and fifty millilters of deionized water are added to each germination tray. Germination counts are taken 10th, 11th, 12th, 13th, 14th, 17th, 19th, 21st, and 24th day after start date of the demonstration. Seeds are considered germinated if the emerged radicle size is 1 cm. From the germination counts germination index is calculated.
  • The germination index is calculated as per:
  • Germination index=(Σ([T+1−ni]*[Pi−Pi-1]))/T where T is the total number of days for which the germination assay is performed. The number of days after planting is defined by n. 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.
  • Transgenic corn plants and soybean plants prepared in Examples 6 and 7 are screened for water use efficiency. Transgenic plants having at least a 5% increase in germination index as compared to control plants are identified as having enhanced cold stress tolerance and are selected as having a nucleus of this invention. Transgenic corn and soybean plants having in their nucleus DNA identified in Table 3 as imparting cold tolerance enhancement (CK or CS) and homologous DNA are identified as showing increased cold stress tolerance as compared to control plants and are selected as having a nucleus of this invention.
  • E. Screens for Transgenic Plant Seeds with Increased Protein and/or Oil Levels
  • The following is a high-throughput selection method 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 analyzer 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. Calculations are performed 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.
  • TABLE 23
    Typical sample(s): Whole grain com and soybean seeds
    Analytical time to run Less than 0.75 min per sample
    method:
    Total elapsed time per 1.5 minute per sample
    run:
    Typical and minimum Com typical: 50 cc; minimum 30 cc
    sample size: Soybean typical: 50 cc; minimum 5 cc
    Typical analytical range: Determined in part by the specific calibration.
    Com—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%.
  • Transgenic corn plants and soybean plants prepared in Examples 6 and 7 are screened for increased protein and oil in seed. Transgenic inbred corn and soybean plants having an increase of at least 1 percentage point in the total percent seed protein or at least 0.3 percentage point in total seed oil and transgenic hybrid corn plants having an increase of at least 0.4 percentage point in the total percent seed protein as compared to control plants are identified as having enhanced seed protein or enhanced seed oil and are selected as having a nucleus of this invention.
    • Example 9 Cotton Transgenic Plants with Enhanced Agronomic Traits
  • Cotton transformation is performed as generally described in WO0036911 and in U.S. Pat. No. 5,846,797 and are incorporated herein by reference. Transgenic cotton plants containing each of the recombinant DNA having a sequence of SEQ ID NO: 1 through SEQ ID NO: 139 are obtained by transforming with recombinant DNA from each of the genes identified in Table 1. Progeny transgenic plants are selected from a population of transgenic cotton events under specified growing conditions and are compared with control cotton plants. Control cotton plants are substantially the same cotton genotype but without the recombinant DNA, for example, either a parental cotton plant of the same genotype that was not transformed with the identical recombinant DNA or a negative isoline of the transformed plant. Additionally, a commercial cotton cultivar adapted to the geographical region and cultivation conditions, i.e. cotton variety ST474, cotton variety FM 958, and cotton variety Siokra L-23, are used to compare the relative performance of the transgenic cotton plants containing the recombinant DNA. The specified culture conditions are growing a first set of transgenic and control plants under “wet” conditions, e.g., irrigated in the range of 85 to 100 percent of evapotranspiration to provide leaf water potential of −14 to −18 bars, and growing a second set of transgenic and control plants under “dry” conditions, e.g., irrigated in the range of 40 to 60 percent of evapotranspiration to provide a leaf water potential of −21 to −25 bars. Pest control, such as weed and insect control is applied equally to both wet and dry treatments as needed. Data gathered during the trial includes weather records throughout the growing season including detailed records of rainfall; soil characterization information; any herbicide or insecticide applications; any gross agronomic differences observed such as leaf morphology, branching habit, leaf color, time to flowering, and fruiting pattern; plant height at various points during the trial; stand density; node and fruit number including node above white flower and node above crack boll measurements; and visual wilt scoring. Cotton boll samples are taken and analyzed for lint fraction and fiber quality. The cotton is harvested at the normal harvest timeframe for the trial area. Enhanced water use efficiency is indicated by increased yield, improved relative water content, enhanced leaf water potential, increased biomass, enhanced leaf extension rates, and improved fiber parameters.
  • The transgenic cotton plants of this invention are identified from among the transgenic cotton plants by agronomic trait screening as having increased yield and enhanced water use efficiency.
    • Example 10 Canola Plants with Enhanced Agrominic Traits
  • This example illustrates plant transformation useful in producing the transgenic canola plants of this invention and the production and identification of transgenic seed for transgenic canola having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • Tissues from in vitro grown canola seedlings are prepared and inoculated with a suspension of overnight grown Agrobacterium containing plasmid DNA with the gene of interest cassette and a plant selectable marker cassette. Following co-cultivation with Agrobacterium, the infected tissues are allowed to grow on selection to promote growth of transgenic shoots, followed by growth of roots from the transgenic shoots. The selected plantlets are then transferred to the greenhouse and potted in soil. Molecular characterizations are performed to confirm the presence of the gene of interest, and its expression in transgenic plants and progenies. Progeny transgenic plants are selected from a population of transgenic canola events under specified growing conditions and are compared with control canola plants. Control canola plants are substantially the same canola genotype but without the recombinant DNA, for example, either a parental canola plant of the same genotype that is not transformed with the identical recombinant DNA or a negative isoline of the transformed plant
  • Transgenic canola plant cells are transformed with recombinant DNA from each of the genes identified in Table 2. Transgenic progeny plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
    • Example 11 Monocot and Dicot Plant Transformation for the Suppression of Endogeneous protein
  • This example illustrates monocot and dicot plant transformation to produce nuclei of this invention in cells of a transgenic plant by transformation where the recombinant DNA suppresses the expression of an endogenous protein identified in Table 24.
  • Corn, soybean, cotton, or canola tissue are transformed as describe in Examples 6, 7, 9 or 10 using recombinant DNA in the nucleus with DNA that transcribes to RNA that forms double-stranded RNA targeted to an endogenous gene with DNA encoding the protein. The genes for which the double-stranded RNAs are targeted are the native gene in corn and soybean that are homolog of the genes encoding the protein of Arabidopsis thaliana as identified in table 24.
  • Populations of transgenic plants prepared in Examples 5, 6, 7, 9 or 10 with DNA for suppressing a gene identified in Table 2 as providing an enhanced trait by gene suppression are screened to identify an event from those plants with a nucleus of the invention by selecting the trait identified in this specification.
  • TABLE 24
    PEP
    SEQ ID Pfam module Construct ID Traits
    142 RWP-RK 70733 SP
    144 AUX_IAA 15707 SS
    151 SRF-TF 10106 LN
    197 zf-C3HC4 10456 LL
    198 Myb_DNA-binding 11115 PEG
    206 CCT 10362 HS
    250 PHD 12179 HS
    273 EIN3 10114 SS
    275 AP2 10804 LN

Claims (15)

What is claimed is:
1. A plant cell nucleus with stably-integrated, recombinant DNA comprising a promoter that is functional in plant cells and that is operably linked to protein coding DNA encoding a protein having an amino acid sequence comprising a Pfam domain module Linker_histone::AT_hook::AT_hook::AT_hook::AT_hook;
wherein said plant cell nucleus is selected by screening a population of transgenic plants that have said recombinant DNA in its nuclei and express said protein for an enhanced trait as compared to control plants that do not have said recombinant DNA in their nuclei; and
wherein said 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.
2. A plant cell nucleus with stably integrated, recombinant DNA, wherein
a. said recombinant DNA comprises a promoter that is functional in said plant cell and that is operably linked to a protein coding DNA encoding a protein having an amino acid sequence comprising a Pfam domain module selected from the group consisting of WRKY::WRKY, AP2, AUX_IAA, WRKY, WRKY, HLH, Myb_DNA-binding::Linker_histone, zf-B_box::zf-B_box, Ank::Ank::Ank::Chromo, NAM, zf-C2H2, Myb_DNA-binding, bZIP—1, PHD, Linker_histone::AT_hook::AT_hook::AT_hook::AT_hook, B3::Auxin_resp, HLH, zf-Dof, AT_hook::DUF296, AT_hook::AT_hook::DUF296, NAM, GATA, NAM, Myb_DNA-binding, zf-B_box::CCT, POX::Homeobox, B3::Auxin_resp::AUX_IAA, Myb_DNA-binding::Myb_DNA-binding, Myb_DNA-binding::Myb_DNA-binding, zf-C2H2, zf-C2H2, Myb_DNA-binding::Myb_DNA-binding, Myb_DNA-binding::Myb_DNA-binding, TCP, KNOX1::KNOX2, zf-ZPR1::zf-ZPR1, Myb_DNA-binding::Myb_DNA-binding, DUF630::DUF632, WRKY, Myb_DNA-binding, zf-C2H2, HLH, AP2, AT_hook::DUF296, Ank::Ank::Ank::Ank::Ank, WRKY, zf-C2H2, NAM, AP2, NAM, Myb_DNA-binding::Myb_DNA-binding::Myb_DNA-binding, NAM, HLH, Myb_DNA-binding::Myb_DNA-binding, Myb_DNA-binding, HLH, bZIP—2, bZIP—2, BAH::PHD, HLH, NAM, GATA, SSrecog::Rtt106::HMG_box, DUF573, zf-B_box::CCT, HLH, RWP-RK, AP2::B3, AUX_IAA, SRF-TF, AP2, AP2, HSF_DNA-bind, AP2, SRF-TF::K-box, Myb_DNA-binding, zf-LSD1::zf-LSD1::zf-LSD1, KNOX1::KNOX2::ELK, zf-C3HC4, MFMR::bZIP—1, DUF573, Myb_DNA-binding, HLH, NAM, Myb_DNA-binding::Myb_DNA-binding, SRF-TF::K-box, zf-C3HC4, zf-B_box, WRKY, zf-B_box::CCT, EIN3, HSF_DNA-bind, AUX_IAA, TCP, Myb_DNA-binding::Myb_DNA-binding, AP2, KNOX1::KNOX2::ELK::Homeobox, HSF_DNA-bind, HSF_DNA-bind, AP2::B3, NAM, SBP, AP2, zf-C2H2, SRF-TF::K-box, zf-C2H2, GRAS, AP2, Myb_DNA-binding, AP2, AP2::AP2, HLH, CXC::CXC, AP2, NAM, zf-C3HC4, Myb_DNA-binding::Myb_DNA-binding, GRAS, Homeobox::HALZ, Myb_DNA-binding, NAM, WRKY, zf-C2H2, zf-C2H2, NAM, zf-C2H2, AP2::AP2, zf-C3HC4, RWP-RK::PB1, SRF-TF::K-box, and zf-B_box;
b. said recombinant DNA comprises a promoter that is functional in said plant cell and that is operably linked to a protein coding DNA encoding a protein comprising an amino acid sequence with at least 90% identity to a consensus amino acid sequence selected from the group consisting of SEQ TD NO: 6027 through 6034; or
c. said recombinant DNA suppresses comprises a promoter that is functional in said plant cell and operably linked to DNA that transcribe into RNA that suppresses the level of an endogenous protein wherein said endogenous protein has an amino acid sequence comprising a pfam domain module selected from the group consisting of RWP-RK, AUX_IAA, SRF-TF, zf-C3HC4, Myb_DNA-binding, CCT, PHD, EIN3, and AP2;
and wherein said plant cell nucleus is selected by screening a population of transgenic plants that have said recombinant DNA and an enhanced trait as compared to control plants that do not have said recombinant DNA in their nuclei; and wherein said enhanced trait is selected from group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced resistance to salt exposure, enhanced shade tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
3. The plant cell nucleus of claim 2 wherein said protein coding DNA encodes a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 140 through SEQ ID NO: 6023.
4. The plant cell nucleus of claim 2 further comprising 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.
5. The plant cell nucleus of claim 4 wherein said herbicide is a glyphosate, dicamba, or glufosinatc compound.
6. A transgenic plant cell or plant comprising a plurality of plant cells with the plant cell nucleus of claim 2.
7. The transgenic plant cell or plant of claim 6 which is homozygous for said recombinant DNA.
8. A transgenic seed comprising a plurality of plant cells with a plant cell nucleus of claim 2.
9. The transgenic seed of claim 8 from a corn, soybean, cotton, canola, alfalfa, wheat or rice plant.
10. A transgenic pollen grain comprising a haploid derivative of a plant cell nucleus of claim 2.
11. A method 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 recombinant DNA in a nucleus of claim 2, wherein said method for manufacturing said transgenic seed comprising:
(a) screening a population of plants for said enhanced trait and said recombinant DNA, wherein individual plants in said population can exhibit said trait at a level less than, essentially the same as or greater than the level that said trait is exhibited in control plants which do not contain the recombinant DNA, wherein said enhanced trait is selected from the group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced high salinity tolerance, enhanced shade tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil,
(b) selecting from said population one or more plants that exhibit said trait at a level greater than the level that said trait is exhibited in control plants, and
(c) collecting seeds from selected plant selected from step b.
12. The method of claim 11 wherein said method for manufacturing said transgenic seed further comprising
(a) verifying that said recombinant DNA is stably integrated in said selected plants, and
(b) analyzing tissue of said selected plant to determine the expression or suppression of a protein having the function of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO:140-278.
13. The method of claim 11 wherein said seed is corn, soybean, cotton, alfalfa, canola wheat or rice seed.
14. A method of producing hybrid corn seed comprising:
(a) acquiring hybrid corn seed from a herbicide tolerant corn plant which also has stably-integrated, recombinant DNA in a nucleus of claim 2;
(b) 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;
(c) selecting corn plants which are homozygous and hemizygous for said recombinant DNA by treating with an herbicide;
(d) collecting seed from herbicide-treated-surviving corn plants and planting said seed to produce further progeny corn plants;
(e) repeating steps (c) and (d) at least once to produce an inbred corn line; and
(f) crossing said inbred corn line with a second corn line to produce hybrid seed.
15. A transgenic plant comprising recombinant DNA constructs encoding amino acid sequence that have at least 90% identity over at least 90% of the length of a reference sequence selected from the group consisting of SEQ ID NOs: 140-278 when the amino acid sequence is aligned to the reference sequence.
US13/999,850 2008-12-22 2014-03-27 Genes and uses for plant enhancement Abandoned US20140331357A1 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
US13/999,850 US20140331357A1 (en) 2008-12-22 2014-03-27 Genes and uses for plant enhancement
US15/211,720 US10301642B2 (en) 2008-12-22 2016-07-15 Genes and uses for plant enhancement

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US20352908P 2008-12-22 2008-12-22
PCT/US2009/068351 WO2010075143A1 (en) 2008-12-22 2009-12-17 Genes and uses for plant enhancement
US201113140920A 2011-06-21 2011-06-21
US13/999,850 US20140331357A1 (en) 2008-12-22 2014-03-27 Genes and uses for plant enhancement

Related Parent Applications (2)

Application Number Title Priority Date Filing Date
PCT/US2009/068351 Continuation WO2010075143A1 (en) 2008-12-22 2009-12-17 Genes and uses for plant enhancement
US13/140,920 Continuation US20110258735A1 (en) 2008-12-22 2009-12-17 Genes and uses for plant enhancement

Related Child Applications (1)

Application Number Title Priority Date Filing Date
US15/211,720 Division US10301642B2 (en) 2008-12-22 2016-07-15 Genes and uses for plant enhancement

Publications (1)

Publication Number Publication Date
US20140331357A1 true US20140331357A1 (en) 2014-11-06

Family

ID=41667184

Family Applications (3)

Application Number Title Priority Date Filing Date
US13/140,920 Abandoned US20110258735A1 (en) 2008-12-22 2009-12-17 Genes and uses for plant enhancement
US13/999,850 Abandoned US20140331357A1 (en) 2008-12-22 2014-03-27 Genes and uses for plant enhancement
US15/211,720 Active 2030-04-19 US10301642B2 (en) 2008-12-22 2016-07-15 Genes and uses for plant enhancement

Family Applications Before (1)

Application Number Title Priority Date Filing Date
US13/140,920 Abandoned US20110258735A1 (en) 2008-12-22 2009-12-17 Genes and uses for plant enhancement

Family Applications After (1)

Application Number Title Priority Date Filing Date
US15/211,720 Active 2030-04-19 US10301642B2 (en) 2008-12-22 2016-07-15 Genes and uses for plant enhancement

Country Status (2)

Country Link
US (3) US20110258735A1 (en)
WO (1) WO2010075143A1 (en)

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10301642B2 (en) 2008-12-22 2019-05-28 Monsanto Technology Llc Genes and uses for plant enhancement
WO2022226341A1 (en) * 2021-04-23 2022-10-27 Viridos, Inc. Chlorophyte algae having improved productivity

Families Citing this family (35)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN102311491B (en) * 2010-07-08 2014-10-22 中国科学院上海生命科学研究院 Plant heat-resistant gene HSF1 and application thereof
WO2012047970A1 (en) * 2010-10-05 2012-04-12 Board Of Trustees Of Michigan State University Regulatory factors controlling oil biosynthesis in microalgae and their use
WO2012063338A1 (en) * 2010-11-10 2012-05-18 国立大学法人京都工芸繊維大学 Protein having chitinase activity and uses thereof
CN102146126B (en) * 2011-01-07 2013-04-03 中国科学院遗传与发育生物学研究所 Protein related to insect resistance and encoding gene and application thereof
AU2012297562B2 (en) * 2011-08-12 2016-05-19 Commonwealth Scientific And Industrial Research Organisation Methods of controlling fructan synthesis in plants
EP2604694A1 (en) * 2011-12-14 2013-06-19 Genoplante-Valor Method for plant improvement
ES2903185T3 (en) 2012-05-08 2022-03-31 Monsanto Technology Llc Corn event MON 87411
CN104812903A (en) 2012-09-20 2015-07-29 先锋国际良种公司 Compositions and methods conferring resistance of maize to corn rootworm I
RU2015114446A (en) 2012-09-20 2016-11-10 Е.И.Дюпон Де Немур Энд Компани COMBATING THE CEREAL ROOT WORM AND OTHER PEST INSECTS
US10240164B2 (en) * 2012-12-05 2019-03-26 British American Tobacco (Investments) Limited Transgenic plants having altered lignin density
WO2014102773A1 (en) 2012-12-25 2014-07-03 Evogene Ltd. Isolated polynucleotides and polypeptides, and methods of using same for increasing nitrogen use efficiency of plants
CN104004767B (en) * 2013-02-25 2020-04-14 先锋海外公司 Vector and method for WRKY transcription factor polypeptide gene application
WO2014164014A1 (en) * 2013-03-11 2014-10-09 Pioneer Hi-Bred International, Inc. Genes for improving nutrient uptake and abiotic stress tolerance in plants
WO2015018459A1 (en) * 2013-08-09 2015-02-12 Wageningen Universiteit Plants with modified vascular tissue
US9101100B1 (en) 2014-04-30 2015-08-11 Ceres, Inc. Methods and materials for high throughput testing of transgene combinations
BR112016026136A2 (en) * 2014-05-12 2018-02-20 Donald Danforth Plant Science Center compositions and methods for increasing plant growth and yield
US20170253886A1 (en) * 2014-08-26 2017-09-07 Københavns Universitet Plants with reduced ethylene sensitivity
GB2552657A (en) * 2016-07-29 2018-02-07 Elsoms Dev Ltd Wheat
CA3080022A1 (en) * 2017-11-21 2019-05-31 Monsanto Technology Llc Modified plants with enhanced traits
CN109293758B (en) * 2018-10-30 2021-06-08 中国农业科学院棉花研究所 Anti-verticillium wilt related protein GbVIP1, and coding gene and application thereof
CN111793119A (en) * 2019-04-04 2020-10-20 中国科学院遗传与发育生物学研究所 Protein for regulating and controlling plant drought resistance, coding gene and application thereof
CN110904117B (en) * 2019-10-24 2022-12-06 中国科学院遗传与发育生物学研究所 Application of plant PHL2 gene in regulation of plant seed size, dry weight and fatty acid accumulation
CN113880927A (en) * 2020-07-01 2022-01-04 中国科学院植物研究所 Method for enhancing low-temperature tolerance of rice by over-expressing zinc finger protein OsCIP3
CN112279904B (en) * 2020-11-04 2022-05-10 中国农业科学院作物科学研究所 Application of protein GL12.2 in regulation and control of rice yield
CN114644693B (en) * 2020-12-17 2023-04-07 中国农业大学 ZmWRKY44 protein, coding gene thereof and application of ZmWRKY44 protein in regulation of plant drought resistance
CN112961231B (en) * 2021-03-12 2023-07-14 北京科技大学 Male sterile gene ZmbHLH122 and application thereof in creating maize male sterile line
AR125348A1 (en) * 2021-04-22 2023-07-12 Plantarc Bio Ltd TRANSGENIC PLANTS WITH IMPROVED CHARACTERISTICS
CN113621039B (en) * 2021-08-19 2023-03-17 云南农业大学 Anthocyanin synthesis related protein IbMYB113 and coding gene and application thereof
CN113774067A (en) * 2021-09-15 2021-12-10 南昌大学 Cymbidium kanran gene expression vector for promoting seed germination, construction method and application
CN114591969B (en) * 2022-03-22 2023-08-15 赣南师范大学 Drought-resistant gene CrWRKY57 and application thereof in drought-resistant improvement of plants
CN114656547B (en) * 2022-04-01 2023-05-23 四川农业大学 Strawberry FaBBX21 transcription factor, and encoding protein and application thereof
CN115838404B (en) * 2022-07-18 2023-09-26 西南大学 EjMYB44 gene for regulating and controlling flowering phase of loquat, and encoding protein and application thereof
CN116254290A (en) * 2022-08-03 2023-06-13 西南大学 Application of PtoPLT5a gene in improving biomass and fiber cell length of populus tomentosa
CN116590337B (en) * 2023-04-21 2023-12-05 中国科学院华南植物园 Rice transcription factor OsbZIP13 and application of coding sequence thereof
CN116640201B (en) * 2023-07-21 2023-10-24 内蒙古大学 Application of regulating and controlling MfERF026 gene in alfalfa growth and development and stress tolerance

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20070033671A1 (en) * 2002-09-18 2007-02-08 Cai-Zhong Jiang Polynucleotides and polypeptides in plants
US20150135358A1 (en) * 2007-10-31 2015-05-14 Monsanto Technology Llc Genes and uses for plant enhancement

Family Cites Families (68)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US591445A (en) 1897-10-12 Water-tube steam-boiler
US5034322A (en) 1983-01-17 1991-07-23 Monsanto Company Chimeric genes suitable for expression in plant cells
US5352605A (en) 1983-01-17 1994-10-04 Monsanto Company Chimeric genes for transforming plant cells using viral promoters
DE3587548T2 (en) 1984-12-28 1993-12-23 Plant Genetic Systems Nv Recombinant DNA that can be introduced into plant cells.
US5420034A (en) 1986-07-31 1995-05-30 Calgene, Inc. Seed-specific transcriptional regulation
NZ217113A (en) 1985-08-07 1988-06-30 Monsanto Co Production of eucaryotic plants which are glyphosate resistant, vectors (transformation and expression), chimeric gene and plant cells
CA1293460C (en) 1985-10-07 1991-12-24 Brian Lee Sauer Site-specific recombination of dna in yeast
US5188958A (en) 1986-05-29 1993-02-23 Calgene, Inc. Transformation and foreign gene expression in brassica species
US5004863B2 (en) 1986-12-03 2000-10-17 Agracetus Genetic engineering of cotton plants and lines
US5015580A (en) 1987-07-29 1991-05-14 Agracetus Particle-mediated transformation of soybean plants and lines
US5322938A (en) 1987-01-13 1994-06-21 Monsanto Company DNA sequence for enhancing the efficiency of transcription
US5359142A (en) 1987-01-13 1994-10-25 Monsanto Company Method for enhanced expression of a protein
US5250515A (en) 1988-04-11 1993-10-05 Monsanto Company Method for improving the efficacy of insect toxins
US5416011A (en) 1988-07-22 1995-05-16 Monsanto Company Method for soybean transformation and regeneration
EP1103616A3 (en) 1989-02-24 2001-06-27 Monsanto Company Synthetic plant genes and method for preparation
US7705215B1 (en) 1990-04-17 2010-04-27 Dekalb Genetics Corporation Methods and compositions for the production of stably transformed, fertile monocot plants and cells thereof
US5550318A (en) 1990-04-17 1996-08-27 Dekalb Genetics Corporation Methods and compositions for the production of stably transformed, fertile monocot plants and cells thereof
ATE196318T1 (en) 1989-10-31 2000-09-15 Monsanto Co PROMOTER FOR TRANSGENIC PLANTS
US5641876A (en) 1990-01-05 1997-06-24 Cornell Research Foundation, Inc. Rice actin gene and promoter
US5484956A (en) 1990-01-22 1996-01-16 Dekalb Genetics Corporation Fertile transgenic Zea mays plant comprising heterologous DNA encoding Bacillus thuringiensis endotoxin
JP3209744B2 (en) 1990-01-22 2001-09-17 デカルブ・ジェネティクス・コーポレーション Transgenic corn with fruiting ability
US5837848A (en) 1990-03-16 1998-11-17 Zeneca Limited Root-specific promoter
AU655197B2 (en) 1990-06-25 1994-12-08 Monsanto Technology Llc Glyphosate tolerant plants
US5633435A (en) 1990-08-31 1997-05-27 Monsanto Company Glyphosate-tolerant 5-enolpyruvylshikimate-3-phosphate synthases
DK0539563T3 (en) 1991-05-15 2001-11-12 Monsanto Technology Llc Process for Creating a Transformed Rice Plant
WO1994000977A1 (en) 1992-07-07 1994-01-20 Japan Tobacco Inc. Method of transforming monocotyledon
EP0578627A1 (en) 1992-07-09 1994-01-12 Monsanto Company Virus resistant plants
US5527695A (en) 1993-01-29 1996-06-18 Purdue Research Foundation Controlled modification of eukaryotic genomes
US6118047A (en) 1993-08-25 2000-09-12 Dekalb Genetic Corporation Anthranilate synthase gene and method of use thereof for conferring tryptophan overproduction
US5631152A (en) 1994-10-26 1997-05-20 Monsanto Company Rapid and efficient regeneration of transgenic plants
US5846797A (en) 1995-10-04 1998-12-08 Calgene, Inc. Cotton transformation
DK0812917T3 (en) 1995-12-27 2005-10-17 Japan Tobacco Inc Cold-inducible promoter sequences
EA199800212A1 (en) 1996-06-21 1998-10-29 Монсанто Компани METHODS OF OBTAINING SUSTAINABLE TRANSFORMABLE HIGH-PRODUCTIVE WHEAT BY TRANSFORMATION MEDIATED BY AGROBACTERIUM AND THE COMBINATION OBTAINED BY THEM
EP0865496A1 (en) 1996-09-05 1998-09-23 Unilever N.V. Salt-inducible promoter derivable from a lactic acid bacterium, and its use in a lactic acid bacterium for production of a desired protein
JPH10117776A (en) 1996-10-22 1998-05-12 Japan Tobacco Inc Transformation of indica rice
JP2001508661A (en) 1997-01-20 2001-07-03 プラント ジエネテイツク システムズ エヌ．ブイ Pathogen-induced plant promoter
US5922564A (en) 1997-02-24 1999-07-13 Performance Plants, Inc. Phosphate-deficiency inducible promoter
US6376754B1 (en) 1997-03-07 2002-04-23 Asgrow Seed Company Plants having resistance to multiple herbicides and its use
EP1056862A1 (en) 1998-02-26 2000-12-06 Pioneer Hi-Bred International, Inc. Family of maize pr-1 genes and promoters
WO1999043797A2 (en) 1998-02-26 1999-09-02 Pioneer Hi-Bred International, Inc. Constitutive maize promoters
US6107549A (en) 1998-03-10 2000-08-22 Monsanto Company Genetically engineered plant resistance to thiazopyr and other pyridine herbicides
US5914451A (en) 1998-04-06 1999-06-22 Monsanto Company Efficiency soybean transformation protocol
US6307123B1 (en) 1998-05-18 2001-10-23 Dekalb Genetics Corporation Methods and compositions for transgene identification
AUPP370498A0 (en) 1998-05-25 1998-06-18 Nalco Chemical Company Dextran, starch and flocculant combination for improving red mud clarification
JP2000083680A (en) 1998-07-16 2000-03-28 Nippon Paper Industries Co Ltd Introduction of gene into plant utilizing adventitious bud redifferentiation gene put under control due to photoinduction type promoter as selection marker gene and vector for transduction of gene into plant used therefor
US20120137382A1 (en) 1998-09-22 2012-05-31 Mendel Biotechnology, Inc. Stress tolerance in plants
US7956242B2 (en) * 1998-09-22 2011-06-07 Mendel Biotechnology, Inc. Plant quality traits
US8030546B2 (en) 1998-09-22 2011-10-04 Mendel Biotechnology, Inc. Biotic and abiotic stress tolerance in plants
US7960612B2 (en) 1998-09-22 2011-06-14 Mendel Biotechnology, Inc. Plant quality with various promoters
US6506599B1 (en) 1999-10-15 2003-01-14 Tai-Wook Yoon Method for culturing langerhans islets and islet autotransplantation islet regeneration
EP2042603A1 (en) 1998-11-17 2009-04-01 Monsanto Technology, LLC Phosphonate metabolizing plants
WO2000036911A2 (en) 1998-12-18 2000-06-29 Monsanto Technology Llc Method for the regeneration of cotton
US6559357B1 (en) * 1999-01-08 2003-05-06 The Regents Of The University Of California Methods for altering mass and fertility in plants
WO2000042207A2 (en) 1999-01-14 2000-07-20 Monsanto Technology Llc Soybean transformation method
US20110138499A1 (en) 1999-03-23 2011-06-09 Mendel Biotechnology, Inc. Plant quality traits
US6429357B1 (en) 1999-05-14 2002-08-06 Dekalb Genetics Corp. Rice actin 2 promoter and intron and methods for use thereof
US6232526B1 (en) 1999-05-14 2001-05-15 Dekalb Genetics Corp. Maize A3 promoter and methods for use thereof
US6194636B1 (en) 1999-05-14 2001-02-27 Dekalb Genetics Corp. Maize RS324 promoter and methods for use thereof
US6207879B1 (en) 1999-05-14 2001-03-27 Dekalb Genetics Corporation Maize RS81 promoter and methods for use thereof
US20020192813A1 (en) 1999-08-18 2002-12-19 Timothy W. Conner Plant expression vectors
US7294759B2 (en) * 2001-06-29 2007-11-13 E. I. Du Pont De Nemours And Company Alteration of oil traits in plants
US20030150017A1 (en) 2001-11-07 2003-08-07 Mesa Jose Ramon Botella Method for facilitating pathogen resistance
US8541665B2 (en) 2002-09-18 2013-09-24 Mendel Biotechnology, Inc. Polynucleotides and polypeptides in plants
US7682829B2 (en) 2003-05-30 2010-03-23 Monsanto Technology Llc Methods for corn transformation
JP4324220B2 (en) 2006-03-06 2009-09-02 パナソニック株式会社 Photomask, method for producing the same, pattern forming method using the photomask, and method for creating mask data
EP2573178A3 (en) * 2007-07-10 2013-07-24 Monsanto Technology LLC Transgenic plants with enhanced agronomic traits
EP2315774A1 (en) 2008-08-20 2011-05-04 BASF Plant Science GmbH Plants having enhanced yield-related traits and a method for making the same
WO2010075143A1 (en) 2008-12-22 2010-07-01 Monsanto Technology Llc Genes and uses for plant enhancement

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20070033671A1 (en) * 2002-09-18 2007-02-08 Cai-Zhong Jiang Polynucleotides and polypeptides in plants
US20150135358A1 (en) * 2007-10-31 2015-05-14 Monsanto Technology Llc Genes and uses for plant enhancement

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
Friedberg. Automated protein function prediction - the genomic challenge. Briefings in Bioinformatics. 2006. 7(3): 225-242. *
Guo et al. Protein tolerance to random amino acid change. PNAS. 2004. 101(25): 9205-9210. *

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10301642B2 (en) 2008-12-22 2019-05-28 Monsanto Technology Llc Genes and uses for plant enhancement
WO2022226341A1 (en) * 2021-04-23 2022-10-27 Viridos, Inc. Chlorophyte algae having improved productivity

Also Published As

Publication number Publication date
US10301642B2 (en) 2019-05-28
US20110258735A1 (en) 2011-10-20
WO2010075143A1 (en) 2010-07-01
US20160319297A1 (en) 2016-11-03

Similar Documents

Publication Publication Date Title
US10301642B2 (en) Genes and uses for plant enhancement
US20220251593A1 (en) Genes and uses for plant enhancement
US10093943B2 (en) Genes and uses for plant improvement
US20190032073A1 (en) Genes and uses for plant improvement
AU2006204997B2 (en) Genes and uses for plant improvement
US9115368B2 (en) Genes and uses for plant improvement
US20160264980A1 (en) Transgenic plants with enhanced agronomic traits
US8410336B2 (en) Transgenic plants with enhanced agronomic traits
US20150232870A1 (en) Transgenic plants with enhanced agronomic traits
US20060041961A1 (en) Genes and uses for pant improvement
EP1882392A2 (en) Genes and uses for plant improvement
EP2271760A2 (en) Genes and uses for plant enhancement
WO2008153927A2 (en) Genes and uses for plant enhancement
US20150135372A1 (en) Transgenic Plants With Enhanced Agronomic Traits
AU2011253798B2 (en) Genes and uses for plant improvement

Legal Events

Date Code Title Description
AS Assignment

Owner name: MONSANTO TECHNOLOGY LLC, MISSOURI

Free format text: ASSIGNMENT OF ASSIGNORS INTEREST;ASSIGNOR:COFFIN, MARIE;REEL/FRAME:037818/0057

Effective date: 20160201

STCB Information on status: application discontinuation

Free format text: ABANDONED -- FAILURE TO RESPOND TO AN OFFICE ACTION