US20130333068A1 - Genes and uses for plant enhancement - Google Patents

Genes and uses for plant enhancement Download PDF

Info

Publication number
US20130333068A1
US20130333068A1 US12/386,976 US38697609A US2013333068A1 US 20130333068 A1 US20130333068 A1 US 20130333068A1 US 38697609 A US38697609 A US 38697609A US 2013333068 A1 US2013333068 A1 US 2013333068A1
Authority
US
United States
Prior art keywords
sense
ppr
pkinase
lrr
enhanced
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
US12/386,976
Other languages
English (en)
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
Family has litigation
First worldwide family litigation filed litigation Critical https://patents.darts-ip.com/?family=41137730&utm_source=google_patent&utm_medium=platform_link&utm_campaign=public_patent_search&patent=US20130333068(A1) "Global patent litigation dataset” by Darts-ip is licensed under a Creative Commons Attribution 4.0 International License.
Application filed by Monsanto Technology LLC filed Critical Monsanto Technology LLC
Priority to US12/386,976 priority Critical patent/US20130333068A1/en
Assigned to MONSANTO TECHNOLOGY LLC reassignment MONSANTO TECHNOLOGY LLC ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: COFFIN, MARIE
Publication of US20130333068A1 publication Critical patent/US20130333068A1/en
Priority to US14/544,230 priority patent/US20160122783A1/en
Priority to US15/732,766 priority patent/US10696975B2/en
Priority to US16/873,608 priority patent/US11274312B2/en
Priority to US17/803,149 priority patent/US20230048751A1/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
    • C12N15/8242—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
    • 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
    • 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
    • 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
    • C12N15/8261—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
    • C12N15/8274—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 herbicide 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
    • C12N15/8261—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
    • C12N15/8274—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 herbicide resistance
    • C12N15/8275—Glyphosate
    • 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

  • Folder hmmer-2.3.2 contains the source code and other associated file for implementing the HMMer software for Pfam analysis.
  • Folder 495pfamDir contains 495 profile Hidden Markov Models. Both folders were created on the disk on Apr. 24, 2009 having a total size of 39,755,623 bytes when measured in MS-WINDOWS® operating system. 00001
  • recombinant DNA for providing enhanced traits to transgenic plants, seeds, pollen, plant cells and plant nucleui of such transgenic plants, methods of making and using such recombinant DNA, plants, seeds, pollen, plant cells and plant nuclei. Also disclosed are methods of producing hybrid seed comprising such recombinant DNA.
  • This invention provides recombinant DNA comprising polynucleotides characterized by SEQ ID NO: 1-803 and the cognate amino acid sequences of SEQ ID NO: 804-1606.
  • the recombinant DNA is used for providing enhanced traits when stably integrated into the chromosomes and expressed in the nuclei of transgenic plants cells.
  • the recombinant DNA encodes a protein; in other aspects the recombinant DNA is transcribed to RNA that suppresses the expression of a native gene.
  • Such recombinant DNA in a plant cell nuclus 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 20.
  • a Pfam domain module as defined herein below
  • such DNA in the construct is defined a consensus amino acid sequence of an encoded protein that is targeted for production e.g.
  • the recombinant DNA is characterized by its cognate amino acid sequence that has at least 70% identity to any of SEQ ID NO: 804-1606.
  • transgenic plant cell nuclei comprising the recombinant DNA of the invention, transgenic plant cells comprising such nuclei, transgenic plants comprising a plurality of such transgenic plant cells, and transgenic seeds and transgenic pollen of such plants.
  • Such transgenic plants are selected from a population of transgenic plants regenerated from plant cells transformed with recombinant DNA by screening transgenic plants for an enhanced trait as compared to control plants.
  • the enhanced trait is one or more of enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced heat tolerance, enhanced shade tolerance, enhanced high salinity tolerance, enhanced seed protein and enhanced seed oil.
  • Such recombinant DNA in a plant cell nuclus 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 20.
  • 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 e.g. a protein having amino acid sequence with at least 90% identity to a consensus amino acid sequence in the group of SEQ ID NO: 94617 through SEQ ID NO: 94734.
  • the plant cell nuclei, cells, plants, seeds, and pollen further comprise DNA expressing a protein that provides tolerance from exposure to an herbicide applied at levels that are lethal to a wild type plant cell.
  • 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 comprises (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 further comprises steps (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: 1-803; in one aspect of the invention the plants in the population further comprise DNA expressing a protein that provides tolerance to exposure to an herbicide applied at levels that are lethal to wild type plant cells and 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 are used for manufacturing corn, soybean, cotton, canola, alfalfa, wheat, rice seed or any combinations thererof selected as having one of the enhanced traits described above.
  • Another aspect of the invention provides a method of producing hybrid corn seed comprising acquiring hybrid corn seed from a herbicide tolerant corn plant which also has a nucleus of this invention with stably-integrated, recombinant DNA.
  • the method further comprises 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 a fraction of the plants produced from said hybrid corn seed has none of said recombinant DNA; selecting corn plants which are homozygous and hemizygous for said recombinant DNA by treating with an herbicide; collecting seed from herbicide-treated-surviving corn plants and planting said seed to produce further progeny corn plants; repeating the selecting and collecting steps at least once to produce an inbred corn line; and crossing the inbred corn line with a second corn line to produce hybrid seed.
  • this invention provides methods of growing a corn, cotton, soybean, or canola crop without irrigation water comprising planting seed having plant cells of the invention which are selected for enhanced water use efficiency.
  • methods comprise applying reduced irrigation water, e.g. providing up to 300 millimeters of ground water during the production of a corn crop.
  • This invention also provides methods of growing a corn, cotton, soybean or canola crop without added nitrogen fertilizer comprising planting seed having plant cells of the invention which are selected for enhanced nitrogen use efficiency.
  • FIGS. 1 , 2 and 3 illustrate plasmid maps.
  • FIG. 4 illustrates a consensus amino acid sequence of SEQ ID NO: 1325 and its homologs.
  • SEQ ID NO: 1-803 are nucleotide sequences of the coding strand of DNA for “genes” used in the recombinant DNA imparting an enhanced trait in plant cells, where each represents a coding sequence for a protein;
  • SEQ ID NO: 804-1606 are amino acid sequences of the cognate protein of the “genes” with nucleotide coding sequence 1-803;
  • SEQ ID NO: 1607-94613 are amino acid sequences of homologous proteins
  • SEQ ID NO: 94614 is a nucleotide sequence of a plasmid base vector for corn transformation.
  • SEQ ID NO: 94615 is a DNA sequence of a plasmid base vector for soybean transformation.
  • SEQ ID NO: 94616 is a DNA sequence of a plasmid base vector for cotton transformation.
  • SEQ ID NO: 94617-94734 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.
  • a “plant cell” means a plant cell that is transformed with stably-integrated, non-natural, recombinant DNA, e.g. by Agrobacterium -mediated transformation or by bombardment using microparticles coated with recombinant DNA or other means.
  • a plant cell of this invention can be an originally-transformed plant cell that exists as a microorganism or as a progeny plant cell that is regenerated into differentiated tissue, e.g. into a transgenic plant with stably-integrated, non-natural recombinant DNA, or seed or pollen derived from a progeny transgenic plant.
  • transgenic plant means a plant whose genome has been altered by the stable integration of recombinant DNA.
  • a transgenic plant includes a plant regenerated from an originally-transformed plant cell and progeny transgenic plants from later generations or crosses of a transformed plant.
  • recombinant DNA means DNA which has been a genetically engineered and constructed outside of a cell including DNA containing naturally occurring DNA or cDNA or synthetic DNA.
  • 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.
  • Homologous genes include naturally occurring alleles and artificially-created variants. Degeneracy of the genetic code provides the possibility to substitute at least one base of the protein encoding sequence of a gene with a different base without causing the amino acid sequence of the polypeptide produced from the gene to be changed.
  • a polynucleotide in the present invention can have any base sequence that has been changed from SEQ ID NO:1 through SEQ ID NO: 803 through substitution in accordance with degeneracy of the genetic code.
  • Homologs are proteins that, when optimally aligned, have at least about 60% identity, about 70% or higher, at least about 80% and at least about 90% identity over the full length of a protein identified as being associated with imparting an enhanced trait when expressed in plant cells.
  • Homologs include proteins with an amino acid sequence that has at least about 90% 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
  • a reciprocal query is used in the present invention to filter hit sequences with significant E-values for ortholog identification.
  • the reciprocal query entails search of the significant hits against a database of amino acid sequences from the base organism that are similar to the sequence of the query protein.
  • a hit 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 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.
  • 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.
  • 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.
  • promoter means regulatory DNA for initializing transcription.
  • a “plant promoter” is a promoter capable of initiating transcription in plant cells whether or not its origin is a plant cell, e.g. is it well known that Agrobacterium promoters are functional in plant cells.
  • plant promoters include promoter DNA obtained from plants, plant viruses and bacteria such as Agrobacterium and Bradyrhizobium bacteria.
  • Examples of promoters under developmental control include promoters that preferentially initiate transcription in certain tissues, such as leaves, roots, or seeds. Such promoters are referred to as “tissue preferred”. Promoters that initiate transcription only in certain tissues are referred to as “tissue specific”.
  • a “cell type” specific promoter primarily drives expression in certain cell types in one or more organs, for example, vascular cells in roots or leaves.
  • An “inducible” or “repressible” promoter is a promoter which is under environmental control. Examples of environmental conditions that 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 antisense 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.
  • expressed means produced, e.g. a protein is expressed in a plant cell when its cognate DNA is transcribed to mRNA that is translated to the protein.
  • “suppressed” means decreased, e.g. a protein is suppressed in a plant cell when there is a decrease in the amount and/or activity of the protein in the plant cell.
  • the presence or activity of the protein can be decreased by any amount up to and including a total loss of protein expression and/or activity.
  • control plant means a plant that does not contain the recombinant DNA that expressed a protein that imparts an enhanced trait.
  • a control plant is to identify and select a transgenic plant that has an enhance trait.
  • a suitable control plant can be a non-transgenic plant of the parental line used to generate a transgenic plant, e.g. devoid of recombinant DNA.
  • a suitable control plant can in some cases be a progeny of a hemizygous transgenic plant line that is does not contain the recombinant DNA, known as a negative segregant.
  • 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 about 2% difference in an observed trait, at least about 5% desirable difference, at least about 10% difference, at least about 20% difference, at least about 30% difference, at least about 40%, at least about 50% difference, at least about 60%, at least about 70% difference, at least about 80% difference, at least about 90% difference, or at least about a 100% difference, or an even greater difference.
  • the trait enhancement is only measured qualitatively. It is known that there can be a natural variation in a trait.
  • 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.
  • Yield can be affected by many properties including without limitation, plant height, pod number, pod position on the plant, number of internodes, incidence of pod shatter, grain size, efficiency of nodulation and nitrogen fixation, efficiency of nutrient assimilation, resistance to biotic and abiotic stress, carbon assimilation, plant architecture, resistance to lodging, percent seed germination, seedling vigor, and juvenile traits. Yield can also be affected by efficiency of germination (including germination in stressed conditions), growth rate (including growth rate in stressed conditions), ear number, seed number per ear, seed size, composition of seed (starch, oil, protein) and characteristics of seed fill.
  • Increased yield of a transgenic plant of the present invention can be measured in a number of ways, including test weight, seed number per plant, seed weight, seed number per unit area (e.g. seeds, or weight of seeds, per acre), bushels per acre, tonnes per acre, tons per acre, kilo per hectare.
  • maize yield can be measured as production of shelled corn kernels per unit of production area, for example in bushels per acre or metric tons per hectare, often reported on a moisture adjusted basis, for example at 15.5 percent moisture.
  • Increased yield can result from improved utilization of key biochemical compounds, such as nitrogen, phosphorous and carbohydrate, or from improved responses to environmental stresses, such as cold, heat, drought, salt, and attack by pests or pathogens.
  • Recombinant DNA used in this invention can also be used to provide plants having improved growth and development, and ultimately increased yield, as the result of modified expression of plant growth regulators or modification of cell cycle or photosynthesis pathways. Also of interest is the generation of transgenic plants that demonstrate enhanced yield with respect to a seed component that could correspond to an increase in overall plant yield. Such properties include enhancements in seed oil, seed molecules such as tocopherol, protein and starch, or oil particular oil components as can be manifest by alterations in the ratios of seed components.
  • 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.
  • a constitutively active mutant is constructed to achieve the desired effect.
  • a dominant negative gene is constructed to adversely affect the normal, wild-type gene product within the same cell.
  • DNA constructs are assembled using methods well known to persons of ordinary skill in the art and typically comprise a promoter operably linked to DNA, the expression of which provides the enhanced agronomic trait.
  • Other construct components can include additional regulatory elements, such as 5′ leaders and introns for enhancing transcription, 3′ untranslated regions (such as polyadenylation signals and sites), DNA for transit or signal peptides.
  • promoters that are active in plant cells have been described in the literature. These include promoters present in plant genomes as well as promoters from other sources, including nopaline synthase (NOS) promoter and octopine synthase (OCS) promoters carried on tumor-inducing plasmids of Agrobacterium tumefaciens and the CaMV35S promoters from the cauliflower mosaic virus as disclosed in U.S. Pat. Nos. 5,164,316 and 5,322,938. Promoters derived from plant genes are found in U.S. Pat. No. 5,641,876, which discloses a rice actin promoter, U.S. Pat. No.
  • NOS nopaline synthase
  • OCS octopine synthase
  • Promoters of interest for such uses include those from genes such as Arabidopsis thaliana ribulose-1,5-bisphosphate carboxylase (Rubisco) small subunit (Fischhoff et al. (1992) Plant Mol Biol. 20:81-93), aldolase and pyruvate orthophosphate dikinase (PPDK) (Taniguchi et al. (2000) Plant Cell Physiol. 41(1):42-48).
  • Rubisco Arabidopsis thaliana ribulose-1,5-bisphosphate carboxylase
  • PPDK pyruvate orthophosphate dikinase
  • the promoters can be altered to contain multiple “enhancer sequences” to assist in elevating gene expression.
  • enhancers are known in the art.
  • the expression of the selected protein 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 upstream (5′) or downstream (3′) to the coding sequence.
  • these 5′ enhancing elements are introns.
  • enhancers are the 5′ introns of the rice actin 1 (see U.S. Pat. No. 5,641,876) and rice actin 2 genes, the maize alcohol dehydrogenase gene intron, the maize heat shock protein 70 gene intron (U.S. Pat. No. 5,593,874) and the maize shrunken 1 gene.
  • promoters for use for seed composition modification include promoters from seed genes such as napin (U.S. Pat. No. 5,420,034), maize L3 oleosin (U.S. Pat. No. 6,433,252), zein Z27 (Russell et al. (1997) Transgenic Res. 6(2):157-166), globulin 1 (Belanger et al (1991) Genetics 129:863-872), glutelin 1 (Russell (1997) supra), and peroxiredoxin antioxidant (Per1) (Stacy et al. (1996) Plant Mol Biol. 31(6):1205-1216).
  • seed genes such as napin (U.S. Pat. No. 5,420,034), maize L3 oleosin (U.S. Pat. No. 6,433,252), zein Z27 (Russell et al. (1997) Transgenic Res. 6(2):157-166), globulin 1 (Belanger et al (1991) Genetics
  • Recombinant DNA constructs prepared in accordance with the invention will also generally include a 3′ element that typically contains a polyadenylation signal and site.
  • 3′ elements include those from Agrobacterium tumefaciens genes such as nos 3′, tml 3′, tmr 3′, tms 3′, ocs 3′, tr7 3′, for example disclosed in U.S. Pat. No.
  • 3′ elements from plant genes such as wheat ( Triticum aesevitum ) heat shock protein 17 (Hsp17 3′), a wheat ubiquitin gene, a wheat fructose-1,6-biphosphatase gene, a rice glutelin gene, a rice lactate dehydrogenase gene and a rice beta-tubulin gene, all of which are disclosed in U.S. published patent application 2002/0192813 A1, incorporated herein by reference; and the pea ( Pisum sativum ) ribulose biphosphate carboxylase gene (rbs 3′), and 3′ elements from the genes within the host plant.
  • wheat Triticum aesevitum
  • Hsp17 3′ heat shock protein 17
  • rbs 3′ the pea ribulose biphosphate carboxylase gene
  • Constructs and vectors can also include a transit peptide for targeting of a gene to a plant organelle, particularly to a chloroplast, leucoplast or other plastid organelle.
  • a transit peptide for targeting of a gene to a plant organelle particularly to a chloroplast, leucoplast or other plastid organelle.
  • chloroplast transit peptides see U.S. Pat. No. 5,188,642 and U.S. Pat. No. 5,728,925, incorporated herein by reference.
  • the transit peptide region of an Arabidopsis EPSPS gene can be in the present invention, see Klee, H. J. et al ( MGG (1987) 210:437-442).
  • 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.
  • Transgenic plants comprising or derived from plant cells of this invention transformed with recombinant DNA can be further enhanced with stacked traits, e.g. a crop plant having an enhanced trait resulting from expression of DNA disclosed herein in combination with herbicide and/or pest resistance traits.
  • genes of the current invention can be stacked with other traits of agronomic interest, such as a trait providing herbicide resistance, or insect resistance, such as using a gene from Bacillus thuringensis to provide resistance against lepidopteran, coliopteran, homopteran, hemiopteran, and other insects.
  • Herbicides for which transgenic plant tolerance has been demonstrated and the method of the present invention can be applied include, but are not limited to, glyphosate, dicamba, glufosinate, sulfonylurea, bromoxynil and norflurazon herbicides.
  • Polynucleotide molecules encoding proteins involved in herbicide tolerance are well-known in the art and include, but are not limited to, a polynucleotide molecule encoding 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) disclosed in U.S. Pat. Nos.
  • EPSPS 5-enolpyruvylshikimate-3-phosphate synthase
  • Patent Application publication 2003/0135879 A1 for imparting dicamba tolerance a polynucleotide molecule encoding bromoxynil nitrilase (Bxn) disclosed in U.S. Pat. No. 4,810,648 for imparting bromoxynil tolerance; a polynucleotide molecule encoding phytoene desaturase (crtl) described in Misawa et al, (1993) Plant J. 4:833-840 and in Misawa et al, (1994) Plant J.
  • Bxn bromoxynil nitrilase
  • crtl phytoene desaturase
  • Patent Application Publication 2003/010609 A1 for imparting N-amino methyl phosphonic acid tolerance polynucleotide molecules disclosed in U.S. Pat. No. 6,107,549 for impartinig pyridine herbicide resistance; molecules and methods for imparting tolerance to multiple herbicides such as glyphosate, atrazine, ALS inhibitors, isoxoflutole and glufosinate herbicides are disclosed in U.S. Pat. No. 6,376,754 and U.S. Patent Application Publication 2002/0112260, all of said U.S. patents and patent application Publications are incorporated herein by reference. Molecules and methods for imparting insect/nematode/virus resistance are disclosed in U.S. Pat. Nos. 5,250,515; 5,880,275; 6,506,599; 5,986,175 and U.S. Patent Application Publication 2003/0150017 A1, all of which are incorporated herein by reference.
  • 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.
  • 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 can be used 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.
  • Pfam modules for use in this invention, as more specifically disclosed below, are Syntaxin::SNARE, Pro_isomerase, Pkinase, ATP-synt_G, Carboxyl_trans, CDC50, GATase::GMP_synt_C, F-box::WD40::WD40::WD40, dsrm::dsrm, Pyr_redox — 2::Pyr_redox_dim, WAK::Pkinase, Pkinase_Tyr, PTPA, Biotin_lipoyl::E3_binding::2-oxoacid_dh, AAA, LRRNT — 2::LRR — 1::LRR — 1::LRR — 1, PRA1, TIM, YTH, ThiF, Hep — 59, Pkinase, PALP::Thr_dehydrat_C::Thr_dehydrat_C, zf-T
  • Transformation of plant material is practiced in tissue culture on a nutrient media, e.g. 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 can 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.
  • a transgenic plant cell nucleus can be prepared by crossing a first plant having cells with a transgenic nucleus with recombinant DNA with a second plant lacking the trangenci nucleus.
  • recombinant DNA can be introduced into a nucleus from a first plant line that is amenable to transformation to transgenic nucleus in cells that are grown into a transgenic plant which can be crossed with a second plant line to introgress the recombinant DNA into the second plant line.
  • a transgenic plant with recombinant DNA providing an enhanced trait, e.g.
  • transgenic plant line having other recombinant DNA that confers another trait for example herbicide resistance or pest resistance
  • progeny plants having recombinant DNA that confers both traits Typically, in such breeding for combining traits the transgenic plant donating the additional trait is a male line and the transgenic plant carrying the base traits is the female line.
  • the progeny of this cross will segregate such that some of the plants will carry the DNA for both parental traits and some will carry DNA for one parental trait; such plants can be identified by markers associated with parental recombinant DNA, e.g.
  • 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.
  • Explementary 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 is (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 can be used 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 plant cells that have been scored positive in a screening assay, can be cultured in regeneration media and allowed to mature into plants.
  • Developing plantlets regenerated from transformed plant cells can be transferred to plant growth mix, and hardened off, for example, in an environmentally controlled chamber at about 85% relative humidity, 600 ppm CO 2 , and 25-250 microeinsteins m ⁇ 2 S ⁇ 1 of light, prior to transfer to a greenhouse or growth chamber for maturation.
  • Plants are regenerated from about 6 weeks to 10 months after a transformant is identified, depending on the initial tissue, and plant species.
  • Plants can be pollinated using conventional plant breeding methods known to those of skill in the art and seed produced, for example self-pollination is commonly used with transgenic corn.
  • the regenerated transformed plant or its progeny seed or plants can be tested for expression of the recombinant DNA and selected for the presence of enhanced agronomic trait.
  • Transgenic plants derived from transgenic plant cells having a transgenic nucleus of this invention are grown to generate transgenic plants having an enhanced trait as compared to a control plant and produce transgenic seed and haploid pollen of this invention.
  • Such plants with enhanced traits are identified by selection of transformed plants or progeny seed for the enhanced trait.
  • a selection method is designed to evaluate multiple transgenic plants (events) comprising the recombinant DNA, for example multiple plants from 2 to 20 or more transgenic events.
  • Transgenic plants grown from transgenic seed provided herein demonstrate improved agronomic traits that contribute to increased yield or other trait that provides increased plant value, including, for example, improved seed quality.
  • plants having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil are plants having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • 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 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.
  • Table 2 provides a list of protein encoding DNA (“genes”) as recombinant DNA for production of transgenic plants with enhanced agronomic trait, the elements of Table 2 are described by reference to:
  • PEP SEQ ID NO′′ identifies an amino acid sequence from SEQ ID NO: 804 to 1606.
  • NUC SEQ ID NO identifies a DNA sequence from SEQ ID NO:1 to 803
  • 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:803, 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.
  • the nucleotides for gne suppression can be 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more consecutive nucleotides.
  • Oligonucleotides having a sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 803 can be as probes and primers for detection of the polynucleotides used in the invention.
  • 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 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 about 60% nucleotide equivalence; about 70% equivalence; about 80% equivalence; about 85% equivalence; about 90%; about 95%; about 98%, about 99% equivalence or about 99.5 equivalence over a comparison window.
  • a comparison window can be at least 50-100 nucleotides or the entire length of the polynucleotide provided herein.
  • Optimal alignment of sequences for aligning a comparison window can be conducted by algorithms; for example by computerized implementations of these algorithms (such as, 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 used 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: 804 through SEQ ID NO: 1606, as well as homologs of such proteins.
  • Homologs of the proteins in the invention are identified by comparison of the amino acid sequence of the protein to amino acid sequences of proteins from the same or different plant sources, e.g., manually or by using known homology-based search algorithms such as those commonly known and referred to as BLAST, FASTA, and Smith-Waterman.
  • a homolog is a protein from the same or a different organism that performs the same biological function as the polypeptide to which it is compared.
  • An orthologous relation between two organisms is not necessarily manifest as a one-to-one correspondence between two genes, because a gene can be duplicated or deleted after organism phylogenetic separation, such as speciation. For a given protein, there can be no ortholog or more than one ortholog.
  • a local sequence alignment program e.g., BLAST
  • E-value the summary Expectation value
  • BLAST a local sequence alignment program
  • 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 the summary Expectation value
  • a reciprocal BLAST search is used in the present invention to filter hit sequences with significant E-values for ortholog identification.
  • the reciprocal BLAST entails search of the significant hits against a database of amino acid sequences from the base organism that are similar to the sequence of the query protein.
  • a hit is a likely ortholog, when the reciprocal BLAST's best hit is the query protein itself or a protein encoded by a duplicated gene after speciation.
  • homolog is used herein to describe proteins that are assumed to have functional similarity by inference from sequence base similarity.
  • the relationship of homologs with amino acid sequences of SEQ ID NO: 1607 to SEQ ID NO: 94613 to the proteins with amino acid sequences of SEQ ID NO: 804 to SEQ ID NO: 1606 are found in the listing of Table 19.
  • 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 comprises 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.
  • Homologs of the trait-improving proteins provided herein will 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: 804 to SEQ ID NO: 1606.
  • Additional embodiments also include those with higher identity, e.g., about 90%, about 92.5%, about 95%, about 98%, about 99%, or to about 99.5% identity.
  • Identity of protein homologs is determined by optimally 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: 804 to SEQ ID NO: 1606.
  • Protein homologs include proteins with an amino acid sequence that has at least 90% identity to such a consensus amino acid sequence sequences.
  • 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.
  • Arabidopsis has a small genome, and well-documented studies are available. It is easy to grow in large numbers and mutants defining important genetically controlled mechanisms are either available, or can readily be obtained. Various methods to introduce and express isolated homologous genes are available (see Koncz, et al., Methods in Arabidopsis Research et al., (1992), World Scientific, New Jersey, N.J., in “Preface”).
  • a two-step screening process was employed which comprised 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 cognate 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:
  • 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.
  • campestris str ATCC 33913] 931 70130 1.00E ⁇ 161 99 ref
  • subtilis str. 168 1179 73164 0 93 ref
  • tomato str. DC3000 1268 73432 0 94 ref
  • LL tomato str. DC3000 1279 73565 0 95 ref
  • PCC 6803 1293 74485 0 88 ref
  • PCC 6803 1365 74966 0 99 ref
  • PCC 6803 1367 74934 0 96 ref
  • PCC 6803 1469 75920 0 100 ref
  • 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 find particular use 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.
  • 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 et al., (1995) Plant Physiol. 107:125-130).
  • PEG polyethylene glycol
  • a PEG-induced osmotic stress tolerance screen can be a 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.
  • 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.
  • 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 drought 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.
  • two screening conditions e.g., cold shock tolerance screen (CK) and cold germination tolerance screen (CS)
  • CK cold shock tolerance screen
  • CS 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 can be used for the production of transgenic plant that can germinate more robustly in a cold temperature as compared to the wild type plants.
  • 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.
  • 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.
  • PEP SEQ ID NO: 1000 can be used to enhance both salt stress tolerance and heat stress tolerance in plants.
  • plants transformed with PEP SEQ ID NO: 1495 can resist salt and heat stress. Plants transformed with PEP SEQ ID NO: 1483 can also improve growth in early stage and under heat stress.
  • the stress tolerance conferring genes provided by the present invention can be used in combinations to generate transgenic plants that can resist multiple stress conditions.
  • PP-Enhancement of earl 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.
  • early planting and applying fertilizer are the methods used for promoting early seedling vigor.
  • 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 can be used 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: 1043 which can improve the plant early growth and development, and impart heat stress tolerance to plants.
  • PEP SEQ ID NO: 1043 which can improve the plant early growth and development, and impart heat stress 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.
  • 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.
  • 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.
  • Explementary herbicides include glyphosate herbicides, phosphinothricin herbicides, oxynil herbicides, imidazolinone herbicides, dinitroaniline herbicides, pyridine herbicides, sulfonylurea herbicides, bialaphos herbicides, sulfonamide herbicides and gluphosinate herbicides.
  • glyphosate herbicides include 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: 803, or a homologous protein with an amino acid sequence homologous to any of SEQ ID NO: 804 to SEQ ID NO: 1606.
  • the present invention provides the protein sequences of identified homologs for a sequence listed as SEQ ID NO: 1607 through SEQ ID NO: 94613.
  • 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.
  • they are agricultural 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, Ill. 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, et al., 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 transgenic plants and their controls and analyzed as a quantitative response according to example 1M.
  • 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 X 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 (Boyes, et 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: 823, 825, 873, 886, 912, 916, 919, 928, 937, 942, 972, 986, 995, 1074, 1107, 1134, 1136, 1145, 1157, 1173, 1220, 1228, 1242, 1243, 1285, 1377, 1469, 1486, 1489, 1524, 1538, 1546, 1556, 1568, 1571, 1574, 1592, or 1603 showed enhanced heat stress tolerance by the second criteria as illustrated in Example 1L 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 experiment 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 1L.
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 821, 834, 890, 919, 946, 961, 997, 1013, 1080, 1101, 1147, 1160, 1181, 1197, 1200, 1220, 1237, 1248, 1264, 1300, 1313, 1355, 1393, 1397, 1406, 1467, 1496, 1514, 1530 or 1561 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 X MS salts, 1% phytagel, and 10 ⁇ g/ml glufosinate. 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, e.g., 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 day14.
  • 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 1L.
  • 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: 832, 833, 871, 874, 931, 974, 985, 997, 1021, 1024, 1031, 1043, 1053, 1059, 1060, 1091, 1111, 1115, 1118, 1120, 1124, 1127, 1128, 1159, 1172, 1179, 1185, 1197, 1213, 1226, 1230, 1244, 1253, 1265, 1306, 1320, 1327, 1354, 1355, 1357, 1362, 1367, 1381, 1395, 1398, 1399, 1407, 1462, 1494, 1499, 1500, 1523, 1529, 1532, 1544, 1548, 1569, 1572, 1573, 1595, or 1598 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.
  • 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 experiment 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 X 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.
  • 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 826, 863, 864, 941, 985, 1071, 1123, 1170, 1194, 1259, 1312, 1339, 1433, 1465, 1543, 1556 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 X 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: 805, 828, 833, 870, 936, 937, 939, 965, 988, 1007, 1010, 1016, 1038, 1050, 1060, 1070, 1079, 1089, 1095, 1100, 1117, 1125, 1129, 1134, 1135, 1145, 1150, 1154, 1155, 1158, 1184, 1204, 1210, 1214, 1216, 1217, 1225, 1226, 1235, 1248, 1252, 1255, 1260, 1271, 1278, 1282, 1283, 1289, 1292, 1297, 1304, 1311, 1312, 1317, 1328, 1336, 1338, 1348, 1363, 1366, 1383, 1386, 1400, 1428, 1448, 1451, 1453, 1462, 1491, 1493, 1505, 1516, 1520, 1528, 1533, 1545, 1579, or 1588 showed
  • 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 day14 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.
  • Root length Root length Seedling weight PEP at day 10 at day 14 at day 14 NUC SEQ Delta Delta Delta SEQ ID ID ID Orientation mean P-value mean P-value 52 855 SENSE 0.091 0.027 0.071 0.018 0.037 0.744 102 905 SENSE 0.188 0.210 0.104 0.247 0.308 0.021 121 924 SENSE 0.242 0.015 0.128 0.063 0.203 0.078 153 956 SENSE 0.153 0.027 0.122 0.197 0.256 0.010 134 937 SENSE 0.329 0.048 0.250 0.085 0.712 0.020 144 947 SENSE 0.127 0.146 0.045 0.566 0.371 0.023 101 904 SENSE 0.537 0.026 0.356 0.004 0.634 0.021 178 981 SENSE 0.372 0.136 0.273 0.033 0.346 0.082 179 982 SENSE 0.404 0.001 0.222 0.051 0.288 0.111
  • Transgenic plants comprising recombinant DNA expressing a protein as set forth in 810, 831, 844, 857, 865, 884, 892, 917, 950, 954, 970, 983, 992, 998, 1004, 1005, 1029, 1033, 1043, 1072, 1101, 1109, 1115, 1133, 1181, 1200, 1284, 1310, 1340, 1384, 1391, 1443, 1449, 1471, 1480, 1483, 1498, 1506, 1508, 1510, 1529, 1548, 1553, 1555, 1556, 1558, 1559, 1564, 1576, or 1577 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.
  • Table 12 A list of recombinant DNA constructs that improve late plant growth and development illustrated in Table 12.
  • 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.
  • 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 (e.g., 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.
  • seedling status e.g., viable or non-viable
  • 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 1L.
  • 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 807, 808, 817, 820, 829, 839, 847, 848, 850, 854, 858, 859, 866, 872, 875, 878, 889, 902, 908, 911, 922, 938, 944, 953, 963, 974, 980, 993, 1001, 1009, 1035, 1042, 1048, 1049, 1054, 1058, 1068, 1076, 1088, 1094, 1096, 1098, 1103, 1104, 1107, 1112, 1113, 1114, 1121, 1152, 1166, 1175, 1192, 1204, 1207, 1215, 1218, 1240, 1246, 1251, 1256, 1266, 1269, 1281, 1283, 1290, 1296, 1298, 1344, 1345, 1356, 1389, 1396, 1400, 1404, 1409, 1425, 1428, 1438, 1441, 1442, 1454,
  • 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 enhacement 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 ⁇ perform 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
  • the measurements (M) of each plant were transformed by log 2 calculation.
  • the Delta was calculated as log 2 M(transgenic) ⁇ log 2 M(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 2 M(transgenic) ⁇ log 2 M(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 perform 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.
  • This example illustrates the construction of plasmids for transferring recombinant DNA into a plant cell nucleus that can be regenerated into transgenic plants.
  • a base corn transformation vector pMON93039 as set forth in SEQ ID NO: 94614, illustrated in Table 16 and FIG. 1 , is made for use in preparing recombinant DNA for Agrobacterium -mediated transformation into corn tissue.
  • T-AGRtu.nos A 3′ non-translated region of 5849-6101 the nopaline synthase gene of Agrobacterium tumefaciens Ti plasmid which functions to direct polyadenylation of the mRNA.
  • Maintenance 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.
  • 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 or suppressing 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 the base vector.
  • Vectors for use in transformation of soybean and canola can also be prepared. Elements of an exemplary common expression vector pMON82053 (SEQ ID NO: 94615) are shown in Table 17 below and FIG. 2 .
  • 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.
  • OR-Ec.oriV-RK2 The vegetative origin of replication 5661-6057 E. coli from plasmid RK2.
  • OR-Ec.ori-ColE1 The minimal origin of replication 2945-3533 from the E. coli plasmid ColE1.
  • 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 or suppressing 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 the base vector.
  • Plasmids for use in transformation of cotton tissue are prepared with elements of expression vector pMON99053 (SEQ ID NO: 94616) are shown in Table 18 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 or suppressing 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 the base vector.
  • T-AGRtu.nos A 3′ non-translated region of 3011-3263 the nopaline synthase gene of Agrobacterium tumefaciens Ti plasmid which functions to direct polyadenylation of the mRNA.
  • Maintenance in OR-Ec.oriV-RK2 The vegetative origin of 3837-4233 E. coli replication from plasmid RK2.
  • OR-Ec.ori-ColE1 The minimal origin of 6363-6949 replication from the E. coli plasmid ColE1.
  • T-Ec.aadA-SPC/STR Promoter for Tn7 7480-7521 adenylyltransferase (AAD(3′′)) CR-Ec.aadA-SPC/STR Coding region for Tn7 7522-8310 adenylyltransferase (AAD(3′′)) conferring spectinomycin and streptomycin resistance.
  • This example illustrates transformation methods in producing a transgenic nucleus in a corn plant cell and the plants, seeds and pollen produced from a transgenic cell with such a nucleus having an enhanced trait, e.g. enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • Plasmid vectors are prepared by cloning DNA identified in Table 2 in the base vector for use in corn transformation of corn tissue.
  • corn plants of a readily transformable line are grown in the greenhouse and ears are harvested when the embryos are 1.5 to 2.0 mm in length. Ears are surface sterilized by spraying or soaking the ears in 80% ethanol, followed by air drying. Immature embryos are isolated from individual kernels on surface sterilized ears. Prior to inoculation of maize cells, Agrobacterium cells are grown overnight at room temperature. Immature maize embryo cells are inoculated with Agrobacterium shortly after excision, and incubated at room temperature with Agrobacterium for 5-20 minutes. Immature embryo plant cells are then co-cultured with Agrobacterium for 1 to 3 days at 23° C. in the dark.
  • Co-cultured embryos are transferred to selection media and cultured for approximately two weeks to allow embryogenic callus to develop.
  • Embryogenic callus is transferred to culture medium containing 100 mg/L paromomycin and subcultured at about two week intervals.
  • Transformed plant cells are recovered 6 to 8 weeks after initiation of selection.
  • immature embryos are cultured for approximately 8-21 days after excision to allow callus to develop. Callus is then incubated for about 30 minutes at room temperature with the Agrobacterium suspension, followed by removal of the liquid by aspiration. The callus and Agrobacterium are co-cultured without selection for 3-6 days followed by selection on paromomycin for approximately 6 weeks, with biweekly transfers to fresh media. Paromomycin resistant calli are identified about 6-8 weeks after initiation of selection.
  • transgenic corn plants To regenerate transgenic corn plants a callus of transgenic plant cells resulting from transformation and selection is placed on media to initiate shoot development into plantlets which are transferred to potting soil for initial growth in a growth chamber at 26° C. followed by a mist bench before transplanting to 5 inch pots where plants are grown to maturity.
  • the regenerated plants are self-fertilized and seed is harvested for use in one or more methods to select seeds, seedlings or progeny second generation transgenic plants (R2 plants) or hybrids, e.g. by selecting transgenic plants exhibiting an enhanced trait as compared to a control plant.
  • Transgenic corn plant cells are transformed with recombinant DNA from each of the genes identified in Table 2. Progeny transgenic 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 as obtained in Example 7.
  • This example illustrates plant transformation in producing the transgenic soybean plants of this invention and the production and identification of transgenic seed for transgenic soybean having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • soybean seeds are imbided overnight and the meristem explants excised.
  • the explants are placed in a wounding vessel.
  • Soybean explants and induced Agrobacterium cells from a strain containing plasmid DNA with the gene of interest cassette and a plant selectable marker cassette are mixed no later than 14 hours from the time of initiation of seed imbibition, and wounded using sonication.
  • explants are placed in co-culture for 2-5 days at which point they are transferred to selection media for 6-8 weeks to allow selection and growth of transgenic shoots.
  • Resistant shoots are harvested approximately 6-8 weeks and placed into selective rooting media for 2-3 weeks. Shoots producing roots are transferred to the greenhouse and potted in soil.
  • a DNA construct can be transferred into the genome of a soybean cell by particle bombardment and the cell regenerated into a fertile soybean plant as described in U.S. Pat. No. 5,015,580, herein incorporated by reference.
  • Transgenic soybean plant cells 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 as obtained in Example 10.
  • Cotton transformation is performed as generally described in WO0036911 and in U.S. Pat. No. 5,846,797.
  • Transgenic cotton plants containing each recombinant DNA having a sequence of SEQ ID NO: 1 through SEQ ID NO: 803 are obtained by transforming with recombinant DNA from each of the genes identified in Table 2.
  • 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 e.g. 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 is 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 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 overnight-grown Agrobacterium cells 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 characterization is 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 1.
  • 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 as obtained in Example 7.
  • This example illustrates the identification of homologs of proteins encoded by the DNA identified in Table 1 which is used to provide transgenic seed and plants having enhanced agronomic traits. From the sequence of the homologs, homologous DNA sequence can be identified for preparing additional transgenic seeds and plants of this invention with enhanced agronomic traits.
  • An “All Protein Database” 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 polynucleotide sequence provided herein was obtained, an “Organism Protein Database” is constructed of known protein sequences of the organism; it is a subset of the All Protein Database based on the NCBI taxonomy ID for the organism.
  • NCBI National Center for Biotechnology Information
  • the All Protein Database is queried using amino acid sequences provided herein as SEQ ID NO: 804 through SEQ ID NO: 1606 using NCBI “blastp” program with E-value cutoff of 1 e ⁇ 8. Up to 1000 top hits are 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 of the polynucleotides provided herein, and is referred to as the Core List. Another list is 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 polypeptide sequences provided herein as SEQ ID NO: 804 through SEQ ID NO: 1606 using NCBI “blastp” program with E-value cutoff of 1 e ⁇ 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 is queried with each sequence in the Hit List using NCBI “blastp” program with E-value cutoff of leg. 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: 804 and its homologs, through SEQ ID NO: 1606 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: 1325 and its 30 homologs were derived according to the procedure described above and is displayed in FIG. 4 .
  • 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: 804 through 1606 are shown in Table 20 and Table 21 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 cognate encoding DNA to enable the full breadth of the invention for a person of ordinary skill in the art. Certain proteins are identified by a single Pfam domain and others by multiple Pfam domains.
  • the protein with amino acids of SEQ ID NO: 830 is characterized by two Pfam domains, e.g. “Lectin_legB” and “Pkinase”. See also the protein with amino acids of SEQ ID NO: 817 which is characterized by four copies of the Pfam domain “Arm”.
  • “score” is the gathering score for the Hidden Markov Model of the domain which exceeds the gathering cutoff reported in Table 22.
  • Transgenic seed and plants in corn, soybean, cotton or canola with recombinant DNA identified in Table 2 are prepared by plant cells transformed with DNA that is stably integrated into the genome of the corn cell.
  • Transgenic corn plant cells are transformed with recombinant DNA from each of the genes identified in Table 2.
  • Progeny transgenic 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 as compared to control plants
  • Transgenic corn seeds provided by the present invention are planted in fields with three levels of nitrogen (N) fertilizer being applied, e.g. low level (0 N), medium level (80 lb/ac) and high level (180 lb/ac). A variety of physiological traits are monitored. Plants with enhanced NUE provide higher yield as compared to control plants.
  • N nitrogen
  • Effective selection of enhanced yielding transgenic plants uses hybrid progeny of the transgenic plants for corn, cotton, and canola, or inbred progeny of transgenic plants for soybeanplants plant such as corn, cotton, canola, or inbred plant such as soy, canola and cottoncotton over multiple locations with plants grown under optimal production management practices, and maximum pest control.
  • a target for improved yield is about a 5% to 10% increase or more 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.
  • the selection process imposes a water withholding period to induce stressdrought followed by watering.
  • a 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.
  • Cold field efficacy trial A cold field efficacy trial is used to identify gene constructs that confer enhanced cold vigor at germination and early seedling growth under early spring planting field conditions in conventional-till and simulated no-till environments. Seeds are planted into the ground around two weeks before local farmers begin to plant corn so that a significant cold stress is exerted onto the crop, named as cold treatment. Seeds also are planted under local optimal planting conditions such that the crop has little or no exposure to cold condition, named as normal treatment. At each location, seeds are planted under both cold and normal conditions with 3 repetitions per treatment. Two temperature monitors are set up at each location to monitor both air and soil temperature daily.
  • This example sets forth a high-throughput selection for identifying plant seeds with improvement in seed composition using the Infratec 1200 series Grain Analyzer, which is a near-infrared transmittance spectrometer used to determine the composition of a bulk seed sample (Table 26).
  • 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 predicted values as well as information on how well the sample fits in the calibration.
  • Infratec Model 1221, 1225, or 1227 with transport module by Foss North America is used with cuvette, item #1000-4033, Foss North America or for small samples with small cell cuvette, Foss standard cuvette modified by Leon Girard Co. Corn and soy check samples of varying composition maintained in check cell cuvettes are supplied by Leon Girard Co. NIT collection software is provided by Maximum Consulting Inc. Software. Calculations are 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 corn and soybean seeds
  • Analytical time to Less than 0.75 min per sample run method Total elapsed time per run: 1.5 minute per sample
  • Typical analytical range Determined in part by the specific calibration. Corn - moisture 5-15%, oil 5-20%, protein 5-30%, starch 50-75%, and density 1.0-1.3%. Soybean - moisture 5-15%, oil 15-25%, and protein 35-50%.
  • Cotton transformation is performed as generally described in WO0036911 and in U.S. Pat. No. 5,846,797.
  • Transgenic cotton plants containing each of the recombinant DNA having a sequence of SEQ ID NO: 1 through SEQ ID NO: 803 are obtained by transforming with recombinant DNA from each of the genes identified in Table 2.
  • 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 e.g. 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 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 the preparation and identification by selection of transgenic seeds and plants derived from transgenic plant cells of this invention where the plants and seed are identified by screening for a transgenic plant having an enhanced agronomic trait imparted by expression or suppression of a protein selected from the group including the homologous proteins identified in Example 7.
  • Transgenic plant cells of corn, soybean, cotton, canola, alfalfa, wheat and rice are transformed with recombinant DNA for expressing or suppressing each of the homologs identified in Example 7.
  • Plants are regenerated from the transformed plant cells and used to produce progeny plants and seed that are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. Plants are identified exhibiting enhanced traits imparted by expression or suppression of the homologous proteins.
  • 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 described in Examples 2-5 using recombinant DNA in the nucleus with DNA that is transcribed into 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, soybean, cotton or canola that are homologs of the genes encoding the protein that has the function of the protein of Arabidopsis thaliana as identified in Table 24.
  • Pfam module ID Traits 115 AP2 10177 LN 116 zf-C2H2 12155 CS SS 118 F-box::Tub 11873 LN PEG 154 Pex2_Pex12::zf-C3HC4 11113 CS Myb_DNA-binding::Myb_DNA- 188 binding 12325 LN 200 bZIP_1 71228 CK
US12/386,976 2008-04-29 2009-04-24 Genes and uses for plant enhancement Abandoned US20130333068A1 (en)

Priority Applications (5)

Application Number Priority Date Filing Date Title
US12/386,976 US20130333068A1 (en) 2008-04-29 2009-04-24 Genes and uses for plant enhancement
US14/544,230 US20160122783A1 (en) 2008-04-29 2014-12-10 Genes and Uses for Plant Enhancement
US15/732,766 US10696975B2 (en) 2008-04-29 2017-12-22 Genes and uses for plant enhancement
US16/873,608 US11274312B2 (en) 2008-04-29 2020-05-21 Genes and uses for plant enhancement
US17/803,149 US20230048751A1 (en) 2008-04-29 2022-03-03 Genes and uses for plant enhancement

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US12590808P 2008-04-29 2008-04-29
US12/386,976 US20130333068A1 (en) 2008-04-29 2009-04-24 Genes and uses for plant enhancement

Related Child Applications (1)

Application Number Title Priority Date Filing Date
US14/544,230 Continuation US20160122783A1 (en) 2008-04-29 2014-12-10 Genes and Uses for Plant Enhancement

Publications (1)

Publication Number Publication Date
US20130333068A1 true US20130333068A1 (en) 2013-12-12

Family

ID=41137730

Family Applications (5)

Application Number Title Priority Date Filing Date
US12/386,976 Abandoned US20130333068A1 (en) 2008-04-29 2009-04-24 Genes and uses for plant enhancement
US14/544,230 Abandoned US20160122783A1 (en) 2008-04-29 2014-12-10 Genes and Uses for Plant Enhancement
US15/732,766 Active US10696975B2 (en) 2008-04-29 2017-12-22 Genes and uses for plant enhancement
US16/873,608 Active US11274312B2 (en) 2008-04-29 2020-05-21 Genes and uses for plant enhancement
US17/803,149 Pending US20230048751A1 (en) 2008-04-29 2022-03-03 Genes and uses for plant enhancement

Family Applications After (4)

Application Number Title Priority Date Filing Date
US14/544,230 Abandoned US20160122783A1 (en) 2008-04-29 2014-12-10 Genes and Uses for Plant Enhancement
US15/732,766 Active US10696975B2 (en) 2008-04-29 2017-12-22 Genes and uses for plant enhancement
US16/873,608 Active US11274312B2 (en) 2008-04-29 2020-05-21 Genes and uses for plant enhancement
US17/803,149 Pending US20230048751A1 (en) 2008-04-29 2022-03-03 Genes and uses for plant enhancement

Country Status (4)

Country Link
US (5) US20130333068A1 (de)
EP (4) EP2336332A3 (de)
BR (1) BRPI0911501A2 (de)
WO (1) WO2009134339A2 (de)

Cited By (26)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20130160165A1 (en) * 2010-06-24 2013-06-20 BASF Plant Science Company BmbH Plants Having Enhanced Yield-Related Traits and Method for Making the Same
US20150143585A1 (en) * 2012-06-08 2015-05-21 Postech Academy-Industry Foundation Biomass Production Increasing Gene And Transgenic Plant Using Same
US9085776B2 (en) * 2013-08-13 2015-07-21 Plant Response Biotech S.L. Method for enhancing drought tolerance in plants
US9198416B2 (en) 2013-08-13 2015-12-01 Plant Response Biotech S.L. Method for enhancing drought tolerance in plants
WO2015181823A1 (en) * 2014-05-28 2015-12-03 Evogene Ltd. Isolated polynucleotides, polypeptides and methods of using same for increasing abiotic stress tolerance, biomass and yield of plants
WO2016077331A1 (en) * 2014-11-12 2016-05-19 The Rockefeller University Improved agronomic characteristics under water limiting conditions for plants expressing pub10 polypeptides
US20170029829A1 (en) * 2014-04-09 2017-02-02 The Scripps Research Institute Import of unnatural or modified nucleoside triphosphates into cells via nucleic acid triphosphate transporters
WO2017023486A1 (en) * 2015-08-06 2017-02-09 Pioneer Hi-Bred International, Inc. Plant derived insecticidal proteins and methods for their use
CN106432447A (zh) * 2016-10-31 2017-02-22 南京农业大学 一种植物淀粉合成相关蛋白OsPKp1及其编码基因与应用
WO2017124001A3 (en) * 2016-01-14 2017-08-17 Memorial Sloan-Kettering Cancer Center T cell receptor-like antibodies specific for foxp3-derived peptides
WO2017141248A1 (en) * 2016-02-17 2017-08-24 Pepticom Ltd Peptide agonists and antagonists of tlr4 activation
WO2017176277A1 (en) * 2016-04-07 2017-10-12 Plant Sensory Systems, Llc Algal and fungal genes and their uses for taurine biosynthesis in cells
WO2018067244A1 (en) * 2016-10-07 2018-04-12 Brim Biotechnology, Inc. Compositions comprising pedf-derived short peptides and uses thereof
WO2019040411A1 (en) * 2017-08-21 2019-02-28 Indiana University Research And Technology Corporation PROTEIN EXPRESSION SYSTEMS ENHANCING SOLUBILITY
US10472642B2 (en) 2015-02-05 2019-11-12 British American Tobacco (Investments) Limited Method for the reduction of tobacco-specific nitrosamines or their precursors in tobacco plants
CN110627869A (zh) * 2019-10-08 2019-12-31 河南省农业科学院 与禽法氏囊病毒vp2蛋白特异性结合的多肽序列及其应用
US10610571B2 (en) 2017-08-03 2020-04-07 Synthorx, Inc. Cytokine conjugates for the treatment of proliferative and infectious diseases
US10696975B2 (en) 2008-04-29 2020-06-30 Monsanto Technology Llc Genes and uses for plant enhancement
US11077195B2 (en) 2019-02-06 2021-08-03 Synthorx, Inc. IL-2 conjugates and methods of use thereof
CN113583100A (zh) * 2021-09-09 2021-11-02 西北农林科技大学 一种苹果离子转运体MdCCX2及其转基因植株和应用
CN114395020A (zh) * 2021-12-31 2022-04-26 华南农业大学 GmRALF1蛋白在促进植物对磷元素吸收中的应用
CN114751967A (zh) * 2022-04-15 2022-07-15 西南大学 水稻籽粒大小和灌浆的调控基因gfd2及其应用
CN115851779A (zh) * 2022-10-29 2023-03-28 昆明理工大学 一种葡萄糖-6-磷酸脱氢酶基因RkZWF1及其应用
CN116286952A (zh) * 2023-03-08 2023-06-23 南京农业大学 大豆GmSAMMT基因在调控植物蛋白含量和/或产量中的应用
CN116768991A (zh) * 2022-03-10 2023-09-19 中国科学院遗传与发育生物学研究所 与油脂代谢调控相关的大豆四跨膜区蛋白GmTET270及其编码基因与应用
US11834689B2 (en) 2017-07-11 2023-12-05 The Scripps Research Institute Incorporation of unnatural nucleotides and methods thereof

Families Citing this family (63)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
ES2716864T3 (es) * 2007-06-06 2019-06-17 Monsanto Technology Llc Genes y usos para la mejora de plantas
US20130305398A1 (en) 2012-02-16 2013-11-14 Marie Coffin Genes and uses for plant enhacement
BRPI0917889A2 (pt) * 2008-08-29 2018-01-30 Los Alamos Nat Security Llc gene glutamina fenilpiruvato transaminase de planta e plantas transgênicas compreendendo o mesmo
US20110030104A1 (en) 2008-08-29 2011-02-03 Los Alamos National Security, Llc Nucleic acids encoding plant glutamine phenylpyruvate transaminase (GPT) and uses thereof
US20110030089A1 (en) 2008-08-29 2011-02-03 Los Alamos National Security, Llc Transgenic plants with enhanced growth characteristics
EP2386634A4 (de) * 2009-01-07 2012-07-18 Mitsubishi Chem Corp Sterolseitenketten spaltendes enzymprotein und verwendung davon
DE112010001805T5 (de) * 2009-04-29 2012-09-06 Basf Plant Science Company Gmbh Pflanzen mit gesteigerten Ertragsmerkmalen und Verfahren zu deren Herstellung
US20120096593A1 (en) * 2009-05-06 2012-04-19 Yves Hatzfeld Plants Having Enhanced Yield-Related Traits And/Or Enhanced Abiotic Stress Tolerance And A Method For Making The Same
BRPI1008189A2 (pt) * 2009-06-30 2015-08-25 Du Pont Planta transgenica semente transgenica obtida a partir da planta transgencia semente transgencia metodo de produção de uma planta transgenica metodo de produção de sementes transgenicas metodo de produto e ou subproduto da semente transgenica e semente transgenica obtida pelo metodo
CN101899459B (zh) * 2009-12-22 2014-04-16 石河子大学 天山雪莲sikRbcS2基因在培育抗寒植物中的应用
NZ601341A (en) 2010-01-22 2014-02-28 Bayer Ip Gmbh Acaricide and/or insecticide active substance combinations
EP2371845A1 (de) * 2010-03-22 2011-10-05 BASF Plant Science Company GmbH Installations dotées de caractéristiques de rendement améliorées et procédé de fabrication de celles-ci
BR122021002340B1 (pt) 2010-04-28 2022-04-05 Evogene Ltd Método de aumento de biomassa, taxa de crescimento e/ou eficiência de uso de nitrogênio de uma planta
CN105296530A (zh) * 2010-10-28 2016-02-03 纳幕尔杜邦公司 涉及编码dtp6多肽的基因的耐旱植物以及相关构建体和方法
EP2665819A4 (de) * 2011-01-20 2014-09-10 Basf Plant Science Co Gmbh Pflanzen mit verbesserten ertragseigenschaften und verfahren zu ihrer herstellung
EP2681307A1 (de) * 2011-02-28 2014-01-08 Novozymes, Inc. Mikroorganismus zur herstellung von c4-dicarbonsäure
CN102747048B (zh) * 2011-04-20 2013-12-04 中国医学科学院病原生物学研究所 一种结核杆菌候选抗原及其应用
WO2012156760A1 (en) * 2011-05-19 2012-11-22 Consejo Superior De Investigaciones Cientificas Process for modifying the architecture and improving the yield of crop plants
EP2734625A4 (de) * 2011-07-19 2015-01-21 Basf Plant Science Co Gmbh Pflanzen mit verbesserten ertragseigenschaften und verfahren zu ihrer herstellung
US9265252B2 (en) 2011-08-10 2016-02-23 Bayer Intellectual Property Gmbh Active compound combinations comprising specific tetramic acid derivatives
MX2014006326A (es) * 2011-11-25 2014-07-09 Basf Plant Science Co Gmbh Plantas que tienen mejores rasgos relacionados con el rendimiento y un metodo para producirlas.
BR112014013853A2 (pt) 2011-12-09 2020-01-14 Ceres Inc uso de um ácido nucleico isolado, método de obtenção de uma célula vegetal transgênica, método de obtenção de uma planta transgênica, método de produção de uma planta, método de produção de biomassa, método de processamento de biomassa, método de alteração da composição de biomassa, método de modulação de composição de biomassa, método de produção de um produto de forragem
WO2014024102A1 (en) 2012-08-09 2014-02-13 Basf Plant Science Company Gmbh Fungal resistant plants expressing rlk2
WO2014037376A1 (en) 2012-09-04 2014-03-13 C5 Ligno Technologies In Lund Ab Stereoselective biosynthesis in microbial host cells
WO2015002588A1 (en) * 2013-07-05 2015-01-08 Oxthera Intellectual Property Ab Secretagogues derived from oxalobacter formigenes
CA2916060A1 (en) * 2013-08-27 2015-03-05 Evogene Ltd. Isolated polynucleotides and polypeptides, and methods of using same for increasing plant yield and/or agricultural characteristics
BR112016012125A2 (pt) 2013-11-27 2018-09-18 E.I. Du Pont De Nemours And Company métodos para identificar uma planta de milho com tolerância diminuída ao estresse salino, para identificar um planta de milho com tolerância ao estresse salino, para aumentar a tolerância ao estresse salino, para identificar e introduzir uma variante do gene transportador de ìons, constructo de dna recombinante, célula vegetal transgênica, planta transgênica e semente transgênica
EP4227685A3 (de) 2013-12-03 2024-02-28 Evaxion Biotech A/S Proteine und nukleinsäuren für impfstoffe gegen staphylococcus aureus
JP2017529063A (ja) * 2014-07-18 2017-10-05 フィリップ・モーリス・プロダクツ・ソシエテ・アノニム たばこプロテアーゼ遺伝子
CN104628839B (zh) * 2015-02-04 2018-03-02 南京农业大学 一种水稻胚乳造粉体发育相关蛋白及其编码基因和应用
KR101869432B1 (ko) * 2015-04-08 2018-06-20 연세대학교 산학협력단 케톤에 대한 활성이 증대된 오메가 트랜스아미네이즈의 변이체 및 이것을 이용한 광학활성 아민의 제조방법
CN106520849B (zh) * 2015-09-11 2022-08-09 杭州酶易生物技术有限公司 一种制备手性2-氯-3,4-二氟苯乙醇的方法
CN105132440B (zh) * 2015-09-23 2018-08-21 安徽农业大学 与小麦叶片叶绿素含量和粒重相关的基因、其Indel标记及应用
WO2017172996A1 (en) * 2016-03-29 2017-10-05 Sapphire Energy, Inc. Biomass genes
CN110366594B (zh) * 2016-12-16 2023-12-15 丹尼斯科美国公司 双功能磷酸转酮酶-磷酸转乙酰酶融合多肽
CN106749580B (zh) * 2017-02-14 2019-07-02 中国农业科学院作物科学研究所 植物耐盐相关蛋白TaPUB15-D及其编码基因与应用
CN107164387B (zh) * 2017-06-16 2020-08-04 南京农业大学 一种低锰利用基因、蛋白、重组表达载体及其制备与应用
EP3733689B1 (de) * 2018-02-05 2022-10-26 Asymchem Life Science (Tianjin) Co., Ltd Transaminase-mutant und anwendung davon
BR112020019198A2 (pt) * 2018-03-23 2021-02-17 Pioneer Hi-Bred International, Inc. método para identificar um gene r em uma planta, método para obter uma planta resistente a doenças, planta modificada tendo resistência aumentada a uma doença, método para introduzir uma variante alélica de um gene nlr01, construto de dna recombinante, célula de planta transgênica e planta transgênica
MA52591A (fr) * 2018-07-12 2021-06-02 Hexamer Therapeutics Inc Échafaudage peptidique autoassemblé
CN109207495B (zh) * 2018-09-18 2021-05-11 华中农业大学 超表达GhCIPK6基因提高植物水分利用效率促进可溶性糖积累
CN110938119B (zh) * 2018-09-20 2021-05-18 中国农业科学院作物科学研究所 大豆抗逆相关蛋白GmBES及其编码基因的应用
CN109608528B (zh) * 2018-12-11 2021-05-25 天津师范大学 一种通过转化旱柳SmZIP蛋白提高植物重金属Cd转运能力及抗性的方法
FR3102186B1 (fr) * 2019-10-17 2021-11-05 Biolaffort Levures œnologiques permettant le contrôle de la teneur en acide des vins et méthodes de sélection de telles levures.
CN110804088A (zh) * 2019-11-18 2020-02-18 维塔恩(广州)医药有限公司 巨细胞病毒相关抗原短肽及其应用
CN110746497A (zh) * 2019-11-18 2020-02-04 维塔恩(广州)医药有限公司 肺炎衣原体相关抗原短肽及其应用
CN110938607B (zh) * 2019-12-18 2023-03-28 美康生物科技股份有限公司 热稳定性好的甘油-3-磷酸氧化酶及其在试剂盒中的应用
CN111676275A (zh) * 2020-06-10 2020-09-18 湖南杂交水稻研究中心 检测水稻HIS1基因是否存在T1510G突变的方法和dCAPS标记引物
WO2021178350A1 (en) * 2020-03-03 2021-09-10 Innate Immunity LLC Antiviral chimeric peptides
US20210292732A1 (en) * 2020-03-18 2021-09-23 Lanzatech, Inc. Fermentative production of 2-phenylethanol from gaseous substrates
CN111235163B (zh) * 2020-03-20 2022-05-31 南京农业大学 水稻减数分裂发育相关基因OsMFS1及其应用
CN111647590B (zh) * 2020-07-06 2023-02-17 西北农林科技大学 含有fyve结构域的腺苷酸环化酶及其编码基因与应用
CN111808872B (zh) * 2020-07-24 2022-06-24 中国科学院遗传与发育生物学研究所农业资源研究中心 调控黍亚科植物株型的基因dpy1及其应用和方法
CN112442115B (zh) * 2020-12-08 2022-03-04 中国农业科学院作物科学研究所 小麦TaPRR95-B蛋白或其编码基因在调控植物株高中的应用
CN112608928B (zh) * 2021-01-05 2021-08-20 重庆文理学院 一种龙眼单果重性状调控基因DlCNR8及其蛋白与应用
CN112625102A (zh) * 2021-01-08 2021-04-09 中国农业科学院作物科学研究所 水稻抽穗期基因OsPRR73及其应用
WO2023148476A1 (en) * 2022-02-03 2023-08-10 Nicoventures Trading Limited Method of modulating alkaloid content in tobacco plants
WO2023201129A1 (en) * 2022-04-12 2023-10-19 NMC Inc. Antibacterial chimeric peptides and their methods of therapeutic use
CN115490762B (zh) * 2022-05-11 2023-06-27 西南大学 蜡梅CpCBL8基因及其编码的蛋白与应用
CN114807218B (zh) * 2022-05-12 2023-06-02 中国科学院海洋研究所 一种转入外源基因来提高三角褐指藻藻种高温抗性的方法
US20240110221A1 (en) * 2022-09-30 2024-04-04 Illumina, Inc. Methods of modulating clustering kinetics
CN115838746B (zh) * 2022-11-14 2024-04-09 东北林业大学 拟南芥bdr3基因在调控植物耐盐性中的应用
CN116217686B (zh) * 2023-01-05 2024-03-08 海南大学 一种来自水稻的OsUVR8基因及其应用

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030233675A1 (en) * 2002-02-21 2003-12-18 Yongwei Cao Expression of microbial proteins in plants for production of plants with improved properties

Family Cites Families (72)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5094945A (en) 1983-01-05 1992-03-10 Calgene, Inc. Inhibition resistant 5-enolpyruvyl-3-phosphoshikimate synthase, production and use
US5034322A (en) 1983-01-17 1991-07-23 Monsanto Company Chimeric genes suitable for expression in plant cells
US5428147A (en) 1983-04-15 1995-06-27 Mycogen Plant Science, Inc. Octopine T-DNA promoters
DE3587548T2 (de) 1984-12-28 1993-12-23 Plant Genetic Systems Nv Rekombinante DNA, die in pflanzliche Zellen eingebracht werden kann.
US5420034A (en) 1986-07-31 1995-05-30 Calgene, Inc. Seed-specific transcriptional regulation
EP0218571B1 (de) 1985-08-07 1993-02-03 Monsanto Company Glyphosat resistente Pflanzen
US4810648A (en) 1986-01-08 1989-03-07 Rhone Poulenc Agrochimie Haloarylnitrile degrading gene, its use, and cells containing the gene
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
US5164316A (en) 1987-01-13 1992-11-17 The University Of British Columbia DNA construct for enhancing the efficiency of transcription
US5359142A (en) 1987-01-13 1994-10-25 Monsanto Company Method for enhanced expression of a protein
US5322938A (en) 1987-01-13 1994-06-21 Monsanto Company DNA sequence for enhancing the efficiency of transcription
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
ATE206462T1 (de) 1989-02-24 2001-10-15 Monsanto Technology Llc Synthetische pflanzengene und verfahren zu ihrer herstellung
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
US5641876A (en) 1990-01-05 1997-06-24 Cornell Research Foundation, Inc. Rice actin gene and promoter
WO1991010725A1 (en) 1990-01-22 1991-07-25 Dekalb Plant Genetics Fertile transgenic corn plants
US5484956A (en) 1990-01-22 1996-01-16 Dekalb Genetics Corporation Fertile transgenic Zea mays plant comprising heterologous DNA encoding Bacillus thuringiensis endotoxin
EP0536330B1 (de) 1990-06-25 2002-02-27 Monsanto Technology LLC Glyphosattolerante pflanzen
US5633435A (en) 1990-08-31 1997-05-27 Monsanto Company Glyphosate-tolerant 5-enolpyruvylshikimate-3-phosphate synthases
DE69232132T3 (de) 1991-05-15 2008-08-14 Monsanto Technology Llc. Verfahren zur schöpfung einer transformierten reispflanze
US5593874A (en) 1992-03-19 1997-01-14 Monsanto Company Enhanced expression in plants
DE69334225D1 (de) 1992-07-07 2008-07-31 Japan Tobacco Inc Verfahren zur transformation einer monokotyledon pflanze
CA2100116C (en) 1992-07-09 2001-09-18 Joseph M. Jilka Virus resistant plants
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
CZ86798A3 (cs) 1996-06-21 1999-03-17 Monsanto Company Fertilní transgenní rostlina pšenice, způsob její přípravy, buňky a semena této rostliny
JPH10117776A (ja) 1996-10-22 1998-05-12 Japan Tobacco Inc インディカイネの形質転換方法
US6809235B2 (en) * 1996-11-18 2004-10-26 University Of Florida Research Foundation, Inc. Heat stable mutants of starch biosynthesis enzymes
US6376754B1 (en) 1997-03-07 2002-04-23 Asgrow Seed Company Plants having resistance to multiple herbicides and its use
US6040497A (en) 1997-04-03 2000-03-21 Dekalb Genetics Corporation Glyphosate resistant maize lines
US7105724B2 (en) 1997-04-04 2006-09-12 Board Of Regents Of University Of Nebraska Methods and materials for making and using transgenic dicamba-degrading organisms
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
FR2779433B1 (fr) * 1998-06-08 2002-08-16 Centre Nat Rech Scient Proteine vegetale a motifs wd40 repetes, acide nucleique codant pour ladite proteine, et leurs applications
JP3051874B2 (ja) * 1998-06-19 2000-06-12 農林水産省農業生物資源研究所長 植物を矮性化させる方法
US6506599B1 (en) 1999-10-15 2003-01-14 Tai-Wook Yoon Method for culturing langerhans islets and islet autotransplantation islet regeneration
DE69941009D1 (de) 1998-11-17 2009-07-30 Monsanto Technology Llc Phosphonat metabolisierende pflanzen
WO2000036911A2 (en) 1998-12-18 2000-06-29 Monsanto Technology Llc Method for the regeneration of cotton
CA2359868A1 (en) 1999-01-14 2000-07-20 Monsanto Company Soybean transformation method
US20090265815A1 (en) 2000-08-09 2009-10-22 Nickolai Alexandrov Sequence-determined DNA fragments and corresponding polypeptides encoded therapy
EP1586645A3 (de) 1999-02-25 2006-02-22 Ceres Incorporated DNA-Fragmente mit bestimmter Sequenz und die dadurch kodierte Polypeptide
EP1033405A3 (de) * 1999-02-25 2001-08-01 Ceres Incorporated DNS-fragmente mit bestimmter Sequenz und die dadurch kodierte Polypeptide
US20040031072A1 (en) * 1999-05-06 2004-02-12 La Rosa Thomas J. Soy nucleic acid molecules and other molecules associated with transcription plants and uses thereof for plant improvement
EP2055779A3 (de) * 1999-05-07 2009-08-12 E.I. Dupont De Nemours And Company Auxiontransportproteine
US6194636B1 (en) 1999-05-14 2001-02-27 Dekalb Genetics Corp. Maize RS324 promoter and methods for use thereof
US6232526B1 (en) 1999-05-14 2001-05-15 Dekalb Genetics Corp. Maize A3 promoter and methods for use thereof
US20020192813A1 (en) 1999-08-18 2002-12-19 Timothy W. Conner Plant expression vectors
EP1313867A2 (de) * 2000-08-24 2003-05-28 The Scripps Research Institute Stressregulierte nukleotidsequenzen aus pflanzen, diese enthaltende transgene pflanzen und verfahren zu deren verwendung
AU2002220181B2 (en) 2000-10-30 2007-12-20 E. I. Du Pont De Nemours And Company Novel glyphosate n-acetyltransferase (gat) genes
US7151204B2 (en) 2001-01-09 2006-12-19 Monsanto Technology Llc Maize chloroplast aldolase promoter compositions and methods for use thereof
JP2003031077A (ja) 2001-07-16 2003-01-31 Sunarrow Ltd 多段多方向キー及びこれを用いた多段多方向キースイッチ
WO2003014348A1 (en) 2001-08-06 2003-02-20 Monsanto Technology Llc Dna molecules from maize and methods of use thereof
AU2001289843A1 (en) 2001-08-28 2002-02-13 Bayer Cropscience Ag Polypeptides for identifying herbicidally active compounds
US20030150017A1 (en) 2001-11-07 2003-08-07 Mesa Jose Ramon Botella Method for facilitating pathogen resistance
WO2005019425A2 (en) * 2003-08-18 2005-03-03 University Of Florida Research Foundation, Inc. Heat stable variants of adenosine diphosphate glucose pyrophosphorylase
US20060048240A1 (en) * 2004-04-01 2006-03-02 Nickolai Alexandrov Sequence-determined DNA fragments and corresponding polypeptides encoded thereby
US20060107345A1 (en) * 2003-09-30 2006-05-18 Nickolai Alexandrov Sequence-determined DNA fragments and corresponding polypeptides encoded thereby
US7989676B2 (en) 2006-08-31 2011-08-02 Ceres, Inc. Nucleotide sequences and corresponding polypeptides conferring modulated plant characteristics
WO2006081029A2 (en) 2004-12-22 2006-08-03 Ceres, Inc. Nucleotide sequences and corresponding polypeptides conferring modulated plant size and biomass and other characteristics in plants
EP2584033A1 (de) * 2005-01-12 2013-04-24 Monsanto Technology LLC Gene und ihre Verwendung zur Pflanzenverbesserung
EP1882392A4 (de) * 2005-05-10 2009-07-01 Monsanto Technology Llc Gene und ihre verwendung zur pflanzenverbesserung
EP2441839A1 (de) * 2006-05-30 2012-04-18 CropDesign N.V. Pflanzen mit reduzierter Expression von REVOLUTA-Gen mit verbesserten Ertragseigenschaften und Verfahren zu ihrer Herstellung
EP2380988A3 (de) * 2007-07-10 2012-04-11 Mosanto Technology LLC Transgene Pflanzen mit erweiterten agronomischen Merkmalen
US20130333068A1 (en) 2008-04-29 2013-12-12 Marie Coffin Genes and uses for plant enhancement
US20120117685A1 (en) * 2009-02-27 2012-05-10 Wei Wu Isolated Novel Nucleic Acid and Protein Molecules from Soybeans and Methods of Using Thos Molecules

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030233675A1 (en) * 2002-02-21 2003-12-18 Yongwei Cao Expression of microbial proteins in plants for production of plants with improved properties

Cited By (39)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10696975B2 (en) 2008-04-29 2020-06-30 Monsanto Technology Llc Genes and uses for plant enhancement
US11274312B2 (en) 2008-04-29 2022-03-15 Monsanto Technology Llc Genes and uses for plant enhancement
US20130160165A1 (en) * 2010-06-24 2013-06-20 BASF Plant Science Company BmbH Plants Having Enhanced Yield-Related Traits and Method for Making the Same
US20150143585A1 (en) * 2012-06-08 2015-05-21 Postech Academy-Industry Foundation Biomass Production Increasing Gene And Transgenic Plant Using Same
US9862961B2 (en) * 2012-06-08 2018-01-09 Postech Academy-Industry Foundation Biomass production increasing gene and transgenic plant using same
US9085776B2 (en) * 2013-08-13 2015-07-21 Plant Response Biotech S.L. Method for enhancing drought tolerance in plants
US9198416B2 (en) 2013-08-13 2015-12-01 Plant Response Biotech S.L. Method for enhancing drought tolerance in plants
US11466279B2 (en) 2014-04-09 2022-10-11 The Scripps Research Institute Import of unnatural or modified nucleoside triphosphates into cells via nucleic acid triphosphate transporters
US20170029829A1 (en) * 2014-04-09 2017-02-02 The Scripps Research Institute Import of unnatural or modified nucleoside triphosphates into cells via nucleic acid triphosphate transporters
US10513706B2 (en) * 2014-04-09 2019-12-24 The Scripps Research Institute Import of unnatural or modified nucleoside triphosphates into cells via nucleic acid triphosphate transporters
WO2015181823A1 (en) * 2014-05-28 2015-12-03 Evogene Ltd. Isolated polynucleotides, polypeptides and methods of using same for increasing abiotic stress tolerance, biomass and yield of plants
US10975383B2 (en) 2014-05-28 2021-04-13 Evogene Ltd. Isolated polynucleotides, polypeptides and methods of using same for increasing abiotic stress tolerance, biomass and yield of plants
WO2016077331A1 (en) * 2014-11-12 2016-05-19 The Rockefeller University Improved agronomic characteristics under water limiting conditions for plants expressing pub10 polypeptides
US10472642B2 (en) 2015-02-05 2019-11-12 British American Tobacco (Investments) Limited Method for the reduction of tobacco-specific nitrosamines or their precursors in tobacco plants
WO2017023486A1 (en) * 2015-08-06 2017-02-09 Pioneer Hi-Bred International, Inc. Plant derived insecticidal proteins and methods for their use
RU2762832C2 (ru) * 2015-08-06 2021-12-23 Пайонир Хай-Бред Интернэшнл, Инк. Инсектицидные белки растительного происхождения и способы их применения
US11198709B2 (en) 2015-08-06 2021-12-14 E. I. Du Pont De Nemours And Company Plant derived insecticidal proteins and methods for their use
WO2017124001A3 (en) * 2016-01-14 2017-08-17 Memorial Sloan-Kettering Cancer Center T cell receptor-like antibodies specific for foxp3-derived peptides
US11505599B2 (en) 2016-01-14 2022-11-22 Memorial Sloan-Kettering Cancer Center T cell receptor-like antibodies specific for Foxp3-derived peptides
US11155578B2 (en) 2016-02-17 2021-10-26 Pepticom Ltd. Peptide agonists and antagonists of TLR4 activation
WO2017141248A1 (en) * 2016-02-17 2017-08-24 Pepticom Ltd Peptide agonists and antagonists of tlr4 activation
US11078547B2 (en) 2016-04-07 2021-08-03 Plant Sensory Systems, Llc Algal and fungal genes and their uses for taurine biosynthesis in cells
WO2017176277A1 (en) * 2016-04-07 2017-10-12 Plant Sensory Systems, Llc Algal and fungal genes and their uses for taurine biosynthesis in cells
EA037698B1 (ru) * 2016-10-07 2021-05-12 Брим Байотекнолоджи, Инк. Композиции, содержащие короткие пептиды, полученные из pedf, и их применение
WO2018067244A1 (en) * 2016-10-07 2018-04-12 Brim Biotechnology, Inc. Compositions comprising pedf-derived short peptides and uses thereof
CN106432447A (zh) * 2016-10-31 2017-02-22 南京农业大学 一种植物淀粉合成相关蛋白OsPKp1及其编码基因与应用
US11834689B2 (en) 2017-07-11 2023-12-05 The Scripps Research Institute Incorporation of unnatural nucleotides and methods thereof
US11622993B2 (en) 2017-08-03 2023-04-11 Synthorx, Inc. Cytokine conjugates for the treatment of autoimmune diseases
US11701407B2 (en) 2017-08-03 2023-07-18 Synthorx, Inc. Cytokine conjugates for the treatment of proliferative and infectious diseases
US10610571B2 (en) 2017-08-03 2020-04-07 Synthorx, Inc. Cytokine conjugates for the treatment of proliferative and infectious diseases
WO2019040411A1 (en) * 2017-08-21 2019-02-28 Indiana University Research And Technology Corporation PROTEIN EXPRESSION SYSTEMS ENHANCING SOLUBILITY
US11077195B2 (en) 2019-02-06 2021-08-03 Synthorx, Inc. IL-2 conjugates and methods of use thereof
CN110627869A (zh) * 2019-10-08 2019-12-31 河南省农业科学院 与禽法氏囊病毒vp2蛋白特异性结合的多肽序列及其应用
CN113583100A (zh) * 2021-09-09 2021-11-02 西北农林科技大学 一种苹果离子转运体MdCCX2及其转基因植株和应用
CN114395020A (zh) * 2021-12-31 2022-04-26 华南农业大学 GmRALF1蛋白在促进植物对磷元素吸收中的应用
CN116768991A (zh) * 2022-03-10 2023-09-19 中国科学院遗传与发育生物学研究所 与油脂代谢调控相关的大豆四跨膜区蛋白GmTET270及其编码基因与应用
CN114751967A (zh) * 2022-04-15 2022-07-15 西南大学 水稻籽粒大小和灌浆的调控基因gfd2及其应用
CN115851779A (zh) * 2022-10-29 2023-03-28 昆明理工大学 一种葡萄糖-6-磷酸脱氢酶基因RkZWF1及其应用
CN116286952A (zh) * 2023-03-08 2023-06-23 南京农业大学 大豆GmSAMMT基因在调控植物蛋白含量和/或产量中的应用

Also Published As

Publication number Publication date
US11274312B2 (en) 2022-03-15
US20160122783A1 (en) 2016-05-05
EP2537937A2 (de) 2012-12-26
EP2336332A3 (de) 2011-11-09
US20190249198A1 (en) 2019-08-15
EP2716763A3 (de) 2014-07-02
US20230048751A1 (en) 2023-02-16
US20210032647A1 (en) 2021-02-04
EP2716763A2 (de) 2014-04-09
BRPI0911501A2 (pt) 2015-07-28
US10696975B2 (en) 2020-06-30
EP2537937A3 (de) 2013-04-10
WO2009134339A3 (en) 2010-03-11
WO2009134339A2 (en) 2009-11-05
WO2009134339A8 (en) 2013-06-13
EP2271760A2 (de) 2011-01-12
EP2336332A2 (de) 2011-06-22

Similar Documents

Publication Publication Date Title
US11274312B2 (en) Genes and uses for plant enhancement
US10538781B2 (en) Mate family genes and uses for plant improvement
US11371054B2 (en) Genes and uses for plant enhancement
US11479783B2 (en) Transgenic plants with enhanced agronomic traits
US20180258442A1 (en) Transgenic plants with enhanced agronomic traits
US20160272994A1 (en) Transgenic Plants With Enhanced Agronomic Traits
US20110214199A1 (en) Genes and uses for plant enhancement
US20170292131A1 (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:022777/0171

Effective date: 20090522

STCB Information on status: application discontinuation

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