# Patent

## Title
Transgenic plants with enhanced agronomic traits

## Abstract

This invention provides transgenic plant cells with recombinant DNA for expression of proteins that are useful for imparting enhanced agronomic trait(s) to transgenic crop plants. This invention also provides transgenic plants and progeny seed comprising the transgenic plant cells where the plants are selected for having an enhanced trait selected from the group of traits consisting of enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. Also disclosed are methods for manufacturing transgenic seed and plants with enhanced traits.

## Background
RELATED APPLICATIONS
This application is a continuation application of Ser. No. 11/982,680, filed Nov. 2, 2007 (pending). Application Ser. No. 11/982,680 is a continuation in part of application Ser. No. 10/678,588 (abandoned), filed Oct. 2, 2003, which claims the benefit under 35 U.S.C. 119(e) of provisional application Ser. Nos. 60/415,758, filed Oct. 2, 2002, 60/425,157, filed Nov. 8, 2002 and 60/463,787, filed Apr. 18, 2003, the disclosures of which are incorporated herein by reference in their entirety.
Application Ser. No. 11/982,680 (pending) is also a continuation in part of application Ser. No. 10/679,063 (abandoned), filed Oct. 2, 2003, which claims the benefit under 35 U.S.C. 119(e) of provisional application 60/415,758, filed Oct. 2, 2002, the disclosures of which are incorporated herein by reference in their entirety.


INCORPORATION OF SEQUENCE LISTING
Three copies of the a sequence listing (Copy 1 and Copy 2 and a computer readable form), in a text file named “38-21 (52054)A_seqList.txt” which is 100.3 MB (measured in MS-WINDOWS) are provided on separate CD-ROMs which were created on Oct. 30, 2007 and are herein incorpated by reference.
INCORPORATION OF COMPUTER PROGRAM LISTING
Two copies of Computer Program Listing (Copy 1 and Copy 2) containing folders “hmmer-2.3.2” and “241pfam” are provided on separate CD-ROMs that were created on Oct. 30, 2007, and have a total file size of 20.3 MB (measured in MS-WINDOWS). The “hmmer-2.3.2” folder contains the source code and other associated ASCII files for implementing the HMMer software for Pfam analysis; the “241 pfam” folder contains ASCII files of 241 Pfam Hidden. Markov Models; as well as the material on replacement CDs (Copy 1 and Copy 2) containing folders “hmmer-2.3.2” and “241pfamDir” are provided on separate CD-ROMs that were created on Dec. 12, 2011, and have a total file size of 20,480,616 bytes, created on Dec. 12, 2011, all of which are incorporated herein by reference in their entirety.
INCORPORATION OF TABLES
Two copies of Table 7 (Copy 1 and Copy 2) are provided on CDROMs that were created on Sep. 6, 2011 and contain the file named “38-21(52054)D_table7.txt” which is 369 KB (measured in MS-WINDOWS) which comprises 71 pages when viewed in MS Word®, are herein incorporated by reference. 







LENGTHY TABLES




The patent contains a lengthy table section. A copy of the table is available in electronic form from the USPTO web site (http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US09290773B2). An electronic copy of the table will also be available from the USPTO upon request and payment of the fee set forth in 37 CFR 1.19(b)(3).






FIELD OF THE INVENTION
Disclosed herein are inventions in the field of plant genetics and developmental biology. More specifically, the present inventions provide plant cells with recombinant DNA for providing an enhanced trait in a transgenic plant, plants comprising such cells, seed and pollen derived from such plants, methods of making and using such cells, plants, seeds and pollen.
SUMMARY OF THE INVENTION
This invention provides plant cell nuclei with recombinant DNA that imparts enhanced agronomic traits in transgenic plants having the nuclei in their cells, e.g. enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein or enhanced seed oil. Such recombinant DNA in a plant cell nucleus of this invention is provided in as a construct comprising a promoter that is functional in plant cells and that is operably linked to DNA that encodes a protein or to DNA that results in gene suppression. Such DNA in the construct is sometimes defined by protein domains of an encoded protein targeted for production or suppression, e.g. a “Pfam domain module” (as defined herein below) from the group of Pfam domain modules identified in Table 21 (page 94). Alternatively, e.g. where a Pfam domain module is not available, such DNA in the construct is defined a consensus amino acid sequence of an encoded protein that is targeted for production 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: 27377 through SEQ ID NO: 27426. Alternatively, in other cases where neither a Pfam domain module nor a consensus amino acid sequence is available, such DNA in the construct is defined by the sequence of a specific encoded and or its homologue proteins.
Other aspects of the invention are specifically directed to transgenic plant cells comprising the recombinant DNA of the invention, transgenic plants comprising a plurality of such plant cells, progeny transgenic seed, embryo and transgenic pollen from such plants. Such transgenic plants are selected from a population of transgenic plants regenerated from plant cells transformed with recombinant DNA and expressed the protein by screening transgenic plants in the population for an enhanced trait as compared to control plants that do not have said recombinant DNA, where the enhanced trait is selected from group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
In yet another aspect of the invention the plant cells, plants, seeds, embryo 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. Such tolerance is especially useful not only as an advantageous trait in such plants but is also useful in a selection step in the methods of the invention. In aspects of the invention the agent of such herbicide is a glyphosate, dicamba, or glufosinate compound.
Yet other aspects of the invention provide transgenic plants which are homozygous for the recombinant DNA and transgenic seed of the invention from corn, soybean, cotton, canola, alfalfa, wheat or rice plants.
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: 1-614; 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 especially useful for manufacturing corn, soybean, cotton, alfalfa, wheat or rice seed selected as having one of the enhanced traits described above.
Another aspect of the invention provides a method of producing hybrid corn seed comprising acquiring hybrid corn seed from a herbicide tolerant corn plant which also has stably-integrated, recombinant DNA comprising a promoter that is (a) functional in plant cells and (b) is operably linked to DNA that encodes a protein having at least one domain of amino acids in a sequence that exceeds the Pfam gathering cutoff for amino acid sequence alignment with a protein domain family identified by a Pfam name in the group of Pfam names identified in Table 22. The methods further comprise producing corn plants from said hybrid corn seed, wherein a fraction of the plants produced from said hybrid corn seed is homozygous for said recombinant DNA, a fraction of the plants produced from said hybrid corn seed is hemizygous for said recombinant DNA, and a fraction of the plants produced from said hybrid corn seed has none of said recombinant DNA; selecting corn plants which are homozygous and hemizygous for said recombinant DNA by treating with an herbicide; collecting seed from herbicide-treated-surviving corn plants and planting said seed to produce further progeny corn plants; repeating the selecting and collecting steps at least once to produce an inbred corn line; and crossing the inbred corn line with a second corn line to produce hybrid seed.
Another aspect of the invention provides a method of selecting a plant comprising plant cells of the invention by using an immunoreactive antibody to detect the presence of protein expressed by recombinant DNA in seed or plant tissue. Yet another aspect of the invention provides anti-counterfeit milled seed having, as an indication of origin, a plant cell of this invention.
Still other aspects of this invention relate to transgenic plants with enhanced water use efficiency or enhanced nitrogen use efficiency. For instance, this invention provides methods of growing a corn, cotton or soybean crop without irrigation water comprising planting seed having plant cells of the invention which are selected for enhanced water use efficiency. Alternatively methods comprise applying reduced irrigation water, e.g. providing up to 300 millimeters of ground water during the production of a corn crop. This invention also provides methods of growing a corn, cotton or soybean crop without added nitrogen fertilizer comprising planting seed having plant cells of the invention which are selected for enhanced nitrogen use efficiency.



BRIEF DESCRIPTION OF THE DRAWINGS
FIGS. 1A and 1B are a consensus amino acid sequence of SEQ ID NO: 932 and its homologs.
FIGS. 2-4 are plasmid maps.



DETAILED DESCRIPTION OF THE INVENTION
In the attached sequence listing:
SEQ ID NO:1-614 are nucleotide sequences of the coding strand of DNA for “genes” used in the recombinant DNA imparting an enhanced trait in plant cells, i.e. each represents a coding sequence for a protein;
SEQ ID NO: 615-1228 are amino acid sequences of the cognate protein of the “genes” with nucleotide coding sequences 1-614;
SEQ ID NO: 1229-27373 are amino acid sequences of homologous proteins;
SEQ ID NO: 27374 is a nucleotide sequence of a base plasmid vector useful for corn transformation;
SEQ ID NO: 27375 is a nucleotide sequence of a base plasmid vector useful for soybean and canola transformation;
SEQ ID NO: 27376 is a nucleotide sequence of a base plasmid vector useful for cotton transformation;
SEQ ID NO: 27377-27426 are consensus sequences.









TABLE 1





PEP SEQ 

Consensus


ID NO
Gene ID
SEQ ID

















684
PHE0000499
27377


704
PHE0000520
27378


705
PHE0000521
27379


706
PHE0000523
27380


710
PHE0000528
27381


719
PHE0000537
27382


734
PHE0000552
27383


735
PHE0000553
27384


738
PHE0000556
27385


743
PHE0000561
27386


744
PHE0000562
27387


745
PHE0000563
27388


746
PHE0000564
27389


761
PHE0000579
27390


777
PHE0000601
27391


779
PHE0000604
27392


793
PHE0000618
27393


804
PHE0000629
27394


824
PHE0000649
27395


891
PHE0000798
27396


896
PHE0000803
27397


900
PHE0000807
27398


918
PHE0000826
27399


924
PHE0000832
27400


932
PHE0000840
27401


957
PHE0000865
27402


961
PHE0000869
27403


1001
PHE0000913
27404


1015
PHE0000927
27405


1016
PHE0000928
27406


1026
PHE0000938
27407


1027
PHE0000939
27408


1032
PHE0000944
27409


1033
PHE0000945
27410


1036
PHE0000948
27411


1043
PHE0000955
27412


1044
PH E0000956
27413


1045
PHE0000957
27414


1051
PHE0000963
27415


1054
PHE0000966
27416


1059
PHE0000972
27417


1087
PHE0001006
27418


1119
PHE0001039
27419


1123
PHE0001043
27420


1135
PHE0001162
27421


1136
PHE0001163
27422


1137
PHE0001164
27423


1138
PHE0001165
27424


1139
PHE0001166
27425


1165
PHE0001435
27426









DETAILED DESCRIPTION OF THE INVENTION
As used herein 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.
As used herein a “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.
As used herein “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.
As used herein “consensus sequence” means an artificial sequence of amino acids in a conserved region of an alignment of amino acid sequences of homologous proteins, e.g. as determined by a CLUSTALW alignment of amino acid sequence of homolog proteins.
As used herein a “homolog” means a protein in a group of proteins that perform the same biological function, e.g. proteins that belong to the same Pfam protein family and that provide a common enhanced trait in transgenic plants of this invention. Homologs are expressed by homologous genes. 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. Hence, a useful polynucleotide may have base sequence changes from SEQ ID NO:1 through SEQ ID NO: 614 in accordance with degeneracy of the genetic code. Homologs are proteins that, when optimally aligned, have at least 60% identity, more preferably about 70% or higher, more preferably at least 80% and even more preferably at least 90% identity, e.g. 95 to 98% 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 have at least 90% identity, e.g. at least 95 to 98% identity, to a consensus amino acid sequence of proteins and homologs disclosed herein.
Homologs are identified by comparison of amino acid sequence, e.g. manually or by use of a computer-based tool using known homology-based search algorithms such as those commonly known and referred to as BLAST, FASTA, and Smith-Waterman. A local sequence alignment program, e.g. BLAST, can be used to search a database of sequences to find similar sequences, and the summary Expectation value (E-value) used to measure the sequence base similarity. As a protein hit with the best E-value for a particular organism may not necessarily be an ortholog or the only ortholog, a reciprocal query is used in the present invention to filter hit sequences with significant E-values for ortholog identification. The reciprocal query entails search of the significant hits against a database of amino acid sequences from the base organism that are similar to the sequence of the query protein. A hit is a likely ortholog, when the reciprocal query's best hit is the query protein itself or a protein encoded by a duplicated gene after speciation. A further aspect of the invention comprises functional homolog proteins that differ in one or more amino acids from those of disclosed protein as the result of conservative amino acid substitutions, for example substitutions are among: acidic (negatively charged) amino acids such as aspartic acid and glutamic acid; basic (positively charged) amino acids such as arginine, histidine, and lysine; neutral polar amino acids such as glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine; neutral nonpolar (hydrophobic) amino acids such as alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine; amino acids having aliphatic side chains such as glycine, alanine, valine, leucine, and isoleucine; amino acids having aliphatic-hydroxyl side chains such as serine and threonine; amino acids having amide-containing side chains such as asparagine and glutamine; amino acids having aromatic side chains such as phenylalanine, tyrosine, and tryptophan; amino acids having basic side chains such as lysine, arginine, and histidine; amino acids having sulfur-containing side chains such as cysteine and methionine; naturally conservative amino acids such as valine-leucine, valine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, aspartic acid-glutamic acid, and asparagine-glutamine. A further aspect of the homologs encoded by DNA useful in the transgenic plants of the invention are those proteins that differ from a disclosed protein as the result of deletion or insertion of one or more amino acids in a native sequence.
As used herein, “percent identity” means the extent to which two optimally aligned DNA or protein segments are invariant throughout one or more windows of alignment of components, for example nucleotide sequence or amino acid sequence, allowing for gaps to account to insertions and deletions. 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 aligned parts of the reference segment over window(s) 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.
The “Pfam” database is a large collection of multiple sequence alignments and hidden Markov models covering many common protein families, e.g. Pfam version 19.0 (December 2005) contains alignments and models for 8183 protein families and is based on the Swissprot 47.0 and SP-TrEMBL 30.0 protein sequence databases. See S. R. Eddy, “Profile Hidden Markov Models”, Bioinformatics 14:755-763, 1998. The Pfam database is currently maintained and updated by the Pfam Consortium. The alignments represent some evolutionary conserved structure that has implications for the protein's function. Profile hidden Markov models (profile HMMs) built from the protein family alignments are useful for automatically recognizing that a new protein belongs to an existing protein family even if the homology by alignment appears to be low.
A “Pfam domain module” is a representation of Pfam domains in a protein, in order from N terminus to C terminus. In a Pfam domain module individual Pfam domains are separated by double colons “::”. The order and copy number of the Pfam domains from N to C terminus are attributes of a Pfam domain module. Although the copy number of repetitive domains is important, varying copy number often enables a similar function. Thus, a Pfam domain module with multiple copies of a domain should define an equivalent Pfam domain module with variance in the number of multiple copies. A Pfam domain module is not specific for distance between adjacent domains, but contemplates natural distances and variations in distance that provide equivalent function. The Pfam database contains both narrowly- and broadly-defined domains, leading to identification of overlapping domains on some proteins. A Pfam domain module is characterized by non-overlapping domains. Where there is overlap, the domain having a function that is more closely associated with the function of the protein (based on the E value of the Pfam match) is selected.
Once one DNA is identified as encoding a protein which imparts an enhanced trait when expressed in transgenic plants, other DNA encoding proteins with the same Pfam domain module are identified by querying the amino acid sequence of protein encoded by candidate DNA against the Hidden Markov Models which characterizes the Pfam domains using HMMER software, a current version of which is provided in the appended computer listing. Candidate proteins meeting the same Pfam domain module are in the protein family and have cognate DNA that is useful in constructing recombinant DNA for the use in the plant cells of this invention. Hidden Markov Model databases for use with HMMER software in identifying DNA expressing protein with a common Pfam domain module for recombinant DNA in the plant cells of this invention are also included in the appended computer listing. Version 19.0 of the HMMER software and Pfam databases were used to identify known domains in the proteins corresponding to amino acid sequence of SEQ ID NO: 615 through SEQ ID NO: 1228. All DNA encoding proteins that have scores higher than the gathering cutoff disclosed in Table 23 by Pfam analysis disclosed herein can be used in recombinant DNA of the plant cells of this invention, e.g. for selecting transgenic plants having enhanced agronomic traits. The relevant Pfams modules for use in this invention, as more specifically disclosed below, are DUF6::DUF6, Sterol_desat, HMG_box, GAF::HisKA::HATPase_c, Sugar_tr, Mito_carr::Mito_carr::Mito_carr, RRM_1, 14-3-3, Globin, F-box::Kelch_1::Kelch_2::Kelch_1::Kelch_2::Kelch_2, Pkinase, zf-CHY::zf-C3HC4, AUX_IAA, Cu-oxidase_3::Cu-oxidase::Cu-oxidase_2, Sigma70_r2::Sigma70_r3::Sigma70_r4, AT_hook::DUF296, Exo_endo_phos, H_PPase, Aldo_ket_red, CHASE::HisKA::HATPase_c::Response_reg, Myb_DNA-binding, AP2::AP2, Flavodoxin_2, P-II, zf-CCCH::zf-CCCH::KH_1::zf-CCCH, PSK, adh_short, Myb_DNA-binding::Myb_DNA-binding, FLO_LFY, LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::Pkinase, Zein, Response_reg::Myb_DNA-binding, LEA_4, DAD, DUF6::DUF6, F-box::LRR_2, LEA_2, zf-C3HC4, 20G-FeII_Oxy, WD40::WD40, DUF231, Cullin, CBFD_NFYB_HMF, Histone, U-box, HSF_DNA-bind, GH3, LIM::LIM, RPE65, GST_N::GST_C, IMPDH, Mlo, Copine, Rieske::PaO, ADH_N::ADH_zinc_N, PBP, F-box, Prp19::WD40::WD40::WD40, Glycos_transf_1::S6PP, PfkB, ABA_WDS, AP2, Asp, Hydrolase, OPT, TFIIS::TFIIS_M::TFTIIS_C, Peptidase_C14, TPT, NAM, SRF-TF::K-box, G-alpha, Lactamase_B, LRR_2::LRR_2, PTR2, PB1, Pkinase::Pkinase_C, S-methyl_trans, Phytochrome::HisKA::HATPase_c, Ank::Ank::Ank::Ank::Ank::zf-C3HC4, F-box::Kelch_2::Kelch_2::Kelch_1::Kelch_2, Cyclin_N, Dor1, F-box::LRR_1, BCCT, B_lectin::S_locus_glycop::PAN_2::Pkinase, SAC3_GANP, F-box::Kelch_1::Kelch_1::Kelch_1, DUF6, MFMR::bZIP_1, Skp1_POZ::Skp1, U-box::Arm::Arm::Arm, NAF1, Ribosomal_L18p, SET, F-box::LysM, Pyridoxal_deC, PPDK_N::PEP-utilizers::PEP-utilizers_C, Transket_pyr::Transketolase_C, IPP-2, zf-B_box::zf-B_box::CCT, MFS_1, zf-D of, RRM_1::zf-CCHC, F-box::Tub, SATase_N::Hexapep::Hexapep::Hexapep, PEMT, B_lectin::PAN_2::Pkinase, Peptidase_S10, SOH1, Methyltransf_11, bZIP_1, DXP_reductoisom::DXP_redisom_C, Flavoprotein, MatE::MatE, Homeobox::HALZ, U-box::Arm::Arm::Arm::Arm::Arm, zf-B_box::zf-B_box, Glycos_transf_1, zf-LSD1::zf-LSD1::zf-LSD1, Aldedh, Melibiase, HEAT::HEAT::HEAT::FAT::Rapamycin_bind::PI3_PI4_kinase::FATC, MtN3_slv::MtN3_slv, DUF1313, S6PP, HD-ZIP_N::Homeobox::HALZ, WRKY, FBPase_glpX, MIF4G::MIF4G_like::MIF4G_like_2, zf-B_box::CCT, FAD_binding_4, Hpt, TLC, CK_II_beta, TPR_1::TPR_1::TPR_2::U-box, Response_reg, AdoHcyase_NAD, P1-PLC-X::PI-PLC-Y::C2, Pkinase::Ribonuc_2-5A, Globin::FAD_binding_6::NAD_binding_1, PMEI, Myb_DNA-binding::Linker_histone, LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::Pkinase, Pkinase::efhand::efhand::efhand::efhand, Pescadillo_N::BRCT, SPX::zf-C3HC4, AdoHcyase, zf-CCCH::zf-CCCH::zf-CCCH::zf-CCCH::zf-CCCH, SBP56, DUF850, NAS, UPF0005, Alpha-amylase::Alpha-amyl_C2, Na_H_Exchanger, PAN_1::Pkinase, F-box::Kelch_1::Kelch_1, Remorin_C, Skp1, DUF580, zf-C2H2, zf-LSD1::Peptidase_C14, Ribosomal_L10:: Ribosomal_60s, Frigida, Methyltransf_11::Methyltransf_11, dCMP_cyt_deam_1, DUF914, Enolase_N::Enolase_C, p450, Cellulose_synt, Cu_bind_like, S6PP::S6PP_C, BRAP2::zf-C3HC4::zf-UBP, BIR::BIR, C1_1::DAGK_cat::DAGK_acc, PA::zf-C3HC4, DPBB_1::Pollen_allerg_1, LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_11::LRR_1::LRR_11::LRR_1::LRR_1::LRR_1::Pkinase, WD40::WD40::WD40::WD40::WD40::WD40, bZIP_2, FBPase, HLH, GRAS, SBP, Sina, Remorin_N::Remorin_C, BTB::NPH3, Glutaredoxin, AA_permease, Cyclin_N::Cyclin_C, DUF810, LRR_2, B_ectin::S_locus_glycop::PAN_2::PAN_1::Pkinase, Put_Phosphatase, DUF221, Response_reg::CCT, EMP24_GP25L, VDE, Orn_Arg_deC_N::Orn_DAP_Arg_deC, HEAT::HEAT::HEAT::HEAT::HEAT::HEAT::HEAT, PHD, UPF0041, Bromodomain, Bap31, UDPGP, Pkinase::NAF, Pirin::Pirin_C, MED7.
As used herein “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. Thus, 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 may effect transcription by inducible promoters include anaerobic conditions, or certain chemicals, or the presence of light. Tissue specific, tissue preferred, cell type specific, and inducible promoters constitute the class of “non-constitutive” promoters. A “constitutive” promoter is a promoter which is active under most conditions.
As used herein “operably linked” means the association of two or more DNA fragments in a DNA construct so that the function of one, e.g. protein-encoding DNA, is controlled by the other, e.g. a promoter.
As used herein “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.
As used herein a “control plant” means a plant that does not contain the recombinant DNA that expressed a protein that impart an enhanced trait. A control plant is to identify and select a transgenic plant that has an enhance trait. A suitable control plant can be a non-transgenic plant of the parental line used to generate a transgenic plant, i.e. devoid of recombinant DNA. A suitable control plant may in some cases be a progeny of a hemizygous transgenic plant line that is does not contain the recombinant DNA, known as a negative segregant.
As used herein an “enhanced trait” means a characteristic of a transgenic plant that includes, but is not limited to, an enhance agronomic trait characterized by enhanced plant morphology, physiology, growth and development, yield, nutritional enhancement, disease or pest resistance, or environmental or chemical tolerance. In more specific aspects of this invention enhanced trait is selected from group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. In an important aspect of the invention the enhanced trait is enhanced yield including increased yield under non-stress conditions and increased yield under environmental stress conditions. Stress conditions may include, for example, drought, shade, fungal disease, viral disease, bacterial disease, insect infestation, nematode infestation, cold temperature exposure, heat exposure, osmotic stress, reduced nitrogen nutrient availability, reduced phosphorus nutrient availability and high plant density. “Yield” can be affected by many properties including without limitation, plant height, pod number, pod position on the plant, number of internodes, incidence of pod shatter, grain size, efficiency of nodulation and nitrogen fixation, efficiency of nutrient assimilation, resistance to biotic and abiotic stress, carbon assimilation, plant architecture, resistance to lodging, percent seed germination, seedling vigor, and juvenile traits. Yield can also 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 (i.e. seeds, or weight of seeds, per acre), bushels per acre, tons per acre, kilo per hectare. For example, maize yield may be measured as production of shelled corn kernels per unit of production area, for example in bushels per acre or metric tons per hectare, often reported on a moisture adjusted basis, for example at 15.5 percent moisture. Increased yield may result from improved utilization of key biochemical compounds, such as nitrogen, phosphorous and carbohydrate, or from improved responses to environmental stresses, such as cold, heat, drought, salt, and attack by pests or pathogens. Recombinant DNA used in this invention can also be used to provide plants having improved growth and development, and ultimately increased yield, as the result of modified expression of plant growth regulators or modification of cell cycle or photosynthesis pathways. Also of interest is the generation of transgenic plants that demonstrate enhanced yield with respect to a seed component that may or may not correspond to an increase in overall plant yield. Such properties include enhancements in seed oil, seed molecules such as tocopherol, protein and starch, or oil particular oil components as may be manifest by an alteration in the ratios of seed components.
A subset of the nucleic molecules of this invention includes fragments of the disclosed recombinant DNA consisting of oligonucleotides of at least 15, preferably at least 16 or 17, more preferably at least 18 or 19, and even more preferably at least 20 or more, consecutive nucleotides. Such oligonucleotides are fragments of the larger molecules having a sequence selected from the group consisting of SEQ ID NO:1 through SEQ ID NO: 614, and find use, for example as probes and primers for detection of the polynucleotides of the present invention.
DNA constructs are assembled using methods well known to persons of ordinary skill in the art and typically comprise a promoter operably linked to DNA, the expression of which provides the enhanced agronomic trait. Other construct components may include additional regulatory elements, such as 5′ leaders and introns for enhancing transcription, 3′ untranslated regions (such as polyadenylation signals and sites), DNA for transit or signal peptides.
Numerous promoters that are functional in plant cells have been described in the literature. These include promoters present in plant genomes as well as promoters from other sources, including nopaline synthase (NOS) promoter and octopine synthase (OCS) promoters carried on tumor-inducing plasmids of Agrobacterium tumefaciens, caulimovirus promoters from the cauliflower mosaic virus. For instance, see U.S. Pat. Nos. 5,858,742 and 5,322,938, which disclose versions of the constitutive promoter derived from cauliflower mosaic virus (CaMV35S), U.S. Pat. No. 5,641,876, which discloses a rice actin promoter, U.S. Patent Application Publication 2002/0192813A1, which discloses 5′, 3′ and intron elements useful in the design of effective plant expression vectors, U.S. patent application Ser. No. 09/757,089, which discloses a maize chloroplast aldolase promoter, U.S. patent application Ser. No. 08/706,946, which discloses a rice glutelin promoter, U.S. patent application Ser. No. 09/757,089, which discloses a maize aldolase (FDA) promoter, and U.S. Patent Application Ser. No. 60/310,370, which discloses a maize nicotianamine synthase promoter, all of which are incorporated herein by reference. These and numerous other promoters that function in plant cells are known to those skilled in the art and available for use in recombinant polynucleotides of the present invention to provide for expression of desired genes in transgenic plant cells.
In other aspects of the invention, preferential expression in plant green tissues is desired. Promoters for such use 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).
A promoter may be altered to contain multiple “enhancer sequences” to assist in elevating gene expression. Such enhancers are known in the art. By including an enhancer sequence with a promoter, expression may be enhanced. These enhancers often are found 5′ to the start of transcription in a promoter that functions in eukaryotic cells, but can often be inserted upstream (5′) or downstream (3′) to the coding sequence. In some instances, these 5′ enhancing elements are introns. Particularly useful as enhancers are the 5′ introns of the rice actin 1 (see U.S. Pat. No. 5,641,876) and rice actin 2 genes, the maize alcohol dehydrogenase gene intron, the maize heat shock protein 70 gene intron (U.S. Pat. No. 5,593,874) and the maize shrunken 1 gene.
In other aspects of the invention, sufficient expression in plant seed tissues is desired to affect improvements in seed composition. Exemplary promoters for use for seed composition modification include promoters from seed genes such as napin (U.S. Pat. No. 5,420,034), maize L3 oleosin (U.S. Pat. No. 6,433,252), zein Z27 (Russell et al. (1997) Transgenic Res. 6(2): 157-166), globulin 1 (Belanger et al (1991) Genetics 129:863-872), glutelin 1 (Russell supra), and peroxiredoxin antioxidant (Perl) (Stacy et al. (1996) Plant Mol Biol. 31(6):1205-1216).
Recombinant DNA constructs prepared in accordance with the invention will also generally include a 3′ element that typically contains a polyadenylation signal and site. Well-known 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. 6,090,627, incorporated herein by reference; 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.
Constructs and vectors may also include a transit peptide for targeting of a gene to a plant organelle, particularly to a chloroplast, leucoplast or other plastid organelle. For descriptions of the use of chloroplast transit peptides see U.S. Pat. No. 5,188,642 and U.S. Pat. No. 5,728,925, incorporated herein by reference.
Transgenic plants comprising or derived from plant cells of this invention transformed with recombinant DNA can be further enhanced by incorporating DNA providing other traits, e.g. herbicide and/or pest resistance traits. DNA for insect resistance can be derived from Bacillus thuringensis to provide resistance against lepidopteran, coliopteran, homopteran, hemiopteran, and other insects. DNA for herbicide resistance can provide resistance to glyphosate, dicamba, glufosinate, sulfonylurea, bromoxynil or norflurazon herbicides. For example, DNA encoding 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) disclosed in U.S. Pat. Nos. 5,094,945; 5,627,061; 5,633,435 and 6,040,497 can impart glyphosate tolerance; DNA encoding a glyphosate oxidoreductase (GOX) disclosed in U.S. Pat. No. 5,463,175 and a glyphosate-N-acetyl transferase (GAT) disclosed in U.S. Patent Application publication 2003/0083480 A1 can also impart glyphosate tolerance; DNA encoding a dicamba monooxygenase disclosed in U.S. Patent Application publication 2003/0135879 A1 can impart dicamba tolerance; DNA encoding bromoxynil nitrilase (Bxn) disclosed in U.S. Pat. No. 4,810,648 can impart bromoxynil tolerance; DNA encoding phytoene desaturase (crtI) described in Misawa et al, (1993) Plant J. 4:833-840 can impart norflurazon tolerance; DNA encoding acetohydroxyacid synthase described in Sathasiivan et al. (1990) Nucl. Acids Res. 18:2188-2193 can impart sulfonylurea herbicide tolerance; DNA encoding a BAR protein as disclosed in DeBlock, et al. (1987) EMBO J. 6:2513-2519 can impart glufosinate and bialaphos tolerance; DNA disclosed in U.S. Patent Application Publication 2003/010609 A1 can impart N-amino methyl phosphonic acid tolerance; DNA disclosed in U.S. Pat. No. 6,107,549 can impart pyridine herbicide resistance; DNA 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.
Plant Cell Transformation Methods
Numerous methods for transforming plant cells with recombinant DNA are known in the art and may be used to make the transgenic plants, cells and nuclei of this invention. Two commonly used methods for plant transformation are Agrobacterium-mediated transformation and microprojectile bombardment. Microprojectile bombardment methods are illustrated in U.S. Pat. No. 5,015,580 (soybean); U.S. Pat. No. 5,550,318 (corn); U.S. Pat. No. 5,538,880 (corn); U.S. Pat. No. 5,914,451 (soybean); U.S. Pat. No. 6,160,208 (corn); U.S. Pat. No. 6,399,861 (corn); U.S. Pat. No. 6,153,812 (wheat) and U.S. Pat. No. 6,365,807 (rice) and Agrobacterium-mediated transformation is described in U.S. Pat. No. 5,159,135 (cotton); U.S. Pat. No. 5,824,877 (soybean); U.S. Pat. No. 5,463,174 (canola); U.S. Pat. No. 5,591,616 (corn); U.S. Pat. No. 6,384,301 (soybean), U.S. Pat. No. 7,026,528 (wheat) and U.S. Pat. No. 6,329,571 (rice), all of which are incorporated herein by reference. For Agrobacterium tumefaciens based plant transformation systems, additional elements present on transformation constructs will include T-DNA left and right border sequences to facilitate incorporation of the recombinant polynucleotide into the plant genome.
In general it is useful to introduce recombinant DNA randomly, i.e. at a non-specific location, in the genome of a target plant line. In special cases it may be useful to target recombinant DNA insertion in order to achieve site-specific integration, for example, to replace an existing gene in the genome, to use an existing promoter in the plant genome, or to insert a recombinant polynucleotide at a predetermined site known to be active for gene expression. Several site specific recombination systems exist which are known to function in plants including cre-lox as disclosed in U.S. Pat. No. 4,959,317 and FLP-FRT as disclosed in U.S. Pat. No. 5,527,695, both incorporated herein by reference.
Transformation methods of this invention are preferably practiced in tissue culture on media and in a controlled environment. “Media” refers to the numerous nutrient mixtures that are used to grow cells in vitro, that is, outside of the intact living organism. Recipient cell targets include, but are not limited to, meristem cells, hypocotyls, calli, immature embryos and gametic cells such as microspores, pollen, sperm and egg cells. It is contemplated that any cell from which a fertile plant may be regenerated is useful as a recipient cell. Callus may be initiated from tissue sources including, but not limited to, immature embryos, hypocotyls, seedling apical meristems, microspores and the like. Cells capable of proliferating as callus are also recipient cells for genetic transformation. Practical transformation methods and materials for making transgenic plants of this invention, for example various media and recipient target cells, transformation of immature embryo cells and subsequent regeneration of fertile transgenic plants are disclosed in U.S. Pat. Nos. 6,194,636 and 6,232,526, which are incorporated herein by reference.
The seeds of transgenic plants can be harvested from fertile transgenic plants and be used to grow progeny generations of transformed plants of this invention including hybrid plants line for selection of plants having an enhanced trait. In addition to direct transformation of a plant with a recombinant DNA, transgenic plants can be prepared by crossing a first plant having a recombinant DNA with a second plant lacking the DNA. For example, recombinant DNA can be introduced into a first plant line that is amenable to transformation to produce a transgenic plant which can be crossed with a second plant line to introgress the recombinant DNA into the second plant line. A transgenic plant with recombinant-DNA providing an enhanced trait, e.g. enhanced yield, can be crossed with transgenic plant line having other recombinant DNA that confers another trait, for example herbicide resistance or pest resistance, to produce progeny plants having recombinant DNA that confers both traits. Typically, in such breeding for combining traits the transgenic plant donating the additional trait is a male line and the transgenic plant carrying the base traits is the female line. The progeny of this cross will segregate such that some of the plants will carry the DNA for both parental traits and some will carry DNA for one parental trait; such plants can be identified by markers associated with parental recombinant DNA, e.g. marker identification by analysis for recombinant DNA or, in the case where a selectable marker is linked to the recombinant, by application of the selecting agent such as a herbicide for use with a herbicide tolerance marker, or by selection for the enhanced trait. Progeny plants carrying DNA for both parental traits can be crossed back into the female parent line multiple times, for example usually 6 to 8 generations, to produce a progeny plant with substantially the same genotype as one original transgenic parental line but for the recombinant DNA of the other transgenic parental line.
In the practice of transformation DNA is typically introduced into chromosomes in the nuclei of only a small percentage of target plant cells in any one transformation experiment. Marker genes are used to provide an efficient system for identification of those cells that are stably transformed by receiving and integrating a recombinant DNA molecule into their genomes. Preferred marker genes provide selective markers which confer resistance to a selective agent, such as an antibiotic or an herbicide. Any of the herbicides to which plants of this invention may be resistant are useful agents for selective markers. Plant cells containing potentially transformed nuclei are exposed to the selective agent. In the population of surviving cells will be those cells where, generally, the resistance-conferring gene is integrated and expressed at sufficient levels to permit cell survival. Cells may be tested further to confirm stable integration of the exogenous DNA. Commonly used selective marker genes include those conferring resistance to antibiotics such as kanamycin and paromomycin (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 (aroA or 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. Selectable markers which provide an ability to visually identify transformants can also be employed, for example, a gene expressing a colored or fluorescent protein such as a luciferase or green fluorescent protein (GFP) or a gene expressing a beta-glucuronidase or uidA gene (GUS) for which various chromogenic substrates are known.
Plant cells that survive exposure to the selective agent, or plant cells that have been scored positive in a screening assay, may be cultured in regeneration media and allowed to mature into plants having the transformed nuclei. 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 CO2, 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 the plant species. Plants may be pollinated using conventional plant breeding methods known to those of skill in the art and seed produced, for example self-pollination is commonly used with transgenic corn. The regenerated transformed plant or its progeny seed or plants can be tested for expression of the recombinant DNA and selected for the presence of enhanced agronomic trait.
Transgenic Plants and Seeds
Transgenic plants derived from the plant cells of this invention are grown to generate transgenic plants having an enhanced trait as compared to a control plant and produce transgenic seed and haploid pollen of this invention. Such plants with enhanced traits are identified by selection of transformed plants or progeny seed for the enhanced trait. For efficiency a selection method is designed to evaluate multiple transgenic plants (events) comprising the recombinant DNA, for example multiple plants from 2 to 20 or more transgenic events. Transgenic plants grown from transgenic seed provided herein demonstrate improved agronomic traits that contribute to increased yield or other trait that provides increased plant value, including, for example, improved seed quality. Of particular interest are plants having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
Table 2 provides a list of proteins SEQ ID NO: 615 through SEQ ID NO: 1228 encoding DNA (“genes”) that are useful as recombinant DNA for production of transgenic plants with enhanced agronomic trait.
Column headings in Table 2 refer to the following information: “PEP SEQ ID” refers to a particular number of amino acid sequence in the Sequence Listing. “PHE ID” refers to an arbitrary number used to identify a particular recombinant polynucleotide corresponding to the translated protein encoded by the polynucleotide. “NUC SEQ ID” refers to a particular number of a nucleic acid sequence in the Sequence Listing which defines a polynucleotide used in a recombinant polynucleotide of this invention. “GENE NAME” refers to a common name for the recombinant polynucleotide. “GENE EFFECT” refers to the effect of the expressed polypeptide in providing yield improvement or other enhanced property. “CODING SEQUENCE” refers to peptide coding segments of the polynucleotide. “SPECIES” refers to the organism from which the polynucleotide DNA was derived.













TABLE 2





PEP

NUC






SEQ

SEQ


ID
PHE ID
ID
Gene Name
Gene Effect
Coding Sequence
Species





















615
PHE0000002
1
Arabidopsis AtHAP3a
Stress tolerance
103-525
Arabidopsis thaliana


616
PHE0000003
2
corn AtHAP3a-like1
Stress tolerance
149-817
Zea mays


617
PHE0000004
3
corn AtHAP3a-like2
Stress tolerance
196-750
Zea mays


618
PHE0000005
4
corn AtHAP3a-like3
Stress tolerance
 91-588
Zea mays


619
PHE0000021
5
Arabidopsis CCA1
Stress tolerance
 238-2061
Arabidopsis thaliana


620
PHE0000041
6
corn hemoglobin 2
Stress tolerance
 67-639
Zea mays


621
PHE0000066
7
At TOR1-like
Stress tolerance
1462-1626, 1850-2188,
Arabidopsis thaliana







2267-2341, 2519-2691,







3060-3158, 3442-3634,







3703-3846, 3984-4153,







4233-4437, 4511-4699,







4907-5059, 5528-5649,







5735-5837, 5912-6007,







6309-6439, 7148-7250,







7326-7508, 7583-7675,







7914-8012, 8096-8194,







8247-8451, 8764-8888,







8999-9051, 9493-9616,







9734-9904, 10380-10532,







10599-10751, 11235-11306,







11414-11548,







11625-11686, 11819-11916,







12172-12281,







12358-12531, 12647-12712,







13059-13127,







13235-13345, 13685-13825,







13917-14045,







14168-14333, 14421-14629,







14795-15001,







15165-15278, 15383-15613,







15896-15976,







16081-16155, 16234-16300,







16400-16560,







16707-16880, 16967-17095,







17187-17270,







17379-17440, 17521-17593,







17678-18001,







18086-18385


622
PHE0000078
8
E. coli glnB
Carbon and/or
 35-373
Escherichia coli






nitrogen






metabolism


623
PHE0000080
9
G28/BAA32418
Stress tolerance
 3-803
Arabidopsis thaliana


624
PHE0000081
10
G378
Stress tolerance
 1-723
Arabidopsis thaliana


625
PHE0000094
11
G464
Stress tolerance
 41-661
Arabidopsis thaliana


626
PHE0000112
12
Curly Leaf-variant 1
Apomixis
108-901, 1084-1177,
Zea mays







1251-3055


627
PHE0000113
13
Curly Leaf-variant 2
Apomixis
113-912, 1083-1191,
Zea mays







1257-2806


628
PHE0000140
14
casein kinase II alpha
Flower
 202-1200
Zea mays





subunit
development


629
PHE0000151
15
Adenosylhomo
Stress tolerance
 71-1525
Zea mays





cysteinase


630
PHE0000199
16
ethylene response
Ethylene
 79-1986
Zea mays





sensor
signaling


631
PHE0000214
17
maize glycine rich
Stress tolerance
 70-540
Zea mays





protein


632
PHE0000364
18
wilt-like 1
Stress tolerance
 316-1644
Zea mays


633
PHE0000365
19
wilt-like 2
Stress tolerance
 334-1512
Zea mays


634
PHE0000366
20
wilt-like 3
Stress tolerance
 263-1552
Zea mays


635
PHE0000367
21
wilt-like 4
Stress tolerance
 202-1419
Zea mays


636
PHE0000373
23
G1411
Plant growth and
 1-747
Arabidopsis thaliana






development


637
PHE0000374
24
G1449
Plant growth and
 1-474
Arabidopsis thaliana






development


638
PHE0000375
25
G1635
Plant growth and
  1-1161
Arabidopsis thaliana






development


639
PHE0000376
26
G188
Stress tolerance
  1-1044
Arabidopsis thaliana


640
PHE0000377
27
G19
Stress tolerance
 1-747
Arabidopsis thaliana


641
PHE0000378
28
G559
Plant growth and
  1-1194
Arabidopsis thaliana






development


642
PHE0000379
29
G865
Plant growth and
 1-636
Arabidopsis thaliana






development


643
PHE0000381
30
corn G214
Stress tolerance
  1-2160
Zea mays


644
PHE0000383
31
700151210_FLI-corn
Plant growth and
 61-966
Zea mays





L5 a
development


645
PHE0000384
32
LIB3957-023-C10_FLI-
Plant growth and
134-904
Zea mays





corn C-type cyclin
development


646
PHE0000405
33
ASH2-F17I14_190
Stress tolerance
 370-1965
Arabidopsis thaliana





(Suppressor of hog1)


647
PHE0000406
34
soy ASH2-like 1
Stress tolerance
 67-1329
Glycine max


648
PHE0000407
35
soy ASH2-like 3
Stress tolerance
 37-1464
Glycine max


649
PHE0000408
36
soy ASH2-like 4
Stress tolerance
 49-1971
Glycine max


650
PHE0000409
37
corn pescadillo-like 1
Plant growth and
 55-1911
Zea mays






development


651
PHE0000410
38
yeast pescadillo
Plant growth and
 657-2474
Saccharomyces





homologue-Z72888
development

cerevisiae


652
PHE0000424
39
soy GA2-oxidase
Plant growth and
 38-1036
Glycine max






development


653
PHE0000447
40
corn phospholipase C 1
Stress tolerance
 228-1985
Zea mays


654
PHE0000448
41
corn diacylglycerol
Stress tolerance
 141-2282
Zea mays





kinase 2


655
PHE0000449
42
corn Ins(1,4,5)P(3) 5-
Stress tolerance
 116-1849
Zea mays





phosphatase 1


656
PHE0000459
43
Anabaena SPP
Carbon and/or
 1-747
Nostoc PCC7120






nitrogen






metabolism


657
PHE0000460
44
Corn SPP
Carbon and/or
  1-1269
Zea mays






nitrogen






metabolism


658
PHE0000461
45
UDPgpp
Carbon and/or
  1-1419
Zea mays






nitrogen






metabolism


659
PHE0000464
46
soy U-box protein 1
Plant growth and
 137-2119
Glycine max






development


660
PHE0000465
47
soy U-box protein 2
Plant growth and
 63-1355
Glycine max






development


661
PHE0000466
48
soy U-box protein 3
Plant growth and
 26-2053
Glycine max






development


662
PHE0000467
49
corn U-box protein 3
Plant growth and
 197-1774
Zea mays






development


663
PHE0000468
50
corn U-box protein 4
Plant growth and
 104-1183
Zea mays






development


664
PHE0000474
51
yeast ado1
Stress tolerance
 567-1589
Saccharomyces








cerevisiae


665
PHE0000475
52
corn adenosine kinase 1
Stress tolerance
 264-1289
Zea mays


666
PHE0000476
53
soy adenosine kinase 2
Stress tolerance
 90-1112
Glycine max


667
PHE0000477
54
Synechocystis
Stress tolerance
 86-1087
Synechocystis sp.





hypothetical sugar


PCC 6803





kinase-BAA10827


668
PHE0000478
55
corn
Stress tolerance
 38-1492
Zea mays





adenosylhomocysteinase 1


669
PHE0000479
56
yeast S-adenosyl-L-
Stress tolerance
 142-1491
Saccharomyces





homocysteine


cerevisiae





hydrolase-





NP_010961


670
PHE0000480
57
Synechocystis S-
Stress tolerance
 305-1582
Synechocystis sp.





adenosylhomocysteine


PCC 6803





hydrolase-BAA18079


671
PHE0000481
58
soy RING finger
Plant growth and
 64-1494
Glycine max





protein 1 [BCRA1]
development


672
PHE0000482
59
Aspergillus yA
Stress tolerance
913-1107, 1162-1217,
Emericella nidulans





(laccase 1)-X52552

1289-1459, 1535-1705,







1759-1884, 1949-3059


673
PHE0000483
60
Synechocystis Sucrose
Carbon and/or
  1-2160
Synechocystis sp.





phosphate synthase
nitrogen

PCC 6803






metabolism


674
PHE0000487
61
yeast HAL3-Z28297
Plant growth and
 64-1752
Saccharomyces






development

cerevisiae


675
PHE0000488
62
yeast GLC8-P41818
Plant growth and
2556-3245
Saccharomyces






development

cerevisiae


676
PHE0000489
63
corn HAL3-like 1-
Plant growth and
 24-659
Zea mays





LIB3060-046-
development





G12_FLI


677
PHE0000490
64
corn HAL3-like 2-
Plant growth and
237-881
Zea mays






development


678
PHE0000491
65
corn GLC8-like 2
Plant growth and
232-726
Zea mays






development


679
PHE0000492
66
corn GLC8-like 1
Plant growth and
 98-625
Zea mays






development


680
PHE0000495
69
Agrobacterium aiiA-
Stress tolerance
 98-865
Agrobacterium





like protein [attM]-


tumefaciens





AAD43990


681
PHE0000496
70
Xylella aiiA-like
Stress tolerance
 365-1204
Xylella fastidiosa





protein-XF1361


682
PHE0000497
71
Xanthomonas aiiA-
Stress tolerance
 121-1044





like protein


683
PHE0000498
72
corn histone H4
Seed
 83-391
Zea mays






development


684
PHE0000499
73
high sulfur zein protein
Seed
 29-661
Zea mays





precursor
development


685
PHE0000500
74
corn RING finger
Plant growth and
 353-1771
Zea mays





protein 25
development


686
PHE0000501
75
corn MKP 1 [MAP
Signal
 157-1278
Zea mays





kinase 4]
transduction


687
PHE0000502
76
corn MKP 3 [MAP
Signal
 110-1300
Zea mays





kinase 5]
transduction


688
PHE0000503
77
corn MKP 4
Signal
 76-1185
Zea mays






transduction


689
PHE0000504
78
corn MKP 6
Signal
 411-2174
Zea mays






transduction


690
PHE0000505
79
corn MKP 7
Signal
 382-1854
Zea mays






transduction


691
PHE0000506
80
corn MKP 8 [cdc2
Signal
 217-1098
Zea mays





kinase]
transduction


692
PHE0000507
81
soy MKP 1
Signal
 175-1293
Glycine max






transduction


693
PHE0000508
82
soy MKP 4
Signal
 334-1446
Glycine max






transduction


694
PHE0000509
83
corn ABF2-like 1
Stress tolerance
141-350, 440-1315
Zea mays


695
PHE0000510
84
soy ABF2-like 1
Stress tolerance
 114-1046
Glycine max


696
PHE0000511
85
maize PPDK
Carbon and/or
 131-3043
Zea mays






nitrogen






metabolism


697
PHE0000512
86
yeast YOR161c-
Stress tolerance
1002-2621
Saccharomyces





Z75069


cerevisiae


698
PHE0000513
87
yeast HNM1-Z72599
Stress tolerance
 419-2110
Saccharomyces








cerevisiae


699
PHE0000514
88
Xylella SAG13-like-
Plant growth and
 67-843
Xylella fastidiosa





E82748
development


700
PHE0000515
89
corn SAG13-like 1
Plant growth and
 74-862
Zea mays






development


701
PHE0000516
90
soy SAG13-like 1
Plant growth and
 49-855
Glycine max






development


702
PHE0000517
91
soy SAG13-like 2
Plant growth and
 25-837
Glycine max






development


703
PHE0000518
92
Nostoc punctiforme
Plant growth and
 68-853
Nostoc punctiforme





SAG13-like
development


704
PHE0000520
93
corn clavata3-like
Plant growth and
145-384
Zea mays






development


705
PHE0000521
94
corn clavata3-like
Plant growth and
 22-255
Zea mays






development


706
PHE0000523
96
corn clv3-like 2
Plant growth and
 69-356
Zea mays






development


707
PHE0000525
98
corn violaxanthin de-
Stress tolerance
 77-1414
Zea mays





epoxidase


708
PHE0000526
99
rice serine
Stress tolerance
 51-1070
Oryza sativa





acetyltransferase 1


709
PHE0000527
100
rice serine
Stress tolerance
 131-1192
Oryza sativa





acetyltranferase 2


710
PHE0000528
101
corn CEO-like protein
Stress tolerance
 134-1873
Zea mays


711
PHE0000529
102
wheat nicotianamine
Iron uptake
 43-1041
Triticum aestivum





aminotransferase


712
PHE0000530
103
corn nicotianamine
Iron uptake
 55-1146
Zea mays





synthase 1


713
PHE0000531
104
corn ys1-like1
Iron uptake
 277-2292
Zea mays


714
PHE0000532
105
rice glutamate
Plant growth and
 77-1552
Oryza sativa





decarboxylase
development


715
PHE0000533
106
rice GA2 oxidase
Plant growth and
 74-1219
Oryza sativa






development


716
PHE0000534
107
corn mlo-like 1
Plant growth and
 57-1583
Zea mays






development


717
PHE0000535
108
corn G alpha 1
Plant growth and
 220-1329
Zea mays






development


718
PHE0000536
109
corn G beta 2
Plant growth and
 58-1059
Zea mays






development


719
PHE0000537
110
corn g gamma-like 1
Plant growth and
64-407, 514-655
Zea mays






development


720
PHE0000538
111
rice tubby 1
Plant growth and
  4-1221
Oryza sativa






development


721
PHE0000539
112
maize tubby 3
Plant growth and
 49-1122
Zea mays






development


722
PHE0000540
113
maize tubby 4
Plant growth and
 257-1600
Zea mays






development


723
PHE0000541
114
corn tubby 5
Plant growth and
 100-1200
Zea mays






development


724
PHE0000542
115
maize tubby 6
Plant growth and
 83-1390
Zea mays






development


725
PHE0000543
116
maize tubby 7
Plant growth and
 125-1327
Zea mays






development


726
PHE0000544
117
corn tubby 9
Plant growth and
 333-1700
Zea mays






development


727
PHE0000545
118
rice LRR.F-box protein 1
Plant growth and
 83-1867
Oryza sativa






development


728
PHE0000546
119
corn LRR.F-box
Plant growth and
 167-1936
Zea mays





protein 7
development


729
PHE0000547
120
cotton ttg1-1
Stress tolerance
 19-1056
Gossypium hirsutum


730
PHE0000548
121
corn nucellin-like
Seed
 42-1424
Zea mays





protein 1
development


731
PHE0000549
122
rice nucellin-like
Seed
 37-1443
Oryza sativa





protein 1
development


732
PHE0000550
123
rice G1449-like 1
Plant growth and
107-652
Oryza sativa






development


733
PHE0000551
124
rice LEA 1
Stress tolerance
 87-686
Oryza sativa


734
PHE0000552
125
rice LEA 2 [wsi18]
Stress tolerance
 70-714
Oryza sativa


735
PHE0000553
126
corn LEA 1
Stress tolerance
 94-1008
Zea mays


736
PHE0000554
127
corn LEA 2
Stress tolerance
 85-777
Zea mays


737
PHE0000555
128
corn adenylate
Plant growth and
 49-1938
Zea mays





transporter 1
development


738
PHE0000556
129
Xylella adenylate
Plant growth and
 54-1376
Xylella fastidiosa





transporter-XF1738
development


739
PHE0000557
130
yeast AAC2-Z35791
Plant growth and
 66-1022
Saccharomyces






development

cerevisiae


740
PHE0000558
131
yeast TFS1-X62105
Flower
 16-675
Saccharomyces






development

cerevisiae


741
PHE0000559
132
yeast YLR179C-
Flower
124-729
Saccharomyces





AAB67472
development

cerevisiae


742
PHE0000560
133
ZmSPS2-2
Carbon and/or
 29-2920
Zea mays






nitrogen






metabolism


743
PHE0000561
134
rice FPF1-like 1
Flower
 93-458
Oryza sativa






development


744
PHE0000562
135
rice FPF1-like 3
Flower
 60-413
Oryza sativa






development


745
PHE0000563
136
corn FPF1-like 1
Flower
132-473
Zea mays






development


746
PHE0000564
137
corn FPF1-like 6
Flower
 31-345
Zea mays






development


747
PHE0000565
138
corn FLC-like 3
Flower
210-905
Zea mays






development


748
PHE0000566
139
corn FLC-like 9
Flower
305-976
Zea mays






development


749
PHE0000567
140
corn selenium-binding
Stress tolerance
 239-1717
Zea mays





protein


750
PHE0000568
141
maize glutathione S-
Stress tolerance
103-771
Zea mays





transferase IV


751
PHE0000569
142
calcium-dependent
Stress tolerance
 177-1844
Zea mays





protein kinase


752
PHE0000570
143
protein kinase CK2
Stress tolerance
178-993
Zea mays





regulatory subunit





CK2B3


753
PHE0000571
144
19K zein precursor
Stress tolerance
 46-747
Zea mays


754
PHE0000572
145
corn EREBP/AP2-like
Stress tolerance
 114-1196
Zea mays





transcription factor


755
PHE0000573
146
G-box binding factor 1
Stress tolerance
 145-1275
Zea mays


756
PHE0000574
147
corn high mobility
Stress tolerance
145-615
Zea mays





group protein


757
PHE0000575
148
corn glycine-rich
Stress tolerance
 70-492
Zea mays





RNA-binding protein


758
PHE0000576
149
corn enolase 1
Stress tolerance
 86-1423
Zea mays


759
PHE0000577
150
maize RING finger
Stress tolerance
 72-680
Zea mays





protein


760
PHE0000578
151
maize 60S acidic
Stress tolerance
 123-1079
Zea mays





ribosomal protein P0


761
PHE0000579
152
corn nucleotide-
Stress tolerance
 223-1266
Zea mays





binding protein


762
PHE0000580
153
MADS affecting
Flower
 31-618
Arabidopsis thaliana





flowering 1-
development





AAK37527


763
PHE0000581
154
G1760-Q9SZJ6
Flower
 50-733
Arabidopsis thaliana






development


764
PHE0000582
155
G2010-CAB56582
Flower
 1-522
Arabidopsis thaliana






development


765
PHE0000583
156
SAG13-AAF09487
Plant growth and
 1-903
Arabidopsis thaliana






development


766
PHE0000584
157
Rice SAG13-like
Plant growth and
 7-786
Oryza sativa






development


767
PHE0000585
158
corn FLT-like 1
Flower
317-835
Zea mays






development


768
PHE0000586
159
corn FLT-like 2
Flower
 65-595
Zea mays






development


769
PHE0000587
160
corn FLT-like 3
Flower
72-263, 626-994
Zea mays






development


770
PHE0000588
161
rice leafy-AB005620
Flower
 76-1245
Oryza sativa






development


771
PHE0000589
162
corn HD1-like 1
Flower
 93-926
Zea mays






development


772
PHE0000590
163
rice plastidic
Plant growth and
109-915, 2211-2480,
Oryza sativa





ATP/ADP-transporter-
development
2563-2706, 2792-3145,





BAB40979

3591-3950


773
PHE0000591
164
rice L5 a
Plant growth and
 80-991
Oryza sativa






development


774
PHE0000592
165
corn L5
Plant growth and
 61-966
Zea mays






development


775
PHE0000593
166
corn L5-like
Plant growth and
 8-871
Zea mays






development


776
PHE0000594
167
Agrobacterium
Plant growth and
 24-1562
Agrobacterium





ornithine
development

tumefaciens





decarboxylase


777
PHE0000601
168
corn IAP-like RING
Plant growth and
 179-1291
Zea mays





finger protein 1
development


778
PHE0000603
170
corn BAX inhibitor 1-
Plant growth and
157-906
Zea mays





like 1
development


779
PHE0000604
171
corn Bax inhibitor 1-
Plant growth and
113-697
Zea mays





like 2
development


780
PHE0000605
172
corn Bax inhibitor 1-
Plant growth and
144-890
Zea mays





like 3
development


781
PHE0000606
173
corn caspase-like 1
Plant growth and
 141-1193
Zea mays






development


782
PHE0000607
174
corn caspase-like 2
Plant growth and
 86-1018
Zea mays






development


783
PHE0000608
175
corn caspase-like 3
Plant growth and
 74-1141
Zea mays






development


784
PHE0000609
176
yeast YOR197w
Plant growth and
 186-1547
Saccharomyces






development

cerevisiae


785
PHE0000610
177
soy Lls1-like
Plant growth and
  7-1695
Glycine max






development


786
PHE0000611
178
Synechocystis Rieske
Plant growth and
 38-1447
Synechocystis sp.





iron-sulfur protein
development

PCC 6803


787
PHE0000612
179
Arabidopsis AGL15
Plant growth and
 80-892
Arabidopsis thaliana






development


788
PHE0000613
180
yeast OST2
Plant growth and
 24-425
Saccharomyces






development

cerevisiae


789
PHE0000614
181
corn DAD1
Plant growth and
 72-413
Zea mays






development


790
PHE0000615
182
corn pirin
Plant growth and
 98-1222
Zea mays






development


791
PHE0000616
183
corn betaine-aldehyde
Stress tolerance
 17-1531
Zea mays





dehydrogenase


792
PHE0000617
184
rice betaine aldehyde
Stress tolerance
 93-1610
Oryza sativa





dehydrogenase


793
PHE0000618
185
yeast PEM1/CHO2
Stress tolerance
 617-3226
Saccharomyces








cerevisiae


794
PHE0000619
186
yeast PEM2/OPI3
Stress tolerance
160-780
Saccharomyces








cerevisiae


795
PHE0000620
187
corn
Stress tolerance
 392-1894
Zea mays





phosphoethanolamine





N-methyltransferase 2


796
PHE0000621
188
E. coli betT
Stress tolerance
 36-2069
Escherichia coli


797
PHE0000622
189
Xenorhabdus BetT-like 1
Stress tolerance
 29-2068
Xenorhabdus sp.


798
PHE0000623
190
corn NHX1-like 1
Stress tolerance
 38-1675
Zea mays


799
PHE0000624
191
OsNHX1-AB021878
Stress tolerance
 297-1904
Oryza sativa


800
PHE0000625
192
corn vacuolar H+-
Stress tolerance
 124-2409
Zea mays





pyrophosphatase 1


801
PHE0000626
193
corn vacuolar H+-
Stress tolerance
 93-2390
Zea mays





pyrophosphatase 2


802
PHE0000627
194
corn vacuolar H+-
Stress tolerance
 35-2329
Zea mays





pyrophosphatase 5


803
PHE0000628
195
soy homeobox-leucine
Light response
 66-920
Glycine max





zipper protein homolog





h1-


804
PHE0000629
196
soy zinc finger protein
Light response
 98-622
Glycine max


805
PHE0000630
197
soy TGACG-motif-
Light response
 82-1053
Glycine max





binding protein STF2


806
PHE0000631
198
corn putative zinc
Light response
225-842
Zea mays





finger protein


807
PHE0000632
199
soy AP2 domain
Light response
227-928
Glycine max





transcription factor


808
PHE0000633
200
soy pseudo-response
Light response
 27-2060
Glycine max





regulator


809
PHE0000634
201
soy CONSTANS-like
Light response
 108-1229
Glycine max





B-box zinc finger





protein


810
PHE0000635
202
soy RPT2-like
Light response
 23-1762
Glycine max


811
PHE0000636
203
corn myb-related
Light response
 34-1101
Zea mays





protein


812
PHE0000637
204
Arabidopsis salt-
Light response
 274-1017
Arabidopsis thaliana





tolerance protein


813
PHE0000638
205
soy AP2 domain
Light response
 98-1555
Glycine max





transcription factor


814
PHE0000639
206
soy late elongated
Light response
 626-2875
Glycine max





hypocotyl


815
PHE0000640
207
soy zinc finger protein
Light response
 139-1416
Glycine max


816
PHE0000641
208
soy putative protein
Light response
 73-1764
Glycine max





kinase


817
PHE0000642
209
soy auxin-responsive
Light response
 42-1820
Glycine max





GH3 protein


818
PHE0000643
210
corn ripening-related
Light response
131-775
Zea mays





protein


819
PHE0000644
211
corn beta-expansin 4
Light response
 97-1020
Zea mays


820
PHE0000645
212
corn hypothetical
Light response
330-716
Zea mays





protein


821
PHE0000646
213
corn unknown protein
Light response
 69-710
Zea mays


822
PHE0000647
214
corn unknown protein
Light response
234-563
Zea mays


823
PHE0000648
215
corn unknown protein
Light response
 169-1542
Zea mays


824
PHE0000649
216
soy unknown protein
Light response
 585-1889
Glycine max


825
PHE0000650
217
corn unknown protein
Light response
 211-2514
Zea mays


826
PHE0000651
218
rice Lls1 (CAO)-
Light response
 100-1722
Oryza sativa





AF284781


827
PHE0000654
219
G896
Plant growth and
 47-1147
Arabidopsis thaliana






development


828
PHE0000655
220
G1435
Plant growth and
 8-901
Arabidopsis thaliana






development


829
PHE0000656
221
LIB4074-003-H1_FLI-
Plant growth and
 83-856
Zea mays





corn G1435-like
development


830
PHE0000658
222
G1496
Plant growth and
 116-1120
Arabidopsis thaliana






development


831
PHE0000660
223
700072387_FLI-
Carbon and/or
 89-3265
Zea mays





ZmSPS3-1
nitrogen






metabolism


832
PHE0000661
224
GATE90-ZmSPS2-3
Carbon and/or
 72-2987
Zea mays






nitrogen






metabolism


833
PHE0000662
225
corn ELI17-like
Disease
  7-1350
Zea mays





protein 1
resistance


834
PHE0000663
226
soy ELI17-like protein 1
Disease
 63-1355
Glycine max






resistance


835
PHE0000664
227
X58872-E. coli hmp1
Nitric oxide
 293-1483
Escherichia coli






signaling


836
PHE0000665
228
Nostoc sp. PCC 7120
Carbon and/or
1074-1412
Nostoc PCC7120





glnB
nitrogen






metabolism


837
PHE0000666
229
Brassica P-II
Carbon and/or
 49-639
Brassica napus






nitrogen






metabolism


838
PHE0000700
230
Arabidopsis eskimo 1
Stress tolerance
 592-2052
Arabidopsis thaliana


839
PHE0000701
231
soy 1-deoxy-D-
Isoprenoid
 76-1500
Glycine max





xylulose-5-phosphate
biosynthesis





reductoisomerase-


840
PHE0000702
232
Synechocystis 1-
Isoprenoid
 100-1284
Synechocystis sp.





deoxy-D-xylulose-5-
biosynthesis

PCC 6803





phosphate





reductoisomerase-





D64000


841
PHE0000703
233
Agrobacterium 1-
Isoprenoid
 52-1245
Agrobacterium





deoxy-D-xylulose 5-
biosynthesis

tumefaciens





phosphate





reductoisomerase-





AAK88334


842
PHE0000704
234
corn 1-deoxy-D-
Isoprenoid
 289-2445
Zea mays





xylulose-5-phosphate
biosynthesis





synthase-


843
PHE0000705
235
Agrobacterium 1-
Isoprenoid
 13-1932
Agrobacterium





deoxy-D-xylulose-5-
biosynthesis

tumefaciens





phosphate synthase-





AAK86554


844
PHE0000706
236
Xylella 1-
Isoprenoid
 38-2050
Xylella fastidiosa





deoxyxylulose-5-
biosynthesis





phosphate synthase-





AAF85048


845
PHE0000709
237
corn HMT 1 (N-
Stress tolerance
 102-1070
Zea mays





methyltransferase)


846
PHE0000710
238
corn HMT 2 (N-
Stress tolerance
 94-1107
Zea mays





methyltransferase)


847
PHE0000711
239
E. coli yagD
Stress tolerance
 21-953
Escherichia coli





homocysteine S-





methyltransferase-





Q47690


848
PHE0000712
240
yeast Mht1-
Stress tolerance
 60-1034
Saccharomyces





NP_013038


cerevisiae


849
PHE0000713
241
corn H2A.F/Z 1
DNA integration
102-515
Zea mays


850
PHE0000714
242
corn H2A 1
DNA integration
 56-457
Zea mays


851
PHE0000715
243
corn H2A 3
DNA integration
 71-541
Zea mays


852
PHE0000716
244
corn H2A 7
DNA integration
 33-512
Zea mays


853
PHE0000717
245
wilt-1256
Stress tolerance
 316-1980
Zea mays


854
PHE0000735
246
corn NAD(P)H
Stress tolerance
 67-834
Zea mays





quinone





oxidoreductase


855
PHE0000736
247
rice CBP80-
Stress tolerance
 76-2808
Oryza sativa





AY017415


856
PHE0000737
248
yeast GCR3-D10224
Stress tolerance
 908-3484
Saccharomyces








cerevisiae


857
PHE0000738
249
corn CBP20
Stress tolerance
 8-736
Zea mays


858
PHE0000739
250
yeast CBC2-Z73534
Stress tolerance
2352-2978
Saccharomyces








cerevisiae


859
PHE0000740
251
rice serine
Stress tolerance
37-289, 1008-1239, 1601-1794,
Oryza sativa





decarboxylase-

1915-2048, 2422-2621,





AAG12476

2796-2943, 3677-3790


860
PHE0000741
252
corn serine
Stress tolerance
 21-1376
Zea mays





decarboxylase


861
PHE0000742
253
soy serine
Stress tolerance
 94-1542
Glycine max





decarboxylase


862
PHE0000743
254
yeast DBF2-P22204
Plant growth and
  1-1716
Saccharomyces






development

cerevisiae


863
PHE0000744
255
yeast DBF20-P32328
Plant growth and
  1-1692
Saccharomyces






development

cerevisiae


864
PHE0000745
256
Arabidopsis agl8-
Plant growth and
 1-726
Arabidopsis thaliana





Q38876
development


865
PHE0000746
257
corn AGL8-like B
Plant growth and
 1-753
Zea mays






development


866
PHE0000747
258
corn PHR1-like 1
Plant growth and
 150-1496
Zea mays






development


867
PHE0000748
259
corn PHR1-like 2
Plant growth and
 55-1302
Zea mays






development


868
PHE0000749
260
Nitrosomonas
Carbon and/or
 94-1095
Nitrosomonas





europaea dual function
nitrogen

europaea





SBPase/FBPase-
metabolism


869
PHE0000750
261
rice VP14-like 1
Stress tolerance
 23-1936
Oryza sativa


870
PHE0000751
262
rice VP14-like 2
Stress tolerance
 220-1947
Oryza sativa


871
PHE0000754
263
rice ANT-like
Flower
  1-1926
Oryza sativa






development


872
PHE0000755
264
Nostoc sp. PCC 7120
Carbon and/or
  1-1035
Nostoc PCC7120





GlpX protein
nitrogen






metabolism


873
PHE0000756
265
Nostoc punctiforme
Carbon and/or
  1-1035
Nostoc punctiforme





strain ATCC 29133
nitrogen





GlpX protein-
metabolism





NOS1c0617


874
PHE0000757
266
Anabaena SPS C154
Carbon and/or
  1-1275
Nostoc PCC7120






nitrogen






metabolism


875
PHE0000758
267
Anabaena SPS C287
Carbon and/or
  1-1266
Nostoc PCC7120






nitrogen






metabolism


876
PHE0000762
268
G557 (HY5)
Light response
 1-507
Arabidopsis thaliana


877
PHE0000763
269
G189
Plant growth and
 1-951
Arabidopsis thaliana






development


878
PHE0000764
270
G736
Plant growth and
 1-510
Arabidopsis thaliana






development


879
PHE0000766
272
G671
Plant growth and
  1-1056
Arabidopsis thaliana






development


880
PHE0000767
273
G247
Plant growth and
 1-660
Arabidopsis thaliana






development


881
PHE0000768
274
G1384
Plant growth and
 1-942
Arabidopsis thaliana






development


882
PHE0000769
275
G779
Plant growth and
 1-594
Arabidopsis thaliana






development


883
PHE0000770
276
G1795
Plant growth and
 1-393
Arabidopsis thaliana






development


884
PHE0000771
277
G977
Plant growth and
 1-543
Arabidopsis thaliana






development


885
PHE0000772
278
G568
Plant growth and
 1-858
Arabidopsis thaliana






development


886
PHE0000773
279
G1269
Plant growth and
 1-861
Arabidopsis thaliana






development


887
PHE0000774
280
G1050
Plant growth and
  1-1557
Arabidopsis thaliana






development


888
PHE0000779
281
yeast GPA2
Stress tolerance
  1-1347
Saccharomyces








cerevisiae


889
PHE0000796
282
phytosulfokine 4-
Plant growth and
 67-315
Oryza sativa





13399211
development


890
PHE0000797
283
rice phytosulfokine 2-
Plant growth and
107-463
Oryza sativa





13399209
development


891
PHE0000798
284
rice phytosulfokine-
Plant growth and
102-368
Oryza sativa





alpha-11907498
development


892
PHE0000799
285
rice phytosulphokine
Plant growth and
 9-314
Oryza sativa





SH27A-3201971
development


893
PHE0000800
286
AtSUC1
Carbon and/or
  1-1539
Arabidopsis thaliana






nitrogen






metabolism


894
PHE0000801
287
Arabidopsis SUT2
Carbon and/or
  1-1773
Arabidopsis thaliana






nitrogen






metabolism


895
PHE0000802
288
Arabidopsis SUT4
Carbon and/or
  1-1530
Arabidopsis thaliana






nitrogen






metabolism


896
PHE0000803
289
OsSUT1-D87819
Carbon and/or
 67-1680
Oryza sativa






nitrogen






metabolism


897
PHE0000804
290
OsSUT3-AB071809
Carbon and/or
 85-1605
Oryza sativa






nitrogen






metabolism


898
PHE0000805
291
Aspergillis
Light response
  1-2013
Emericella nidulans





phytochrome


899
PHE0000806
292
corn histidine
Plant growth and
103-561
Zea mays





phosphotransfer
development





protein 1


900
PHE0000807
293
corn histidine
Plant growth and
 57-512
Zea mays





phosphotransfer
development





protein 2


901
PHE0000808
294
soy histidine
Plant growth and
 63-527
Glycine max





phosphotransfer
development





protein 1


902
PHE0000809
295
YPD1-Z74283
Plant growth and
320-823
Saccharomyces






development

cerevisiae


903
PHE0000810
296
rice ethylene receptor-
Plant growth and
 66-1976
Oryza sativa





AF013979
development


904
PHE0000811
297
rice ethylene
Plant growth and
9-917, 1160-1528, 1646-1912,
Oryza sativa





responsive factor-
development
2188-2312, 2425-2662





AAK70909


905
PHE0000812
298
CYP79F1 (supershoot)-
Plant growth and
 75-1688
Arabidopsis thaliana





AF370512
development


906
PHE0000813
299
AtSUC2
Carbon and/or
  1-1536
Arabidopsis thaliana






nitrogen






metabolism


907
PHE0000814
300
soy G28 like
Stress tolerance
 1-753
Glycine max


908
PHE0000815
301
corn G1792-like 2
Stress tolerance
104-661
Zea mays


909
PHE0000816
302
G1792
Stress tolerance
 77-493
Arabidopsis thaliana


910
PHE0000817
303
corn duf6 2
Carbon and/or
 54-1394
Zea mays






nitrogen






metabolism


911
PHE0000818
304
corn duf6 3
Carbon and/or
 30-1112
Zea mays






nitrogen






metabolism


912
PHE0000819
305
corn duf6
Carbon and/or
 62-1324
Zea mays






nitrogen






metabolism


913
PHE0000820
306
corn duf6 6
Carbon and/or
 174-1271
Zea mays






nitrogen






metabolism


914
PHE0000822
307
corn duf6 11
Carbon and/or
  5-1072
Zea mays






nitrogen






metabolism


915
PHE0000823
308
corn duf6 12
Carbon and/or
 113-1261
Zea mays






nitrogen






metabolism


916
PHE0000824
309
corn duf6 13
Carbon and/or
 48-1127
Zea mays






nitrogen






metabolism


917
PHE0000825
310
corn duf6 14
Carbon and/or
 112-1290
Zea mays






nitrogen






metabolism


918
PHE0000826
311
corn duf6 15
Carbon and/or
 197-1327
Zea mays






nitrogen






metabolism


919
PHE0000827
312
corn duf6 16
Carbon and/or
 111-1142
Zea mays






nitrogen






metabolism


920
PHE0000828
313
corn duf6 17
Carbon and/or
  6-1097
Zea mays






nitrogen






metabolism


921
PHE0000829
314
corn duf6 18
Carbon and/or
 149-1375
Zea mays






nitrogen






metabolism


922
PHE0000830
315
corn duf6 19
Carbon and/or
 153-1193
Zea mays






nitrogen






metabolism


923
PHE0000831
316
corn duf6 20
Carbon and/or
 145-1641
Zea mays






nitrogen






metabolism


924
PHE0000832
317
soy duf6 1
Carbon and/or
 52-1170
Glycine max






nitrogen






metabolism


925
PHE0000833
318
soy duf6 2
Carbon and/or
 151-1203
Glycine max






nitrogen






metabolism


926
PHE0000834
319
soy duf6 3
Carbon and/or
 36-1073
Glycine max






nitrogen






metabolism


927
PHE0000835
320
soy duf6 4
Carbon and/or
 69-1118
Glycine max






nitrogen






metabolism


928
PHE0000836
321
soy duf6 5
Carbon and/or
 55-1140
Glycine max






nitrogen






metabolism


929
PHE0000837
322
soy duf6 6
Carbon and/or
 36-1271
Glycine max






nitrogen






metabolism


930
PHE0000838
323
soy duf6 7
Carbon and/or
 228-1226
Glycine max






nitrogen






metabolism


931
PHE0000839
324
soy duf6 8
Carbon and/or
 140-1126
Glycine max






nitrogen






metabolism


932
PHE0000840
325
soy duf6 9
Carbon and/or
 61-1173
Glycine max






nitrogen






metabolism


933
PHE0000841
326
soy duf6 10
Carbon and/or
 99-1265
Glycine max






nitrogen






metabolism


934
PHE0000842
327
soy duf6 11
Carbon and/or
 167-1084
Glycine max






nitrogen






metabolism


935
PHE0000843
328
soy duf6 12
Carbon and/or
 158-1258
Glycine max






nitrogen






metabolism


936
PHE0000844
329
soy duf6 13
Carbon and/or
 250-1284
Glycine max






nitrogen






metabolism


937
PHE0000845
330
soy duf6 15
Carbon and/or
 96-1157
Glycine max






nitrogen






metabolism


938
PHE0000846
331
rice Crinkly4-
Seed
 805-3510
Oryza sativa





AB057787
development


939
PHE0000847
332
rice S-domain
Seed
 89-2395
Oryza sativa





receptor-like protein
development





kinase 1-BAA94516


940
PHE0000848
333
rice S-domain
Seed
 89-2437
Oryza sativa





receptor-like protein
development





kinase 2-BAB07906.1


941
PHE0000849
334
rice S-domain
Seed
 98-2539
Oryza sativa





receptor-like protein
development





kinase 3-BAB07905.1


942
PHE0000850
335
rice S-domain
Seed
 72-2321
Oryza sativa





receptor-like protein
development





kinase 4-BAB07904.1


943
PHE0000851
336
rice S-domain
Seed
28-44, 145-173, 272-397,
Oryza sativa





receptor-like protein
development
1180-3476





kinase 5


944
PHE0000852
337
rice S-receptor kinase
Seed
 67-2562
Oryza sativa





PK3-BAB64641.1
development


945
PHE0000853
338
OsPK10-L27821
Seed
  1-2475
Oryza sativa






development


946
PHE0000854
339
soy 14-3-3 22
Stress tolerance
 32-802
Glycine max


947
PHE0000855
340
soy 14-3-3 22 N-
Stress tolerance
 32-382
Glycine max





terminus


948
PHE0000856
341
14-3-3-like protein N-
Stress tolerance
 6-365
Oryza sativa





terminus


949
PHE0000857
342
sorghum 14-3-3 10
Stress tolerance
116-874
Sorghum bicolor


950
PHE0000858
343
sorghum 14-3-3 10 N-
Stress tolerance
116-460
Sorghum bicolor





terminus


951
PHE0000859
344
rice 14-3-3 15
Stress tolerance
 70-855
Oryza sativa


952
PHE0000860
345
rice 14-3-3 15 N-
Stress tolerance
 70-429
Oryza sativa





terminus


953
PHE0000861
346
corn 14-3-3 13
Stress tolerance
 62-808
Zea mays


954
PHE0000862
347
corn 14-3-3 13 N-
Stress tolerance
 62-409
Zea mays





terminus


955
PHE0000863
348
14-3-3 protein N-
Stress tolerance
 42-389
Glycine max





terminus


956
PHE0000864
349
rice 14-3-3 10
Stress tolerance
105-875
Oryza sativa


957
PHE0000865
350
rice 14-3-3 10 N-
Stress tolerance
105-449
Oryza sativa





terminus


958
PHE0000866
351
soy 14-3-3 21
Stress tolerance
 84-860
Glycine max


959
PHE0000867
352
soy 14-3-3 21 N-
Stress tolerance
 84-443
Glycine max





terminus


960
PHE0000868
353
wheat 14-3-3 10
Stress tolerance
 64-840
Triticum aestivum


961
PHE0000869
354
wheat 14-3-3 10 N-
Stress tolerance
 64-420
Triticum aestivum





terminus


962
PHE0000870
355
corn 14-3-3 17
Stress tolerance
132-929
Zea mays


963
PHE0000871
356
corn 14-3-3 17 N-
Stress tolerance
132-506
Zea mays





terminus


964
PHE0000872
357
rice G alpha XL-
Plant growth and
48-1040, 1127-1264,
Oryza sativa





BAA93022
development
2100-2204, 2500-2682,







3113-3290, 3374-3618,







3937-4109, 4430-4627,







4988-5378


965
PHE0000873
358
yeast casein kinase II
Flower
  2-1120
Saccharomyces





alpha-CAA86916
development

cerevisiae


966
PHE0000874
359
rice casein kinase
Flower
29-363, 471-600, 1034-1228,
Oryza sativa





alpha subunit-
development
2564-2721, 3082-3172,





AAL34126

3250-3315, 3657-3739,







3821-3884, 3967-4035,







4124-4159


967
PHE0000875
360
soy casein kinase alpha
Flower
 129-1127
Glycine max






development


968
PHE0000876
361
rice casein kinase II
Flower
52-262, 2992-3213, 3477-3586,
Oryza sativa





beta subunit-
development
3679-3844, 4365-4498





AAG60201


969
PHE0000877
362
yeast CKB1-Z72541
Flower
 286-1122
Saccharomyces






development

cerevisiae


970
PHE0000878
363
corn casein kinase beta 1
Flower
 231-1055
Zea mays






development


971
PHE0000879
364
corn casein kinase beta 2
Flower
178-993
Zea mays






development


972
PHE0000884
365
CAR1-like 1
Stress tolerance
 82-546
Zea mays


973
PHE0000885
366
corn CAR1-like 3
Stress tolerance
161-775
Zea mays


974
PHE0000886
367
corn CAR1-like 4
Stress tolerance
192-659
Zea mays


975
PHE0000887
368
corn CAR1-like 5
Stress tolerance
 86-484
Zea mays


976
PHE0000888
369
yeast hnRNP
Stress tolerance
 76-1122
Saccharomyces





methyltransferase-


cerevisiae





CAA53689


977
PHE0000889
370
corn arginine N-methyl
Stress tolerance
 44-1318
Zea mays





transferase 1


978
PHE0000890
371
corn arginine N-methyl
Stress tolerance
 102-1232
Zea mays





transferase 2


979
PHE0000891
372
CAR1-corn ABA
Stress tolerance
 68-538
Zea mays





inducible RNA-





binding protein


980
PHE0000892
373
corn RING finger 100
Plant growth and
 292-1404
Zea mays






development


981
PHE0000893
374
corn RING finger 101
Plant growth and
 103-1077
Zea mays






development


982
PHE0000894
375
corn RING finger 103
Plant growth and
 20-1093
Zea mays






development


983
PHE0000895
376
corn RING finger 102
Plant growth and
 252-1295
Zea mays






development


984
PHE0000896
377
corn RING finger 104
Plant growth and
293-925
Zea mays






development


985
PHE0000897
378
corn RING finger 105
Plant growth and
 95-934
Zea mays






development


986
PHE0000898
379
corn RING finger 106
Plant growth and
 99-563
Zea mays






development


987
PHE0000899
380
corn RING finger 108
Plant growth and
 308-1054
Zea mays






development


988
PHE0000900
381
corn RING finger 109
Plant growth and
 71-622
Zea mays






development


989
PHE0000901
382
corn RING finger 110
Plant growth and
 215-1756
Zea mays





[ReMembR-H2 protein
development





JR702]-


990
PHE0000902
383
corn RING finger 111
Plant growth and
162-599
Zea mays






development


991
PHE0000903
384
corn RING finger 112
Plant growth and
 411-2375
Zea mays






development


992
PHE0000904
385
corn RING finger 113
Plant growth and
 269-1828
Zea mays






development


993
PHE0000905
386
corn RING finger 114
Plant growth and
167-781
Zea mays






development


994
PHE0000906
387
corn RING finger 115
Plant growth and
294-806
Zea mays






development


995
PHE0000907
388
corn RING finger 116
Plant growth and
 187-1374
Zea mays






development


996
PHE0000908
389
corn Skp1-like 118
Plant growth and
 94-597
Zea mays





[UIP2]
development


997
PHE0000909
390
corn Skp1-like 119
Plant growth and
 158-1159
Zea mays






development


998
PHE0000910
391
corn Skp1-like 120
Plant growth and
106-633
Zea mays





[UIP2]
development


999
PHE0000911
392
corn F-box 123
Plant growth and
 184-1980
Zea mays






development


1000
PHE0000912
393
corn F-box 124 [TIR1]
Plant growth and
 167-1936
Zea mays






development


1001
PHE0000913
394
corn F-box 125 [TIR1]
Plant growth and
 174-1892
Zea mays






development


1002
PHE0000914
395
corn F-box 126
Plant growth and
 107-1894
Zea mays






development


1003
PHE0000915
396
corn RING finger 128
Plant growth and
 42-746
Zea mays





[response regulator 6]
development


1004
PHE0000916
397
corn RING finger 132
Plant growth and
107-985
Zea mays






development


1005
PHE0000917
398
corn RING finger 133
Plant growth and
 597-1496
Zea mays






development


1006
PHE0000918
399
corn ASH1
Stress tolerance
144-899
Zea mays


1007
PHE0000919
400
corn RING finger 136
Plant growth and
 95-1012
Zea mays






development


1008
PHE0000920
401
corn RING finger 138
Plant growth and
117-902
Zea mays






development


1009
PHE0000921
402
corn F-box 141
Plant growth and
 487-1428
Zea mays






development


1010
PHE0000922
403
corn F-box 142
Plant growth and
 227-1114
Zea mays






development


1011
PHE0000923
404
corn F-box 143
Plant growth and
 352-1410
Zea mays






development


1012
PHE0000924
405
corn F-box 144
Plant growth and
 96-1406
Zea mays






development


1013
PHE0000925
406
corn F-box 145
Plant growth and
 436-1524
Zea mays






development


1014
PHE0000926
407
corn RING finger 147
Plant growth and
 79-927
Zea mays






development


1015
PHE0000927
408
corn RING finger 149
Plant growth and
128-379
Zea mays





[anaphase promoting
development





complex subunit 11]-


1016
PHE0000928
409
corn RING finger 151
Plant growth and
 77-442
Zea mays





[ROC1]
development


1017
PHE0000929
410
corn U-box 153
Plant growth and
 166-1743
Zea mays






development


1018
PHE0000930
411
corn RING finger 154
Plant growth and
 262-1560
Zea mays





[VIP2]
development


1019
PHE0000931
412
corn RING finger 155
Plant growth and
 161-1498
Zea mays





[VIP2]
development


1020
PHE0000932
413
rice U-box 100
Plant growth and
121-939
Oryza sativa






development


1021
PHE0000933
414
corn RING finger
Plant growth and
168-857
Zea mays





protein 157
development


1022
PHE0000934
415
corn F-box 159 [FKF1-
Plant growth and
 195-2021
Zea mays





like]
development


1023
PHE0000935
416
corn F-box 160 [FKF-
Plant growth and
 77-1930
Zea mays





like]
development


1024
PHE0000936
417
corn RING finger 161
Plant growth and
 78-3026
Zea mays





[cellulose synthase]
development


1025
PHE0000937
418
corn RING finger 162
Plant growth and
 193-3414
Zea mays





[cellulose synthase]
development


1026
PHE0000938
419
corn RING finger 163
Plant growth and
 277-1059
Zea mays






development


1027
PHE0000939
420
corn RING finger 164
Plant growth and
 218-1033
Zea mays






development


1028
PHE0000940
421
corn RING finger 165
Plant growth and
167-754
Zea mays






development


1029
PHE0000941
422
corn F-box 166
Plant growth and
 62-814
Zea mays






development


1030
PHE0000942
423
corn RING finger 167
Plant growth and
 266-1288
Zea mays





[seven in absentia-like]
development


1031
PHE0000943
424
corn F-box 168
Plant growth and
 203-1402
Zea mays






development


1032
PHE0000944
425
corn RING finger 169
Plant growth and
 103-1113
Zea mays





[S-ribonuclease
development





binding protein]


1033
PHE0000945
426
corn F-box 170
Plant growth and
 123-1184
Zea mays






development


1034
PHE0000946
427
corn F-box 172
Plant growth and
 42-803
Zea mays






development


1035
PHE0000947
428
corn RING finger 174
Plant growth and
 255-1280
Zea mays






development


1036
PHE0000948
429
corn RING 175
Plant growth and
 179-1291
Zea mays






development


1037
PHE0000949
430
corn Cullin 176
Plant growth and
221-931
Zea mays






development


1038
PHE0000950
431
corn RING finger 177
Plant growth and
 33-863
Zea mays






development


1039
PHE0000951
432
corn RING finger 178
Plant growth and
 227-1492
Zea mays






development


1040
PHE0000952
433
corn RING finger 179
Plant growth and
 68-1342
Zea mays





[alpha-galactosidase]
development


1041
PHE0000953
434
corn RING finger 180
Plant growth and
 265-1431
Zea mays






development


1042
PHE0000954
435
corn F-box 181
Plant growth and
 354-1397
Zea mays






development


1043
PHE0000955
436
corn RING finger 182
Plant growth and
 113-1282
Zea mays






development


1044
PHE0000956
437
corn RING finger 183
Plant growth and
293-997
Zea mays






development


1045
PHE0000957
438
corn RING finger 185
Plant growth and
104-829
Zea mays






development


1046
PHE0000958
439
corn F-box 186
Plant growth and
 47-1303
Zea mays






development


1047
PHE0000959
440
corn F-box 187
Plant growth and
 195-1199
Zea mays






development


1048
PHE0000960
441
corn RING/U-box 188
Plant growth and
 63-1142
Zea mays






development


1049
PHE0000961
442
corn SPS2-4
Carbon and/or
 105-3035
Zea mays






nitrogen






metabolism


1050
PHE0000962
443
rice IRE1-AB031396
Seed
 239-2920
Oryza sativa






development


1051
PHE0000963
444
rice IRE1 N-terminal
Seed
 239-1483
Oryza sativa





domain-AB031396
development


1052
PHE0000964
445
rice IRE1 C-terminal
Seed
1481-2920
Oryza sativa





domain-AB031396
development


1053
PHE0000965
446
yeast IRE1-P32361
Seed
 80-3427
Saccharomyces






development

cerevisiae


1054
PHE0000966
447
yeast IRE1 N-terminal
Seed
 80-1798
Saccharomyces





domain-P32361
development

cerevisiae


1055
PHE0000967
448
yeast IRE1 C-terminal
Seed
1799-3427
Saccharomyces





domain-P32361
development

cerevisiae


1056
PHE0000968
449
corn cytosine
Seed
 80-1339
Zea mays





deaminase-like
development


1057
PHE0000969
450
corn aldose reductase
Seed
 106-1041
Zea mays






development


1058
PHE0000970
451
soy NADPH dependent
Seed
 32-958
Glycine max





mannose 6-phosphate
development





reductase-


1059
PHE0000972
453
yeast Ydr210w-
Seed
101-325
Saccharomyces





NP_010496
development

cerevisiae


1060
PHE0000974
455
yeast Soh1-
Seed
101-481
Saccharomyces





NP_011388
development

cerevisiae


1061
PHE0000975
456
yeast TAD2-
Seed
101-850
Saccharomyces





NP_012499
development

cerevisiae


1062
PHE0000978
459
yeast Ynl010w-
Seed
101-823
Saccharomyces





NP_014388
development

cerevisiae


1063
PHE0000979
460
yeast Ynl124w-
Seed
 101-1576
Saccharomyces





NP_014275
development

cerevisiae


1064
PHE0000980
461
yeast Ydl124w-
Seed
 101-1036
Saccharomyces





NP_010159
development

cerevisiae


1065
PHE0000984
465
yeast Glutaredoxin-
Seed
101-430
Saccharomyces





NP_009895
development

cerevisiae


1066
PHE0000985
466
soy unknown protein
Seed
 228-1226
Saccharomyces






development

cerevisiae


1067
PHE0000986
467
soy putative protein
Seed
 265-1002
Glycine max






development


1068
PHE0000987
468
corn CLC1
Stress tolerance
102-599
Zea mays


1069
PHE0000988
469
corn CLD1
Stress tolerance
 69-461
Zea mays


1070
PHE0000989
470
rice Asr1-AF039573
Stress tolerance
 71-487
Oryza sativa


1071
PHE0000990
471
rice CLC1-like 1-
Stress tolerance
37-326, 451-703
Oryza sativa





BAB19059


1072
PHE0000991
472
corn Asr1-like 1
Stress tolerance
151-690
Zea mays


1073
PHE0000992
473
corn Asr1-like 5
Stress tolerance
 89-511
Zea mays


1074
PHE0000993
474
corn sigma factor 1
Plant growth and
 219-1715
Zea mays






development


1075
PHE0000994
475
corn sigma factor 2
Plant growth and
 166-1815
Zea mays





[Sig3]
development


1076
PHE0000995
476
corn sigma factor 3
Plant growth and
 101-1717
Zea mays





[Sig1]
development


1077
PHE0000996
477
corn bromodomain
Seed
 417-2147
Zea mays





protein
development


1078
PHE0000997
478
corn homeodomain
Seed
 292-1269
Zea mays





leucine zipper protein
development


1079
PHE0000998
479
corn bZIP protein 3
Seed
 63-908
Zea mays






development


1080
PHE0000999
480
corn bZIP protein 4
Seed
 95-1225
Zea mays





[G-box binding factor
development





1]


1081
PHE0001000
481
corn remorin like
Seed
 84-1637
Zea mays





DNA-binding protein 1
development


1082
PHE0001001
482
corn remorin like
Seed
 43-639
Zea mays





DNA-binding protein 2
development


1083
PHE0001002
483
corn Gld-Tea protein 2
Seed
 47-811
Zea mays






development


1084
PHE0001003
484
corn homeobox protein 1
Seed
 370-1179
Zea mays






development


1085
PHE0001004
485
corn homeobox protein 3
Seed
 485-1300
Zea mays






development


1086
PHE0001005
486
corn heat shock
Seed
 75-875
Zea mays





transcription factor 1
development


1087
PHE0001006
487
corn heat shock
Seed
 895-1575
Zea mays





transcription factor 2
development


1088
PHE0001007
488
corn heat shock
Seed
195-965
Zea mays





transcription factor 3
development


1089
PHE0001008
489
corn heat shock
Seed
 383-1276
Zea mays





transcription factor 4
development


1090
PHE0001009
490
corn IAA-like 1
Seed
 65-724
Zea mays






development


1091
PHE0001010
491
corn IAA-like 4
Seed
 762-1448
Zea mays






development


1092
PHE0001011
492
corn MADS box
Seed
114-286, 383-819
Zea mays





protein 100
development


1093
PHE0001012
493
corn MADS box
Seed
 293-1027
Zea mays





protein 102
development


1094
PHE0001013
494
corn MADS box
Seed
 63-731
Zea mays





protein 103
development


1095
PHE0001014
495
corn MADS box
Seed
213-890
Zea mays





protein 104
development


1096
PHE0001015
496
corn MADS box
Seed
101-853
Zea mays





protein 105
development


1097
PHE0001016
497
corn MADS box
Seed
115-741
Zea mays





protein 108
development


1098
PHE0001018
498
corn MADS box
Seed
246-980
Zea mays





protein 114
development


1099
PHE0001019
499
corn LIM domain
Seed
 99-1160
Zea mays





protein 1
development


1100
PHE0001020
500
corn LIM domain
Seed
171-782
Zea mays





protein 2
development


1101
PHE0001021
501
corn myb-like DNA
Seed
 248-1105
Zea mays





binding protein
development


1102
PHE0001022
502
corn myb domain
Seed
112-945
Zea mays





protein 1
development


1103
PHE0001023
503
corn myb domain
Seed
 125-1030
Zea mays





protein 3
development


1104
PHE0001024
504
corn myb domain
Seed
 34-1101
Zea mays





protein 4
development


1105
PHE0001025
505
corn NAM-like protein
Seed
 139-1563
Zea mays






development


1106
PHE0001026
506
corn transcriptional co-
Seed
165-686
Zea mays





activator-like protein 1
development


1107
PHE0001027
507
corn LSD1-like protein 1
Seed
222-650
Zea mays






development


1108
PHE0001028
508
corn GS1-like protein
Seed
 84-806
Zea mays






development


1109
PHE0001029
509
corn RING finger 200
Seed
 268-1470
Zea mays






development


1110
PHE0001030
510
corn RING finger
Seed
 187-1158
Zea mays





protein 202
development


1111
PHE0001031
511
corn PGPD14-like
Seed
107-985
Zea mays





protein
development


1112
PHE0001032
512
corn Ankyrin protein 1
Seed
 440-1891
Zea mays






development


1113
PHE0001033
513
corn zinc finger protein
Seed
 424-1644
Zea mays





10 [corn G325-like 3]
development


1114
PHE0001034
514
corn scarecrow protein
Seed
 242-1903
Zea mays





100
development


1115
PHE0001035
515
corn transcription
Seed
 131-1234
Zea mays





elongation factor
development


1116
PHE0001036
516
corn constans-like
Seed
128-904
Zea mays





protein 10
development


1117
PHE0001037
517
corn copine-like
Seed
 518-1861
Zea mays





protein 1
development


1118
PHE0001038
518
corn copine-like
Seed
 281-1513
Zea mays





protein 2
development


1119
PHE0001039
519
corn RING finger
Seed
 311-1579
Zea mays





protein 201
development


1120
PHE0001040
520
corn zinc finger protein
Seed
 65-1138
Zea mays






development


1121
PHE0001041
521
corn IAA-like 10
Seed
146-823
Zea mays






development


1122
PHE0001042
522
corn constans-like 5
Seed
215-829
Zea mays






development


1123
PHE0001043
523
soy G-gamma subunit
Plant growth and
210-518
Glycine max





DC-terminus
development


1124
PHE0001044
524
soy AGL8-like 1
Plant growth and
 346-1077
Glycine max






development


1125
PHE0001045
525
soy AGL8-like 3
Plant growth and
147-863
Glycine max






development


1126
PHE0001046
526
corn Agl8D (LIB5131-
Plant growth and
 1-735
Zea mays





001-H1)
development


1127
PHE0001047
527
corn Agl8E (LIB5131-
Plant growth and
 1-798
Zea mays





001-H2)
development


1128
PHE0001048
528
corn Agl8F (LIB5131-
Plant growth and
 1-798
Zea mays





001-H3)
development


1129
PHE0001050
529
Arabidopsis LFY
Flower
 40-1311
Arabidopsis thaliana






development


1130
PHE0001103
530
corn Isr
Plant growth and
 220-1254
Zea mays






development


1131
PHE0001104
531
soy Isr-like 1
Plant growth and
 365-1495
Glycine max






development


1132
PHE0001105
532
rice Isr-like 1
Plant growth and
 110-1159
Oryza sativa






development


1133
PHE0001160
533
soy G1792-like
Stress tolerance
 20-391
Glycine max


1134
PHE0001161
534
corn sucrose export
Carbon and/or
  1-1425
Zea mays





defective 1 (sdx1)-
nitrogen





AF302187
metabolism


1135
PHE0001162
535
rice sdx1 delta ctp
Carbon and/or
345-409, 581-692, 710-827,
Oryza sativa






nitrogen
2019-2098, 3567-3646,






metabolism
5059-5228, 5675-5772,







6541-6645, 7487-7603,







7908-8057, 9155-9328


1136
PHE0001163
536
Arabidopsis sucrose
Carbon and/or
  1-1467
Arabidopsis thaliana





export defective 1-
nitrogen





AF302188
metabolism


1137
PHE0001164
537
Nostoc sp. PCC 7120
Carbon and/or
  1-1092
Nostoc PCC7120





sdx1-like-17134979
nitrogen






metabolism


1138
PHE0001165
538
Synechocystis sp. PCC
Carbon and/or
  1-1092
Synechocystis sp.





6803 sdx1-like-
nitrogen

PCC 6803





1652844
metabolism


1139
PHE0001166
539
Nostoc punctiforme
Carbon and/or
 294-1388
Nostoc punctiforme





sdx1-like
nitrogen






metabolism


1140
PHE0001173
540
corn CVY-CIK
Stress tolerance
 217-1563
Zea mays


1141
PHE0001187
541
corn spa1-like
Light response
 104-2467
Zea mays


1142
PHE0001188
542
corn calcium
Stress tolerance
 649-2424
Zea mays





dependant protein





kinase


1143
PHE0001189
543
corn unknown protein
Stress tolerance
127-813
Zea mays


1144
PHE0001190
544
corn putative splicing
Stress tolerance
153-671
Zea mays





factor


1145
PHE0001191
545
rice hydroxyproline-
Stress tolerance
 120-1769
Oryza sativa





rich glycoprotein


1146
PHE0001192
546
rice unknown protein-
Stress tolerance
605-719, 800-864, 1161-1503,
Oryza sativa





AAK14418

1666-1732, 1833-1986,







2283-2450, 2553-2663,







2773-2883, 3025-3042,







3078-3179, 3748-3978,







4551-4625, 4905-4976,







5758-5943, 6029-6187,







6412-6504, 6891-6962,







7497-7587, 7830-8008,







8413-8494, 8687-8797,







8876-8982, 9355-9432,







9518-9613, 9788-9883,







11533-11700


1147
PHE0001193
547
corn unknown protein
Stress tolerance
87-1147, 1229-1919
Zea mays


1148
PHE0001194
548
corn alpha-amylase
Stress tolerance
 553-1797
Zea mays


1149
PHE0001233
549
rice G1073-like 1
Plant growth and
  1-1008
Oryza sativa






development


1150
PHE0001234
550
rice inosine
Plant growth and
45-1040, 2559-2738,
Oryza sativa





monophosphate
development
3841-4098, 4927-4998





dehydrogenase-





AAK09225


1151
PHE0001235
551
yeast IMP
Plant growth and
 101-1669
Saccharomyces





dehydrogenase
development

cerevisiae





[Imd2p]-NP_012088


1152
PHE0001236
552
E. coli guaB-
Plant growth and
  1-1467
Escherichia coli





NP_417003
development


1153
PHE0001237
553
Agrobacterium GuaB-
Plant growth and
  7-1512
Agrobacterium





AE007996
development

tumefaciens


1154
PHE0001276
554
corn Transcription
Seed
 1-921
Zea mays





Factor #1
development


1155
PHE0001277
555
corn Transcription
Seed
  1-2028
Zea mays





Factor #2
development


1156
PHE0001325
556
corn RING finger
Plant growth and
 353-1771
Zea mays





protein 25
development


1157
PHE0001326
557
yeast VHT1-
Carbon and/or
 101-1879
Saccharomyces





YGR065C
nitrogen

cerevisiae






metabolism


1158
PHE0001327
558
Arabidopsis Suc5-
Carbon and/or
 63-1592
Arabidopsis thaliana





AJ252133
nitrogen






metabolism


1159
PHE0001400
559
soy G1792-like 2
Stress tolerance
 18-431
Glycine max


1160
PHE0001401
560
corn G1792-like 3
Stress tolerance
247-639
Zea mays


1161
PHE0001423
561
Glutamate
Plant growth and
 268-1761
Zea mays





Decarboxylase
development


1162
PHE0001432
562
putative
Plant growth and
 94-909
Zea mays





carnitine/acylcarnitine
development





translocase-


1163
PHE0001433
563
corn cycA-like
Plant growth and
 196-1230
Zea mays





[GATE80]
development


1164
PHE0001434
564
corn cycA-like
Plant growth and
 188-1306
Zea mays





[GAT81]
development


1165
PHE0001435
565
corn E4/E8 binding
Plant growth and
 253-2259
Zea mays





protein-like [GATE68]
development


1166
PHE0001438
566
Arabidopsis G748
Plant growth and
 98-1441
Arabidopsis thaliana






development


1167
PHE0001439
567
Arabidopsis NAM (no
Plant growth and
 175-1293
Arabidopsis thaliana





apical meristem)-like
development





protein-


1168
PHE0001440
568
soy G1452-like protein
Plant growth and
 207-1319
Glycine max






development


1169
PHE0001497
569
corn cytochrome P450
Plant growth and
 143-1588
Zea mays






development


1170
PHE0001498
570
rice receptor-like
Plant growth and
  1-3885
Oryza sativa





protein
development


1171
PHE0001499
571
rice receptor-like
Plant growth and
  1-3333
Oryza sativa





protein kinase
development


1172
PHE0001500
572
rice putative
Plant growth and
  1-3366
Oryza sativa





brassinosteroid-
development





insensitive protein


1173
PHE0001501
573
rice cell elongation
Plant growth and
  1-1686
Oryza sativa





protein DIMINUTO
development


1174
PHE0001502
574
corn Dwarf1-like 1
Plant growth and
 138-1823
Zea mays






development


1175
PHE0001503
575
rice putative sterol-
Plant growth and
 1-717
Oryza sativa





C5(6)-desaturase
development


1176
PHE0001504
576
corn sterol-C5(6)-
Plant growth and
 60-881
Zea mays





desaturase 2
development


1177
PHE0001505
577
corn sterol-C5(6)-
Plant growth and
 43-870
Zea mays





desaturase 1
development


1178
PHE0001506
578
soy sterol-C5(6)-
Plant growth and
 158-1006
Glycine max





desaturase
development


1179
PHE0001507
579
rice BRS1-like
Plant growth and
 78-1490
Oryza sativa





protease 4
development


1180
PHE0001508
580
corn BRS1-like
Plant growth and
 109-1548
Zea mays





protease 1
development


1181
PHE0001509
581
soy FKF1-like protein
Plant growth and
 19-1878
Glycine max






development


1182
PHE0001510
582
corn FKF-like protein 2
Plant growth and
 70-2115
Zea mays






development


1183
PHE0001552
583
yeast YDL168W/SFA1-
Nitric oxide
 101-1258
Saccharomyces





NP_010113
signaling

cerevisiae


1184
PHE0001543
584
E. coli adhC-
Nitric oxide
  1-1110
Escherichia coli





AE000142
signaling


1185
PHE0001544
585
Nostoc sp. PCC 7120
Nitric oxide
  1-1110
Nostoc PCC7120





glutathione dependent
signaling





formaldehyde





dehydrogenase-





BAB74509


1186
PHE0001545
586
rice glutathione
Nitric oxide
204-243, 391-527, 1160-1206,
Oryza sativa





dependent
signaling
1296-1621, 1946-2028,





formaldehyde

2107-2182, 2805-2962,





dehydrogenase-

3285-3446, 3541-3657





U77637


1187
PHE0001546
587
corn glutathione-
Nitric oxide
 82-1227
Zea mays





dependent
signaling





formaldehyde





dehydrogenase-





Y11029


1188
PHE0001547
588
corn corn glutathione-
Nitric oxide
 108-1265
Zea mays





dependent
signaling





formaldehyde





dehydrogenase 2-


1189
PHE0001548
589
corn corn glutathione-
Nitric oxide
 95-1231
Zea mays





dependent
signaling





formaldehyde





dehydrogenase 3-


1190
PHE0001549
590
soy glutathione
Nitric oxide
 30-1166
Glycine max





dependent
signaling





formaldehyde





dehydrogenase-


1191
PHE0001550
591
rice putative phosphate
Carbon and/or
  1-1113
Oryza sativa





translocator-
nitrogen





AAK21346
metabolism


1192
PHE0001551
592
rice glucose-6-
Carbon and/or
  1-1071
Oryza sativa





phosphate/phosphate-
nitrogen





tranlocator-13486660
metabolism


1193
PHE0001552
593
corn glucose-6-
Carbon and/or
 165-1184
Zea mays





phosphate/phosphate-
nitrogen





tranlocator-
metabolism


1194
PHE0001553
594
rice putative sugar
Carbon and/or
  3-1736
Oryza sativa





transporter-AF416867
nitrogen






metabolism


1195
PHE0001554
595
soy cycD4-like protein
Plant growth and
 222-1277
Glycine max






development


1196
PHE0001578
596
rice RPN12-
Plant growth and
 76-879
Oryza sativa





AB037153
development


1197
PHE0001579
597
YFR052W/RPN12-
Plant growth and
101-922
Saccharomyces





NP_116710
development

cerevisiae


1198
PHE0001580
598
corn rpn12
Plant growth and
 83-883
Zea mays






development


1199
PHE0001581
599
soy rpn12
Plant growth and
113-913
Glycine max






development


1200
PHE0001583
600
sorghum TTG1-like
Stress tolerance
 107-1288
Sorghum bicolor


1201
PHE0001584
601
corn TTG1-like protein 2
Stress tolerance
 141-1388
Zea mays


1202
PHE0001595
602
ZmHK1
Plant growth and
 77-3001
Zea mays






development


1203
PHE0001596
603
Arabidopsis CRE1b
Plant growth and
 69-3311
Arabidopsis thaliana






development


1204
PHE0001597
604
Arabidopsis HK2
Plant growth and
  1-3531
Arabidopsis thaliana






development


1205
PHE0001598
605
Arabidopsis HK3
Plant growth and
  1-3111
Arabidopsis thaliana






development


1206
PHE0001607
606
maize nitrate
Seed
 494-2068
Zea mays





transporter like 1
development





sequence


1207
PHE0001608
607
rice nitrate transporter
Seed
 97-1698
Oryza sativa





like 1 sequence
development


1208
PHE0001609
608
rice nitrate transporter
Seed
  1-1551
Oryza sativa





like 2 sequence
development


1209
PHE0001667
609
rice histidine kinase
Plant growth and
 201-3239
Oryza sativa






development


1210
PHE0002018
610
Arabidopsis nitrate
Seed
 76-1833
Arabidopsis thaliana





transporter NTL1 like
development





sequence


1211
PHE0002019
611
maize nitrate
Seed
 75-1907
Zea mays





transporter NTL1 like
development





sequence


1212
PHE0002020
612
maize nitrate
Seed
 212-1954
Zea mays





transporter NTL1 like
development





2 sequence


1213
PHE0002021
613
rice nitrate transporter
Seed
 163-1944
Oryza sativa





NTL1 like 1 sequence
development


1214
PHE0002022
614
rice nitrate transporter
Seed
  1-1743
Oryza sativa





NTL1 like 2 sequence
development


1215
PHE0000372
22
G1073
Plant growth and
 1-810
Arabidopsis thaliana






development


1216
PHE0000493
67
Synechocystis ssr3189-
Stress tolerance
 54-221
Synechocystis sp.





BAA17701


PCC 6803


1217
PHE0000494
68
Synechocystis ssr2315-
Stress tolerance
242-457
Synechocystis sp.





BAA17190


PCC 6803


1218
PHE0000522
95
wheat clv3-like
Plant growth and
102-365
Triticum aestivum






development


1219
PHE0000524
97
corn ESR2
Plant growth and
 46-441
Zea mays






development


1220
PHE0000602
169
yeast BIR1
Plant growth and
 345-3209
Saccharomyces






development

cerevisiae


1221
PHE0000765
271
G1073
Plant growth and
 1-810
Arabidopsis thaliana






development


1222
PHE0000971
452
yeast YBL107c-
Seed
 29-619
Saccharomyces





Z35868
development

cerevisiae


1223
PHE0000973
454
yeast YDR209c-
Seed
101-511
Saccharomyces





S61572
development

cerevisiae


1224
PHE0000976
457
yeast Yet1-
Seed
101-718
Saccharomyces





NP_012858
development

cerevisiae


1225
PHE0000977
458
yeast Ylr162w-
Seed
101-454
Saccharomyces





NP_013263
development

cerevisiae


1226
PHE0000981
462
yeast Ygr039w-
Seed
101-409
Saccharomyces





NP_011553
development

cerevisiae


1227
PHE0000982
463
yeast Usa1-
Seed
 101-2614
Saccharomyces





NP_013683
development

cerevisiae


1228
PHE0000983
464
yeast Ynr061c-
Seed
101-757
Saccharomyces





NP_014459
development

cerevisiae









Selection Methods for Transgenic Plants with Enhanced Agronomic Trait

Within a population of transgenic plants regenerated from plant cells transformed with the recombinant DNA in their nucleus many plants that survive to fertile transgenic plants that produce seeds and progeny plants will not exhibit an enhanced agronomic trait. Selection from the population is necessary to identify one or more transgenic plant cells that can provide plants with the enhanced trait. Transgenic plants having enhanced traits are selected from populations of plants regenerated or derived from plant cells transformed as described herein by evaluating the plants in a variety of assays to detect an enhanced trait, e.g. enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. These assays also may take many forms including, but not limited to, direct screening for the trait in a greenhouse or field trial or by screening for a surrogate trait. Such analyses can be directed to detecting changes in the chemical composition, biomass, physiological properties, morphology of the plant. Changes in chemical compositions such as nutritional composition of grain can be detected by analysis of the seed composition and content of protein, free amino acids, oil, free fatty acids, starch or tocopherols. Changes in biomass characteristics can be made on greenhouse or field grown plants and can include plant height, stem diameter, root and shoot dry weights; and, for corn plants, ear length and diameter. Changes in physiological properties can be identified by evaluating responses to stress conditions, for example assays using imposed stress conditions such as water deficit, nitrogen deficiency, cold growing conditions, pathogen or insect attack or light deficiency, or increased plant density. Changes in morphology can be measured by visual observation of tendency of a transformed plant with an enhanced agronomic trait to also appear to be a normal plant as compared to changes toward bushy, taller, thicker, narrower leaves, striped leaves, knotted trait, chlorosis, albino, anthocyanin production, or altered tassels, ears or roots. Other selection properties include days to pollen shed, days to silking, leaf extension rate, chlorophyll content, leaf temperature, stand, seedling vigor, internode length, plant height, leaf number, leaf area, tillering, brace roots, stay green, stalk lodging, root lodging, plant health, barreness/prolificacy; green snap, and pest resistance. In addition, phenotypic characteristics of harvested grain may be evaluated, including number of kernels per row on the ear, number of rows of kernels on the ear, kernel abortion, kernel weight, kernel size, kernel density and physical grain quality.
Although the transgenic plant nuclei, plant cells, plant pollen, plants and methods of this invention can be applied to a wide variety of plant species such as fruits, vegetables, grasses and trees, they are particularly useful when applied to crops such as corn, soybean, cotton, oilseed rape (canola), alfalfa, rice, wheat, sugar beet, sugar cane and sunflower.
The following examples illustrate aspects of the inventions.
Example 1
Plant Expression Constructs
This example illustrates the construction of a several alternative base transformation vectors for transferring recombinant DNA into the nucleus of a plant cell which can be regenerated into a transgenic plant of this invention.
A base transformation vector for bombardment transformation is produced using GATEWAYTM Destination (Invitrogen Life Technologies, Carlsbad, Calif.) vectors. pMON65154 is constructed for use in preparation of constructs comprising recombinant polynucleotides for corn transformation. The elements of the expression vector are summarized in Table 3 below. Generally, pMON65154 comprises a selectable marker expression cassette comprising a Cauliflower Mosaic Virus 35S promoter operably linked to a gene encoding neomycin phosphotransferase II (nptII). The 3′ region of the selectable marker expression cassette comprises the 3′ region of the Agrobacterium tumefaciens nopaline synthase gene (nos) followed 3′ by the 3′ region of the potato proteinase inhibitor II (pinII) gene. The plasmid pMON 65154 further comprises a plant expression cassette into which a gene of interest may be inserted using GATEWAYTM cloning methods. The GATEWAYTM cloning cassette is flanked 5′ by a rice actin 1 promoter, exon and intron and flanked 3′ by the 3′ region of the potato pinII gene. Using GATEWAYTM methods, the cloning cassette may be replaced with a gene of interest. The vector pMON65154, and derivatives thereof comprising a gene of interest, are particularly useful in methods of plant transformation via direct DNA delivery, such as microprojectile bombardment.







TABLE 3







Elements of Plasmid pMON65154









FUNCTION
ELEMENT
REFERENCE





Plant gene of interest
Rice actin 1 promoter
U.S. Pat. No. 5,641,876


expression cassette
Rice actin 1 exon 1, 
U.S. Pat. No. 5,641,876



intron 1 enhancer



Gene of interest
AttR1
GATEWAY TMCloning 


insertion site

Technology Instruction 




Manual



CmR gene
GATEWAY TMCloning 




Technology Instruction 




Manual



ccdA, ccdB genes
GATEWAY TMCloning 




Technology Instruction 




Manual



attR2
GATEWAY TMCloning 




Technology Instruction 




Manual


Plant gene of interest
Potato pinII 3′ region
An et al. (1989) Plant 


expression cassette

Cell 1:115-122


Plant selectable
CaMV 35S promoter
U.S. Pat. No. 5,858,742


marker expression
nptII selectable marker
U.S. Pat. No. 5,858,742


cassette
nos 3′ region
U.S. Pat. No. 5,858,742



PinII 3′ region
An et al. (1989) Plant 




Cell 1:115-122


Maintenance in 
ColE1 origin 



E. coli
of replication




F1 origin of 




replication




Bla ampicillin 




resistance









A similar plasmid vector, pMON72472, is constructed for use in Agrobacterium-mediated methods of plant transformation. pMON72472 comprises the gene of interest plant expression cassette, GATEWAYTM cloning, and plant selectable marker expression cassettes present in pMON65154. In addition, left and right T-DNA border sequences from Agrobacterium are added to the plasmid (Zambryski et al. (1982)). The right border sequence is located 5′ to the rice actin 1 promoter and the left border sequence is located 3′ to the pinII 3′ sequence situated 3′ to the nptII gene. Furthermore, pMON72472 comprises a plasmid backbone to facilitate replication of the plasmid in both E. coli and Agrobacterium tumefaciens. The backbone has an oriV wide host range origin of DNA replication functional in Agrobacterium, a pBR322 origin of replication functional in E. coli, and a spectinomycin/streptomycin resistance gene for selection in both E. coli and Agrobacterium. 
Vectors similar to those described above may be constructed for use in Agrobacterium or microprojectile bombardment maize transformation systems where the rice actin 1 promoter in the plant expression cassette portion is replaced with other desirable promoters including, but not limited to a corn globulin 1 promoter, a maize oleosin promoter, a glutelin 1 promoter, an aldolase promoter, a zein Z27 promoter, a pyruvate orthophosphate dikinase (PPDK) promoter, a soybean 7S alpha promoter, a peroxiredoxin antioxidant (Perl) promoter and a CaMV 35S promoter. Protein coding segments are amplified by PCR prior to insertion into vectors such as described above. Primers for PCR amplification can be 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. For GATEWAY cloning methods, PCR products are tailed with attB1 and attB2 sequences, purified then recombined into a destination vectors to produce an expression vector for use in transformation.
An alternative base transformation vector specifically useful for inserting a recombinant DNA construct into a chromosome in a nucleus in a corn plant cell by Agrobacterium-mediated transformation is pMON93039 which has the DNA in the nucleotide sequence of SEQ ID NO:27374 and the elements described in Table 4 and illustrated in FIG. 2.










TABLE 4








Coordinates 





of SEQ ID 


Function 
Name
Annotation
NO: 27374







Agrobacterium
B-AGRtu.right border
Agro right border sequence,
11364-11720


T-DNA transfer

essential for transfer of T-DNA.



Gene of interest
E-Os.Act1
Upstream promoter region of the
  19-775


expression

rice actin 1 gene



cassette
E-CaM V.35S.2xA1-
Duplicated35S A1-B3 domain
 788-1120 



B3
without TATA box




P-Os.Act1
Promoter region of the rice actin 1
 1125-1204




gene




L-Ta.Lhcb1
5′ untranslated leader of wheat
 1210-1270




major chlorophyll a/b binding





protein




I-Os.Act1
First intron and flanking UTR exon
 1287-1766




sequences from the rice actin 1





gene




T-St.Pis4
3′ non-translated region of the
 1838-2780




potato proteinase inhibitor II gene





which functions to direct





polyadenylation of the mRNA



Plant selectable
P-Os.Act1
Promoter from the rice actin 1 gene
 2830-3670


marker
L-Os.Act1
First exon of the rice actin 1 gene
 3671-3750


expression
I-Os.Act1
First intron and flanking UTR exon
 3751-4228


cassette

sequences from the rice actin 1





gene




TS-At.ShkG-CTP2
Transit peptide region of
 4238-4465




Arabidopsis EPSPS




CR-AGRtu.aroA-
Coding region for bacterial strain
 4466-5833



CP4.nat
CP4 native aroA gene.




T-AGRtu.nos
A 3′ non-translated region of the
 5849-6101




nopaline synthase gene of





Agrobacterium tumefaciens Ti





plasmid which functions to direct





polyadenylation of the mRNA.



Agrobacterium
B-AGRtu.left border.
Agro left border sequence, essential
 6168-6609


T-DNA transfer

for transfer of T-DNA.



Maintenance in
OR-Ec.oriV-RK2
The vegetative origin of replication
 6696-7092


E. coli

from plasmid RK2.




CR-Ec.rop
Coding region for repressor of
 8601-8792




primer from the ColE1 plasmid.





Expression of this gene product





interferes with primer binding at the





origin of replication, keeping





plasmid copy number low.




OR-Ec.ori-ColE1
The minimal origin of replication
 9220-9808




from the E. coli plasmid ColE1.




P-Ec.aadA-SPC/STR
Promoter for Tn7
10339-10380




adenylyltransferase (AAD(3′′))




CR-Ec.aadA-
Coding region for Tn7
10381-11169



SPC/STR
adenylyltransferase (AAD(3′′))





conferring spectinomycin and





streptomycin resistance.




T-Ec.aadA-SPC/STR
3′ UTR from the Tn7
11170-11227




adenylyltransferase (AAD(3′′))





gene of E. coli.









An alternative base transformation vector specifically useful for inserting a recombinant DNA construct into a chromosome in a nucleus in a dicot plant cell, e.g. soybean or oilseed rape, by Agrobacterium-mediated transformation is pMON82053 which has the DNA in the nucleotide sequence of SEQ ID NO:27375 and the elements described in Table 5 and illustrated in FIG. 3.










TABLE 5








Coordinates 





of SEQ ID 


Function
Name
Annotation
NO: 27375







Agrobacterium T-
B-AGRtu.left 
Agro left border sequence, essential for
6144-6585


DNA transfer
border
transfer of T-DNA.



Plant selectable
P-At.Act7
Promoter from the Arabidopsis actin 7 gene
6624-7861


marker expression
L-At.Act7
5′UTR of Arabidopsis Act7 gene



cassette
I-At.Act7
Intron from the Arabidopsis actin7 gene




TS-At.ShkG-
Transit peptide region of Arabidopsis
7864-8091



CTP2
EPSPS




CR-AGRtu.aroA-
Synthetic CP4 coding region with dicot
8092-9459



CP4.nno_At
preferred codon usage.




T-AGRtu.nos
A 3′ non-translated region of the nopaline
9466-9718




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



expression cassette

containing a duplication of the −90 to −350
  1-613




region.




T-Gb.E6-3b
3′ untranslated region from the fiber protein
 688-1002 




E6 gene of sea-island cotton.



Agrobacterium T-
B-AGRtu.right
Agro right border sequence, essential for
1033-1389


DNA transfer
border
transfer of T-DNA.



Maintenance in 
OR-Ec.oriV-RK2
The vegetative origin of replication from
5661-6057


E. coli

plasmid RK2.




CR-Ec.rop
Coding region for repressor of primer from
3961-4152




the ColE1 plasmid. Expression of this gene





product interferes with primer binding at the





origin of replication, keeping plasmid copy





number low.




OR-Ec.ori-ColE1
The minimal origin of replication from the
2945-3533




E. coli plasmid ColE1.




P-Ec.aadA-
Promoter for Tn7 adenylyltransferase
2373-2414



SPC/STR
(AAD(3′′))




CR-Ec.aadA-
Coding region for Tn7 adenylyltransferase
1584-2372



SPC/STR
(AAD(3′′)) conferring spectinomycin and





streptomycin resistance.




T-Ec.aadA-
3' UTR from the Tn7 adenylyltransferase
1526-1583



SPC/STR
(AAD(3′′)) gene of E. coli.









An alternative base transformation vector specifically useful for inserting a recombinant DNA construct into a chromosome in a nucleus in a dicot plant cell, e.g. cotton, by Agrobacterium-mediated transformation is pMON99053 which has the DNA in the nucleotide sequence of SEQ ID NO:27376 and the elements described in Table 6 and illustrated in FIG. 4.










TABLE 6








Coordinates of





SEQ ID NO:


Function
Name
Annotation
27376







Agrobacterium T-
B-AGRtu.right border
Agro right border sequence, essential
11364-11720


DNA transfer

for transfer of T-DNA.


Gene of interest
Exp-CaMV.35S-
Enhanced version of the 35S RNA
7794-8497


expression
enh + Ph.DnaK
promoter from CaMV plus the


cassette

petunia hsp70 5′ untranslated region



T-Ps.RbcS2-E9
The 3′ non-translated region of the
 67-699




pea RbcS2 gene which functions to




direct polyadenylation of the mRNA.


Plant selectable
Exp-CaMV.35S
Promoter and 5′ untranslated region
 730-1053


marker

from the 35S RNA of CaMV


expression
CR-Ec.nptII-Tn5
Coding region for neomycin
1087-1881


cassette

phosphotransferase gene from




transposon Tn5 which confers




resistance to neomycin and




kanamycin.



T-AGRtu.nos
A 3′ non-translated region of the
1913-2165




nopaline synthase gene of




Agrobacterium tumefaciens Ti




plasmid which functions to direct




polyadenylation of the mRNA.


Agrobacterium T-
B-AGRtu.left border
Agro left border sequence, essential
2211-2652


DNA transfer

for transfer of T-DNA.


Maintenance in
OR-Ec.oriV-RK2
The vegetative origin of replication
2739-3135


E. coli

from plasmid RK2.



CR-Ec.rop
Coding region for repressor of primer
4644-4835




from the ColE1 plasmid. Expression




of this gene product interferes with




primer binding at the origin of




replication, keeping plasmid copy




number low.



OR-Ec.ori-ColE1
The minimal origin of replication
5263-5851




from the E. coli plasmid ColE1.



P-Ec.aadA-SPC/STR
Promoter for Tn7
6382-6423




adenylyltransferase (AAD(3′′))



CR-Ec.aadA-SPC/STR
Coding region for Tn7
6424-7212




adenylyltransferase (AAD(3′′))




conferring spectinomycin and




streptomycin resistance.



T-Ec.aadA-SPC/STR
3′ UTR from the Tn7
7213-7270




adenylyltransferase (AAD(3′′)) gene




of E. coli.









Primers for PCR amplification of protein coding nucleotides of recombinant DNA are designed at or near the start and stop codons of the coding sequence, in order to eliminate most of the 5′ and 3′ untranslated regions. Each recombinant DNA coding for a protein identified in Table 2 is amplified by PCR prior to insertion into the insertion site within the gene of interest expression cassette of one of the base transformation vectors.
Example 2
Corn Transformation
This example illustrates transformation methods useful in introducing recombinant DNA into corn chromosomes to produce the transgenic nuclei, plant cells, plants and pollen and the production and identification of transgenic corn plants and seed with an enhanced trait, i.e. enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. Plasmid vectors were prepared by cloning DNA identified in Table 1 and inserting the cloned DNA into a base transformation vector.
In Agrobacterium-mediated transformation corn embryo cells from a corn line that is readily transformable (e.g. corn line designated LH59) are grown in a greenhouse to produce ears that are harvested when the embryos are 1.5 to 2.0 mm in length. The ears are surface sterilized by spraying or soaking 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.
For transformation by microprojectile bombardment maize immature embryos are isolated and cultured 3-4 days prior to bombardment. Prior to microprojectile bombardment, a suspension of gold particles is prepared onto which the desired recombinant DNA expression cassettes are precipitated. DNA is introduced into maize cells as described in U.S. Pat. Nos. 5,550,318 and 6,399,861 using the electric discharge particle acceleration gene delivery device. Following microprojectile bombardment, tissue is cultured in the dark at 27° C. Additional transformation methods and materials for making transgenic plants of this invention, for example, various media and recipient target cells, transformation of immature embryos and subsequence regeneration of fertile transgenic plants are disclosed in U.S. Pat. Nos. 6,194,636 and 6,232,526 and U.S. patent application Ser. No. 09/757,089, which are incorporated herein by reference.
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 1, e.g. with DNA having the nucleotide sequence of SEQ ID NO:1-614. 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 reported in Example 7.
Example 3
Soybean Transformation
This example illustrates transformation methods useful in introducing recombinant DNA into soybean chromosomes to produce the transgenic nuclei, plant cells, plants and pollen and the production and identification of transgenic soybean plants and seed with an enhanced trait, i.e. enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. Plasmid vectors were prepared by cloning DNA identified in Table 1 and inserting the cloned DNA into a base transformation vector.
For Agrobacterium-mediated transformation, soybean seeds are imbibed 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. Following wounding, 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. Shoots that remain healthy on selection, but do not produce roots are transferred to non-selective rooting media for an additional two weeks. Roots from any shoots that produce roots off selection are tested for expression of the plant selectable marker before they are transferred to the greenhouse and potted in soil. Additionally, 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, i.e. with DNA having the nucleotide sequence of SEQ ID NO: 1-614. 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 reported in Example 7.
Example 4
Cotton Transgenic Plants with Enhanced Agronomic Traits
This example illustrates transformation methods useful in introducing recombinant DNA into cotton chromosomes to produce the transgenic nuclei, plant cells, plants and pollen and the production and identification of transgenic cotton plants and seed with an enhanced trait, i.e. enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. Plasmid vectors were prepared by cloning DNA identified in Table 1 and inserting the cloned DNA into a base transformation vector.
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: 614 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. Additionally, a commercial cotton cultivar adapted to the geographical region and cultivation conditions, i.e. cotton variety ST474, cotton variety FM 958, and cotton variety Siokra L-23, are used to compare the relative performance of the transgenic cotton plants containing the recombinant DNA. The specified culture conditions are growing a first set of transgenic and control plants under “wet” conditions, i.e. 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, i.e. irrigated in the range of 40 to 60 percent of evapotranspiration to provide a leaf water potential of −21 to −25 bars. Pest control, such as weed and insect control is applied equally to both wet and dry treatments as needed. Data gathered during the trial includes weather records throughout the growing season including detailed records of rainfall; soil characterization information; any herbicide or insecticide applications; any gross agronomic differences observed such as leaf morphology, branching habit, leaf color, time to flowering, and fruiting pattern; plant height at various points during the trial; stand density; node and fruit number including node above white flower and node above crack boll measurements; and visual wilt scoring. Cotton boll samples are taken and analyzed for lint fraction and fiber quality. The cotton is harvested at the normal harvest timeframe for the trial area. Enhanced water use efficiency is indicated by increased yield, improved relative water content, enhanced leaf water potential, increased biomass, enhanced leaf extension rates, and improved fiber parameters.
The transgenic cotton plants of this invention are identified from among the transgenic cotton plants by agronomic trait screening as having increased yield and enhanced water use efficiency.
Example 5
Oilseed Rape Transformation
This example illustrates transformation methods useful in introducing recombinant DNA into oilseed-rape (canola) chromosomes to produce the transgenic nuclei, plant cells, plants and pollen and the production and identification of transgenic canola plants and seed with an enhanced trait, i.e. enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
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 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 as reported in Example 7.
Example 6
Homolog Identification
This example illustrates the identification of homologs of proteins encoded by the DNA identified in Table 2 which is used to provide transgenic seed and plants having enhanced agronomic traits. From the sequence of the homologs, homologous DNA sequence can be identified for preparing additional transgenic seeds and plants of this invention with enhanced agronomic traits.
An “All Protein Database” was constructed of known protein sequences using a proprietary sequence database and the National Center for Biotechnology Information (NCBI) non-redundant amino acid database (nr.aa). For each organism from which a polynucleotide sequence provided herein was obtained, an “Organism Protein Database”.was constructed of known protein sequences of the organism; it is a subset of the All Protein Database based on the NCBI taxonomy ID for the organism.
The All Protein Database was queried using amino acid sequences provided herein as SEQ ID NO: 615 through SEQ ID NO: 1228 using NCBI “blastp” program with E-value cutoff of 1e-8. Up to 1000 top hits were kept, and separated by organism names. For each organism other than that of the query sequence, a list was kept for hits from the query organism itself with a more significant E-value than the best hit of the organism. The list contains likely duplicated genes of the polynucleotides provided herein, and is referred to as the Core List. Another list was kept for all the hits from each organism, sorted by E-value, and referred to as the Hit List.
The Organism Protein Database was queried using polypeptide sequences provided herein as SEQ ID NO: 615 through SEQ ID NO: 1228 using NCBI “blastp” program with E-value cutoff of 1e-4. Up to 1000 top hits were kept. A BLAST searchable database was constructed based on these hits, and is referred to as “SubDB”. SubDB was queried with each sequence in the Hit List using NCBI “blastp” program with E-value cutoff of 1e-8. The hit with the best E-value was compared with the Core List from the corresponding organism. The hit is deemed a likely ortholog if it belongs to the Core List, otherwise it is deemed not a likely ortholog and there is no further search of sequences in the Hit List for the same organism. Homologs from a large number of distinct organisms were identified and are reported by amino acid sequences of SEQ ID NO: 1229 through SEQ ID NO: 27373. These relationships of proteins of SEQ ID NO: 615 through 1228 and homologs of SEQ ID NO: 1229 through 27373 are identified in Table 7. The source organism for each homolog is found in the Sequence Listing.
Example 7
Selection of Transgenic Plants with Enhanced Agronomic Trait(s)
This example illustrates identification of plant cells of the invention by screening derived plants and seeds for enhanced trait. Transgenic corn, soybean, cotton and canola seeds and plants with recombinant DNA from each of the genes identified in Table 2 are prepared using plant cells transformed with DNA that is stably integrated into a chromosome of the nuclei in a plant cell. 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.
A. Selection for Enhanced Nitrogen Use Efficiency
The physiological efficacy of transgenic plants, e.g. transgenic corn plants (tested as hybrids), can be tested for nitrogen use efficiency (NUE) traits in a high-throughput nitrogen (N) selection method compared to the measurements from testing of control plants.
Plants are allowed to grow for 28 days in a low nitrogen nutrient environment or for 23 days in a high nitrogen nutrient environment. The nitrogen nutrients are dispensed in the form of a macronutrient solution (see composition below) containing different amounts of nitrogen nutrient (2 mM NH4NO3 for a low nitrogen environment or 20 mM NH4NO3 for a high nitrogen environment). Pots with corn plants a provided with 100 ml of nutrient solution three times a week on alternate days starting at eight days after planting for low nitrogen and ten days after planting for high nitrogen. Matting under the pots should be changed as needed to avoid nitrogen accumulation and buildup of root matter. Table 8 shows the amount of nutrients in the low and high nitrogen solutions.











TABLE 8








2 mM NH4NO3
20 mM NH4NO3



Nutrient Stock
solution (mL/L)
solution (mL/L)




















1M NH4NO3
2
20



1M KH2PO4
0.5
0.5



1M MgSO4•7H2O
2
2



1M CaCl2
2.5
2.5



1M K2SO4
1
1







pH adjusted to 5.6 with HCl or KOH






After 28 days of plant growth under low nitrogen and 23 days of plant growth under high nitrogen, the following variables are measured: total shoot fresh mass (SFM) in grams (g), V6 leaf chlorophyll (LC) measured by Minolta SPAD meter in “relative units”, V6 leaf area (LA) measured in square centimeters (cm2), V6 leaf fresh mass (LFM) measured in grams and V6 leaf dry mass (LDM) measured in grams. Leaf fresh mass is measure on leaves that have been dried in a forced air oven at 80° C. for 3 days. From the collected data, two derived measurements are made: (1) Leaf chlorophyll area (LCA), which is a product of V6 relative chlorophyll content and its leaf area (relative units), indicates the spread of chlorophyll over the entire leaf area; and (2) specific leaf area (LSA), which is the ratio of V6 leaf area to its dry mass (cm2/g dry mass), serves as an indicator of nitrogen use efficiency (NUE).
A list of recombinant DNA constructs which improved growth in high nitrogen environments in transgenic plants is reported in Table 9.











TABLE 9









Confirmed





Positive
events/Actual





events/Total
events with


NUC


events
confirmation


SEQ ID
PHE ID
Construct
screened
attempted



















3
PHE0000004
PMON67819
2/2
2/2


4
PHE0000005
PMON67820
2/2
2/2


9
PHE0000080
PMON68366
1/1
0/0


22
PHE0000372
PMON72460
2/4
1/1


43
PHE0000459
PMON68390
2/2
0/0


44
PHE0000460
PMON73751
3/3
2/2


66
PHE0000492
PMON69490
3/3
2/3


67
PHE0000493
PMON68403
2/5
0/0


72
PHE0000498
PMON76305
5/5
0/5


74
PHE0000500
PMON69495
1/4
0/0


124
PHE0000551
PMON74450
1/2
0/0


137
PHE0000564
PMON68619
6/7
0/2


165
PHE0000592
PMON68639
4/4
2/4


166
PHE0000593
PMON68634
5/5
1/5


220
PHE0000655
PMON68607
5/7
1/5


227
PHE0000664
PMON69471
4/4
3/4


229
PHE0000666
PMON68398
6/9
2/9


285
PHE0000799
PMON75317
1/4
0/0


293
PHE0000807
PMON76309
1/3
0/0


295
PHE0000809
PMON76311
3/8
0/0


296
PHE0000810
PMON75319
1/2
0/0


339
PHE0000854
PMON73795
1/1
0/0


340
PHE0000855
PMON75347
1/2
0/0


347
PHE0000862
PMON75335
2/2
0/0


348
PHE0000863
PMON75349
1/2
0/0


354
PHE0000869
PMON75339
1/2
0/0


476
PHE0000995
PMON77871
1/3
0/0


487
PHE0001006
PMON73814
1/1
0/0


508
PHE0001028
PMON73823
1/1
0/0


560
PHE0001401
PMON84122
7/9
0/0


587
PHE0001546
PMON79717
2/5
0/0


589
PHE0001548
PMON75547
2/6
0/0









A list of recombinant DNA constructs which improved growth in a low (limiting) nitrogen environment in transgenic plants is reported in Table 10.











TABLE 10









Confirmed





Positive
events/Actual





events/Total
events with


NUC SEQ


events
confirmation


ID
PHE ID
Construct
screened
attempted



















1
PHE0000002
PMON80861
3/4
2/4


3
PHE0000004
PMON67819
2/3
0/3


4
PHE0000005
PMON67820
3/7
0/4


9
PHE0000080
PMON68366
2/3
0/2


13
PHE0000113
PMON68365
1/3
0/0


14
PHE0000140
PMON73157
1/1
0/0


22
PHE0000372
PMON72460
3/8
1/5


25
PHE0000375
PMON73153
1/2
0/1


28
PHE0000378
PMON72461
1/2
0/0


30
PHE0000381
PMON72469
1/1
0/0


32
PHE0000384
PMON68621
2/3
1/3


43
PHE0000459
PMON68390
3/5
0/5


44
PHE0000460
PMON73751
4/6
2/3


45
PHE0000461
PMON67829
2/2
2/2


56
PHE0000479
PMON68402
4/8
0/0


58
PHE0000481
PMON75472
5/7
2/7


61
PHE0000487
PMON80267
2/3
0/0


62
PHE0000488
PMON75473
3/5
0/5


65
PHE0000491
PMON72489
1/2
0/2


66
PHE0000492
PMON69490
3/3
0/3


67
PHE0000493
PMON68403
3/5
1/5


68
PHE0000494
PMON75459
1/1
0/1


72
PHE0000498
PMON76305
4/5
2/5


74
PHE0000500
PMON69495
3/5
1/4


77
PHE0000503
PMON69493
1/5
0/0


81
PHE0000507
PMON69492
4/2
0/0


90
PHE0000516
PMON72492
1/2
0/0


91
PHE0000517
PMON72493
1/2
0/1


96
PHE0000523
PMON69487
1/2
0/0


102
PHE0000529
PMON69482
1/4
1/1


106
PHE0000533
PMON84135
1/7
0/0


113
PHE0000540
PMON75451
1/4
0/0


116
PHE0000543
PMON69499
1/4
0/0


124
PHE0000551
PMON74450
2/2
0/2


125
PHE0000552
PMON75460
1/2
1/2


131
PHE0000558
PMON68637
1/3
0/0


132
PHE0000559
PMON74431
2/3
0/0


134
PHE0000561
PMON68620
4/7
1/7


134
PHE0000561
PMON68620
4/7
1/7


135
PHE0000562
PMON75303
3/9
0/0


137
PHE0000564
PMON68619
3/3
1/3


139
PHE0000566
PMON75304
5/6
0/0


144
PHE0000571
PMON69484
3/4
0/0


151
PHE0000578
PMON69485
2/6
0/0


153
PHE0000580
PMON68611
1/4
0/0


157
PHE0000584
PMON68610
1/2
1/2


165
PHE0000592
PMON68639
2/4
2/4


166
PHE0000593
PMON68634
5/5
5/5


171
PHE0000604
PMON68625
2/3
0/0


178
PHE0000611
PMON68405
2/3
0/0


190
PHE0000623
PMON74438
2/7
0/0


196
PHE0000629
PMON68631
3/5
0/0


197
PHE0000630
PMON68648
2/3
0/0


198
PHE0000631
PMON75454
1/3
0/0


206
PHE0000639
PMON75457
3/5
2/5


216
PHE0000649
PMON78901
1/3
0/0


219
PHE0000654
PMON68605
1/6
1/1


220
PHE0000655
PMON84121
11/18
 2/15


221
PHE0000656
PMON80923
 6/17
2/8


227
PHE0000664
PMON69471
4/4
3/4


228
PHE0000665
PMON84120
 5/13
0/0


229
PHE0000666
PMON68398
7/9
4/7


233
PHE0000703
PMON75517
1/1
0/0


234
PHE0000704
PMON76315
1/4
0/0


238
PHE0000710
PMON84772
1/2
0/0


259
PHE0000748
PMON75479
5/9
4/9


260
PHE0000749
PMON84133
 1/12
0/0


268
PHE0000762
PMON75464
1/1
1/1


285
PHE0000799
PMON75317
4/4
2/4


293
PHE0000807
PMON76309
3/3
3/3


295
PHE0000809
PMON76311
7/8
2/8


296
PHE0000810
PMON75319
2/2
0/2


334
PHE0000849
PMON82608
1/4
1/1


339
PHE0000854
PMON73795
1/3
1/1


340
PHE0000855
PMON75347
2/4
2/2


342
PHE0000857
PMON75348
2/5
2/5


344
PHE0000859
PMON73798
1/8
0/0


347
PHE0000862
PMON75335
2/2
1/2


348
PHE0000863
PMON75349
2/5
0/2


350
PHE0000865
PMON75336
1/5
0/1


351
PHE0000866
PMON84970
 2/10
0/0


354
PHE0000869
PMON75339
1/2
0/0


366
PHE0000885
PMON77853
3/3
0/3


378
PHE0000897
PMON73833
4/5
3/4


384
PHE0000903
PMON77865
1/4
0/0


390
PHE0000909
PMON73845
1/3
1/2


391
PHE0000910
PMON73846
1/3
0/0


394
PHE0000913
PMON78201
2/3
2/3


400
PHE0000919
PMON73848
1/2
0/0


406
PHE0000925
PMON73835
1
0/0


421
PHE0000940
PMON76317
1/1
0/1


425
PHE0000944
PMON76319
1/3
1/2


428
PHE0000947
PMON75493
1/1
1/1


434
PHE0000953
PMON76322
1/2
0/0


436
PHE0000955
PMON76324
1/1
0/0


445
PHE0000964
PMON77867
2/3
0/0


465
PHE0000984
PMON73809
1/2
0/0


470
PHE0000989
PMON80515
2/7
0/7


471
PHE0000990
PMON77858
6/9
2/9


476
PHE0000995
PMON77871
3/8
0/3


487
PHE0001006
PMON73814
1/2
1/2


488
PHE0001007
PMON84742
2/4
0/0


499
PHE0001019
PMON73817
1/3
0/0


508
PHE0001028
PMON73823
2/5
2/2


523
PHE0001043
PMON77881
1/2
1/2


524
PHE0001044
PMON77876
1/3
0/0


525
PHE0001045
PMON77872
2/7
0/7


528
PHE0001048
PMON80862
1/2
1/2


540
PHE0001173
PMON80469
 6/11
0/1


548
PHE0001194
PMON78918
1/5
0/0


550
PHE0001234
PMON82646
2/6
0/0


554
PHE0001276
PMON79652
2/2
1/2


560
PHE0001401
PMON84122
6/6
5/6


561
PHE0001423
PMON79672
2/7
0/0


575
PHE0001503
PMON84706
1/8
0/4


577
PHE0001505
PMON75536
2/2
0/2


578
PHE0001506
PMON75537
1
0/0


581
PHE0001509
PMON75540
1/3
0/0


587
PHE0001546
PMON79717
3/6
1/6


588
PHE0001547
PMON79184
1/3
0/2


589
PHE0001548
PMON75547
6/6
2/6


600
PHE0001583
PMON84780
6/7
0/0


608
PHE0001609
PMON84709
7/7
1/7


611
PHE0002019
PMON84744
1/3
0/0


612
PHE0002020
PMON84769
9/9
5/9


613
PHE0002021
PMON80309
1/4
1/1


614
PHE0002022
PMON84753
2/3
0/0









Nitrogen Use Efficacy Field Assay

Transgenic plants of this invention and control plants are planted in field without any supplemental nitrogen being applied. Nitrogen levels in the fields are analyzed in early April pre-planting, e.g. by collecting 30 sample soil cores from 0-24′′ and 24 to 48′′ soil layer and analyzing for nitrate-nitrogen, phosphorus (P), potassium (K), organic matter and pH. P, K and micronutrients are applied based upon soil test recommendations. Recombinant DNA constructs which improved growth without any nitrogen source in transgenic plants is reported in Table 11.











TABLE 11








Positive
Confirmed


NUC


events/Total
events/Actual events


SEQ


events
with confirmation


ID
PHE ID
Construct
screened
attempted







166
PHE0000593
PMON68634
1/3
0/3


302
PHE0000816
PMON93867
2/3
0/0


560
PHE0001401
PMON84122
3/9
0/0


561
PHE0001423
PMON79672
1/5
0/0


608
PHE0001609
PMON84709
1/3
0/0


612
PHE0002020
PMON84769
2/9
0/0


614
PHE0002022
PMON84753
1/3
0/0









B. Selection for Increased Yield

Many transgenic plants with recombinant DNA of this invention in a chromosome in the nucleus of their cells exhibit improved yield as compared to a control plant. Recombinant DNA constructs which show improved yield or enhancement in a surrogate indicators for yield in transgenic corn plants is reported in Table 12. Useful surrogate indicators for yield include source capacity (biomass), source output (sucrose and photosynthesis), sink components (kernel size, ear size, starch in the seed), development (light response, height, density tolerance), maturity, early flowering trait and physiological responses to high density planting, e.g., at 45,000 plants per acre.











TABLE 12








Positive
Confirmed





events/Total
events/Actual events


NUC


events
with confirmation


SEQ ID
PHE ID
Construct
screened
attempted



















3
PHE0000004
PMON67819
1/7
0/3


4
PHE0000005
PMON67820
 1/11
0/6


4
PHE0000005
PMON73601
1/2
0/1


8
PHE0000078
PMON77877
1/4
0/3


9
PHE0000080
PMON68366
1/3
0/2


22
PHE0000372
PMON72460
2/7
0/3


26
PHE0000376
PMON73154
1/3
0/1


43
PHE0000459
PMON68390
1/5
0/4


61
PHE0000487
PMON80267
1/4
0/4


66
PHE0000492
PMON69490
1/3
0/3


69
PHE0000495
PMON73763
1/3
0/1


91
PHE0000517
PMON72493
3/4
0/2


106
PHE0000533
PMON84135
1/6
0/0


108
PHE0000535
PMON68615
1/5
1/2


109
PHE0000536
PMON74447
1/7
0/1


138
PHE0000565
PMON69483
1/3
0/2


166
PHE0000593
PMON68634
1/5
0/3


178
PHE0000611
PMON68405
2/3
0/3


181
PHE0000614
PMON68632
1/8
0/3


190
PHE0000623
PMON74438
2/7
1/5


196
PHE0000629
PMON68631
1/5
0/1


219
PHE0000654
PMON68605
1/6
0/4


220
PHE0000655
PMON68607
 1/12
1/8


221
PHE0000656
PMON80923
 1/11
0/0


227
PHE0000664
PMON69471
1/4
0/3


237
PHE0000709
PMON68643
1/6
0/1


240
PHE0000712
PMON73753
1/7
0/3


242
PHE0000714
PMON68642
2/6
1/4


246
PHE0000735
PMON75481
1/3
0/2


254
PHE0000743
PMON71005
3/4
0/0


254
PHE0000743
PMON81215
1/9
0/6


259
PHE0000748
PMON75479
1/9
0/6


262
PHE0000751
PMON75321
1/4
0/3


296
PHE0000810
PMON75319
1/1
0/1


314
PHE0000829
PMON73800
1/1
0/1


352
PHE0000867
PMON75337
1/2
0/2


355
PHE0000870
PMON75340
1/1
0/1


425
PHE0000944
PMON76319
2/3
1/2


465
PHE0000984
PMON73809
1/2
0/2


467
PHE0000986
PMON80929
2/4
0/2


527
PHE0001047
PMON75318
1/6
0/1


548
PHE0001194
PMON78918
1/5
0/2


550
PHE0001234
PMON82646
1/6
0/0


574
PHE0001502
PMON80908
1/2
0/1


589
PHE0001548
PMON75547
1/6
0/4









C. Selection for Enhanced Water Use Efficiency (WUE)

Water use efficiency can be evaluated by high-throughput methods in greenhouse screening of potted corn plants. This selection process imposes 3 drought/re-water cycles on plants over a total period of 15 days after an initial stress free growth period of 11 days. Each cycle consists of 5 days, with no water being applied for the first four days and water quenching on the 5th day of the cycle. The primary phenotypes analyzed by the selection method are the changes in plant growth rate as determined by height and biomass during a vegetative drought treatment. The hydration status of the shoot tissues following the drought is also measured. The plant height are measured at three time points. The first is taken just prior to the onset drought when the plant is 11 days old, which is the shoot initial height (SIH). The plant height is also measured halfway throughout the drought/re-water regimen, on day 18 after planting, to give rise to the shoot mid-drought height (SMH). Upon the completion of the final drought cycle on day 26 after planting, the shoot portion of the plant is harvested and measured for a final height, which is the shoot wilt height (SWH) and also measured for shoot wilted biomass (SWM). The shoot is placed in water at 40 degrees Celsius in the dark. Three days later, the shoot is weighted to give rise to the shoot turgid weight (STM). After drying in an oven for four days, the shoots are weighted for shoot dry biomass (SDM). The shoot average height (SAH) is the mean plant height across the 3 height measurements.
To correct for slight differences between plants, a size corrected growth value is derived from SIH and SWH. This is the Relative Growth Rate (RGR). Relative Growth Rate (RGR) is calculated for each shoot using the formula [RGR %=(SWH−SIH)/((SWH+SIH)/2)*100]. Relative water content (RWC) is a measurement of how much (%) of the plant was water at harvest. Water Content (RWC) is calculated for each shoot using the formula [RWC %=(SWM−SDM)/(STM−SDM)*100]. Fully watered corn plants of this age run around 98% RWC. Transgenic plants with recombinant DNA constructs which provide improved water use efficiency in transgenic corn plants are reported in Table 15.











TABLE 15








Positive
Confirmed events/





events/Total
Actual events


NUC


events
with confirmation


SEQ ID
PHE ID
Construct
screened
attempted



















3
PHE0000004
PMON67819
3/7
2/4


3
PHE0000004
PMON82452
 6/11
0/0


4
PHE0000004
PMON67820
 4/11
 2/11


8
PHE0000078
PMON77877
1/1
0/0


9
PHE0000080
PMON68366
2/3
2/3


10
PHE0000081
PMON67814
3/6
3/6


13
PHE0000113
PMON68365
2/3
0/3


15
PHE0000151
PMON67822
2/4
0/2


21
PHE0000367
PMON72500
1/1
0/1


22
PHE0000372
PMON72460
5/8
0/7


23
PHE0000373
PMON73151
1/2
1/2


27
PHE0000377
PMON73155
1/1
0/1


29
PHE0000379
PMON72457
3/3
0/2


30
PHE0000381
PMON72469
1/4
0/4


34
PHE0000406
PMON67841
1/1
0/0


43
PHE0000459
PMON68390
2/5
0/5


44
PHE0000460
PMON73751
2/5
0/3


45
PHE0000461
PMON67829
2/2
1/2


54
PHE0000477
PMON68401
2/4
0/0


58
PHE0000481
PMON75472
1/7
0/0


62
PHE0000488
PMON75473
2/6
0/0


63
PHE0000489
PMON74432
1/5
0/5


72
PHE0000498
PMON76305
3/5
0/0


76
PHE0000502
PMON75474
2/9
0/0


81
PHE0000507
PMON69492
1/4
0/0


84
PHE0000510
PMON72491
2/2
0/2


86
PHE0000512
PMON74444
3/9
0/2


91
PHE0000517
PMON72493
1/4
0/3


108
PHE0000535
PMON68615
2/5
0/0


109
PHE0000536
PMON74447
2/5
0/0


124
PHE0000551
PMON74450
1/2
0/2


125
PHE0000552
PMON75460
1/2
0/2


132
PHE0000559
PMON74431
2/4
0/2


135
PHE0000562
PMON75303
7/9
0/0


137
PHE0000564
PMON68619
2/3
0/0


138
PHE0000565
PMON69483
1/3
0/0


139
PHE0000566
PMON75304
6/7
0/0


152
PHE0000579
PMON68623
1/4
0/1


155
PHE0000582
PMON75476
1/4
0/0


165
PHE0000592
PMON68639
1/4
0/4


166
PHE0000593
PMON68634
1/5
0/5


170
PHE0000603
PMON68626
1/6
0/0


177
PHE0000610
PMON75494
1/4
0/0


186
PHE0000619
PMON74435
2/3
0/3


188
PHE0000621
PMON75482
2/3
0/0


190
PHE0000623
PMON74438
2/7
0/0


212
PHE0000645
PMON68640
2/4
0/0


220
PHE0000655
PMON68607
 4/13
0/6


221
PHE0000656
PMON80923
2/9
0/0


229
PHE0000666
PMON68398
 2/10
0/0


234
PHE0000704
PMON76315
2/4
0/0


237
PHE0000709
PMON68643
4/6
1/6


240
PHE0000712
PMON73753
1/7
0/0


242
PHE0000714
PMON68642
1/6
0/0


243
PHE0000715
PMON68641
1/5
0/0


246
PHE0000735
PMON75481
1/3
0/0


252
PHE0000741
PMON80930
2/8
0/0


253
PHE0000742
PMON75478
2/2
0/2


254
PHE0000743
PMON81215
2/9
0/5


256
PHE0000745
PMON73776
2/4
0/0


259
PHE0000748
PMON75479
2/8
0/0


262
PHE0000751
PMON75321
1/4
0/0


268
PHE0000762
PMON75464
1/1
0/1


270
PHE0000764
PMON75465
3/4
0/0


278
PHE0000772
PMON75468
1/3
0/0


281
PHE0000779
PMON76307
1/4
0/0


285
PHE0000799
PMON75317
3/4
0/0


295
PHE0000809
PMON76311
1/7
0/0


313
PHE0000828
PMON75327
1/3
0/0


320
PHE0000835
PMON75344
2/7
0/0


330
PHE0000845
PMON76313
1/3
0/0


339
PHE0000854
PMON73795
1/4
0/2


340
PHE0000855
PMON75347
2/4
0/0


342
PHE0000857
PMON75348
2/6
0/4


348
PHE0000863
PMON75349
2/5
0/0


350
PHE0000865
PMON75336
1/5
0/0


352
PHE0000867
PMON75337
1/2
0/0


354
PHE0000869
PMON75339
1/2
0/0


356
PHE0000871
PMON75341
2/8
0/6


367
PHE0000886
PMON73804
1/2
1/1


369
PHE0000888
PMON73830
1/2
0/0


378
PHE0000897
PMON73833
2/5
0/0


394
PHE0000913
PMON78201
1/3
0/0


445
PHE0000964
PMON77867
2/3
0/0


454
PHE0000973
PMON73827
2/5
0/0


465
PHE0000984
PMON73809
1/2
0/1


476
PHE0000995
PMON77871
1/7
0/0


487
PHE0001006
PMON73814
1/2
0/0


499
PHE0001019
PMON73817
1/3
0/0


508
PHE0001028
PMON73823
2/5
0/0


524
PHE0001044
PMON77876
2/3
0/0


525
PHE0001045
PMON77872
1/7
0/0


527
PHE0001047
PMON75318
4/6
4/6


587
PHE0001546
PMON79717
1/6
0/0


589
PHE0001548
PMON75547
3/6
0/0


613
PHE0002021
PMON80309
1/5
0/0









D. Selection for Growth Under Cold Stress

Plants can be identified as having enhanced growth under cold stress by a cold germination assay using three sets of seeds. The first set consists of seeds that are F1 hybrids that are tested positive for the transgenic events and the recombinant DNA is expressed in the growing seed. The second set consists of control seeds, e.g. a nontransgenic, wild-type negative control made from the same genotype as the seeds in the first set. The third set consists of two cold tolerant and one cold sensitive commercial check lines of corn. All seeds are treated with a fungicide “Captan” (MAESTRO®80DF Fungicide, Arvesta Corporation, San Francisco, Calif., USA), e.g. 0.43 mL Captan is applied per 45 g of corn seeds by mixing it well and drying the fungicide prior to the assay.
Corn seeds are placed embryo side down in deionized water on blotter paper in a tray that is held at 9.7° C. for 24 days (no light) in a growth chamber. Germination counts are taken on days 10, 11, 12, 13, 14, 17, 19, 21, and 24. Seeds are considered germinated if the emerged radicle size is 1 cm. Tissue samples are collected at random on the last day of the experiment for confirmation of RNA expression. A germination index (GI) is calculated after the day 24 count using the formula:

GI=(Σ([T+1−n][Pi−Pi-1]))/T 

where “T” is the number of days for the experiment, i.e. 24; “n” is the number of days after start on which a count is made; “P” is the percentage of seed germinated during a count; and “i” represents a particular count. Statistical differences are calculated between positive and wild type control.

Events of transgenic plants that showed a statistical significance at the p level of less than 0.05 relative to wild-type controls for improved seed growth under cold stress are reported in Table 16.











TABLE 16









Confirmed





Positive
events/Actual





events/Total
events with


NUC


events
confirmation


SEQ ID
PHE ID
Construct
screened
attempted



















3
PHE0000004
PMON67819
1/5
1/1


4
PHE0000005
PMON67820
 7/11
3/9


9
PHE0000080
PMON68366
1/3
0/2


10
PHE0000081
PMON67814
1/6
0/4


13
PHE0000113
PMON68365
2/5
0/4


22
PHE0000372
PMON72460
5/8
2/7


25
PHE0000375
PMON73153
1/2
0/1


27
PHE0000377
PMON73155
1/1
0/1


28
PHE0000378
PMON72461
1/2
1/1


29
PHE0000379
PMON72457
3/4
2/3


30
PHE0000381
PMON72469
3/4
2/3


43
PHE0000459
PMON68390
3/5
2/5


56
PHE0000479
PMON68402
6/9
4/8


58
PHE0000481
PMON75472
1/7
0/1


62
PHE0000488
PMON75473
4/6
3/4


65
PHE0000491
PMON72489
2/2
0/2


68
PHE0000494
PMON75459
1/6
0/0


76
PHE0000502
PMON75474
4/9
1/4


77
PHE0000503
PMON69493
3/5
1/5


81
PHE0000507
PMON69492
3/4
2/3


84
PHE0000510
PMON72491
1/2
0/2


86
PHE0000512
PMON74444
2/7
2/5


91
PHE0000517
PMON72493
1/3
0/3


97
PHE0000524
PMON69491
1/1
1/1


98
PHE0000525
PMON75497
1/2
0/0


102
PHE0000529
PMON69482
3/3
3/3


108
PHE0000535
PMON68615
2/5
0/2


109
PHE0000536
PMON74447
1/5
0/1


116
PHE0000543
PMON69499
1/5
1/4


120
PHE0000547
PMON76304
4/4
0/4


124
PHE0000551
PMON74450
1/2
0/1


125
PHE0000552
PMON75460
1/2
0/0


131
PHE0000558
PMON68637
2/3
0/3


134
PHE0000561
PMON68620
6/7
5/7


138
PHE0000565
PMON69483
 6/10
 3/10


139
PHE0000566
PMON75304
1/7
0/0


146
PHE0000573
PMON68624
2/3
2/2


151
PHE0000578
PMON69485
4/4
4/4


152
PHE0000579
PMON68623
3/4
3/3


153
PHE0000580
PMON68611
5/5
4/5


156
PHE0000583
PMON80926
1/4
0/4


157
PHE0000584
PMON68610
1/3
0/3


166
PHE0000593
PMON68634
4/5
3/4


170
PHE0000603
PMON68626
1/6
0/0


171
PHE0000604
PMON68625
3/3
0/0


176
PHE0000609
PMON74443
1/3
0/0


178
PHE0000611
PMON68405
1/4
0/0


188
PHE0000621
PMON73769
1/4
0/0


193
PHE0000626
PMON68406
1/2
0/2


196
PHE0000629
PMON68631
1/5
0/0


197
PHE0000630
PMON68648
3/5
3/3


202
PHE0000635
PMON68407
1/1
1/1


206
PHE0000639
PMON75457
1/4
0/2


219
PHE0000654
PMON68605
4/6
1/4


220
PHE0000655
PMON68607
 2/12
 1/10


221
PHE0000656
PMON82689
4/8
2/7


221
PHE0000656
PMON84137
1/6
0/6


222
PHE0000658
PMON68606
2/2
2/2


225
PHE0000662
PMON80944
2/5
1/5


229
PHE0000666
PMON68398
 3/10
0/5


237
PHE0000709
PMON68643
1/6
0/0


242
PHE0000714
PMON68642
3/6
0/0


243
PHE0000715
PMON68641
1/4
0/1


252
PHE0000741
PMON80930
3/7
0/7


256
PHE0000745
PMON73776
1/2
0/1


258
PHE0000747
PMON75480
1/2
0/0


259
PHE0000748
PMON75479
3/9
2/4


264
PHE0000755
PMON92853
3/7
2/7


265
PHE0000756
PMON77884
1/1
0/0


268
PHE0000762
PMON75464
1/1
1/1


270
PHE0000764
PMON75465
1/4
1/2


272
PHE0000766
PMON75466
1/1
0/0


277
PHE0000771
PMON84798
1/3
0/0


295
PHE0000809
PMON76311
4/8
2/6


299
PHE0000813
PMON75530
1/1
0/0


307
PHE0000822
PMON73799
1/2
0/0


320
PHE0000835
PMON75344
1/7
0/0


338
PHE0000853
PMON77893
1/2
0/0


340
PHE0000855
PMON75347
1/4
0/0


348
PHE0000863
PMON75349
1/5
0/0


350
PHE0000865
PMON75336
1/1
0/0


351
PHE0000866
PMON84970
1/7
0/0


354
PHE0000869
PMON75339
1/2
0/0


356
PHE0000871
PMON75341
1/1
0/0


358
PHE0000873
PMON79671
1/2
0/0


363
PHE0000878
PMON77852
1/1
0/0


366
PHE0000885
PMON77853
3/3
0/3


373
PHE0000892
PMON77864
1/1
0/0


387
PHE0000906
PMON73842
1/1
0/0


390
PHE0000909
PMON73845
1/3
0/0


425
PHE0000944
PMON76319
1/3
0/0


454
PHE0000973
PMON73827
1/5
0/0


455
PHE0000974
PMON77855
1/1
0/0


457
PHE0000976
PMON78912
1/2
0/0


459
PHE0000978
PMON77856
1/2
0/0


460
PHE0000979
PMON73849
1/1
0/0


461
PHE0000980
PMON77869
1/3
0/0


475
PHE0000994
PMON77870
1/1
0/0


485
PHE0001004
PMON77860
1/1
0/0


488
PHE0001007
PMON84742
4/5
2/4


518
PHE0001038
PMON73839
1/2
0/0


527
PHE0001047
PMON75318
 2/13
 2/12


540
PHE0001173
PMON80469
 1/14
0/1


548
PHE0001194
PMON78918
4/5
1/5


561
PHE0001423
PMON79672
3/5
1/5


575
PHE0001503
PMON84706
5/7
5/7


577
PHE0001505
PMON75536
2/3
0/0


578
PHE0001506
PMON75537
1/1
0/0


587
PHE0001546
PMON79717
4/6
2/6


590
PHE0001549
PMON79185
1/1
0/0


598
PHE0001580
PMON79190
2/2
1/2


599
PHE0001581
PMON79191
1/4
0/1


600
PHE0001583
PMON84780
2/7
0/7


613
PHE0002021
PMON80309
3/5
0/4









Cold stress tolerance for corn plants of this invention is also determined by a field trial under early spring planting around two weeks prior to the time local farmers plant corn to identify recombinant DNA constructs that confer enhanced cold vigor at germination and early seedling growth under cold stress. The same seeds also are planted under local optimal planting conditions such that the crop has little or no exposure to cold condition (normal treatment). Early planting cold field trials were carried out at five locations, Glyndon Minn., Mason Mich., Monmouth Ill., Dayton Iowa and Mystic Conn. At each location seeds are planted under both early and local optimal planting times with 3 repetitions of 20 kernels in a single row in a plot. Seeds are planted 1.5 to 2 inch deep into soil to avoid muddy conditions. Two temperature monitors are set up at each location to monitor both air and soil temperature daily. Seed emergence is defined as the time when the growing shoot breaks the soil surface. The number of emerged seedling in each plot is counted daily from the day the earliest plot begins to emerge until no significant changes in emergence occur. Seedling vigor is also rated on a scale of 1 to 9 at the V3-V4 stage before the average of corn plant height reaches 10 inches, where 1 represents excellent early growth, 5 represents average growth and 9 represents poor growth. Days to 50% emergence, maximum percent emergence and seedling vigor are calculated. Corn plants having recombinant DNA constructs showing enhanced cold vigor at germination and early seedling growth under the early spring planting field conditions are reported in Table 17.











TABLE 17









Confirmed





Positive
events/Actual





events/Total
events with


NUC


events
confirmation


SEQ ID
PHE ID
Construct
screened
attempted



















56
PHE0000479
PMON68402
2/6
0/0


62
PHE0000488
PMON75473
2/3
0/0


77
PHE0000503
PMON69493
2/3
0/0


102
PHE0000529
PMON69482
2/3
0/0


134
PHE0000561
PMON68620
1/5
0/0


138
PHE0000565
PMON69483
2/2
0/0


152
PHE0000579
PMON68623
3/4
0/0


153
PHE0000580
PMON68611
4/5
0/0


197
PHE0000630
PMON68648
2/4
0/0


222
PHE0000658
PMON68606
1/2
0/0


259
PHE0000748
PMON75479
2/2
0/0


295
PHE0000809
PMON76311
1/3
0/0









E. Screens for Transgenic Plant Seeds with Increased Protein and/or Oil Levels

Transgenic plants with recombinant DNA producing seed with increased protein and/or oil content are determined by analyzing harvested seed. For example, near-infrared transmittance spectrometry is used to determine the composition of a bulk seed samples by analyzing for multiple traits in a single scan. Typical analysis parameters are provided in Table 18.








TABLE 18







Typical sample(s):
Whole grain corn and soybean seeds


Analytical time to run method:
Less than 0.75 min per sample


Total elapsed time per run:
1.5 minute per sample


Typical and minimum sample
Corn typical: 50 cc; minimum 30 cc


size:
Soybean typical: 50 cc; minimum 5 cc


Typical analytical range:
Determined in part by the specific



calibration.



Corn - moisture 5-15%, oil 5-20%,



protein 5-30%, starch 50-75%, and



density 1.0-1.3%.



Soybean - moisture 5-15%, oil 15-25%,



and protein 35-50%.









Transgenic plants with recombinant DNA constructs which improve seed compositions in terms of protein content are reported in Table 19.











TABLE 19









Confirmed





Positive
events/Actual





events/Total
events with


NUC


events
confirmation


SEQ ID
PHE ID
Construct
screened
attempted



















3
PHE0000004
PMON67819
1/7
0/0


4
PHE0000005
PMON67820
1/8
0/0


8
PHE0000078
PMON77877
1/4
0/1


10
PHE0000081
PMON67814
2/5
0/0


13
PHE0000113
PMON68365
3/5
3/4


18
PHE0000364
PMON77882
1/2
0/0


22
PHE0000372
PMON72460
1/2
2/4


23
PHE0000373
PMON73151
1/3
0/0


25
PHE0000375
PMON73153
1/2
0/0


26
PHE0000376
PMON73154
2/3
0/1


29
PHE0000379
PMON72457
2/4
0/1


30
PHE0000381
PMON72469
2/4
0/0


32
PHE0000384
PMON68621
3/3
0/0


37
PHE0000409
PMON72496
1/2
0/0


43
PHE0000459
PMON68390
1/5
0/1


44
PHE0000460
PMON73751
1/5
0/0


56
PHE0000479
PMON68402
2/8
1/3


58
PHE0000481
PMON75472
1/7
1/1


61
PHE0000487
PMON80267
1/4
0/1


62
PHE0000488
PMON75473
1/6
0/0


63
PHE0000489
PMON74432
3/5
2/3


67
PHE0000493
PMON68403
1/6
0/1


68
PHE0000494
PMON75459
4/6
0/0


69
PHE0000495
PMON73763
1/3
0/1


73
PHE0000499
PMON72490
 3/12
0/1


74
PHE0000500
PMON69495
1/2
1/1


76
PHE0000502
PMON75474
1/9
0/1


81
PHE0000507
PMON69492
1/4
0/0


86
PHE0000512
PMON74444
2/9
0/0


90
PHE0000516
PMON72492
1/3
0/0


91
PHE0000517
PMON72493
1/4
0/0


96
PHE0000523
PMON69487
1/1
0/0


97
PHE0000524
PMON69491
1/1
1/1


100
PHE0000527
PMON74446
1/1
0/0


102
PHE0000529
PMON69482
2/4
0/2


106
PHE0000533
PMON81274
1/2
0/0


108
PHE0000535
PMON68615
2/5
0/1


109
PHE0000536
PMON74447
1/7
0/1


112
PHE0000539
PMON74448
1/1
1/1


113
PHE0000540
PMON75451
2/4
0/0


115
PHE0000542
PMON68613
2/4
0/1


116
PHE0000543
PMON69499
2/5
0/0


120
PHE0000547
PMON76304
3/7
0/2


125
PHE0000552
PMON75460
1/2
0/0


131
PHE0000558
PMON68637
1/3
0/0


132
PHE0000559
PMON74431
2/3
1/4


134
PHE0000561
PMON68620
2/4
0/0


135
PHE0000562
PMON75303
1/5
0/0


137
PHE0000564
PMON68619
1/3
0/0


138
PHE0000565
PMON69483
1/3
0/2


139
PHE0000566
PMON75304
4/5
0/0


144
PHE0000571
PMON69484
2/4
0/0


146
PHE0000573
PMON68624
3/3
2/3


147
PHE0000574
PMON74442
1/2
0/0


151
PHE0000578
PMON69485
2/5
0/0


153
PHE0000580
PMON68611
3/5
0/4


157
PHE0000584
PMON68610
2/4
1/1


159
PHE0000586
PMON68618
1/1
1/1


165
PHE0000592
PMON68639
2/4
0/0


171
PHE0000604
PMON68625
1/6
0/0


176
PHE0000609
PMON74443
1/3
0/0


177
PHE0000610
PMON75494
2/4
1/1


178
PHE0000611
PMON68405
1/4
0/1


181
PHE0000614
PMON68632
3/8
0/2


186
PHE0000619
PMON74435
1/3
0/1


196
PHE0000629
PMON68631
1/5
0/0


198
PHE0000631
PMON75454
1/4
0/0


206
PHE0000639
PMON75457
3/5
0/0


212
PHE0000645
PMON68640
1/4
0/0


214
PHE0000647
PMON74437
1/2
0/2


216
PHE0000649
PMON78901
1/3
0/0


217
PHE0000650
PMON76303
1/2
1/2


219
PHE0000654
PMON68605
2/6
0/2


220
PHE0000655
PMON68607
 7/12
 0/23


221
PHE0000656
PMON80923
 3/19
0/0


222
PHE0000658
PMON68606
1/2
0/1


227
PHE0000664
PMON69471
1/8
1/1


229
PHE0000666
PMON68398
1/8
0/0


232
PHE0000702
PMON77883
3/4
1/2


234
PHE0000704
PMON76315
1/4
1/1


235
PHE0000705
PMON75516
1/1
0/0


237
PHE0000709
PMON68643
1/6
0/0


240
PHE0000712
PMON73753
3/7
2/4


242
PHE0000714
PMON68642
1/6
0/0


243
PHE0000715
PMON68641
2/5
1/1


244
PHE0000716
PMON68644
1/4
0/0


246
PHE0000735
PMON75481
1/3
0/0


252
PHE0000741
PMON80930
1/1
0/0


254
PHE0000743
PMON71005
 1/12
0/0


257
PHE0000746
PMON73777
1/4
0/0


259
PHE0000748
PMON75479
4/9
0/0


262
PHE0000751
PMON75321
1/4
0/1


268
PHE0000762
PMON75464
1/1
0/0


269
PHE0000763
PMON75956
1/2
0/1


270
PHE0000764
PMON75465
2/4
0/3


280
PHE0000774
PMON75461
1/2
0/0


281
PHE0000779
PMON74489
 1/19
0/0


288
PHE0000802
PMON76337
1/2
0/1


292
PHE0000806
PMON76308
2/4
1/1


295
PHE0000809
PMON76311
2/8
0/0


305
PHE0000819
PMON75324
1/3
0/0


307
PHE0000822
PMON73799
1/2
0/0


320
PHE0000835
PMON75344
2/5
0/0


321
PHE0000836
PMON75328
2/2
0/0


327
PHE0000842
PMON75329
1/2
0/0


342
PHE0000857
PMON75348
5/6
0/2


343
PHE0000858
PMON73797
1/6
0/0


344
PHE0000859
PMON73798
5/8
5/5


348
PHE0000863
PMON75349
2/5
0/0


350
PHE0000865
PMON75336
2/5
1/1


353
PHE0000868
PMON75338
1/4
0/0


355
PHE0000870
PMON75340
1/1
0/2


356
PHE0000871
PMON75341
1/4
0/3


366
PHE0000885
PMON77853
3/3
2/2


367
PHE0000886
PMON73804
1/2
0/0


369
PHE0000888
PMON73830
2/2
0/0


373
PHE0000892
PMON77864
1/1
0/1


374
PHE0000893
PMON73831
2/3
1/1


378
PHE0000897
PMON73833
1/5
0/0


386
PHE0000905
PMON77866
2/2
0/0


394
PHE0000913
PMON78201
2/3
1/1


421
PHE0000940
PMON76317
1/1
0/0


425
PHE0000944
PMON76319
1/3
0/0


436
PHE0000955
PMON76324
1/2
0/0


445
PHE0000964
PMON77867
1/3
0/0


452
PHE0000971
PMON73806
1/2
0/0


454
PHE0000973
PMON73827
1/5
0/0


457
PHE0000976
PMON78912
1/4
0/1


470
PHE0000989
PMON80515
1/7
0/1


471
PHE0000990
PMON77858
2/9
0/1


476
PHE0000995
PMON77871
1/8
0/1


482
PHE0001001
PMON77859
1/4
0/0


485
PHE0001004
PMON77860
1/1
0/0


487
PHE0001006
PMON73814
1/2
0/0


497
PHE0001016
PMON73815
1/2
0/0


499
PHE0001019
PMON73817
2/3
0/0


500
PHE0001020
PMON73818
1/1
0/0


524
PHE0001044
PMON77876
1/3
0/0


525
PHE0001045
PMON77872
5/7
1/1


527
PHE0001047
PMON75318
1/2
0/0


538
PHE0001165
PMON75513
1/2
0/0


540
PHE0001173
PMON80469
 4/11
0/3


548
PHE0001194
PMON78918
3/5
1/1


550
PHE0001234
PMON82646
1/3
0/0


554
PHE0001276
PMON79652
1/2
0/0


561
PHE0001423
PMON79672
2/6
2/2


575
PHE0001503
PMON84706
2/8
0/1


577
PHE0001505
PMON75536
1/3
0/0


581
PHE0001509
PMON75540
1/3
2/2


589
PHE0001548
PMON75547
1/6
0/0


598
PHE0001580
PMON79190
1/3
0/1


599
PHE0001581
PMON79191
1/4
0/0


610
PHE0002018
PMON79677
1/3
0/0









Transgenic plants with recombinant DNA constructs which improve seed compositions in terms of oil content are reported in Table 20.











TABLE 20









Confirmed






events/Actual





Positive
events with


NUC


events/Total
confirmation


SEQ ID
PHE ID
Construct
events screened
attempted



















3
PHE0000004
PMON67819
1/3
0/0


4
PHE0000005
PMON67820
1/6
0/0


9
PHE0000080
PMON68366
1/2
0/0


13
PHE0000113
PMON68365
2/3
0/4


22
PHE0000372
PMON72460
2/4
1/4


29
PHE0000379
PMON72457
1/3
0/0


74
PHE0000500
PMON69495
1/1
0/0


120
PHE0000547
PMON76304
1/2
0/0


122
PHE0000549
PMON75974
1/1
0/0


132
PHE0000559
PMON74431
1/1
0/0


138
PHE0000565
PMON69483
1/2
0/0


155
PHE0000582
PMON75476
1/2
0/0


190
PHE0000623
PMON74438
1/2
0/0


220
PHE0000655
PMON68607
 2/12
0/4


234
PHE0000704
PMON76315
1/1
0/0


240
PHE0000712
PMON73753
1/2
0/0


254
PHE0000743
PMON81215
1/2
0/0


296
PHE0000810
PMON75319
1/1
0/0


344
PHE0000859
PMON73798
1/6
0/0


366
PHE0000885
PMON77853
1/2
0/0


394
PHE0000913
PMON78201
1/1
0/0


457
PHE0000976
PMON78912
1/2
0/0


471
PHE0000990
PMON77858
1/3
0/0


540
PHE0001173
PMON80469
2/7
0/0


587
PHE0001546
PMON79717
2/3
0/0


589
PHE0001548
PMON75547
1/2
0/0









Example 8
Consensus Amino Acid Sequence
This example illustrates the identification of consensus amino acid sequences for the proteins encoded by recombinant DNA in transgenic seeds and plants disclosed herein and homologs.
ClustalW program was selected for multiple sequence alignments of the amino acid sequence of SEQ ID NO: 684, 704, 705, 706, 710, 719, 734, 735, 738, 743, 744, 745, 746, 761, 777, 779, 793, 804, 824, 891, 896, 900, 918, 924, 932, 957, 961, 1001, 1015, 1016, 1026, 1027, 1032, 1033, 1036, 1043, 1044, 1045, 1051, 1054, 1059, 1087, 1119, 1123, 1135, 1136, 1137, 1138, 1139, 1165, and their 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 were chosen for multiple sequence alignment. FIG. 1 shows the consensus sequence of SEQ ID NO: 684 and its homologs. The symbols for consensus sequence are (1) uppercase letters for 100% identity in all positions of multiple sequence alignment output; (2) lowercase letters for >=70% identity; symbol; (3) “X” indicated <70% identity; (4) dashes “-” meaning that gaps were in ≧70% of the sequences.
The consensus amino acid sequence can be used to identify DNA corresponding to the full scope of this invention that is useful in providing transgenic plants, for example corn and soybean plants with enhanced agronomic traits, for example improved nitrogen use efficiency, improved yield, improved water use efficiency and/or improved growth under cold stress, due to the expression in the plants of DNA encoding a protein with amino acid sequence identical to the consensus amino acid sequence.
Example 9
Pfam Domain Module Annotation
This example illustrates the identification by Pfam analysis of domain and domain module in proteins encoded by recombinant DNA in the transgenic plants and seeds disclosed herein. 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: 615 through 1228 are shown in Table 21 and Table 22 respectively. The Hidden Markov model databases for the identified protein families are also in the appended computer listing allowing identification of other homologous proteins and their cognate encoding DNA to enable the full breadth of the invention for a person of ordinary skill in the art. Certain proteins are identified by a single Pfam domain and others by multiple Pfam domains. For instance, the protein with amino acids of SEQ ID NO: 668 is characterized by three Pfam domains, i.e., AdoHcyase, 2-Hacid_dh_C and AdoHcyase_NAD. See also the protein with amino acids of SEQ ID NO: 659 which is characterized by five copies of the Pfam domain “Arm”. In Table 22 “score” is the gathering score for the Hidden Markov Model of the domain which exceeds the gathering cutoff reported in Table 23.









TABLE 21





PEP




SEQ


ID
Pfam module
Position

















615
CBFD_NFYB_HMF
24-89


616
CBFD_NFYB_HMF
26-91


617
CBFD_NFYB_HMF
 34-106


618
CBFD_NFYB_HMF
22-87


619
Myb_DNA-binding
24-69


620
Globin
 7-147


621
HEAT::HEAT::HEAT::FAT::Rapamycin_bind::
204-240::303-338::748-



PI3_PI4_kinase::FATC
785::1463-1829::1934-




2046::2113-2363::2472-2504


622
P-II
 4-105


623
AP2
143-208


624
zf-C3HC4
196-237


625
AUX_IAA
 21-196


626
SET
772-900


627
SET
739-867


628
Pkinase
 34-319


629
AdoHcyase
 12-484


630
GAF::HisKA::HATPase_c
159-308::344-409::456-587


631
RRM_1
10-81


632
DUF231
283-433


633
DUF231
210-384


634
DUF231
254-427


635
DUF231
232-404


636
AP2
 88-152


637
AUX_IAA
 4-155


638
Myb_DNA-binding
 55-100


639
WRKY
164-224


640
AP2
 77-141


641
bZIP_1
201-263


642
AP2
 36-100


643
Myb_DNA-binding
24-69


644
Ribosomal_L18p
 27-173


645
Cyclin_N
 4-144


646
PB1
 54-147


647
PB1
 46-136


648
PB1
 55-146


649
PB1
 58-148


650
Pescadillo_N::BRCT
8-286::352-429


651
Pescadillo_N::BRCT
4-285::355-436


652
2OG-Fell_Oxy
176-281


653
PI-PLC-X::PI-PLC-Y::C2
109-253::320-438::459-551


654
C1_1::DAGK_cat::DAGK_acc
139-200::347-476::493-650


655
Exo_endo_phos
109-538


656
S6PP
 2-247


657
S6PP::S6PP_C
8-261::262-393


658
UDPGP
 29-441


659
U-box::Arm::Arm::Arm::Arm::Arm
256-329::383-423::424-464::465-




505::506-546::547-587


660
U-box
 29-102


661
U-box::Arm::Arm::Arm
270-342::398-441::442-483::526-567


662
Prp19::WD40::WD40::WD40
64-133::253-291::298-336::384-421


663
U-box
 5-78


664
PfkB
 21-336


665
PfkB
 24-340


666
PfkB
 23-339


667
PfkB
 23-323


668
AdoHcyase
 12-484


669
AdoHcyase
 6-448


670
AdoHcyase_NAD
192-353


671
BRAP2::zf-C3HC4::zf-UBP
51-161::168-207::219-290


672
Cu-oxidase_3::Cu-oxidase::Cu-
28-145::169-374::469-606



oxidase_2


673
Glycos_transf_1::S6PP
241-428::466-713


674
Flavoprotein
264-428


676
Flavoprotein
 18-138


677
Flavoprotein
 18-163


678
IPP-2
 7-148


679
IPP-2
 2-137


680
Lactamase_B
 27-240


681
Lactamase_B
 45-264


682
Lactamase_B
 50-244


683
Histone
25-94


685
zf-C3HC4
251-291


686
Pkinase
 40-327


687
Pkinase
 71-351


688
Pkinase
 32-319


689
Pkinase
 33-324


690
Pkinase
 13-304


691
Pkinase
 4-287


692
Pkinase
 39-325


693
Pkinase
 32-319


694
WRKY
199-259


695
WRKY
158-218


696
PPDK_N::PEP-utilizers::PEP-
100-460::511-601::613-971



utilizers_C


697
DUF580
187-539


698
AA_permease
 59-525


699
adh_short
 11-180


700
adh_short
 15-187


701
adh_short
 19-188


702
adh_short
 18-186


703
adh_short
 17-184


707
VDE
163-360


708
SATase_N::Hexapep::Hexapep::Hexapep
73-177::231-248::257-274::275-292


709
SATase_N::Hexapep::Hexapep::Hexapep
80-184::238-255::264-281::282-299


711
NAS
 3-285


712
NAS
 39-319


713
OPT
 43-656


714
Pyridoxal_deC
 33-381


715
2OG-Fell_Oxy
190-321


716
Mlo
 4-501


717
G-alpha
 22-366


718
WD40::WD40::WD40::WD40::WD40::
8-47::65-103::107-145::155-



WD40
195::199-237::288-326


720
F-box::Tub
53-108::119-406


721
F-box::Tub
34-90::101-358


722
F-box::Tub
51-106::117-448


723
F-box::Tub
45-100::111-367


724
F-box::Tub
73-128::139-436


725
F-box::Tub
48-103::114-401


726
F-box::Tub
58-113::124-456


727
LRR_2
297-321


728
F-box::LRR_1
15-63::168-190


729
WD40::WD40
168-205::257-296


730
Asp
127-460


731
Asp
130-466


732
AUX_IAA
 2-182


733
LEA_4
 5-48


736
LEA_4
 57-100


737
TLC
 65-563


739
Mito_carr::Mito_carr::Mito_carr
22-119::126-222::226-316


740
PBP
 28-218


741
PBP
 22-191


742
Glycos_transf_1::S6PP
452-635::676-930


747
SRF-TF::K-box
9-59::74-172


748
SRF-TF::K-box
9-59::73-173


749
SBP56
 24-493


750
GST_N::GST_C
4-79::108-203


751
Pkinase::efhand::efhand::efhand::efhand
93-351::398-426::434-462::470-




498::504-532


752
CK_II_beta
 87-260


753
Zein
 1-234


754
AP2
113-177


755
MFMR::bZIP_1
1-156::244-308


756
HMG_box
 41-110


757
RRM_1
10-81


758
Enolase_N::Enolase_C
4-140::148-443


759
zf-C3HC4
118-160


760
Ribosomal_L10::Ribosomal_60s
6-110::227-317


762
SRF-TF::K-box
9-59::75-166


763
SRF-TF::K-box
9-59::75-172


764
SBP
 53-131


765
adh_short
 18-218


766
adh_short
 16-184


767
PBP
 18-163


768
PBP
 20-165


769
PBP
 17-162


770
FLO_LFY
 1-379


771
zf-B_box::CCT
14-60::193-231


772
TLC
 91-587


773
Ribosomal_L18p
 27-173


774
Ribosomal_L18p
 27-173


775
Ribosomal_L18p
 26-172


776
Orn_Arg_deC_N::Orn_DAP_Arg_deC
158-396::399-512


778
UPF0005
 28-237


780
UPF0005
 37-249


781
zf-LSD1::Peptidase_C14
7-31::64-347


782
Peptidase_C14
 65-310


783
Peptidase_C14
 73-352


784
Peptidase_C14
157-450


785
Rieske::PaO
116-225::325-432


786
Rieske::PaO
33-139::244-336


787
SRF-TF::K-box
9-59::69-169


788
DAD
 11-133


789
DAD
 3-114


790
Pirin::Pirin_C
91-188::244-356


791
Aldedh
 18-487


792
Aldedh
 18-488


794
PEMT
 10-205


795
Methyltransf_11::Methyltransf_11
69-167::298-394


796
BCCT
 17-503


797
BCCT
 19-505


798
Na_H_Exchanger
 22-444


799
Na_H_Exchanger
 24-443


800
H_PPase
 6-748


801
H_PPase
 9-752


802
H_PPase
 6-751


803
HD-ZIP_N::Homeobox::HALZ
1-96::123-177::178-222


805
bZIP_1
244-308


806
zf-B_box::zf-B_box
1-47::51-96


807
AP2
 62-126


808
Response_reg::CCT
26-142::628-666


809
zf-B_box::zf-B_box::CCT
17-64::65-107::308-346


810
BTB::NPH3
20-119::181-443


811
Myb_DNA-binding::Myb_DNA-
14-61::67-112



binding


812
zf-B_box::zf-B_box
1-47::52-99


813
AP2::AP2
159-222::251-315


814
Myb_DNA-binding
24-69


815
zf-CCCH::zf-CCCH::zf-CCCH::zf-
39-65::84-110::130-156::287-



CCCH::zf-CCCH
313::333-359


816
Pkinase
 7-262


817
GH3
 15-570


818
PMEI
 33-207


819
DPBB_1::Pollen_allerg_1
117-199::211-292


820
DUF1313
 23-112


821
Cu_bind_like
 35-120


822
UPF0041
 1-109


823
MatE::MatE
15-172::233-396


825
DUF221
303-726


826
Rieske::PaO
219-316::407-501


827
zf-LSD1::Peptidase_C14
18-42::80-363


828
Myb_DNA-binding
143-193


829
Myb_DNA-binding
138-188


830
HLH
192-242


831
Glycos_transf_1::S6PP
481-664::773-1047


832
Glycos_transf_1::S6PP
460-643::683-937


833
U-box
 29-103


834
U-box
 29-102


835
Globin::FAD_binding_6::NAD_binding_1
6-131::154-253::263-373


836
P-II
4-105


837
P-II
 78-180


838
DUF231
310-483


839
DXP_reductoisom::DXP_redisom_C
81-209::223-306


840
DXP_reductoisom::DXP_redisom_C
5-134::148-231


841
DXP_reductoisom::DXP_redisom_C
11-138::152-235


842
Transket_pyr::Transketolase_C
392-559::573-696


843
Transket_pyr::Transketolase_C
318-485::497-620


844
Transket_pyr::Transketolase_C
354-520::532-648


845
S-methyl_trans
 14-319


846
S-methyl_trans
 24-328


847
S-methyl_trans
 16-310


848
S-methyl_trans
 17-322


849
Histone
 33-107


850
Histone
19-92


851
Histone
 29-102


852
Histone
 28-101


853
DUF231
364-540


854
Flavodoxin_2
 5-218


855
MIF4G::MIF4G_like::MIF4G_like_2
9-228::304-467::483-770


856
MIF4G::MIF4G_like::MIF4G_like_2
33-261::343-539::580-820


857
RRM_1
 36-107


858
RRM_1
 48-119


859
Pyridoxal_deC
 87-361


860
Pyridoxal_deC
 80-381


861
Pyridoxal_deC
110-412


862
Pkinase::Pkinase_C
177-477::495-549


863
Pkinase::Pkinase_C
169-469::487-541


864
SRF-TF::K-box
9-59::75-174


865
SRF-TF::K-box
9-59::76-173


866
Myb_DNA-binding
233-284


867
Myb_DNA-binding
244-294


868
FBPase
 5-334


869
RPE65
131-630


870
RPE65
 68-569


871
AP2::AP2
289-362::391-456


872
FBPase_glpX
 2-334


873
FBPase_glpX
 2-334


874
Glycos_transf_1
211-388


875
Glycos_transf_1
211-388


876
bZIP_1
 87-151


877
WRKY
239-299


878
zf-Dof
 53-115


879
Myb_DNA-binding::Myb_DNA-
15-62::68-113



binding


880
Myb_DNA-binding::Myb_DNA-
15-62::68-113



binding


881
AP2
140-204


882
HLH
121-168


883
AP2
12-77


884
AP2
May-69


885
bZIP_2
213-267


886
Myb_DNA-binding
36-81


887
bZIP_1
368-432


888
G-alpha
103-447


889
PSK
13-83


890
PSK
 20-118


892
PSK
 20-101


893
Sugar_tr
 33-473


894
MFS_1
 63-548


895
MFS_1
 46-466


898
Phytochrome::HisKA::HATPase_c
48-227::237-302::349-486


899
Hpt
 44-129


901
Hpt
 44-122


902
Hpt
 30-112


903
GAF::HisKA::HATPase_c
158-307::343-408::455-586


904
GAF::HisKA::HATPase_c
159-308::344-409::456-586


905
p450
 45-523


906
Sugar_tr
 32-472


907
AP2
131-196


908
AP2
17-81


909
AP2
17-82


910
DUF6::DUF6
115-233::253-394


911
TPT
183-335


912
TPT
231-379


913
DUF6::DUF6
24-157::204-333


914
DUF6::DUF6
19-146::198-326


915
DUF6::DUF6
21-154::198-328


916
DUF6::DUF6
26-160::202-333


917
DUF6::DUF6
28-161::202-331


919
TPT
156-298


920
DUF6::DUF6
22-155::201-330


921
DUF6::DUF6
26-159::205-334


922
DUF914
 1-328


923
HEAT::HEAT::HEAT::HEAT::HEAT::
22-57::97-133::181-217::218-



HEAT::HEAT
253::259-295::341-376::381-416


925
DUF6
 22-154


926
TPT
167-307


927
DUF6
 15-148


928
DUF6::DUF6
27-160::201-330


929
DUF6::DUF6
128-252::277-407


930
TPT
156-299


931
DUF914
 2-327


933
DUF6::DUF6
31-164::215-344


934
TPT
156-300


935
DUF6::DUF6
16-149::193-322


936
TPT
163-303


937
TPT
200-344


938
Pkinase
504-777


939
B_lectin::PAN_2::Pkinase
81-189::322-387::470-736


940
B_lectin::PAN_2::Pkinase
80-187::326-391::473-742


941
B_lectin::PAN_2::Pkinase
110-225::360-425::507-776


942
B_lectin::PAN_2::Pkinase
67-176::311-373::450-718


943
B_lectin::S_locus_glycop::PAN_2::PAN_1::
74-188::202-333::350-415::362-



Pkinase
433::499-784


944
B_lectin::S_locus_glycop::PAN_2::Pkinase
75-199::212-340::357-425::506-790


945
PAN_1::Pkinase
336-417::500-770


946
14-3-3
 6-243


947
14-3-3
 6-117


948
14-3-3
 8-120


949
14-3-3
 3-240


950
14-3-3
 3-115


951
14-3-3
 9-246


952
14-3-3
 9-120


953
14-3-3
 5-240


954
14-3-3
 5-116


955
14-3-3
 7-116


956
14-3-3
 4-239


958
14-3-3
 8-245


959
14-3-3
 8-120


960
14-3-3
 8-245


962
14-3-3
 8-249


963
14-3-3
 8-125


964
G-alpha
431-841


965
Pkinase
 40-363


966
Pkinase
117-402


967
Pkinase
 34-319


968
CK_II_beta
 93-267


969
CK_II_beta
 26-233


970
CK_II_beta
 89-263


971
CK_II_beta
 87-260


972
RRM_1
10-81


973
RRM_1::zf-CCHC
9-80::128-145


974
RRM_1
 39-110


975
RRM_1
 33-104


976
Methyltransf_11
 63-162


977
Methyltransf_11
 85-184


978
Methyltransf_11
 70-169


979
RRM_1
10-81


980
zf-C3HC4
253-293


981
zf-C3HC4
190-230


982
zf-C3HC4
234-274


983
zf-C3HC4
221-261


984
zf-C3HC4
156-196


985
zf-C3HC4
218-258


986
zf-C3HC4
 94-135


987
zf-C3HC4
204-245


988
zf-C3HC4
126-169


989
PA::zf-C3HC4
51-149::237-278


990
zf-C3HC4
 87-128


991
zf-C3HC4
607-647


992
zf-C3HC4
467-507


993
zf-C3HC4
155-195


994
zf-C3HC4
127-167


995
zf-C3HC4
33-73


996
Skp1_POZ::Skp1
5-65::91-168


997
Skp1
 90-164


998
Skp1_POZ::Skp1
8-68::99-176


999
LRR_2::LRR_2
174-201::301-325


1000
F-box::LRR_1
15-63::168-190


1002
F-box::LRR_2
17-64::299-323


1003
Response_reg
 42-177


1004
zf-CHY::zf-C3HC4
35-113::166-208


1005
zf-CHY::zf-C3HC4
59-142::195-237


1006
MtN3_slv::MtN3_slv
9-98::132-218


1007
zf-C3HC4
215-256


1008
PHD
198-248


1009
F-box
17-64


1010
F-box
22-69


1011
F-box::Kelch_1::Kelch_1::Kelch_1
9-56::97-153::155-201::285-339


1012
F-box::Kelch_1::Kelch_1
76-123::167-213::215-262


1013
F-box::Kelch_1::Kelch_1
26-73::116-162::164-210


1014
zf-C3HC4
49-91


1017
Prp19::WD40::WD40::WD40
64-133::253-291::298-336::384-421


1018
zf-C3HC4
36-81


1019
zf-C3HC4
 58-103


1020
TPR_1::TPR_1::TPR_2::U-box
14-47::48-81::82-115::195-269


1021
zf-C3HC4
24-64


1022
F-
195-243::292-340::345-392::397-



box::Kelch_1::Kelch_2::Kelch_1::Kelch_2::
445::449-501::516-564



Kelch_2


1023
F-
205-253::300-348::353-400::405-



box::Kelch_1::Kelch_2::Kelch_1::Kelch_2::
453::458-509::518-566



Kelch_2


1024
Cellulose_synt
167-977


1025
Cellulose_synt
 254-1069


1028
zf-C3HC4
22-64


1029
F-box::LysM
32-79::109-152


1030
Sina
121-320


1031
F-box
18-65


1034
F-box
18-66


1035
SPX::zf-C3HC4
1-167::238-286


1037
Cullin
 15-237


1038
zf-C3HC4
227-270


1039
zf-C3HC4
361-398


1040
Melibiase
 34-362


1041
Copine
 80-227


1042
F-box
36-83


1046
F-box::LRR_2
1-47::150-174


1047
F-box
11-59


1048
U-box
 5-78


1049
Glycos_transf_1::S6PP
465-648::701-942


1050
Pkinase::Ribonuc_2-5A
491-759::764-890


1052
Pkinase::Ribonuc_2-5A
77-345::350-476


1053
Pkinase::Ribonuc_2-5A
674-980::985-1115


1055
Pkinase::Ribonuc_2-5A
101-407::412-542


1056
dCMP_cyt_deam_1
218-319


1057
Aldo_ket_red
 7-285


1058
Aldo_ket_red
 5-292


1060
SOH1
 18-112


1061
dCMP_cyt_deam_1
 1-107


1062
Put_Phosphatase
 4-229


1063
NAF1
104-273


1064
Aldo_ket_red
 10-289


1065
Glutaredoxin
19-85


1066
TPT
156-299


1067
DUF850
 2-230


1068
LEA_2
 17-166


1069
ABA_WDS
43-96


1070
ABA_WDS
 51-104


1071
LEA_2
 30-179


1072
LEA_2
 30-179


1073
ABA_WDS
 54-107


1074
Sigma70_r2::Sigma70_r3::Sigma70_r4
260-330::334-414::433-485


1075
Sigma70_r2::Sigma70_r3::Sigma70_r4
314-384::388-469::482-535


1076
Sigma70_r2::Sigma70_r3::Sigma70_r4
302-372::376-457::469-522


1077
Bromodomain
 61-150


1078
Homeobox::HALZ
70-124::125-169


1079
bZIP_1
118-179


1080
MFMR::bZIP_1
1-156::244-308


1081
Remorin_C
402-512


1082
Remorin_N::Remorin_C
23-83::85-194


1083
Myb_DNA-binding
39-90


1084
Homeobox::HALZ
77-131::132-176


1085
Homeobox::HALZ
77-131::132-176


1086
HSF_DNA-bind
 11-170


1088
HSF_DNA-bind
 13-167


1089
HSF_DNA-bind
 15-219


1090
AUX_IAA
 18-218


1091
AUX_IAA
 19-219


1092
SRF-TF::K-box
9-59::48-144


1093
SRF-TF::K-box
9-59::75-174


1094
SRF-TF::K-box
9-59::73-173


1095
SRF-TF::K-box
9-59::71-170


1096
SRF-TF::K-box
9-59::76-173


1097
SRF-TF::K-box
9-59::71-170


1098
SRF-TF::K-box
9-59::75-174


1099
zf-C2H2
35-58


1100
LIM::LIM
10-67::105-162


1101
Myb_DNA-binding::Linker_histone
5-57::122-190


1102
Myb_DNA-binding::Myb_DNA-
14-61::67-112



binding


1103
Myb_DNA-binding::Myb_DNA-
11-57::63-108



binding


1104
Myb_DNA-binding::Myb_DNA-
14-61::67-112



binding


1105
NAM
 23-158


1106
MED7
 4-169


1107
zf-LSD1::zf-LSD1::zf-LSD1
27-51::66-90::104-128


1108
Hydrolase
 18-209


1109
zf-C3HC4
349-389


1110
zf-C3HC4
244-284


1111
zf-CHY::zf-C3HC4
35-113::166-208


1112
Ank::Ank::Ank::Ank::Ank::zf-C3HC4
50-82::83-115::117-148::180-




212::223-255::321-370


1113
zf-B_box::zf-B_box::CCT
1-47::48-90::356-394


1114
GRAS
154-464


1115
TFIIS::TFIIS_M::TFIIS_C
1-93::189-317::328-366


1116
zf-B_box::zf-B_box
1-47::55-102


1117
Copine
111-259


1118
Copine
111-259


1120
zf-CCCH::zf-CCCH::KH_1::zf-CCCH
35-61::95-121::246-310::324-349


1121
AUX_IAA
 7-222


1122
zf-B_box::zf-B_box
1-47::51-96


1124
SRF-TF::K-box
9-59::75-174


1125
SRF-TF::K-box
9-59::75-174


1126
SRF-TF::K-box
9-59::75-174


1127
SRF-TF::K-box
9-59::75-174


1128
SRF-TF::K-box
9-59::75-174


1129
FLO_LFY
 1-395


1130
Hydrolase
114-295


1131
Hydrolase
130-317


1132
Hydrolase
110-298


1133
AP2
15-80


1140
Pkinase::NAF
20-275::314-374


1141
WD40::WD40
560-599::646-683


1142
Pkinase
139-401


1143
EMP24_GP25L
 76-137


1144
RRM_1::zf-CCHC
4-70::86-103


1145
Frigida
112-414


1146
DUF810
 175-1046


1147
Dor1
 21-369


1148
Alpha-amylase::Alpha-amyl_C2
26-356::357-415


1149
AT_hook::DUF296
99-111::126-246


1150
IMPDH
 23-491


1151
IMPDH
 35-512


1152
IMPDH
 7-473


1153
IMPDH
 12-486


1154
zf-CCCH::zf-CCCH::KH_1::zf-CCCH
38-64::105-131::174-236::274-299


1155
Response_reg::Myb_DNA-binding
21-134::214-264


1156
zf-C3HC4
251-291


1157
MFS_1
129-549


1158
Sugar_tr
 34-472


1159
AP2
15-80


1160
AP2
 7-72


1161
Pyridoxal_deC
 35-383


1162
AUX_IAA
 7-263


1163
Cyclin_N::Cyclin_C
92-207::209-336


1164
Cyclin_N
183-321


1166
zf-Dof
105-167


1167
NAM
 52-179


1168
NAM
 18-145


1169
p450
 41-477


1170
LRRNT_2::LRR_1::LRR_1::LRR_1::
23-63::90-112::114-136::162-



LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::
184::186-208::234-256::258-



LRR_1::LRR_1::LRR_1::LRR_1::
280::282-304::306-328::354-



LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::
376::402-425::448-470::472-



LRR_1::LRR_1::LRR_1::LRR_1::
494::519-541::543-565::567-



Pkinase
589::591-613::615-638::748-




771::772-791::824-846::848-




870::1002-1275


1171
LRRNT_2::LRR_1::LRR_1::LRR_1::
21-60::139-158::185-207::209-



LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::
231::233-255::259-281::283-



LRR_1::LRR_1::LRR_1::LRR_1::
306::308-330::332-354::357-



LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::
379::381-403::429-451::453-



Pkinase
475::477-499::501-520::593-




615::617-639::641-663::824-1098


1172
LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::
199-219::221-244::246-268::270-



LRR_1::LRR_1::LRR_1::LRR_1::
293::295-317::319-342::345-



LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::
367::369-391::393-415::417-



LRR_1::LRR_1::Pkinase
439::441-463::465-487::489-




511::582-604::630-652::653-




674::807-1080


1173
FAD_binding_4
 55-200


1174
FAD_binding_4
 55-200


1175
Sterol_desat
 35-210


1176
Sterol_desat
 35-246


1177
Sterol_desat
 37-248


1178
Sterol_desat
 43-254


1179
Peptidase_S10
 41-465


1180
Peptidase_S10
 56-474


1181
F-
205-253::300-348::353-400::405-



box::Kelch_2::Kelch_2::Kelch_1::Kelch_2
453::524-572


1182
F-
272-320::367-415::420-467::472-



box::Kelch_1::Kelch_2::Kelch_1::Kelch_2::
520::525-576::586-634



Kelch_2


1183
ADH_N::ADH_zinc_N
36-165::196-342


1184
ADH_N::ADH_zinc_N
27-155::186-332


1185
ADH_N::ADH_zinc_N
27-155::186-328


1186
ADH_N::ADH_zinc_N
36-165::196-338


1187
ADH_N::ADH_zinc_N
36-165::196-338


1188
ADH_N::ADH_zinc_N
35-163::197-343


1189
ADH_N::ADH_zinc_N
34-163::194-336


1190
ADH_N::ADH_zinc_N
34-163::194-336


1191
TPT
156-298


1192
TPT
154-296


1193
TPT
151-293


1194
Sugar_tr
 91-552


1195
Cyclin_N::Cyclin_C
61-193::195-326


1196
SAC3_GANP
 24-209


1197
SAC3_GANP
 20-211


1198
SAC3_GANP
 24-209


1199
SAC3_GANP
 24-209


1200
WD40::WD40
183-220::289-328


1201
WD40::WD40
204-241::311-350


1202
CHASE::HisKA::HATPase_c::Response_reg
86-298::359-424::471-654::829-963


1203
CHASE::HisKA::HATPase_c::Response_reg
198-411::472-537::584-759::945-1068


1204
CHASE::HisKA::HATPase_c::Response_reg
302-526::587-652::699-




866::1035-1170


1205
CHASE::HisKA::HATPase_c::Response_reg
163-389::450-515::562-722::890-1025


1206
MFS_1
 66-429


1207
MFS_1
 69-432


1208
MFS_1
 51-415


1209
CHASE::HisKA::HATPase_c::Response_reg
110-321::382-447::494-682::869-1004


1210
PTR2
113-517


1211
PTR2
118-521


1212
PTR2
 97-499


1213
PTR2
122-526


1214
PTR2
 98-500


1215
AT_hook::DUF296
34-46::61-180


1220
BIR::BIR
20-117::153-241


1221
AT_hook::DUF296
34-46::61-180


1224
Bap31
 1-188





















TABLE 22





PEP SEQ







ID
Pfam domain
Start
End
score
E-value




















615
CBFD_NFYB_HMF
24
89
126.8
5.90E−35


616
CBFD_NFYB_HMF
26
91
130.9
3.50E−36


617
CBFD_NFYB_HMF
34
106
117.8
3.10E−32


618
CBFD_NFYB_HMF
22
87
131
3.40E−36


619
Myb_DNA-binding
24
69
54.5
3.50E−13


620
Globin
7
147
127.6
3.50E−35


621
HEAT
204
240
23.5
7.80E−04


621
HEAT
303
338
11.6
1.60E+00


621
HEAT
748
785
17.7
4.20E−02


621
FAT
1463
1829
498.6
7.00E−147


621
Rapamycin_bind
1934
2046
187.1
4.40E−53


621
PI3_PI4_kinase
2113
2363
365.6
7.80E−107


621
FATC
2472
2504
44.7
3.10E−10


622
P-II
4
105
244
3.10E−70


623
AP2
143
208
145.4
1.50E−40


624
zf-C3HC4
196
237
19.6
1.50E−03


625
AUX_IAA
21
196
2.8
1.20E−09


626
SET
772
900
157.6
3.20E−44


627
SET
739
867
157.6
3.20E−44


628
Pkinase
34
319
302.5
7.70E−88


629
AdoHcyase
12
484
826.2
1.70E−245


629
2-Hacid_dh_C
219
399
−77
1.30E−03


629
AdoHcyase_NAD
240
403
393.3
3.60E−115


630
GAF
159
308
98.7
1.70E−26


630
HisKA
344
409
87.6
3.80E−23


630
HATPase_c
456
587
131.8
2.00E−36


631
RRM_1
10
81
108.2
2.40E−29


632
DUF231
283
433
139.3
1.10E−38


633
DUF231
210
384
210.9
2.90E−60


634
DUF231
254
427
265.7
9.50E−77


635
DUF231
232
404
99.1
1.30E−26


636
AP2
88
152
147.9
2.70E−41


637
AUX_IAA
4
155
28.5
1.80E−11


638
Myb_DNA-binding
55
100
58
3.20E−14


639
WRKY
164
224
139.9
7.00E−39


640
AP2
77
141
142.7
1.00E−39


641
bZIP_2
199
253
29.9
8.90E−06


641
bZIP_1
201
263
31.2
3.70E−06


642
AP2
36
100
148
2.50E−41


643
Myb_DNA-binding
24
69
54.2
4.20E−13


644
Ribosomal_L18p
27
173
263.6
3.90E−76


645
Cyclin_N
4
144
47.9
3.50E−11


646
PB1
54
147
103
9.00E−28


647
PB1
46
136
91.6
2.50E−24


648
PB1
55
146
90.6
4.90E−24


649
PB1
58
148
92.7
1.10E−24


650
Pescadillo_N
8
286
523.1
3.10E−154


650
BRCT
352
429
47.9
3.50E−11


651
Pescadillo_N
4
285
667.1
1.40E−197


651
BRCT
355
436
48.4
2.50E−11


652
2OG-FeII_Oxy
176
281
135
2.00E−37


653
PI-PLC-X
109
253
146.2
8.90E−41


653
PI-PLC-Y
320
438
84.2
4.10E−22


653
C2
459
551
81.4
2.90E−21


654
C1_1
139
200
38.3
2.60E−08


654
DAGK_cat
347
476
130.6
4.50E−36


654
DAGK_acc
493
650
144.9
2.20E−40


655
Exo_endo_phos
109
538
148
2.50E−41


656
S6PP
2
247
493.5
2.60E−145


656
Hydrolase_3
6
242
−20.7
5.50E−06


657
S6PP
8
261
556.5
2.60E−164


657
Hydrolase_3
12
242
−15.4
2.70E−06


657
S6PP_C
262
393
322.8
6.00E−94


658
UDPGP
29
441
981.2
3.70E−292


659
U-box
256
329
93
9.30E−25


659
Arm
383
423
48.9
1.80E−11


659
Arm
424
464
21.9
2.20E−03


659
Arm
465
505
40.9
4.30E−09


659
Arm
506
546
18.5
2.40E−02


659
Arm
547
587
34.2
4.50E−07


660
U-box
29
102
84.8
2.70E−22


661
U-box
270
342
81.2
3.30E−21


661
Arm
398
441
19.1
1.60E−02


661
Arm
442
483
17.5
4.90E−02


661
Arm
526
567
21.2
3.80E−03


662
Prp19
64
133
161.6
2.10E−45


662
WD40
253
291
47.2
5.40E−11


662
WD40
298
336
33.4
8.10E−07


662
WD40
384
421
32.2
1.80E−06


663
U-box
5
78
69.7
9.30E−18


664
PfkB
21
336
284.2
2.50E−82


665
PfkB
24
340
279.5
6.70E−81


666
PfkB
23
339
282.4
8.70E−82


667
PfkB
23
323
269
9.80E−78


668
AdoHcyase
12
484
828
4.90E−246


668
2-Hacid_dh_C
219
399
−77
1.30E−03


668
AdoHcyase_NAD
240
403
393.3
3.60E−115


669
AdoHcyase
6
448
744.6
6.30E−221


669
AdoHcyase_NAD
194
355
393.2
3.90E−115


670
AdoHcyase
8
424
133.5
5.90E−37


670
2-Hacid_dh_C
171
341
−56.8
4.40E−05


670
AdoHcyase_NAD
192
353
252.7
7.60E−73


670
IlvN
211
360
−67.8
1.40E−03


671
BRAP2
51
161
136.6
7.00E−38


671
zf-C3HC4
168
207
40.1
7.40E−09


671
zf-UBP
219
290
119.4
1.00E−32


672
Cu-oxidase_3
28
145
200.1
5.30E−57


672
Cu-oxidase
169
374
59.4
1.20E−14


672
Cu-oxidase_2
469
606
39.1
1.50E−08


673
Glycos_transf_1
241
428
78.2
2.60E−20


673
S6PP
466
713
451.8
9.10E−133


673
Hydrolase_3
470
708
−13.7
2.10E−06


674
Flavoprotein
264
428
204.8
2.00E−58


676
Flavoprotein
18
138
141.2
2.90E−39


677
Flavoprotein
18
163
105.7
1.30E−28


678
IPP-2
7
148
−29.9
1.50E−03


679
IPP-2
2
137
−23.9
4.70E−04


680
Lactamase_B
27
240
61.3
3.20E−15


681
Lactamase_B
45
264
78.5
2.10E−20


682
Lactamase_B
50
244
82.1
1.80E−21


683
Histone
25
94
67.1
5.70E−17


685
zf-C3HC4
251
291
37.3
5.10E−08


686
Pkinase
40
327
322.6
6.90E−94


687
Pkinase
71
351
313.1
4.90E−91


688
Pkinase
32
319
321.7
1.30E−93


689
Pkinase
33
324
308.5
1.20E−89


690
Pkinase
13
304
296.9
3.80E−86


691
Pkinase
4
287
395.1
1.10E−115


692
Pkinase
39
325
314.1
2.40E−91


693
Pkinase
32
319
342.5
7.10E−100


694
WRKY
199
259
135.3
1.70E−37


695
WRKY
158
218
132.3
1.40E−36


696
PPDK_N
100
460
599
4.20E−177


696
PEP-utilizers
511
601
167.6
3.20E−47


696
PEP-utilizers_C
613
971
732.1
3.60E−217


697
DUF580
187
539
516.7
2.50E−152


698
AA_permease
59
525
−44.7
1.50E−04


699
adh_short
11
180
113.5
5.90E−31


699
Epimerase
13
244
−42.3
2.10E−03


700
adh_short
15
187
111.5
2.50E−30


700
KR
15
204
−29.4
1.20E−05


700
NAD_binding_4
19
236
−73.6
7.20E−04


701
adh_short
19
188
81.3
3.10E−21


701
KR
19
205
−66.7
1.70E−03


702
adh_short
18
186
110.5
5.00E−30


702
KR
18
201
−57.3
5.00E−04


703
adh_short
17
184
90.2
6.20E−24


707
VDE
163
360
553.4
2.40E−163


708
SATase_N
73
177
210
5.30E−60


708
Hexapep
231
248
18.5
2.40E−02


708
Hexapep
257
274
14.9
3.00E−01


708
Hexapep
275
292
9.7
9.60E+00


709
SATase_N
80
184
220
5.40E−63


709
Hexapep
238
255
12
2.20E+00


709
Hexapep
264
281
8.3
1.40E+01


709
Hexapep
282
299
2.9
6.40E+01


711
NAS
3
285
688
7.20E−204


712
NAS
39
319
615.6
4.30E−182


713
OPT
43
656
560.7
1.40E−165


714
Pyridoxal_deC
33
381
538.4
7.80E−159


715
2OG-FeII_Oxy
190
321
91.1
3.40E−24


716
Mlo
4
501
735
4.80E−218


717
G-alpha
22
366
473.3
3.00E−139


718
WD40
8
47
34.2
4.60E−07


718
WD40
65
103
39.8
9.50E−09


718
WD40
107
145
47.8
3.50E−11


718
WD40
155
195
47.6
4.20E−11


718
WD40
199
237
42.4
1.60E−09


718
WD40
288
326
25.1
2.50E−04


720
F-box
53
108
29.4
1.30E−05


720
Tub
119
406
566.3
3.00E−167


721
F-box
34
90
17.8
3.80E−02


721
Tub
101
358
418.7
8.10E−123


722
F-box
51
106
31.6
2.70E−06


722
Tub
117
448
571.9
6.10E−169


723
F-box
45
100
28
3.40E−05


723
Tub
111
367
414.3
1.70E−121


724
F-box
73
128
23.1
9.90E−04


724
Tub
139
436
500.5
2.00E−147


725
F-box
48
103
15.6
1.80E−01


725
Tub
114
401
594.1
1.30E−175


726
F-box
58
113
26.9
7.20E−05


726
Tub
124
456
614.6
8.90E−182


727
LRR_1
297
323
8
9.00E+00


727
LRR_2
297
321
10.3
6.10E−01


728
F-box
15
63
21.2
3.70E−03


728
LRR_1
168
190
12.6
1.30E+00


729
WD40
168
205
26.6
8.80E−05


729
WD40
257
296
35.5
1.90E−07


730
Asp
127
460
−46.6
7.40E−11


731
Asp
130
466
−79.2
6.20E−09


732
AUX_IAA
2
182
25.2
3.10E−11


733
LEA_4
5
48
26.7
8.20E−05


736
LEA_4
57
100
22.9
1.10E−03


737
TLC
65
563
994.5
3.70E−296


739
Mito_carr
22
119
127.2
4.60E−35


739
Mito_carr
126
222
112.8
1.00E−30


739
Mito_carr
226
316
102.5
1.30E−27


740
PBP
28
218
293.1
5.40E−85


741
PBP
22
191
121
3.40E−33


742
Glycos_transf_1
452
635
61.5
2.80E−15


742
S6PP
676
930
−86.2
1.10E−04


747
SRF-TF
9
59
114.1
4.10E−31


747
K-box
74
172
79.3
1.20E−20


748
SRF-TF
9
59
111.5
2.40E−30


748
K-box
73
173
58.3
2.60E−14


749
SBP56
24
493
1290.6
0.00E+00


750
GST_N
4
79
91.5
2.60E−24


750
GST_C
108
203
80.1
6.80E−21


751
Pkinase
93
351
334
2.50E−97


751
efhand
398
426
37.3
5.20E−08


751
efhand
434
462
25.5
1.90E−04


751
efhand
470
498
34.2
4.50E−07


751
efhand
504
532
35.1
2.40E−07


752
CK_II_beta
87
260
445.5
7.10E−131


753
Zein
1
234
121.6
2.30E−33


754
AP2
113
177
134.8
2.40E−37


755
MFMR
1
156
268.4
1.40E−77


755
bZIP_2
244
298
37
6.30E−08


755
bZIP_1
244
308
89.4
1.10E−23


756
HMG_box
41
110
115.2
1.80E−31


757
RRM_1
10
81
108.2
2.40E−29


758
Enolase_N
4
140
244
3.20E−70


758
Enolase_C
148
443
729.3
2.50E−216


759
zf-C3HC4
118
160
35.8
1.50E−07


760
Ribosomal_L10
6
110
168.2
2.00E−47


760
Ribosomal_60s
227
317
70.2
6.60E−18


762
SRF-TF
9
59
78.3
2.40E−20


762
K-box
75
166
8.4
8.50E−05


763
SRF-TF
9
59
99.2
1.30E−26


763
K-box
75
172
92.4
1.30E−24


764
SBP
53
131
190.3
4.80E−54


765
adh_short
18
218
72.6
1.30E−18


766
adh_short
16
184
116.4
7.90E−32


766
KR
16
201
−11
1.00E−06


767
PBP
18
163
220.5
3.70E−63


768
PBP
20
165
193.4
5.30E−55


769
PBP
17
162
162.2
1.30E−45


770
FLO_LFY
1
379
1005.9
1.40E−299


771
zf-B_box
14
60
47
6.30E−11


771
CCT
193
231
70.4
5.80E−18


772
TLC
91
587
1002.7
1.30E−298


773
Ribosomal_L18p
27
173
265.2
1.30E−76


774
Ribosomal_L18p
27
173
263.6
3.90E−76


775
Ribosomal_L18p
26
172
246.3
6.30E−71


776
Orn_Arg_deC_N
158
396
211.9
1.40E−60


776
Orn_DAP_Arg_deC
399
512
108.5
2.00E−29


778
UPF0005
28
237
70.1
7.20E−18


780
UPF0005
37
249
37.9
3.50E−08


781
zf-LSD1
7
31
49.4
1.20E−11


781
Peptidase_C14
64
347
225.1
1.50E−64


782
Peptidase_C14
65
310
90
7.20E−24


783
Peptidase_C14
73
352
132.8
9.70E−37


784
Peptidase_C14
157
450
268.6
1.20E−77


785
Rieske
116
225
88.5
2.10E−23


785
PaO
325
432
171.8
1.80E−48


786
Rieske
33
139
109
1.40E−29


786
PaO
244
336
155.9
1.10E−43


787
SRF-TF
9
59
108.3
2.30E−29


787
K-box
69
169
112.1
1.60E−30


788
DAD
11
133
309.1
8.10E−90


789
DAD
3
114
219.5
7.70E−63


790
Pirin
91
188
131.1
3.00E−36


790
Pirin_C
244
356
113.3
6.90E−31


791
Aldedh
18
487
820.1
1.20E−243


792
Aldedh
18
488
829.6
1.70E−246


794
PEMT
10
205
548.9
5.10E−162


795
Methyltransf_11
69
167
74
4.90E−19


795
Methyltransf_12
69
165
51.3
3.20E−12


795
CMAS
240
501
−149.9
5.50E−05


795
Ubie_methyltran
275
445
−111.2
2.70E−04


795
Methyltransf_12
298
392
70.4
5.90E−18


795
Methyltransf_11
298
394
100.9
3.80E−27


796
BCCT
17
503
1106.5
0.00E+00


797
BCCT
19
505
970.6
6.00E−289


798
Na_H_Exchanger
22
444
185.2
1.60E−52


799
Na_H_Exchanger
24
443
183.2
6.30E−52


800
H_PPase
6
748
1649.7
0.00E+00


801
H_PPase
9
752
1606.8
0.00E+00


802
H_PPase
6
751
1479.9
0.00E+00


803
HD-ZIP_N
1
96
151.2
2.80E−42


803
Homeobox
123
177
65.2
2.10E−16


803
HALZ
178
222
86.1
1.10E−22


805
bZIP_1
244
308
58.5
2.30E−14


805
bZIP_2
244
298
51.7
2.50E−12


806
zf-B_box
1
47
39
1.70E−08


806
zf-B_box
51
96
47.1
5.90E−11


807
AP2
62
126
129.6
8.70E−36


808
Response_reg
26
142
96.2
9.90E−26


808
CCT
628
666
73.6
6.40E−19


809
zf-B_box
17
64
42.1
1.80E−09


809
zf-B_box
65
107
48.3
2.60E−11


809
CCT
308
346
78.8
1.70E−20


810
BTB
20
119
11
4.10E−04


810
NPH3
181
443
372
9.20E−109


811
Myb_DNA-binding
14
61
51.9
2.20E−12


811
Myb_DNA-binding
67
112
50.8
4.50E−12


812
zf-B_box
1
47
36.8
7.50E−08


812
zf-B_box
52
99
46.1
1.20E−10


813
AP2
159
222
102.9
9.80E−28


813
AP2
251
315
80.9
4.10E−21


814
Myb_DNA-binding
24
69
57.9
3.40E−14


815
zf-CCCH
39
65
44.1
4.70E−10


815
zf-CCCH
84
110
43.8
6.00E−10


815
zf-CCCH
130
156
44.5
3.70E−10


815
zf-CCCH
287
313
43.6
6.60E−10


815
zf-CCCH
333
359
46.2
1.10E−10


816
Pkinase
7
262
206.1
8.10E−59


817
GH3
15
570
1262.5
0.00E+00


818
PMEI
33
207
144.5
2.90E−40


819
DPBB_1
117
199
120.1
6.30E−33


819
Pollen_allerg_1
211
292
120
6.90E−33


820
DUF1313
23
112
213.3
5.50E−61


821
Cu_bind_like
35
120
100.2
6.10E−27


822
UPF0041
1
109
135.3
1.70E−37


823
MatE
15
172
121.1
3.10E−33


823
MatE
233
396
164.2
3.40E−46


825
DUF221
303
726
617.9
9.10E−183


826
Rieske
219
316
98.7
1.80E−26


826
PaO
407
501
170.6
3.80E−48


827
zf-LSD1
18
42
53.5
7.00E−13


827
Peptidase_C14
80
363
234.7
2.00E−67


828
Myb_DNA-binding
143
193
43.7
6.10E−10


829
Myb_DNA-binding
138
188
45.8
1.50E−10


830
HLH
192
242
27.9
3.60E−05


831
Glycos_transf_1
481
664
67.9
3.30E−17


831
S6PP
773
1047
−77.2
2.90E−05


832
Glycos_transf_1
460
643
58.7
2.00E−14


832
S6PP
683
937
−90.5
1.90E−04


833
U-box
29
103
97.9
3.10E−26


834
U-box
29
102
84.8
2.70E−22


835
Globin
6
131
103.1
8.10E−28


835
FAD_binding_6
154
253
42.5
1.40E−09


835
NAD_binding_1
263
373
87.5
4.20E−23


836
P-II
4
105
232.8
7.50E−67


837
P-II
78
180
180
6.00E−51


838
DUF231
310
483
233.6
4.40E−67


839
DXP_reductoisom
81
209
238.7
1.20E−68


839
DXP_redisom_C
223
306
210.4
4.10E−60


840
DXP_reductoisom
5
134
247.6
2.60E−71


840
DXP_redisom_C
148
231
216.8
5.00E−62


841
DXP_reductoisom
11
138
212.2
1.20E−60


841
DXP_redisom_C
152
235
206.2
7.60E−59


842
Transket_pyr
392
559
233.7
4.00E−67


842
Transketolase_C
573
696
154.1
3.60E−43


843
Transket_pyr
318
485
187.1
4.20E−53


843
Transketolase_C
497
620
135.5
1.40E−37


844
Transket_pyr
354
520
185
1.90E−52


844
Transketolase_C
532
648
111.7
2.10E−30


845
S-methyl_trans
14
319
324.6
1.70E−94


846
S-methyl_trans
24
328
373.5
3.40E−109


847
S-methyl_trans
16
310
485.1
8.60E−143


848
S-methyl_trans
17
322
485.3
7.50E−143


849
Histone
33
107
93.5
6.40E−25


850
Histone
19
92
111.6
2.30E−30


850
CBFD_NFYB_HMF
25
89
20.5
2.00E−03


851
Histone
29
102
100.4
5.30E−27


852
Histone
28
101
98.7
1.80E−26


853
DUF231
364
540
212.6
8.70E−61


854
Flavodoxin_2
5
218
190.1
5.50E−54


855
MIF4G
9
228
74.8
2.80E−19


855
MIF4G_like
304
467
158
2.50E−44


855
MIF4G_like_2
483
770
349.5
5.70E−102


856
MIF4G
33
261
120.5
4.80E−33


856
MIF4G_like
343
539
246.8
4.50E−71


856
MIF4G_like_2
580
820
322.9
5.80E−94


857
RRM_1
36
107
59.5
1.10E−14


858
RRM_1
48
119
59.7
9.90E−15


859
Pyridoxal_deC
87
361
26.2
5.40E−16


860
Pyridoxal_deC
80
381
66.1
1.30E−18


861
Pyridoxal_deC
110
412
58.5
4.20E−18


862
Pkinase
177
477
204.5
2.50E−58


862
Pkinase_C
495
549
33.7
6.20E−07


863
Pkinase
169
469
206.1
8.00E−59


863
Pkinase_C
487
541
32.8
1.20E−06


864
SRF-TF
9
59
119.2
1.20E−32


864
K-box
75
174
158.4
1.80E−44


865
SRF-TF
9
59
120.7
4.20E−33


865
K-box
76
173
128.5
1.80E−35


866
Myb_DNA-binding
233
284
47.9
3.30E−11


867
Myb_DNA-binding
244
294
41.1
3.70E−09


868
FBPase
5
334
567
1.90E−167


869
RPE65
131
630
696.9
1.50E−206


870
RPE65
68
569
598.4
6.70E−177


871
AP2
289
362
138.7
1.60E−38


871
AP2
391
456
126
1.00E−34


872
FBPase_glpX
2
334
754.2
8.00E−224


873
FBPase_glpX
2
334
730.6
1.00E−216


874
Glycos_transf_1
211
388
177.1
4.50E−50


875
Glyco_transf_20
7
407
−235.8
3.80E−03


875
Glycos_transf_1
211
388
175.7
1.20E−49


876
bZIP_1
87
151
55.7
1.60E−13


876
bZIP_2
87
141
44.4
3.80E−10


877
WRKY
239
299
143.1
7.20E−40


878
zf-Dof
53
115
135.9
1.10E−37


879
Myb_DNA-binding
15
62
49
1.60E−11


879
Myb_DNA-binding
68
113
49.7
9.60E−12


880
Myb_DNA-binding
15
62
51.3
3.20E−12


880
Myb_DNA-binding
68
113
57.7
3.90E−14


881
AP2
140
204
153.6
5.00E−43


882
HLH
121
168
24.3
3.70E−04


883
AP2
12
77
155
1.90E−43


884
AP2
5
69
119.2
1.20E−32


885
bZIP_1
213
276
52.3
1.60E−12


885
bZIP_2
213
267
53.6
6.40E−13


886
Myb_DNA-binding
36
81
56.5
8.60E−14


887
bZIP_1
368
432
38
3.20E−08


887
bZIP_2
368
422
33.4
8.10E−07


888
G-alpha
103
447
509.4
4.00E−150


889
PSK
13
83
94.2
3.90E−25


890
PSK
20
118
149.2
1.10E−41


892
PSK
20
101
143.5
5.60E−40


893
Sugar_tr
33
473
−38.5
1.10E−05


894
MFS_1
63
548
57.3
5.00E−14


895
MFS_1
46
466
28.6
1.60E−05


898
Phytochrome
48
227
27.2
3.20E−06


898
HisKA
237
302
59.6
1.00E−14


898
HATPase_c
349
486
79.2
1.30E−20


899
Hpt
44
129
42.6
1.40E−09


901
Hpt
44
122
55.1
2.30E−13


902
Hpt
30
112
55
2.60E−13


903
GAF
158
307
88.1
2.70E−23


903
HisKA
343
408
87.5
4.10E−23


903
HATPase_c
455
586
134.1
3.90E−37


904
GAF
159
308
75.9
1.20E−19


904
HisKA
344
409
77.9
3.20E−20


904
HATPase_c
456
586
109
1.40E−29


905
p450
45
523
187.4
3.50E−53


906
Sugar_tr
32
472
−71.7
1.30E−04


907
AP2
131
196
139.5
9.10E−39


908
AP2
17
81
121.1
3.10E−33


909
AP2
17
82
142.5
1.10E−39


910
DUF6
115
233
36.3
1.10E−07


910
DUF6
253
394
33.4
7.90E−07


911
TPT
183
335
126.5
7.30E−35


912
UAA
81
385
−117.9
1.60E−04


912
TPT
231
379
169
1.20E−47


913
DUF6
24
157
53.3
8.30E−13


913
DUF6
204
333
26.2
1.10E−04


914
UAA
9
330
−142.8
2.80E−03


914
DUF6
19
146
35.2
2.30E−07


914
TPT
189
326
−10.4
2.30E−03


914
DUF6
198
326
57
6.40E−14


915
DUF6
21
154
55.4
1.80E−13


915
DUF6
198
328
30.4
6.20E−06


916
DUF6
26
160
21.9
2.30E−03


916
TPT
193
333
−5.8
1.20E−03


916
DUF6
202
333
26.8
7.50E−05


917
DUF6
28
161
39.1
1.50E−08


917
DUF6
202
331
64.4
3.80E−16


919
TPT
156
298
142.9
8.40E−40


920
DUF6
22
155
61.9
2.00E−15


920
DUF6
201
330
45.7
1.60E−10


921
DUF6
26
159
62.5
1.30E−15


921
DUF6
205
334
51.9
2.20E−12


922
DUF914
1
328
373.7
2.80E−109


922
UAA
18
304
−142.8
2.80E−03


922
DUF6
22
144
21.3
3.40E−03


923
HEAT
22
57
12.7
1.20E+00


923
HEAT
97
133
19.8
9.90E−03


923
HEAT
181
217
27.9
3.60E−05


923
HEAT
218
253
13.5
8.00E−01


923
HEAT
259
295
11.7
1.60E+00


923
HEAT
341
376
11.5
1.70E+00


923
HEAT
381
416
18.9
1.80E−02


925
DUF6
22
154
39.4
1.20E−08


926
UAA
27
313
−136.4
1.30E−03


926
TPT
167
307
171.9
1.60E−48


927
DUF6
15
148
39
1.70E−08


928
DUF6
27
160
54.3
4.10E−13


928
DUF6
201
330
29.8
9.80E−06


929
DUF6
128
252
84.7
2.80E−22


929
DUF6
277
407
104.4
3.40E−28


930
TPT
156
299
163.8
4.30E−46


931
DUF914
2
327
672
4.60E−199


933
DUF6
31
164
53.1
9.30E−13


933
DUF6
215
344
58.8
1.80E−14


934
UAA
6
306
−56.5
1.40E−07


934
TPT
156
300
171.2
2.60E−48


935
DUF6
16
149
73.5
6.70E−19


935
DUF6
193
322
76
1.20E−19


936
TPT
163
303
167.7
2.90E−47


937
UAA
50
350
−68.7
5.60E−07


937
TPT
200
344
162
1.50E−45


938
Pkinase
504
777
139.8
7.20E−39


938
Pkinase_Tyr
504
777
122.7
1.00E−33


939
B_lectin
81
189
44.9
2.70E−10


939
PAN_2
322
387
49.4
1.20E−11


939
PAN_1
322
404
4.4
5.80E−02


939
Pkinase_Tyr
470
736
115.7
1.30E−31


939
Pkinase
470
736
172.3
1.20E−48


940
B_lectin
80
187
49.4
1.20E−11


940
PAN_2
326
391
74.4
3.70E−19


940
Pkinase
473
742
194.7
2.10E−55


940
Pkinase_Tyr
474
742
106.2
9.80E−29


941
B_lectin
110
225
48.7
2.00E−11


941
PAN_2
360
425
70.8
4.30E−18


941
Pkinase
507
776
188.2
2.00E−53


941
Pkinase_Tyr
508
776
100.9
3.80E−27


942
B_lectin
67
176
77.3
4.90E−20


942
PAN_2
311
373
67.5
4.30E−17


942
Pkinase
450
718
195.6
1.20E−55


942
Pkinase_Tyr
451
718
121.9
1.80E−33


943
B_lectin
74
188
122.8
9.50E−34


943
S_locus_glycop
202
333
111.6
2.20E−30


943
PAN_2
350
415
113.1
8.10E−31


943
PAN_1
362
433
14.4
5.90E−03


943
Pkinase
499
784
161.9
1.70E−45


943
Pkinase_Tyr
500
784
113.8
5.10E−31


944
B_lectin
75
199
126.2
9.10E−35


944
S_locus_glycop
212
340
129.9
7.00E−36


944
PAN_2
357
425
108.7
1.70E−29


944
PAN_1
362
443
13.2
7.70E−03


944
Pkinase
506
790
191.2
2.50E−54


944
Pkinase_Tyr
507
790
106.2
9.30E−29


945
PAN_1
336
417
3.4
7.30E−02


945
Pkinase
500
770
188
2.20E−53


945
Pkinase_Tyr
500
770
111.2
3.00E−30


946
14-3-3
6
243
509.5
3.80E−150


947
14-3-3
6
117
28.5
1.00E−05


948
14-3-3
8
120
34.7
3.20E−07


949
14-3-3
3
240
507.1
2.00E−149


950
14-3-3
3
115
27.9
1.10E−05


951
14-3-3
9
246
512.4
5.10E−151


952
14-3-3
9
120
30.8
4.70E−06


953
14-3-3
5
240
492.1
6.50E−145


954
14-3-3
5
116
31.7
2.50E−06


955
14-3-3
7
116
30.8
4.70E−06


956
14-3-3
4
239
430.4
2.40E−126


958
14-3-3
8
245
517.1
2.00E−152


959
14-3-3
8
120
32
2.10E−06


960
14-3-3
8
245
485.1
8.30E−143


962
14-3-3
8
249
505.4
6.60E−149


963
14-3-3
8
125
31.3
3.50E−06


964
G-alpha
431
841
14.7
2.20E−18


965
Pkinase
40
363
240.5
3.60E−69


966
Pkinase
117
402
287.2
3.00E−83


967
Pkinase
34
319
298.5
1.30E−86


968
CK_II_beta
93
267
451.2
1.30E−132


969
CK_II_beta
26
233
575.7
4.40E−170


970
CK_II_beta
89
263
440.5
2.20E−129


971
CK_II_beta
87
260
445.5
7.10E−131


972
RRM_1
10
81
104.5
3.10E−28


973
RRM_1
9
80
108.7
1.70E−29


973
zf-CCHC
128
145
37.8
3.90E−08


974
RRM_1
39
110
112.7
1.00E−30


975
RRM_1
33
104
111.1
3.10E−30


976
Methyltransf_11
63
162
21.8
3.90E−04


976
Methyltransf_12
63
161
23.9
5.80E−04


977
Methyltransf_11
85
184
32
2.10E−06


977
Methyltransf_12
85
182
29.8
9.60E−06


978
Methyltransf_11
70
169
31.3
3.40E−06


979
RRM_1
10
81
108.2
2.40E−29


980
zf-C3HC4
253
293
40.2
6.90E−09


981
zf-C3HC4
190
230
41.3
3.20E−09


982
zf-C3HC4
234
274
35.4
1.90E−07


983
zf-C3HC4
221
261
48.4
2.30E−11


984
zf-C3HC4
156
196
28.6
2.10E−05


985
zf-C3HC4
218
258
37.9
3.60E−08


986
zf-C3HC4
94
135
41.9
2.10E−09


987
zf-C3HC4
204
245
17.9
2.20E−03


988
zf-C3HC4
126
169
40.1
7.50E−09


989
PA
51
149
62.7
1.20E−15


989
zf-C3HC4
237
278
41.3
3.30E−09


990
zf-C3HC4
87
128
46.1
1.20E−10


991
zf-C3HC4
607
647
39.8
9.50E−09


992
zf-C3HC4
467
507
27.5
4.70E−05


993
zf-C3HC4
155
195
38.7
2.00E−08


994
zf-C3HC4
127
167
27.6
4.60E−05


995
zf-C3HC4
33
73
34.2
4.60E−07


996
Skp1_POZ
5
65
99.6
9.60E−27


996
Skp1
91
168
186.3
7.40E−53


997
Skp1
90
164
53.7
6.00E−13


998
Skp1_POZ
8
68
123.8
4.80E−34


998
Skp1
99
176
192.8
8.40E−55


999
LRR_2
174
201
6.7
1.90E+00


999
LRR_2
301
325
7.2
1.60E+00


1000
F-box
15
63
21.2
3.70E−03


1000
LRR_1
168
190
12.6
1.30E+00


1002
F-box
17
64
17.6
4.70E−02


1002
LRR_1
299
325
8.6
7.10E+00


1002
LRR_2
299
323
14.3
1.80E−01


1003
Response_reg
42
177
69.4
1.20E−17


1004
zf-CHY
35
113
119.1
1.30E−32


1004
zf-C3HC4
166
208
33.3
8.40E−07


1005
zf-CHY
59
142
141.2
2.80E−39


1005
zf-C3HC4
195
237
32.4
1.60E−06


1006
MtN3_slv
9
98
86.2
1.00E−22


1006
MtN3_slv
132
218
124.5
2.90E−34


1007
zf-C3HC4
215
256
16.1
3.40E−03


1008
PHD
198
248
56.1
1.10E−13


1009
F-box
17
64
35.9
1.40E−07


1010
F-box
22
69
26.7
8.20E−05


1011
F-box
9
56
34.8
3.00E−07


1011
Kelch_1
97
153
36.7
8.30E−08


1011
Kelch_2
97
153
21.8
2.50E−03


1011
Kelch_2
155
201
30.3
6.70E−06


1011
Kelch_1
155
201
54.1
4.50E−13


1011
Kelch_1
285
339
30.1
8.00E−06


1012
F-box
76
123
33.2
9.30E−07


1012
Kelch_1
167
213
33.5
7.40E−07


1012
Kelch_1
215
262
52.1
1.80E−12


1012
Kelch_2
215
262
15.7
1.70E−01


1013
F-box
26
73
33.6
6.90E−07


1013
Kelch_2
116
162
19.9
8.90E−03


1013
Kelch_1
116
162
42.2
1.70E−09


1013
Kelch_2
164
210
18.4
2.70E−02


1013
Kelch_1
164
210
21.6
2.90E−03


1014
zf-C3HC4
49
91
40.7
5.00E−09


1017
Prp19
64
133
161.6
2.10E−45


1017
WD40
253
291
47.2
5.40E−11


1017
WD40
298
336
33.4
8.10E−07


1017
WD40
384
421
32.2
1.80E−06


1018
zf-C3HC4
36
81
26.6
8.90E−05


1019
zf-C3HC4
58
103
34.3
4.30E−07


1020
TPR_1
14
47
22.2
1.80E−03


1020
TPR_2
14
47
20.6
5.70E−03


1020
TPR_2
48
81
23.5
7.80E−04


1020
TPR_1
48
81
33.1
9.60E−07


1020
TPR_1
82
115
12.8
1.60E−01


1020
TPR_2
82
115
21.1
4.10E−03


1020
U-box
195
269
132.5
1.20E−36


1021
zf-C3HC4
24
64
27.8
3.90E−05


1022
F-box
195
243
23.8
5.90E−04


1022
Kelch_1
292
340
17.6
3.90E−02


1022
Kelch_2
292
340
15.9
1.50E−01


1022
Kelch_2
345
392
33.6
7.10E−07


1022
Kelch_1
345
392
17.2
4.40E−02


1022
Kelch_1
397
445
13.4
1.20E−01


1022
Kelch_2
449
501
27.6
4.40E−05


1022
Kelch_2
516
564
26.4
9.90E−05


1023
F-box
205
253
28.5
2.40E−05


1023
Kelch_1
300
348
17.8
3.70E−02


1023
Kelch_2
300
348
17.8
3.90E−02


1023
Kelch_2
353
400
24.4
4.10E−04


1023
Kelch_1
405
453
12.7
1.40E−01


1023
Kelch_2
458
509
18.3
2.80E−02


1023
Kelch_2
518
566
32.8
1.20E−06


1024
Cellulose_synt
167
977
2072.7
0.00E+00


1025
Cellulose_synt
254
1069
2130.3
0.00E+00


1028
zf-C3HC4
22
64
22
8.20E−04


1029
F-box
32
79
35.9
1.40E−07


1029
LysM
109
152
29.7
1.00E−05


1030
Sina
121
320
442.6
5.20E−130


1031
F-box
18
65
37.6
4.20E−08


1034
F-box
18
66
31
4.10E−06


1035
SPX
1
167
88.9
1.50E−23


1035
zf-C3HC4
238
286
16.9
2.80E−03


1037
Cullin
15
237
52.9
4.60E−14


1038
zf-C3HC4
227
270
35.6
1.70E−07


1039
zf-C3HC4
361
398
39.6
1.10E−08


1040
Melibiase
34
362
−25.7
2.30E−14


1041
Copine
80
227
281
2.30E−81


1042
F-box
36
83
31.8
2.40E−06


1046
F-box
1
47
20.9
4.70E−03


1046
LRR_2
150
174
14.4
1.70E−01


1047
F-box
11
59
25.9
1.40E−04


1048
U-box
5
78
69.7
9.30E−18


1049
Glycos_transf_1
465
648
59.4
1.20E−14


1049
S6PP
701
942
−88.5
1.40E−04


1050
Pkinase
491
759
187.9
2.50E−53


1050
Ribonuc_2-5A
764
890
261.8
1.40E−75


1052
Pkinase
77
345
187.9
2.50E−53


1052
Ribonuc_2-5A
350
476
261.8
1.40E−75


1053
Pkinase
674
980
198.2
1.90E−56


1053
Ribonuc_2-5A
985
1115
256.7
4.80E−74


1055
Pkinase
101
407
198.2
1.90E−56


1055
Ribonuc_2-5A
412
542
256.7
4.80E−74


1056
dCMP_cyt_deam_1
218
319
145.6
1.30E−40


1057
Aldo_ket_red
7
285
442
8.10E−130


1058
Aldo_ket_red
5
292
465.6
6.20E−137


1060
SOH1
18
112
205.8
9.90E−59


1061
dCMP_cyt_deam_1
1
107
117.9
2.80E−32


1062
Put_Phosphatase
4
229
−87.8
7.10E−04


1063
NAF1
104
273
372.4
7.00E−109


1064
Aldo_ket_red
10
289
204.4
2.70E−58


1065
Glutaredoxin
19
85
72.9
1.10E−18


1066
TPT
156
299
163.8
4.30E−46


1067
DUF850
2
230
517.4
1.60E−152


1068
LEA_2
17
166
309.5
6.20E−90


1069
ABA_WDS
43
96
102.9
9.40E−28


1070
ABA_WDS
51
104
105.7
1.40E−28


1071
LEA_2
30
179
280.9
2.40E−81


1072
LEA_2
30
179
300.6
2.90E−87


1073
ABA_WDS
54
107
105.1
2.10E−28


1074
Sigma70_r2
260
330
69.1
1.50E−17


1074
Sigma70_r3
334
414
67.5
4.20E−17


1074
Sigma70_r4
433
485
38.5
2.30E−08


1075
Sigma70_r2
314
384
83.9
4.80E−22


1075
Sigma70_r3
388
469
76.3
9.60E−20


1075
Sigma70_r4
482
535
73.1
8.80E−19


1076
Sigma70_r2
302
372
70.7
4.80E−18


1076
Sigma70_r3
376
457
95.4
1.70E−25


1076
Sigma70_r4
469
522
98.3
2.30E−26


1077
Bromodomain
61
150
114.6
2.80E−31


1078
Homeobox
70
124
73.7
5.70E−19


1078
HALZ
125
169
43.9
5.50E−10


1079
bZIP_1
118
179
60.2
6.60E−15


1079
bZIP_2
118
172
40.5
5.90E−09


1080
MFMR
1
156
268.9
1.00E−77


1080
bZIP_2
244
298
40
8.10E−09


1080
bZIP_1
244
308
89.8
8.30E−24


1081
Remorin_C
402
512
145
2.00E−40


1082
Remorin_N
23
83
48
3.20E−11


1082
Remorin_C
85
194
165.5
1.40E−46


1083
Myb_DNA-binding
39
90
48.5
2.30E−11


1084
Homeobox
77
131
77.3
4.70E−20


1084
HALZ
132
176
65.4
1.80E−16


1085
Homeobox
77
131
77.3
4.70E−20


1085
HALZ
132
176
70.2
6.40E−18


1086
HSF_DNA-bind
11
170
148.9
1.30E−41


1088
HSF_DNA-bind
13
167
170.8
3.60E−48


1089
HSF_DNA-bind
15
219
144
4.10E−40


1090
AUX_IAA
18
218
231.9
1.40E−66


1091
AUX_IAA
19
219
97.9
3.00E−26


1092
SRF-TF
9
59
111.1
3.30E−30


1092
K-box
48
144
138
2.60E−38


1093
SRF-TF
9
59
120.8
3.90E−33


1093
K-box
75
174
154.8
2.20E−43


1094
SRF-TF
9
59
111.5
2.40E−30


1094
K-box
73
173
55.8
1.50E−13


1095
SRF-TF
9
59
109.7
8.30E−30


1095
K-box
71
170
112.4
1.30E−30


1096
SRF-TF
9
59
120.7
4.20E−33


1096
K-box
76
173
128.5
1.80E−35


1097
SRF-TF
9
59
113.1
8.30E−31


1097
K-box
71
170
105.8
1.30E−28


1098
SRF-TF
9
59
120.8
3.90E−33


1098
K-box
75
174
154.8
2.20E−43


1099
zf-C2H2
35
58
19.5
1.20E−02


1100
LIM
10
67
55.9
1.30E−13


1100
LIM
105
162
67.2
5.10E−17


1101
Myb_DNA-binding
5
57
34.1
5.00E−07


1101
Linker_histone
122
190
14.4
2.80E−04


1102
Myb_DNA-binding
14
61
44.9
2.70E−10


1102
Myb_DNA-binding
67
112
46
1.30E−10


1103
Myb_DNA-binding
11
57
59.3
1.30E−14


1103
Myb_DNA-binding
63
108
48.9
1.70E−11


1104
Myb_DNA-binding
14
61
51.9
2.20E−12


1104
Myb_DNA-binding
67
112
50.8
4.50E−12


1105
NAM
23
158
278.5
1.30E−80


1106
MED7
4
169
270.1
4.40E−78


1107
zf-LSD1
27
51
43.6
6.70E−10


1107
zf-LSD1
66
90
54.8
2.80E−13


1107
zf-LSD1
104
128
55.2
2.20E−13


1108
Hydrolase
18
209
95.4
1.70E−25


1109
zf-C3HC4
349
389
38.5
2.30E−08


1110
zf-C3HC4
244
284
41.2
3.40E−09


1111
zf-CHY
35
113
119.1
1.30E−32


1111
zf-C3HC4
166
208
33.3
8.40E−07


1112
Ank
50
82
34.2
4.60E−07


1112
Ank
83
115
32.9
1.20E−06


1112
Ank
117
148
12.8
4.40E−01


1112
Ank
180
212
40.8
4.80E−09


1112
Ank
223
255
37.4
5.00E−08


1112
zf-C3HC4
321
370
23.9
5.30E−04


1113
zf-B_box
1
47
42.6
1.30E−09


1113
zf-B_box
48
90
24.8
3.00E−04


1113
CCT
356
394
69.7
9.50E−18


1114
GRAS
154
464
462.7
4.60E−136


1115
TFIIS
1
93
31.9
2.20E−06


1115
TFIIS_M
189
317
173.9
4.10E−49


1115
TFIIS_C
328
366
86.5
8.20E−23


1116
zf-B_box
1
47
38.8
1.80E−08


1116
zf-B_box
55
102
38.5
2.30E−08


1117
Copine
111
259
298.9
9.70E−87


1118
Copine
111
259
298.3
1.40E−86


1120
zf-CCCH
35
61
16.6
8.40E−03


1120
zf-CCCH
95
121
30.7
5.20E−06


1120
KH_1
246
310
63.8
5.70E−16


1120
zf-CCCH
324
349
38.8
1.90E−08


1121
AUX_IAA
7
222
240.4
3.90E−69


1122
zf-B_box
1
47
39
1.70E−08


1122
zf-B_box
51
96
46.8
7.50E−11


1124
SRF-TF
9
59
118.2
2.30E−32


1124
K-box
75
174
158.7
1.50E−44


1125
SRF-TF
9
59
110.5
4.80E−30


1125
K-box
75
174
141.1
2.90E−39


1126
SRF-TF
9
59
120.8
3.90E−33


1126
K-box
75
174
162.3
1.20E−45


1127
SRF-TF
9
59
124.4
3.10E−34


1127
K-box
75
174
167.9
2.60E−47


1128
SRF-TF
9
59
124.4
3.10E−34


1128
K-box
75
174
167.9
2.60E−47


1129
FLO_LFY
1
395
1029.1
0.00E+00


1130
Hydrolase
114
295
47.5
4.50E−11


1131
Hydrolase
130
317
50
8.20E−12


1132
Hydrolase
110
298
45.1
2.30E−10


1133
AP2
15
80
145.7
1.20E−40


1140
Pkinase
20
275
350.4
3.00E−102


1140
NAF
314
374
120
6.50E−33


1141
WD40
560
599
34.5
3.70E−07


1141
WD40
646
683
30.4
6.10E−06


1142
Pkinase
139
401
317.6
2.30E−92


1143
EMP24_GP25L
76
137
56.3
1.00E−13


1144
RRM_1
4
70
55.9
1.40E−13


1144
zf-CCHC
86
103
32.5
1.40E−06


1145
Frigida
112
414
431.3
1.30E−126


1146
DUF810
175
1046
1901.1
0.00E+00


1147
Dor1
21
369
478.8
6.60E−141


1148
Alpha-amylase
26
356
188.4
1.70E−53


1148
Alpha-amyl_C2
357
415
103.2
7.90E−28


1149
AT_hook
99
111
7.4
1.20E+00


1149
DUF296
126
246
177.4
3.60E−50


1150
IMPDH
23
491
672.5
3.20E−199


1150
CBS
53
218
21.4
8.00E−04


1151
IMPDH
35
512
774.3
7.60E−230


1151
CBS
119
235
89.6
9.60E−24


1152
IMPDH
7
473
831.3
5.20E−247


1152
CBS
91
206
91.4
2.80E−24


1153
IMPDH
12
486
777.4
8.30E−231


1153
CBS
96
218
104.2
3.70E−28


1154
zf-CCCH
38
64
22.1
1.60E−03


1154
zf-CCCH
105
131
33.5
7.60E−07


1154
KH_1
174
236
56.7
7.50E−14


1154
zf-CCCH
274
299
46.2
1.10E−10


1155
Response_reg
21
134
102.7
1.10E−27


1155
Myb_DNA-binding
214
264
50.1
7.50E−12


1156
zf-C3HC4
251
291
37.3
5.10E−08


1157
MFS_1
129
549
28.1
1.60E−05


1158
Sugar_tr
34
472
−51.8
3.00E−05


1159
AP2
15
80
145.2
1.70E−40


1160
AP2
7
72
145.6
1.30E−40


1161
Pyridoxal_deC
35
383
513.3
2.70E−151


1162
AUX_IAA
7
263
378.3
1.20E−110


1163
Cyclin_N
92
207
148.4
1.90E−41


1163
Cyclin_C
209
336
128.3
2.20E−35


1164
Cyclin_N
183
321
109.6
9.10E−30


1166
zf-Dof
105
167
142.4
1.20E−39


1167
NAM
52
179
232
1.30E−66


1168
NAM
18
145
252.2
1.10E−72


1169
p450
41
477
129.4
9.70E−36


1170
LRRNT_2
23
63
40.6
5.40E−09


1170
LRR_1
90
112
14
5.60E−01


1170
LRR_1
114
136
22.7
1.30E−03


1170
LRR_1
162
184
13.2
9.40E−01


1170
LRR_1
186
208
9.7
4.40E+00


1170
LRR_1
234
256
16
1.30E−01


1170
LRR_1
258
280
12.4
1.40E+00


1170
LRR_1
282
304
12.3
1.40E+00


1170
LRR_1
306
328
13.3
8.70E−01


1170
LRR_1
354
376
13.9
5.90E−01


1170
LRR_1
402
425
11.7
1.80E+00


1170
LRR_1
448
470
13.8
6.10E−01


1170
LRR_1
472
494
9.8
4.20E+00


1170
LRR_1
519
541
14.8
3.10E−01


1170
LRR_1
543
565
9.6
4.50E+00


1170
LRR_1
567
589
16.1
1.20E−01


1170
LRR_1
591
613
18.7
2.20E−02


1170
LRR_1
615
638
10.8
2.70E+00


1170
LRR_1
748
771
13.4
8.20E−01


1170
LRR_1
772
791
9.7
4.50E+00


1170
LRR_1
824
846
16.4
1.00E−01


1170
LRR_1
848
870
11.8
1.80E+00


1170
Pkinase_Tyr
1002
1275
118.5
1.80E−32


1170
Pkinase
1002
1275
145.9
1.10E−40


1171
LRRNT_2
21
60
65.1
2.30E−16


1171
LRR_1
139
158
8.6
7.00E+00


1171
LRR_1
185
207
18.2
3.00E−02


1171
LRR_1
209
231
12.5
1.30E+00


1171
LRR_1
233
255
16.3
1.10E−01


1171
LRR_1
259
281
17.6
4.40E−02


1171
LRR_1
283
306
13.9
5.70E−01


1171
LRR_1
308
330
11.5
2.00E+00


1171
LRR_1
332
354
10.4
3.20E+00


1171
LRR_1
357
379
12.1
1.50E+00


1171
LRR_1
381
403
10
3.90E+00


1171
LRR_1
429
451
14.3
4.30E−01


1171
LRR_1
453
475
12.3
1.40E+00


1171
LRR_1
477
499
12.9
1.10E+00


1171
LRR_1
501
520
11.1
2.40E+00


1171
LRR_1
593
615
15.6
1.80E−01


1171
LRR_1
617
639
15.7
1.70E−01


1171
LRR_1
641
663
12.1
1.50E+00


1171
Pkinase
824
1098
139.3
1.10E−38


1171
Pkinase_Tyr
824
1098
124
4.20E−34


1172
LRR_1
199
219
8.6
7.20E+00


1172
LRR_1
221
244
16.5
9.50E−02


1172
LRR_1
246
268
14.3
4.40E−01


1172
LRR_1
270
293
17.5
4.70E−02


1172
LRR_1
295
317
11.9
1.70E+00


1172
LRR_1
319
342
13.5
8.00E−01


1172
LRR_1
345
367
13.3
9.00E−01


1172
LRR_1
369
391
15.1
2.50E−01


1172
LRR_1
393
415
10.3
3.40E+00


1172
LRR_1
417
439
16.4
1.00E−01


1172
LRR_1
441
463
13.5
7.80E−01


1172
LRR_1
465
487
14.3
4.50E−01


1172
LRR_1
489
511
13.8
6.20E−01


1172
LRR_1
582
604
10.8
2.70E+00


1172
LRR_1
630
652
19.3
1.40E−02


1172
LRR_1
653
674
16.4
1.10E−01


1172
Pkinase_Tyr
807
1080
114.8
2.50E−31


1172
Pkinase
807
1080
161.6
2.00E−45


1173
FAD_binding_4
55
200
30
8.20E−06


1174
FAD_binding_4
55
200
29.3
1.40E−05


1175
Sterol_desat
35
210
87
5.70E−23


1176
Sterol_desat
35
246
180.6
3.90E−51


1177
Sterol_desat
37
248
184.2
3.20E−52


1178
Sterol_desat
43
254
215.6
1.10E−61


1179
Peptidase_S10
41
465
669.2
3.10E−198


1180
Peptidase_S10
56
474
711.4
6.30E−211


1181
F-box
205
253
30.2
7.10E−06


1181
Kelch_1
300
348
18.6
2.20E−02


1181
Kelch_2
300
348
23.7
6.70E−04


1181
Kelch_1
352
400
8.4
4.30E−01


1181
Kelch_2
353
400
26.4
1.00E−04


1181
Kelch_1
405
453
15.4
7.00E−02


1181
Kelch_2
524
572
34.3
4.20E−07


1182
F-box
272
320
28.5
2.40E−05


1182
Kelch_1
367
415
21
4.10E−03


1182
Kelch_2
367
415
20.6
5.50E−03


1182
Kelch_2
420
467
24.4
4.10E−04


1182
Kelch_2
471
520
15.1
2.50E−01


1182
Kelch_1
472
520
12
1.70E−01


1182
Kelch_1
525
576
8.7
4.00E−01


1182
Kelch_2
525
576
20
8.40E−03


1182
Kelch_2
586
634
29.8
9.70E−06


1183
ADH_N
36
165
116.7
6.40E−32


1183
ADH_zinc_N
196
342
117
5.40E−32


1184
ADH_N
27
155
135.6
1.30E−37


1184
ADH_zinc_N
186
332
115.4
1.70E−31


1185
ADH_N
27
155
118.3
2.10E−32


1185
ADH_zinc_N
186
328
139.2
1.10E−38


1186
ADH_N
36
165
130.6
4.50E−36


1186
ADH_zinc_N
196
338
129.9
6.80E−36


1187
ADH_N
36
165
135
2.00E−37


1187
ADH_zinc_N
196
338
124.6
2.70E−34


1188
ADH_N
35
163
116.1
1.00E−31


1188
ADH_zinc_N
197
343
119.6
9.10E−33


1189
ADH_N
34
163
119.4
1.00E−32


1189
ADH_zinc_N
194
336
145.3
1.60E−40


1190
ADH_N
34
163
121.3
2.70E−33


1190
ADH_zinc_N
194
336
126.3
8.30E−35


1191
TPT
156
298
165.2
1.70E−46


1192
TPT
154
296
177.3
3.90E−50


1193
TPT
151
293
150.6
4.10E−42


1194
Sugar_tr
91
552
421.2
1.50E−123


1194
MFS_1
95
511
85.3
1.80E−22


1195
Cyclin_N
61
193
117.1
5.00E−32


1195
Cyclin_C
195
326
36.6
8.70E−08


1196
SAC3_GANP
24
209
90.8
4.10E−24


1197
SAC3_GANP
20
211
214.5
2.30E−61


1198
SAC3_GANP
24
209
106.9
5.90E−29


1199
SAC3_GANP
24
209
122.2
1.40E−33


1200
WD40
183
220
26.2
1.20E−04


1200
WD40
289
328
33.8
5.90E−07


1201
WD40
204
241
26.2
1.20E−04


1201
WD40
311
350
33.8
5.90E−07


1202
CHASE
86
298
339
8.00E−99


1202
HisKA
359
424
83.1
8.50E−22


1202
HATPase_c
471
654
130.1
6.30E−36


1202
Response_reg
829
963
111.6
2.20E−30


1203
CHASE
198
411
356.8
3.40E−104


1203
HisKA
472
537
93.4
6.90E−25


1203
HATPase_c
584
759
124.3
3.50E−34


1203
Response_reg
945
1068
106.2
9.70E−29


1204
CHASE
302
526
342.6
6.40E−100


1204
HisKA
587
652
90.2
6.20E−24


1204
HATPase_c
699
866
132.7
9.90E−37


1204
Response_reg
1035
1170
106.9
6.00E−29


1205
CHASE
163
389
347.6
2.10E−101


1205
HisKA
450
515
89.7
9.00E−24


1205
HATPase_c
562
722
128.9
1.40E−35


1205
Response_reg
890
1025
92.6
1.20E−24


1206
MFS_1
66
429
63.7
5.90E−16


1207
MFS_1
69
432
56.4
9.20E−14


1208
MFS_1
51
415
50.8
4.50E−12


1209
CHASE
110
321
288.1
1.70E−83


1209
HisKA
382
447
88.4
2.20E−23


1209
HATPase_c
494
682
112.8
9.90E−31


1209
Response_reg
869
1004
105.6
1.50E−28


1210
PTR2
113
517
661.3
7.40E−196


1211
PTR2
118
521
399.1
6.60E−117


1212
PTR2
97
499
482.9
3.80E−142


1213
PTR2
122
526
531.9
6.60E−157


1214
PTR2
98
500
500.5
1.90E−147


1215
AT_hook
34
46
7.5
1.20E+00


1215
DUF296
61
180
198.4
1.70E−56


1220
BIR
20
117
62.6
1.30E−15


1220
BIR
153
241
96.5
7.70E−26


1221
AT_hook
34
46
7.5
1.20E+00


1221
DUF296
61
180
198.4
1.70E−56


1224
Bap31
1
188
39.2
4.60E−11



















TABLE 23





Pfam domain name
Accession #
Gathering cutoff
Domain description


















14-3-3
PF00244.10
25.0
14-3-3 protein


2-Hacid_dh_C
PF02826.9
−82.2
D-isomer specific 2-hydroxyacid





dehydrogenase, NAD binding domain


2OG-FeII_Oxy
PF03171.10
11.5
2OG-Fe(II) oxygenase superfamily


AA_permease
PF00324.11
−120.8
Amino acid permease


ABA_WDS
PF02496.6
25.0
ABA/WDS induced protein


ADH_N
PF08240.2
−14.5
Alcohol dehydrogenase GroES-like domain


ADH_zinc_N
PF00107.16
23.8
Zinc-binding dehydrogenase


AP2
PF00847.10
0.0
AP2 domain


AT_hook
PF02178.9
3.6
AT hook motif


AUX_IAA
PF02309.7
−83.0
AUX/IAA family


AdoHcyase
PF05221.7
−205.2
S-adenosyl-L-homocysteine hydrolase


AdoHcyase_NAD
PF00670.12
−23.6
S-adenosyl-L-homocysteine hydrolase, NAD





binding domain


Aldedh
PF00171.12
−209.3
Aldehyde dehydrogenase family


Aldo_ket_red
PF00248.11
−97.0
Aldo/keto reductase family


Alpha-amyl_C2
PF07821.3
25.0
Alpha-amylase C-terminal beta-sheet domain


Alpha-amylase
PF00128.14
−92.6
Alpha amylase, catalytic domain


Ank
PF00023.20
0.0
Ankyrin repeat


Arm
PF00514.13
17.0
Armadillo/beta-catenin-like repeat


Asp
PF00026.14
−153.8
Eukaryotic aspartyl protease


BCCT
PF02028.8
−17.0
BCCT family transporter


BIR
PF00653.12
0.0
Inhibitor of Apoptosis domain


BRAP2
PF07576.2
0.7
BRCA1-associated protein 2


BRCT
PF00533.16
27.8
BRCA1 C Terminus (BRCT) domain


BTB
PF00651.21
6.2
BTB/POZ domain


B_lectin
PF01453.15
28.2
D-mannose binding lectin


Bap31
PF05529.2
−39.4
B-cell receptor-associated protein 31-like


Bromodomain
PF00439.15
8.9
Bromodomain


C1_1
PF00130.12
10.5
Phorbol esters/diacylglycerol binding domain





(C1 domain)


C2
PF00168.20
3.7
C2 domain


CBFD_NFYB_HMF
PF00808.13
18.4
Histone-like transcription factor (CBF/NF-Y)





and archaeal histone


CBS
PF00571.18
17.5
CBS domain pair


CCT
PF06203.4
25.0
CCT motif


CHASE
PF03924.4
25.0
CHASE domain


CK_II_beta
PF01214.9
−106.0
Casein kinase II regulatory subunit


CMAS
PF02353.10
−177.9
Cyclopropane-fatty-acyl-phospholipid





synthase


Cellulose_synt
PF03552.5
−257.9
Cellulose synthase


Copine
PF07002.6
−36.5
Copine


Cu-oxidase
PF00394.12
−18.9
Multicopper oxidase


Cu-oxidase_2
PF07731.4
−5.8
Multicopper oxidase


Cu-oxidase_3
PF07732.5
10.0
Multicopper oxidase


Cu_bind_like
PF02298.8
−16.4
Plastocyanin-like domain


Cullin
PF00888.12
−33.3
Cullin family


Cyclin_C
PF02984.9
−13.0
Cyclin, C-terminal domain


Cyclin_N
PF00134.13
−14.7
Cyclin, N-terminal domain


DAD
PF02109.6
25.0
DAD family


DAGK_acc
PF00609.10
−50.0
Diacylglycerol kinase accessory domain


DAGK_cat
PF00781.14
−5.7
Diacylglycerol kinase catalytic domain





(presumed)


DPBB_1
PF03330.8
5.3
Rare lipoprotein A (RlpA)-like double-psi





beta-barrel


DUF1313
PF07011.2
25.0
Protein of unknown function (DUF1313)


DUF221
PF02714.6
25.0
Domain of unknown function DUF221


DUF231
PF03005.6
−58.0
Arabidopsis proteins of unknown function


DUF296
PF03479.5
−11.0
Domain of unknown function (DUF296)


DUF580
PF04515.3
25.0
Protein of unknown function, DUF580


DUF6
PF00892.11
20.8
Integral membrane protein DUF6


DUF810
PF05664.2
25.0
Protein of unknown function (DUF810)


DUF850
PF05863.3
25.0
Eukaryotic protein of unknown function





(DUF850)


DUF914
PF06027.3
−193.0
Eukaryotic protein of unknown function





(DUF914)


DXP_redisom_C
PF08436.3
25.0
1-deoxy-D-xylulose 5-phosphate





reductoisomerase C-terminal


DXP_reductoisom
PF02670.7
−49.7
1-deoxy-D-xylulose 5-phosphate





reductoisomerase


Dor1
PF04124.3
25.0
Dor1-like family


EMP24_GP25L
PF01105.14
10.0
emp24/gp25L/p24 family/GOLD


Enolase_C
PF00113.12
−71.2
Enolase, C-terminal TIM barrel domain


Enolase_N
PF03952.6
11.3
Enolase, N-terminal domain


Epimerase
PF01370.11
−46.3
NAD dependent epimerase/dehydratase





family


Exo_endo_phos
PF03372.13
11.0
Endonuclease/Exonuclease/phosphatase





family


F-box
PF00646.23
13.9
F-box domain


FAD_binding_4
PF01565.13
−8.1
FAD binding domain


FAD_binding_6
PF00970.14
−11.4
Oxidoreductase FAD-binding domain


FAT
PF02259.13
275.0
FAT domain


FATC
PF02260.10
20.0
FATC domain


FBPase
PF00316.10
−170.3
Fructose-1-6-bisphosphatase


FBPase_glpX
PF03320.4
−198.1
Bacterial fructose-1,6-bisphosphatase, glpX-





encoded


FLO_LFY
PF01698.7
−225.0
Floricaula/Leafy protein


Flavodoxin_2
PF02525.7
−46.4
Flavodoxin-like fold


Flavoprotein
PF02441.9
11.0
Flavoprotein


Frigida
PF07899.2
−62.5
Frigida-like protein


G-alpha
PF00503.10
−230.0
G-protein alpha subunit


GAF
PF01590.16
23.0
GAF domain


GH3
PF03321.4
−336.0
GH3 auxin-responsive promoter


GRAS
PF03514.5
−78.0
GRAS family transcription factor


GST_C
PF00043.15
22.3
Glutathione S-transferase, C-terminal domain


GST_N
PF02798.10
14.6
Glutathione S-transferase, N-terminal domain


Globin
PF00042.12
−8.8
Globin


Glutaredoxin
PF00462.14
17.2
Glutaredoxin


Glyco_transf_20
PF00982.11
−243.6
Glycosyltransferase family 20


Glycos_transf_1
PF00534.10
−7.3
Glycosyl transferases group 1


HALZ
PF02183.8
17.0
Homeobox associated leucine zipper


HATPase_c
PF02518.16
22.4
Histidine kinase-, DNA gyrase B-, and





HSP90-like ATPase


HD-ZIP_N
PF04618.3
25.0
HD-ZIP protein N terminus


HEAT
PF02985.12
11.5
HEAT repeat


HLH
PF00010.16
8.3
Helix-loop-helix DNA-binding domain


HMG_box
PF00505.9
4.1
HMG (high mobility group) box


HSF_DNA-bind
PF00447.8
−70.0
HSF-type DNA-binding


H_PPase
PF03030.7
−377.0
Inorganic H+ pyrophosphatase


Hexapep
PF00132.14
0.3
Bacterial transferase hexapeptide (three





repeats)


HisKA
PF00512.15
10.3
His Kinase A (phosphoacceptor) domain


Histone
PF00125.14
17.4
Core histone H2A/H2B/H3/H4


Homeobox
PF00046.19
−4.1
Homeobox domain


Hpt
PF01627.13
25.0
Hpt domain


Hydrolase
PF00702.16
13.6
haloacid dehalogenase-like hydrolase


Hydrolase_3
PF08282.2
−64.8
haloacid dehalogenase-like hydrolase


IMPDH
PF00478.15
−190.6
IMP dehydrogenase/GMP reductase





domain


IPP-2
PF04979.4
−30.0
Protein phosphatase inhibitor 2 (IPP-2)


IlvN
PF07991.2
−75.8
Acetohydroxy acid isomeroreductase,





catalytic domain


K-box
PF01486.8
0.0
K-box region


KH_1
PF00013.19
10.5
KH domain


KR
PF08659.1
−74.3
KR domain


Kelch_1
PF01344.15
7.8
Kelch motif


Kelch_2
PF07646.5
14.0
Kelch motif


LEA_2
PF03168.4
25.0
Late embryogenesis abundant protein


LEA_4
PF02987.7
22.6
Late embryogenesis abundant protein


LIM
PF00412.12
0.0
LIM domain


LRRNT_2
PF08263.3
18.6
Leucine rich repeat N-terminal domain


LRR_1
PF00560.23
7.7
Leucine Rich Repeat


LRR_2
PF07723.3
6.0
Leucine Rich Repeat


Lactamase_B
PF00753.17
24.6
Metallo-beta-lactamase superfamily


Linker_histone
PF00538.9
−8.0
linker histone H1 and H5 family


LysM
PF01476.10
20.0
LysM domain


MED7
PF05983.2
−39.2
MED7 protein


MFMR
PF07777.2
−46.7
G-box binding protein MFMR


MFS_1
PF07690.6
23.5
Major Facilitator Superfamily


MIF4G
PF02854.9
−6.0
MIF4G domain


MIF4G_like
PF09088.1
25.0
MIF4G like


MIF4G_like_2
PF09090.1
−46.1
MIF4G like


MatE
PF01554.9
−4.8
MatE


Melibiase
PF02065.9
−228.6
Melibiase


Methyltransf_11
PF08241.2
20.9
Methyltransferase domain


Methyltransf_12
PF08242.2
23.0
Methyltransferase domain


Mito_carr
PF00153.17
0.0
Mitochondrial carrier protein


Mlo
PF03094.6
−263.0
Mlo family


MtN3_slv
PF03083.6
9.7
MtN3/saliva family


Myb_DNA-binding
PF00249.21
14.0
Myb-like DNA-binding domain


NAD_binding_1
PF00175.11
−3.9
Oxidoreductase NAD-binding domain


NAD_binding_4
PF07993.2
−87.7
Male sterility protein


NAF
PF03822.5
4.5
NAF domain


NAF1
PF05492.3
−43.3
NAF1 domain


NAM
PF02365.6
−19.0
No apical meristem (NAM) protein


NAS
PF03059.6
−60.0
Nicotianamine synthase protein


NPH3
PF03000.5
25.0
NPH3 family


Na_H_Exchanger
PF00999.11
−67.9
Sodium/hydrogen exchanger family


OPT
PF03169.6
−238.6
OPT oligopeptide transporter protein


Orn_Arg_deC_N
PF02784.7
−76.0
Pyridoxal-dependent decarboxylase,





pyridoxal binding domain


Orn_DAP_Arg_deC
PF00278.12
6.7
Pyridoxal-dependent decarboxylase, C-





terminal sheet domain


P-II
PF00543.12
−29.0
Nitrogen regulatory protein P-II


PA
PF02225.12
13.0
PA domain


PAN_1
PF00024.16
1.4
PAN domain


PAN_2
PF08276.2
−4.9
PAN-like domain


PB1
PF00564.15
12.3
PB1 domain


PBP
PF01161.10
−20.6
Phosphatidylethanolamine-binding protein


PEMT
PF04191.3
25.0
Phospholipid methyltransferase


PEP-utilizers
PF00391.13
0.6
PEP-utilising enzyme, mobile domain


PEP-utilizers_C
PF02896.8
−173.0
PEP-utilising enzyme, TIM barrel domain


PHD
PF00628.19
25.9
PHD-finger


PI-PLC-X
PF00388.9
18.8
Phosphatidylinositol-specific phospholipase





C, X domain


PI-PLC-Y
PF00387.9
−11.0
Phosphatidylinositol-specific phospholipase





C, Y domain


PI3_PI4_kinase
PF00454.17
14.8
Phosphatidylinositol 3- and 4-kinase


PMEI
PF04043.6
25.0
Plant invertase/pectin methylesterase





inhibitor


PPDK_N
PF01326.9
−150.2
Pyruvate phosphate dikinase, PEP/pyruvate





binding domain


PSK
PF06404.3
25.0
Phytosulfokine precursor protein (PSK)


PTR2
PF00854.12
−50.0
POT family


PaO
PF08417.2
25.0
Pheophorbide a oxygenase


Peptidase_C14
PF00656.12
−22.5
Caspase domain


Peptidase_S10
PF00450.12
−198.0
Serine carboxypeptidase


Pescadillo_N
PF06732.2
−167.1
Pescadillo N-terminus


PfkB
PF00294.14
−67.8
pfkB family carbohydrate kinase


Phytochrome
PF00360.10
13.0
Phytochrome region


Pirin
PF02678.6
25.0
Pirin


Pirin_C
PF05726.3
−8.8
Pirin C-terminal cupin domain


Pkinase
PF00069.15
−70.3
Protein kinase domain


Pkinase_C
PF00433.14
14.0
Protein kinase C terminal domain


Pkinase_Tyr
PF07714.7
65.0
Protein tyrosine kinase


Pollen_allerg_1
PF01357.11
17.2
Pollen allergen


Prp19
PF08606.2
−1.5
Prp19/Pso4-like


Put_Phosphatase
PF06888.3
−100.0
Putative Phosphatase


Pyridoxal_deC
PF00282.9
−158.6
Pyridoxal-dependent decarboxylase





conserved domain


RPE65
PF03055.6
−156.5
Retinal pigment epithelial membrane protein


RRM_1
PF00076.12
17.7
RNA recognition motif. (a.k.a. RRM, RBD, or





RNP domain)


Rapamycin_bind
PF08771.1
25.0
Rapamycin binding domain


Remorin_C
PF03763.4
25.0
Remorin, C-terminal region


Remorin_N
PF03766.4
10.1
Remorin, N-terminal region


Response_reg
PF00072.14
4.0
Response regulator receiver domain


Ribonuc_2-5A
PF06479.2
25.0
Ribonuclease 2-5A


Ribosomal_60s
PF00428.9
6.0
60s Acidic ribosomal protein


Ribosomal_L10
PF00466.10
−14.0
Ribosomal protein L10


Ribosomal_L18p
PF00861.12
25.0
Ribosomal L18p/L5e family


Rieske
PF00355.16
−7.0
Rieske [2Fe—2S] domain


S-methyl_trans
PF02574.6
−33.2
Homocysteine S-methyltransferase


S6PP
PF05116.4
−113.7
Sucrose-6F-phosphate phosphohydrolase


S6PP_C
PF08472.1
−34.2
Sucrose-6-phosphate phosphohydrolase C-





terminal


SAC3_GANP
PF03399.6
−15.2
SAC3/GANP/Nin1/mts3/eIF-3 p25 family


SATase_N
PF06426.4
25.0
Serine acetyltransferase, N-terminal


SBP
PF03110.5
25.0
SBP domain


SBP56
PF05694.2
25.0
56 kDa selenium binding protein (SBP56)


SET
PF00856.18
23.5
SET domain


SOH1
PF05669.3
25.0
SOH1


SPX
PF03105.10
−20.0
SPX domain


SRF-TF
PF00319.9
11.0
SRF-type transcription factor (DNA-binding





and dimerisation domain)


S_locus_glycop
PF00954.11
−12.7
S-locus glycoprotein family


Sigma70_r2
PF04542.4
18.6
Sigma-70 region 2


Sigma70_r3
PF04539.6
10.0
Sigma-70 region 3


Sigma70_r4
PF04545.6
21.6
Sigma-70, region 4


Sina
PF03145.7
−48.4
Seven in absentia protein family


Skp1
PF01466.9
−2.0
Skp1 family, dimerisation domain


Skp1_POZ
PF03931.5
14.9
Skp1 family, tetramerisation domain


Sterol_desat
PF01598.8
−13.0
Sterol desaturase


Sugar_tr
PF00083.14
−85.0
Sugar (and other) transporter


TFIIS
PF08711.1
3.0
Transcription elongation factor S-II protein N





terminal


TFIIS_C
PF01096.9
15.0
Transcription factor S-II (TFIIS)


TFIIS_M
PF07500.4
7.4
Transcription factor S-II (TFIIS), central





domain


TLC
PF03219.5
25.0
TLC ATP/ADP transporter


TPR_1
PF00515.18
7.7
Tetratricopeptide repeat


TPR_2
PF07719.7
20.1
Tetratricopeptide repeat


TPT
PF03151.7
−15.3
Triose-phosphate Transporter family


Transket_pyr
PF02779.14
−49.0
Transketolase, pyrimidine binding domain


Transketolase_C
PF02780.10
−15.5
Transketolase, C-terminal domain


Tub
PF01167.8
−98.0
Tub family


U-box
PF04564.6
−7.6
U-box domain


UAA
PF08449.2
−146.2
UAA transporter family


UDPGP
PF01704.8
−265.2
UTP--glucose-1-phosphate





uridylyltransferase


UPF0005
PF01027.11
−6.7
Uncharacterised protein family UPF0005


UPF0041
PF03650.4
−33.6
Uncharacterised protein family (UPF0041)


Ubie_methyltran
PF01209.9
−117.0
ubiE/COQ5 methyltransferase family


VDE
PF07137.2
−40.0
Violaxanthin de-epoxidase (VDE)


WD40
PF00400.22
21.5
WD domain, G-beta repeat


WRKY
PF03106.6
25.0
WRKY DNA-binding domain


Zein
PF01559.7
−21.0
Zein seed storage protein


adh_short
PF00106.15
−40.2
short chain dehydrogenase


bZIP_1
PF00170.11
24.5
bZIP transcription factor


bZIP_2
PF07716.5
15.0
Basic region leucine zipper


dCMP_cyt_deam_1
PF00383.13
−9.0
Cytidine and deoxycytidylate deaminase zinc-





binding region


efhand
PF00036.22
21.7
EF hand


p450
PF00067.12
−105.0
Cytochrome P450


zf-B_box
PF00643.14
15.3
B-box zinc finger


zf-C2H2
PF00096.16
17.7
Zinc finger, C2H2 type


zf-C3HC4
PF00097.15
16.0
Zinc finger, C3HC4 type (RING finger)


zf-CCCH
PF00642.15
0.0
Zinc finger C-x8-C-x5-C-x3-H type (and





similar)


zf-CCHC
PF00098.13
17.9
Zinc knuckle


zf-CHY
PF05495.3
25.0
CHY zinc finger


zf-Dof
PF02701.6
25.0
Dof domain, zinc finger


zf-LSD1
PF06943.3
25.0
LSD1 zinc finger


zf-UBP
PF02148.9
25.0
Zn-finger in ubiquitin-hydrolases and other





protein









Example 9
Selection of Transgenic Plants with Enhanced Agronomic Trait(s)
This example illustrates the preparation and identification by selection of transgenic seeds and plants derived from transgenic plant cells of this invention having recombinant DNA in a chromosome in the nucleus of such cells. The plants and seeds are identified by screening for a transgenic plant having an enhanced agronomic trait imparted by expression of a protein selected from the group including the homologous proteins identified in Example 6. Transgenic plant cells of corn, soybean, cotton, canola, wheat and rice are transformed with recombinant DNA for expressing each of the homologs identified in Example 6. Plants are regenerated from the transformed plant cells and used to produce progeny plants and seed that are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. Plants are identified exhibiting enhanced traits imparted by expression of the homologous proteins.

## Claims

1. A plant cell nucleus with stably integrated, recombinant DNA, wherein said recombinant DNA comprises a promoter that is functional in said plant cell nucleus and that is operably linked to a protein coding recombinant DNA encoding the protein consisting of SEQ ID NO: 1032 or a protein having an amino acid sequence with at least 95% but less than 100% amino acid sequence identity to SEQ ID NO: 1032; and wherein said plant cell nucleus is selected by screening a population of transgenic plants that have said recombinant DNA and an enhanced trait as compared to control plants that do not have said recombinant DNA in their nuclei; and wherein said enhanced trait is selected from the group of enhanced traits consisting of cold tolerance, yield, nitrogen use efficiency, and seed protein.

2. The plant cell nucleus of claim 1 wherein said protein coding DNA encodes the protein having the amino acid sequence of SEQ ID NO:1032.

3. The plant cell nucleus of claim 1 further comprising a DNA expressing a protein that provides tolerance from exposure to an herbicide applied at levels that are lethal to a wild type plant cell of the same species.

4. The plant cell nucleus of claim 3 wherein said herbicide is a glyphosate, dicamba, or glufosinate compound.

5. A transgenic plant comprising a plurality of plant cells with the plant cell nucleus of claim 1.

6. The transgenic plant of claim 5 which is homozygous for said recombinant DNA.

7. A transgenic seed comprising a plurality of plant cells with the plant cell nucleus of claim 1.

8. The transgenic seed of claim 7, wherein said transgenic seed is obtained from a corn, soybean, cotton, canola, alfalfa, wheat or rice transgenic plant comprising said plant cell nucleus.

9. A transgenic pollen grain comprising a haploid gamete of the plant cell nucleus of claim 1, wherein the gamete comprises said recombinant DNA.

10. A method for manufacturing non-natural, transgenic seed, said method comprising the steps of:
(a) providing a population of transgenic plants transformed with a recombinant DNA construct comprising a promoter that is functional in a plant cell and that is operably linked to a protein coding recombinant DNA encoding the protein consisting of SEQ ID NO: 1032 or a protein having an amino acid sequence with at least 95% but less than 100% amino acid sequence identity to SEQ ID NO: 1032, wherein said recombinant DNA construct is stably integrated into the genome of said transgenic plants;
(b) screening the population of transgenic plants provided in step (a) for an enhanced trait and said recombinant DNA, wherein said enhanced trait is selected from the group of enhanced traits consisting of water use efficiency, cold tolerance, heat tolerance, resistance to salt exposure, shade tolerance, yield, nitrogen use efficiency, seed protein and seed oil as compared to control plants of the same species lacking said DNA construct;
(c) selecting one or more transformed plants from said screening of step (b) which exhibit said enhanced trait as compared to said control plants lacking said DNA construct, wherein said enhanced trait is due to the expression of said protein in said selected transformed plants;
(d) verifying that said recombinant DNA is stably integrated in said selected transformed plants;
(e) analyzing tissue of said selected transformed plants to determine the expression of a gene that encodes a protein having the function of a protein having the amino acid sequence of SEQ ID NO:1032; and
(f) collecting seed from said selected transformed plants.

11. A method of producing hybrid corn seed comprising:
(a) acquiring hybrid corn seed from a herbicide tolerant corn plant which also has stably-integrated recombinant DNA construct comprising a promoter that is functional in plant cells and that is operably linked to a protein coding recombinant DNA encoding the protein consisting of SEQ ID NO: 1032 or a protein having an amino acid sequence with at least 95% but less than 100% amino acid sequence identity to SEQ ID NO: 1032, wherein said recombinant DNA construct is stably integrated into the genome of said hybrid corn seed;
(b) producing corn plants from said hybrid corn seed of step a), wherein a fraction of the plants produced from said hybrid corn seed is homozygous for said recombinant DNA, a fraction of the plants produced from said hybrid corn seed is hemizygous for said recombinant DNA, and a fraction of the plants produced from said hybrid corn seed has none of said recombinant DNA;
(c) selecting corn plants which are homozygous and hemizygous for said recombinant DNA by treating with an herbicide;
(d) collecting seed from herbicide-treated-surviving corn plants and planting said seed to produce further progeny corn plants;
(e) repeating steps (c) and (d) at least once to produce an inbred corn line; and
(f) crossing said inbred corn line with a second corn line to produce hybrid seed; and wherein said inbred corn line of step (e) and hybrid seed of step (f) comprise said recombinant DNA.