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.

What is claimed is: 
     
         1 . A plant cell nucleus with stably integrated, recombinant DNA in a chromosome for expressing in said plant cell a Hap3 transcription factor protein having a CAAT box binding domain, wherein the amino acid sequence of said protein has 60 to 100 percent identity to SEQ ID NO: 615, 616, 617 or 618 and at least one other protein. 
     
     
         2 . A plant cell nucleus of  claim 1  wherein said at least one other protein is a protein listed in Table 2. 
     
     
         3 . A plant cell nucleus of  claim 2  wherein said at least one other protein provides water stress tolerance and is selected from the proteins identified in Table 15. 
     
     
         4 . A plant cell nucleus of  claim 1  wherein said at least other protein has at least 90% identity to an amino acid sequence m the group consisting of SEQ ID NO:624, 656, 658, 667, 674, 675, 687, 718, 722, 729, 741, 744, 746, 747, 748, 775, 786, 796, 820, 828, 829, 830, 836, 842, 845, 848, 860, 862, 864, 866, 878, 892, 941, 946, 947, 952, 954, 955, 958, 960, 963, 985, 1064, 1124, 1125, 1127, 1160, 1161, 1177, 1188, 1189, 1199, 1215, and 1223. 
     
     
         5 . A plant cell nucleus with stably integrated, recombinant DNA, wherein
 (a) said recombinant DNA comprises a promoter that is functional in said plant cell and that is operably linked to a protein coding DNA encoding a protein having an amino acid sequence comprising a Pfam domain module selected from the group consisting of 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::L RR_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, DUF23I, 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::TFIIS_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-Dof, 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_sly; 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, PI-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_::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::P kinase, 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-amy1_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_1::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::L RR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_::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_lectin::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;   (b) said recombinant DNA comprises a promoter that is functional in said plant cell and that is operably linked to a protein coding DNA encoding a protein comprising an amino acid sequence with at least 90% identity to a consensus amino acid sequence selected from the group consisting of SEQ ID NO: 23377 through 23426;   (c) said recombinant DNA comprises a promoter that is functional in said plant cell and that is operably linked to a protein coding DNA encoding a protein comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 675, 897 and 1134 and homologs thereof listed in Table 7;   (d) said recombinant DNA comprises a promoter that is functional in said plant cell and that is operably linked to a protein coding recombinant DNA encoding a protein having an amino acid sequence having at least 70% identity to an amino acid sequence selected from the group consisting of 1216,1217, 1218,1219, 1222, 1223, 1225, 1226, 1227 and 1228;   and wherein said plant cell nucleus is selected by screening a population of transgenic plants that have said recombinant DNA and an enhanced trait as compared to control plants that do not have said recombinant DNA in their nuclei; and wherein said enhanced trait is selected from group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced resistance to salt exposure, enhanced shade tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.   
     
     
         6 . The plant cell nucleus of  claim 5  wherein said protein coding DNA encodes a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 615 through SEQ ID NO: 27373. 
     
     
         7 . The plant cell nucleus of  claim 5  further comprising DNA expressing a protein that provides tolerance from exposure to an herbicide applied at levels that are lethal to a wild type of said plant cell. 
     
     
         8 . The plant cell nucleus of  claim 7  wherein the agent of said herbicide is a glyphosate, dicamba, or glufosinate compound. 
     
     
         9 . A transgenic plant cell or plant comprising a plurality of plant cells with the plant cell nucleus of  claim 5 . 
     
     
         10 . The transgenic plant cell or plant of  claim 9  which is homozygous for said recombinant DNA. 
     
     
         11 . A transgenic seed comprising a plurality of plant cells with a plant cell nucleus of  claim 5 . 
     
     
         12 . The transgenic seed of  claim 11  from a corn, soybean, cotton, canola, alfalfa, wheat or rice plant. 
     
     
         13 . A transgenic pollen grain comprising a haploid derivative of a plant cell nucleus of  claim 5 . 
     
     
         14 . A method for manufacturing non-natural, transgenic seed that can be used to produce a crop of transgenic plants with an enhanced trait resulting from expression of stably-integrated recombinant DNA in a nucleus of  claim 5 , wherein said method for manufacturing said transgenic seed comprising:
 (a) screening a population of plants for said enhanced trait and said recombinant DNA, wherein individual plants in said population can exhibit said trait at a level less than, essentially the same as or greater than the level that said trait is exhibited in control plants which do not contain the recombinant DNA, wherein said enhanced trait is selected from the group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced resistance to salt exposure, enhanced shade tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil;   (b) selecting from said population one or more plants that exhibit said trait at a level greater than the level that said trait is exhibited in control plants,   (c) verifying that said recombinant DNA is stably integrated in said selected plants,   (d) analyzing tissue of said selected plant to determine the expression of a gene that encodes a protein having the function of a protein having an amino acid sequence selected from the group consisting of one of SEQ ID NO:615-27373; and   (e) collecting seed from said selected plant.   
     
     
         15 . A method of producing hybrid corn seed comprising:
 (a) acquiring hybrid corn seed from a herbicide tolerant corn plant which also has stably-integrated, recombinant DNA in a nucleus of  claim 5 ;   (b) producing corn plants from said hybrid corn seed, wherein a fraction of the plants produced from said hybrid corn seed is homozygous for said recombinant DNA, a fraction of the plants produced from said hybrid corn seed is hemizygous for said recombinant DNA, and a fraction of the plants produced from said hybrid corn seed has none of said recombinant DNA;   (c) selecting corn plants which are homozygous and hemizygous for said recombinant DNA by treating with an herbicide;   (d) collecting seed from herbicide-treated-surviving corn plants and planting said seed to produce further progeny corn plants;   (e) repeating steps (c) and (d) at least once to produce an inbred corn line; and   (f) crossing said inbred corn line with a second corn line to produce hybrid seed.