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 bZIP—1, AOX, DUF902::DUF906, 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::LRR—1::Pkinase, ABC_tran::ABC2_membrane::PDR_CDR::ABC_tran::ABC2_membrane, Redoxin, RNase_PH::RNase_PH_C, AAA, GFO_IDH_MocA::GFO_IDH_MocA_C, GRAS, Metallophos, Ribosomal_L18p, Sugar_tr, CDC48_N::AAA::AAA, Pkinase, PAS—3::PAS—3::Pkinase, CRAL_TRIO_N::CRAL_TRIO, p450, RRM—1::RRM—1, SRF-TF, G-alpha, TPR—1::TPR—1, FAE1_CUT1_RppA::ACP syn_III_CC, Globin::FAD_binding—6::NAD_binding—1, TPR—1::TPR—2, IF4E, F-box::LRR—2, FBPase, LRR—2::LRR—1::LRR—1::LRR—1, HSF DNA-bind, Dehydrin, TP_methylase, Response_reg::Myb_DNA-binding, KNOX1::KNOX2::ELK::Homeobox, Catalase, GTP_EFTU::GTP_EFTU_D2::GTP_EFTU_D3, TPR—1::TPR—1::TPR—1::TPR—1, ADH_zinc_N, Globin, CS, GH3, HLH, Ribonuclease_T2, TPR—1::TPR—1::TPR—1::U-box, Dicty_CAR, Cyclin_N::Cyclin_C, MFS—1, Acid_phosphat_A. Methyltransf—7. TPR—1::TPR—1::TPR—2, IBN_N, polyprenyl_synt, AhpC-TSA, Oxidored_FMN, Hydrolase, DS, Response_reg::CCT, Aa_trans, peroxidase, E1-E2_ATPase, F-box::Tub, Response_reg, Rho_GD1, E2F TDP, 14-3-3, AT_hook::AT_hook::AT_hook::AT_hook::YDG_SRA::Pre-SET::SET, Tub, KOW::eIF-5a, MtN3_slv::MtN3_slv, GTP_EFTU, UQ_con, MATI, E2F_TDP::E2F_TDP, HEAT::HEAT::HEAT::FAT::PI3_PI4_kinase::FATC, HMG_CoA_synt_N::HMG_CoA_synt_C, TAP42, DEAD::Helicase_C::DSHCT, NDK, Clp_N::Clp_N::AAA::AAA—2, Cyclin_N, OPT, Orn_Arg_deC_N::Orn_DAP_Arg_deC, PAS::Pkinase, FtsH_ext::AAA::Peptidase_M41, Wzy_C, Mlo, AP2::B3, SET, FKBP_C::FKBP_C::FKBP_C::TPR—1::TPR—1, TPR—2::TPR—1::TPR—1::TPR—2::TPR—1::TPR—1, Pyridoxal_deC, RNase_PH, RB_A::RB_B, WD40::WD40::WD40::WD40::WD40::WD40, SNF2_N::Helicase_C, Aminotran—1—2, Gemini_AL1::Gemini_AL1_M, Hexapep::Hexapep::Hexapep::Hexapep, AP2::AP2, Abhydrolase—1, PAS—2::GAF::Phytochrome::PAS::PAS::HisKA::HATPase_c, Cystatin::Cystatin, Pfam module annoation, Cystatin, F-box::FBA—1, 2OG-Fell_Oxy, FA_desaturase, HSP20, FBPase_glpX, E1-E2_ATPase::Hydrolase, Mito_carr:Mito_carr:Mito_carr, Cellulose_synt, Linker_histone::AT_hook::AT_hook::AT_hook::AT_hook, UPF0016::UPF0016, GDI, Glyco_hydro—32N::Glyco_hydro—32C, TPR—1::TPR—1::TPR—2::U-box, ADH_N::ADH_zinc_N, GDA1_CD39, MIP, CRAL_TRIO, TPR—1::TPR—1::TPR—1::TPR—1::TPR—1::TPR—1::TPR—1::TPR—1, LEA—4::LEA—4, Carb_anhydrase, PTR2, Cu_bind_like, HD-ZIP_N::Homeobox::HALZ, eIF-5a, Asp, S1::S1::S1, SAM_decarbox, WD40::WD40, Citrate_synt, SRF-TF::K-box, HSP9_HSP12, P13_P14_kinase, Ferritin, Xan_ur_permease, Myb_DNA-binding::Myb_DNA-binding, zf-NF-X1::zf-NF-X1::zf-NF-X1::zf-NF-X1::zf-NF-X1, AP2, and Myb_DNA-binding;
- 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:
- 24153 through SEQ ID NO:
- 24174;
- c. said recombinant DNA comprises a promoter that is functional ill plant cells and that is operably linked to a protein coding DNA encoding a protein comprising an amino acid sequence selected from the group consisting of 467, 507, 517, 535, 620, and homologs thereof listed in table 7;
- or
- 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 511 and 513;
- 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.