Genes and uses for plant enhancement

A recombinant DNA construct 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 at least one protein having an amino acid sequence comprising a Pfam domain module selected from the group consisting of AOX, UBX, DUF1635, Senescence, zf-Tim10_DDP, IQ, Skp1_POZ::Skp1, NLE::WD40::WD40::WD40::WD40, ArfGap::C2, DUF1639, PBP, PPR::PPR::PPR::PPR::PPR::PPR, zf-C3HC4::YDG_SRA, AAA, F-box::Kelch—1::Kelch—1, PetM, CPDase, Iso_dh, OTU, Sugar_tr, Pro_dh, Pkinase::NAF, HEAT::HEAT::HEAT::HEAT::HEAT::HEAT::HEAT::HEAT::HEAT::HEA T::HEAT::HEAT, Pkinase, Nuc_sug_transp, eIF2A, cobW, DUF538, WD40::WD40::WD40, DUF393, ScpA_ScpB, PCI, SRF-TF, DUF1644, DUF1645, NIF, WD40::WD40::WD40::WD40, WD40::WD40::WD40::WD40::WD40::WD40::WD40, F-box::LRR—2, tRNA-synt—1g, Glutaminase, Dehydrin, TP_methylase, Band—7, LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1, Exo_endo_phos, Ank::Ank::Ank, HLH, DUF617, Uricase::Uricase, ABC_tran::ABC2_membrane::PDR_assoc::ABC_tran::ABC2_membrane, Bystin, AWPM-19, IGPD, PAS—2::GAF::Phytochrome::HisKA::HATPase_c, 60 KD_IMP, DUF6::TPT, Glyco_hydro—1, F-box::Sel1::Sel1::zf-MYND, Cyclin_N::Cyclin_C, MFS—1, Tetraspannin, Cyt-b5, HMA::HMA, zf-CW::MBD, IQ::IQ, PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR, eIF-1a, Pro_isomerase, DUF623, PGM_PMM_I::PGM_PMM_II::PGM_PMM_III::PGM_PMM_IV, Hydrolase, SKI, Aa_trans, Ribosomal_L19, Isoamylase_N::Alpha-amylase, zf-MYND::UCH, Spermine_synth, ABC1, 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, MtN3_slv::MtN3_slv, TPR—2, UQ_con, NIR_SIR_ferr::NIR_SIR::NIR_SIR_ferr::NIR_SIR, Metallothio_PEC, F-box, NUDIX, HEAT::Arm::HEAT::Arm, P21-Arc, 11, KTI12, Acyltransferase, Glutaredoxin, TIM, FKBP_C, NTP_transferase::Hexapep::Hexapep, Transaldolase, Peptidase_M22, TFIIS, Cyclin_N, DZC, Methyltransf—12, PFK, DUF1749, DUF1677, Y_phosphatase2, B3—4::B5, MSF1, Hin1, mTERF, TMEM14, zf-PARP::zf-PARP::PADR1::BRCT::WGR::PARP_reg::PARP, DUF21::CBS, Ribosomal_S8, LysM, Ank::Ank::Ank::Pkinase, SNARE_assoc, DUF640, iPGM_N::Metalloenzyme, Cullin, Glyco_transf—8, GAF::HisKA, Ribosomal_L37, Phi—1, OstA, HD::RelA_SpoT, Pyr_redox—2, Isy1, Peptidase_C26, WRKY, LRRNT—2::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::Pkinase, DUF212, PGI, Pyr_redox—2::efhand, Aminotran—1—2, PGK, FTHFS, PB1::Pkinase_Tyr, GRP, Arf, Radical_SAM, Cystatin, Stig1, UDPGT, Sulfotransfer—1, NADPH_Ox::Ferric_reduct:FAD_binding—8::NAD_binding—6, LRRNT—2::LRR—1::LRR—1::LRR—1::LRR—1::Pkinase, Ank::Ank::Pkinase_Tyr, AMP-binding, DEAD::Helicase_C, LSM, NTP_transferase, DHDPS, Mo25, DUF581, DREPP, Mito_carr:Mito_carr:Mito_carr, ThiC, Aminotran—3, Nramp, Aminotran—4, Pkinase::efhand::efhand::efhand::efhand, MMR_HSR1, B56, Transket_pyr::Transketolase_C, malic::Malic_M, PSI_PsaH, F-box::LRR—2::FBD, BNR::BNR::BNR, ADH_N::ADH_zinc_N, HMG-CoA_red, Pkinase::efhand::efhand, Cyclin, efhand::efhand::efhand, Fer4::Fer4, PTR2, Rib—5-P_isom_A, LRRNT—2::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::Pkinase, Pyr_redox, TLD, Voltage_CLC::CBS, DJ-1_PfpI::DJ-1_PfpI, SIR2, GATase::GMP_synt_C, Citrate_synt, DUF300, DUF231, Molybdop_Fe4S4::Molybdopterin::Molydop_binding, LRR—1::LRR—1::LRR—1::Pkinase, NOI, DAGK_cat, DUF239, V-SNARE, ELFV_dehydrog_N::ELFV_dehydrog, MCM, LRR—1::
• LRR—1::
• LRR—1::
• LRR—1::
• LRR—1::
• LRR—1::
• LRR—1::
• LRR—1::PKinase, FAD_binding—4, SpoIIE, DUF740, Gp_dh_N::Gp_dh_C, FHA::PP2C, Pyr_redox—2::Pyr_redox_dim, CBS, GRAM, DUF676, GILT, AlaDh_PNT_N::AlaDh_PNT_C::Saccharop_dh_N::Saccharop_dh, Peptidase_C54, ArfGap, Metallophos, SH3—1, DUF313, DUF383::DUF384, Brix, Ras, Maf, DUF246, RNA_pol_I_A49, C2, CRAL_TRIO_N::CRAL_TRIO, DUF1350, p450, PP2C, Histone, Enolase_N::Enolase_C, GTP_EFTU::GTP_EFTU_D2::EFG_C, MSP, NTP_transferase::Hexapep::Hexapep::Hexapep::Hexapep, RRM—1::RRM—1, ETC_C1_NDUFA4, Amino_oxidase, DUF827, CCT, BCNT, ubiquitin::UBA::XPC-binding::UBA, Tryp_alpha_amyl, FBPase, ACT::ACT, IPK, Usp::Pkinase, Sina, CTP_transf—1, PPR::PPR::PPR::PPR::PPR::PPR::PPR, PfkB, Sterol_desat, Zip, ADH_zinc_N, WD40::WD40::WD40::WD40::PWP2, Globin, BTB::NPH3, Amidohydro—2, CS, PAP2, Cys_Met_Meta_PP, Gar1, DAO, NDUF_B7, RNA_polI_A14, DUF833, MATH::BTB, DUF1000, DUF1001, TFIIS_C, PLAT::Lipoxygenase, Self-incomp_S1, Thioredoxin, DUF1005, DUF791::MFS—1, DUF6::DUF6, Gal-bind_lectin::Galactosyl_T, Invertase_neut, SAC3_GANP, DUF260, Polyketide_cyc, polyprenyl_synt, DUF23, GHMP_kinases_N::GHMP_kinases_C, Complex1—30kDa::Complex1—49kDa, Transthyretin, TB2_DP1_HVA22, Aldose_epim, H_PPase, SIS::CBS, YjeF_N::Carb_kinase, DUF914, Mov34, UFD1, Ahal_N::AHSA1, Dirigent, Response_reg, 14-3-3, Rho_GDI, Di19, SNARE, DUF778, efhand, Chitin_bind—1::Barwin, Phosphoesterase, zf-CCHC, LRRNT—2::LRR—1::LRR—1::Pkinase, TPT, SOR_SNZ::ThiG, CN_hydrolase::NAD_synthase, PPDK_N::PEP-utilizers::PEP-utilizers_C, PRA-CH::PRA-PH, Glucokinase, adh_short, SapB—1::SapB—2::SapB—1::SapB—2, DEAD::Helicase_C::DSHCT, Fibrillarin, AA_permease, NDK, RRM—1, GATase—2::Asn_synthase, Mago-bind, DHquinase_I::Shikimate_dh_N::Shikimate_DH, OPT, Orn_Arg_deC_N::Orn_DAP_Arg_deC, DUF926, Not3::NOT2—3—5, Pro_CA, Copine, DUF783, RWD, MATH, TOM20_plant, zf-UBR, Cyt-b5::FA_desaturase, DUF788, E1_dh, Saccharop_dh, Glycolytic, Actin, AstE_AspA, ATP_synt_H, SET, Cornichon, Pyridoxal_deC, MGDG_synth::Glyco_tran—28_C, Arm::Arm, DUF860, CorA, DnaJ::DnaJ_CXXCXGXG::DnaJ_C, DUF862, Prefoldin, PEARLI-4, PGAM, Gln-synt_N::Gln-synt_C, DUF793, CPSase_L_chain::CPSase_L_D2::CPSase_L_D3::CPSase_L_chain::CPSase_L_D2::MGS, Abhydrolase—1, Lung—7-TM_R, Abhydrolase—3, Glyco_hydro—17, F-box::FBA—1, DUF506, F-box::FBA—3, efhand_like::PI-PLC-X::PI-PLC-Y::C2, 2OG-Fell_Oxy, Pribosyltran, TFIIS_M::SPOC, FA_desaturase, Nol1_Nop2_Fmu, DUF59, LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1, Cytochrom_C, TPK_catalytic::TPK_B1_binding, DnaJ, Pkinase_Tyr, MIP, Ribonuc_L-PSP, NicO, zf-LSD1::zf-LSD1::zf-LSD1, PC_rep::PC_rep::PC_rep::PC_rep::PC_rep::PC_rep, Trehalose_PPase, LRR—1, WD40::WD40::WD40::WD40::WD40::WD40::WD40::WD40::WD40::WD40::Utp13, Phytochelatin::DUF1984, RNA_pol_A_bac, LRRNT—2::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—1::LRR—1::LRR—1::Pkinas e, Reticulon, XG_FTase, RRM—1::zf-CCHC, Pre-SET::SET, MATH::MATH, Str_synth, SPT2, Lectin_legB::Pkinase, Snf7, Aldedh, HIT, zf-C3HC4, TFIIF_alpha, Transketolase_N::Transket_pyr:Transketolase_C, WD40::WD40, ARM—1, DUF26::DUF26::Pkinase, SRF-TF::K-box, PseudoU_synth—1::PseudoU_synth—1, PI3_PI4 kinase, CAF1, Tim17, Cpn60_TCP1, Xan_ur_permease, Biotin_lipoyl::E3_binding::2-oxoacid_dh, Myb_DNA-binding, AP2, Diphthamide_syn, DUF525, PBD, and Molybdop_Fe4S4::Molybdopterin::Molydop_binding::Fer2_BFD;
• 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:
• 67782 through 67894;
• c. said recombinant DNA comprises a promoter that is functional in 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 918, 932, 1208, 1305, 1375, 1407, and homologs thereof listed in table 16;
• 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 762, 846 and 1055;
• e. said recombinant DNA suppresses comprises a promoter that is functional in said plant cell and operably linked to DNA that transcribe into RNA that suppresses the level of at least one endogenous protein wherein said endogenous protein has an amino acid sequence comprising a pfam domain module selected from the group consisting of RRM—1, Peptidase_C54, AP2, DUF788, RRM—1, NUDIX, adh_short, PTR2, Gar1, Response_reg, DUF86, Glycolytic, Metallophos, ATP_synt_H, SPT2, CTP_transf—1, Ribosomal_L19, DUF740, Di19, Cyt-b5::FA_desaturase, DUF791::MFS—1, PB1::Pkinase_Tyr, F-box::LRR—2, NADPH_Ox::Ferric_reduct::FAD_binding—8::NAD_binding—6, Nuc_sug_transp, HMA::HMA, MATH::MATH, RNA_pol_I_A49, DUF23, p450, ABC1, Hydrolase, Band—7, WD40::WD40::WD40, IGPD, Cyclin_N, Glyco_transf—8, DREPP, SET, DUF6::TPT, SOR_SNZ::ThiG, Pkinase::efhand::efhand::efhand::efhand, Pkinase, Fer4::Fer4, Rho_GDI, bhydrolase—1, Transket_pyr::Transketolase_C, Chitin_bind—1::Barwin, XG_FTase, FTHFS, MGDG_synth::Glyco_tran—28_C, PSI_PsaH, cobW, tRNA-synt—1g, Pro_CA, RRM—1::zf-CCHC, Cyclin_N, Amino_oxidase, H_PPase, Cyt-b5, ArfGap, ABC_tran::ABC2_membrane::
• PDR_assoc::ABC_tran::ABC2_membrane, PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR, WD40::WD40::WD40::WD40::WD40::WD40::WD40, BTB::NPH3RRM—1, Peptidase_C54, AP2, DUF788, RRM—1, NUDIX, adh_short, PTR2, Gar1, Response_reg, DUF86, Glycolytic, Metallophos, ATP_synt_H, SPT2, CTP_transf—1, Ribosomal_L19, DUF740, Di19, Cyt-b5::FA_desaturase, DUF791::MFS—1, PB1::Pkinase_Tyr, F-box::LRR—2, NADPH_Ox::Ferric_reduct::FAD_binding—8::NAD_binding—6, Nuc_sug_transp, HMA::HMA, MATH::MATH, RNA_pol_I_A49, DUF23, p450, ABC1, Hydrolase, Band—7, WD40::WD40::WD40, IGPD, Cyclin_N, Glyco_transf—8, DREPP, SET, DUF6::TPT, SOR_SNZ::ThiG, Pkinase::efhand::efhand::efhand::efhand, Pkinase, Fer4::Fer4, Rho_GDI, bhydrolase—1, Transket_pyr:Transketolase_C, Chitin_bind—1::Barwin, XG_FTase, FTHFS, MGDG_synth::Glyco_tran—28_C, PSI_PsaH, cobW, tRNA-synt—1g, Pro_CA, RRM—1::zf-CCHC, Cyclin_N, Amino_oxidase, H_PPase, Cyt-b5, ArfGap, ABC_tran::ABC2_membrane::PDR_assoc::ABC_tran::ABC2_membrane, PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR, WD40::WD40::WD40::WD40::WD40::WD40::WD40, and BTB::NPH3;
• f. said recombinant DNA comprises a promoter that is functional in said plant cell and operably linked to DNA that transcribe into RNA that suppresses the level of an endogenous protein wherein said endogenous protein has an amino acid sequence with at least 70% identity to an amino acid sequence selected from the group consisting of SEQ ID NO:
• 767, 768, 772, 792, 809, 814, 821, 822, 836, 840, 848, 866, and homologs thereof listed in table 16;
• and wherein said recombinant DNA construct is stably integrated into a chromosome in a plant cell nucleus which 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 high salinity tolerance, enhanced shade tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.