Rice cells and rice plants

1. A method of providing a modified rice cell having a modified genome, comprising effecting in the genome of the rice cell targeted modifications that result in a change of expression in at least two genes, wherein the targeted modifications comprise an insertion of a predetermined sequence encoded by a single stranded DNA donor molecule, and wherein the insertion of the predetermined sequence comprises a transcription factor recognition site sequence;

wherein each targeted modification is located at one or more site-specific double-strand breaks (DSBs) introduced upstream of, downstream of, or within the two genes;

wherein the targeted modifications are effected in a rice cell by a site-specific DSB-inducing agent and at least one single stranded DNA donor molecule encoding the predetermined sequence, wherein the single stranded DNA donor molecule contains no nucleotide sequence that is sufficiently complementary to permit hybridization to genome sequences immediately adjacent to the location of the DSBs;

wherein the at least two genes are associated with the same trait, wherein the trait is selected from the group consisting of abiotic stress, architecture, biotic stress, flowering time, nutrient use, photosynthesis, and senescence; and

wherein the targeted modifications improve the trait in a rice cell comprising the targeted modifications relative to a rice cell having an unmodified genome, or in a rice plant grown from or comprising a rice cell comprising the modifications relative to a rice plant lacking the modifications.

2. The method of claim 1 , wherein the site-specific DSB-inducing agent is selected from the group consisting of:

(a) a nuclease selected from the group consisting of an RNA-guided nuclease, an RNA-guided DNA endonuclease, a type II Cas nuclease, a Cas9, a type V Cas nuclease, a Cpf1, a CasY, a CasX, a C2c1, a C2c3, an engineered nuclease, a codon-optimized nuclease, a zinc-finger nuclease (ZFN), a transcription activator-like effector nuclease (TAL-effector nuclease), an Argonaute, and a meganuclease or engineered meganuclease;

(b) a polynucleotide encoding one or more nucleases capable of effecting site-specific alteration of a target nucleotide sequence; and

(c) a guide RNA (gRNA) for an RNA-guided nuclease, and a DNA encoding a gRNA for an RNA-guided nuclease.

3. The method of claim 1 , wherein the single-stranded DNA donor molecule has a length of 18 to 300 nucleotides.

4. The method of claim 1 , wherein, after the targeted modifications are effected, a loss of epigenetic marks occurs in less than 0.01% of the genome.

5. The method of claim 1 , wherein, after the targeted modifications are effected, the modified genome is more than 99.9% identical to the unmodified genome.

6. The method of claim 1 , further comprising the step of growing or regenerating a modified rice plant from the modified rice cell.

7. The method of claim 1 , wherein the trait is abiotic stress and each of the at least two genes is a gene that encodes a protein having at least 90% identity to a sequence selected from the group consisting of the sequences identified by SEQ ID NOs:932-1172 or is a gene having a sequence selected from SEQ ID NOs:210-450 or is a gene selected from the group consisting of AP2/ERF-N22(2), AP37, ARAG1, ASR1, ASR3, ASRS, COLD1, CTB4a, CYP-like, CYP94C2b, DCA1, DREB1A, DREB1B, DST, EG1, GA2ox6, Ghd2, Ghd7, glyoxalase II, glyoxylase pathway, gr3, GS2, JIOsPR10, LOC_Os03g61750 (OsTRM13), LOS5, LRK2, microRNA319 (miR319), MicroRNA528 (miR528), MIDI, miR169r-5p, miR390, MSD1, NF-YC13, NUS1, OCPI2, OgTT1, ONAC022, ONAC045, ONAC063, ONAC095, ONAC106, OrbHLH001, OrbHLH2, Os09g0410300, osa-MIR393 (miR393), OsABA8ox3, OsABF2, OsABI5, OsABIL2, OsACA6, OsAMTR1, OsANN1, OsAOX1a, OsAP21, OsAPXa, OsAPXb, OsAREB1, OsAsr1, OsbHLH068, OsbHLH148, OsbZIP16, OsbZIP23, OsbZIP46, OsbZIP71, OsbZIP72, OsCA1, OsCAS, OsCBL8, OsCBSX4, OsCDPK13, OsCDPK7, OsCEST, OsChll, OsCIPK03, OsCIPK12, OsCIPK15, OsCKX2, OsC1pD1, OsCNX, OsCOIN, OsCPK21, OsCPK4, OsCPK9, OsCTR1, OsCYP18-2, OsCYP19-4, OsCYP2, OsCYP21-4, OsDERF1, OsDHODH1, OsDi19-4, OsDIL, OsDIS1, OsDREB1A, OsDREB1B, OsDREB1F, OsDREB1G, OsDREB2A, OsDREB2B, OsECS, OsEm1, OsEREBP1, OsERF109, OsERF10a, OsERF3, OsERF48, OsERF4a, OsERF71, OsERF922, OsFAD8, OsFKBP20, OsGGP, OsGL1-2, OsGL1-6, OsGME-1, OsGME-2, OsGRAS23, OsGRX8, OsGS, OsGSTU4, OsHAP2E, OsHBP1b, OsHKT1;1, OsHKT1;5, OsHOX24, OsHSF7, OsHsfB2b, osHsp101, Oshsp16.9, OsHsp17.0, OsHsp23.7, OsICE1, OsICE2, OsIFL, OsIMP, OsiSAP1, OsJAZ9, OsLAC10, OsLEA3-1, OsLEA3-2, OsLOL5, OsMADS87, OsMAPK5, OsMGD, OsMIOX, OsMPG1, OsMSR2, OsMT1a, OsMYB2, OsMYB30, OsMYB3R-2, Osmyb4, OsMYB48-1, OsMYB511, OsMYB55, OsMYB91, OsMYBR1, OsNAC10, OsNAC2, OsNAC5, OsNAC6, OsNAP, OsNDPK2, OsNF-YA7, OsNHX1, OsORAP1, OsOTS1 SUMO protease, OsPCS2, OsPEX11 (Os03g0302000), OsPFA-DSP1, OsPgk2a-P, OsPILl, OsPIP1;3, OsPP108, OsPR4a, OsPRP3, OsPsbR1, OsPUB15, OsPYL3 or OsPYL9, OsRab7, OsRacB, OsRAN1, OsRAN2, OsRbohA, OsRDCP1, OsRINO1, OSRIP18, OsRZ2, OsRZFP34, OsSce1, OsSCP, OsSDIR1, OsSGL, OsSIDP366, OsSIK1, OsSIK2, OsSIT1, OsSIZ1, OsSMCP1, OsSNAC1, OsSPX1, OsSRFP1, OsSta2, OsSUV3, OsTIFY11b, OsTOP6A1, OsTPP1, OsTPS1, OsTZF1, OsVPE3, OsVTC1-1, OsVTE1, OsWR1, OsWRKY11, OsWRKY30, OsWRKY47, OsWRKY74, OsZFP6, OVP1, Rab16A, RGG1, rHsp90, ROC1, Rubisco activase, SAPK4, SAPK6, SAPK9, sHSP17.7, SKC1, SNAC1, SNAC2, SNAC3, SQS, TLD1, WRKY62, ZAT10, ZFP177, ZFP179, ZFP185, ZFP252, and ZFP36.

8. The method of claim 1 , wherein the trait is architecture and each of the at least two genes is a gene that encodes a protein having at least 90% identity to a sequence selected from the group consisting of the sequences identified by SEQ ID NOs:1175-1348 or is a gene having a sequence selected from SEQ ID NOs:453-626 or is a gene selected from the group consisting of MIR172B (miR172b), MIR172D (miR172d), ARGOS, BZIP27, MIR156B (miR156b), MIR156D (miR156d), MIR156E (miR156e), MIR156F (miR156t), SLG, LAZY1, LAX1, CKX3, GN1A, SG1, HAP3A, RAN1, RAN2, PROG1, LG1, SDIR1, FIE2, DRM2, RMC, CDPK9, JAR1, JAR2, ERF108, FZP, G1, G1L5, FON1, FON2, FOR1, APO1, EG1, RAG, MFO1, LFY, SDG708, RFL, HD3A, MADS18, MADS24, MADS50, BRD2, SK2(T)(SCL, FGR), SLR1, ILI5, 1116, BGLU18, BU1, GIF1, GL2, GS5, LK3, RDD1, GW2, GW5, GW8, SPL16, SPL17, SPL7, D18, ETR2, EXPA4, GA20OX1, GA2OX3, GA2OX6, HOX4, IAA13, NAC2, D2, D61, CCA1, PDR6, ACO4, Rab6a, ZFP179, ILA1, OsSERK1, D11, FTL1, NAL2, NAL3, R9-LOX1, BC1, FC1, RTS, SNAT1, AGO1A, AGO1B, AGO1C, AGO3, GRF10, GRF3, GRF5, DL, DEP1, DEP3, DN1, EP2, EP3, MIR529a (miR529a), RAE2, RA, CUC1, CYP734A2, CYP734A4, CYP734A6, RDD4, APC6, BLE3, CEL9D, SD37, SD1, GATA12, PSK, PSK2, PSK3, DRO1, CKX4, CRL1, CRL4, NAC5, ABIL2, CSLD1, CSLD3, EXPA10, EXPA17, EXPA7, LSI1, PHR1, PHR2, PHR3, PT1, PLT1, PLT2, ERF3, EXPA8, SIZ1, RAB16A, NAM, OsCLE402, OSH15, PNH1, QHB, LOG1, SH4, SH5, SHAT1, SH-H, SERK1, PIN, PIN2, SDG701, RSR1, LPA1, NAC106, MADS57, D14, D17, D27, AGR1, EUI1, ric2, GHD7, GS2, IPT2, IPT3, IPTG, IPT8, SGL, MIR398A (miR398a), SPL14, ZIP4, and ZIP5.

9. The method of claim 1 , wherein the trait is biotic stress and each of the at least two genes is a gene that encodes a protein having at least 90% identity to a sequence selected from the group consisting of the sequences identified by SEQ ID NOs:1349-1456 or is a gene having a sequence selected from SEQ ID NOs:627-734 or is a gene selected from the group consisting of SAP1, ONAC122, ONAC131, PI21, PITA, PIZ, VAMP714, WRKY76, PIKH, XA21, XA5, WRKY45, ALD1, CEBiP, RLCK185, PBZ1, WRKY4, WRKY70, LCB2A1, RAC1, DCL2A, DCL2B, RYMV2, WRKY51, ACDR1, ACS2, AOS1, BIHD1, BWMKY1, CIPK14, edr1-rice ortholog, eIF4G, GAP1, GF14e, GH3, GH3-2, GH3-8, GLP1, Gns1, LOX1, LTP1, OSBIDK1, OsBIMK2, OsBIRH1, OsBISCPL1, OSBWMK1, OsCBT, OsCCR1, OsChib1, OsEREBP1, OsLOL2, OsMAPK6, OsMAPKY5, OsMKK4, Osmlo, OsNAC6, OsPLDbeta1, OsPR1a, OsRAC1, OsRar1, OsSBP, OsSGT1, OsTPC1, OsWAK1, OsWRKY 45-1, OsWRKY13, OsWRKY28, OsWRKY45, OsBBI1, OsBIANK1, OsChil1, OsCIPK15, OsCPK12, OsEDR1|EDR1, OsERF3, OsERF922, OsHIR1, OsLRR1, OsMPK3, OsMPK5, OsMPK6, OsNH1, OsNPR1, OsOxi1, OsSGT, OsTGAP1, OsWRKY62, O5WRKY71, OsWRKY76, PDR6, Pi-d2, Pi37, Pi54, PiK, Pita, RAC5, RACK1A, RACK1B, RCH10, RF2B, RIM1, RYMV1, TPS1, WRKY6, WRKY71, Xa13, XB24, and XB3.

10. The method of claim 1 , wherein the trait is flowering time and each of the at least two genes is a gene that encodes a protein having at least 90% identity to a sequence selected from the group consisting of the sequences identified by SEQ ID NOs:1457-1484 or is a gene having a sequence selected from SEQ ID NOs:735-762 or is a gene selected from the group consisting of CHI, DTH2, Ehd2, Ehd3, Ehd4, ETR2, Hd1, Hd14, Hd16, Hd17, Hd2, Hd4, Hd5, Hd6, OsCO3, OsCOL4, OsDof12, OsGI, OsLF, OsLFL1, OsMADS50, OsMADS56, OsPhyB, RCN1, RFT1, SES, Spin1, and SPL11.

11. The method of claim 1 , wherein the trait is nutrient use and each of the at least two genes is a gene that encodes a protein having at least 90% identity to a sequence selected from the group consisting of the sequences identified by SEQ ID NOs:1485-1546 or is a gene having a sequence selected from SEQ ID NOs:763-824 or is a gene selected from the group consisting of LHY, TPS10, PAL, PAL1, OsAGPS1, OsNAC5, NRAMP1, NRAIVIP3, NAS3, ATM3, OsMTP1, OsRMC, OsYSL1, OsYSL2, OsNAS2, IDEF1, IDEF2, NRAMP4, OsIRO2, OsIRO3, OsYSL15, DMAS1, NAAT1, MIPS, OsLpa1, OsMRP5, OsSULTR3;3, RINO1, ABC1, AlaAT, AMT1;1, AMT1;2, AMT1;3, GRX6, GS1;2, GS2, NADH-GOGAT, OsAMT3;1, OsARG, OsENOD93-1 (LOC_Os06g05010), OsGOGAT2, OsGS1;1, OsNRT1.1b, OsNRT2.1, OsNRT2.3b, OsPTR6, OsPTR9, IPT, OsSPX1, RBCS, NLA1, OsLPT1, OsMYB2P-1, OsPT1, OsWRKY74, PHF1, PHR1, CASTOR, INO1, OsARD2, OsIRT1, and OsNAS1.

12. The method of claim 1 , wherein the trait is photosynthesis and each of the at least two genes is a gene that encodes a protein having at least 90% identity to a sequence selected from the group consisting of the sequences identified by SEQ ID NOs:1547-1565, 1728, 1730, and 1732, or is a gene having a sequence selected from SEQ ID NOs:825-843, 1727, 1729, and 1731, or is a gene selected from the group consisting of GA2ox6, NAL2, Os02g0465900, OsBRI1, OsBZR1, OsCBSX4, OsDET1, OsERF71, OsHAP2E, OsHAP3H, OsHox32, OsMGD, OsNAL1, OsSNAC1, OsSUV3, OsTLP27, SsNHX1, SUV3, TIFY11b, PsbS, VDE, and ZEP.

13. The method of claim 1 , wherein the trait is senescence and each of the at least two genes is a gene that encodes a protein having at least 90% identity to a sequence selected from the group consisting of the sequences identified by SEQ ID NOs:1566-1653 or is a gene having a sequence selected from SEQ ID NOs:844-931 or is a gene selected from the group consisting of MADS22, SNAC1, RT, SE1, GAMYB, HSP90, AOC, AOS1, AOS2, ACDR1, WRKY45, SPS1, NYC1, D35, PIMT1, PIMT2, WRKY16, SAUR39, CKX3, GN1A, MADS47, MADS55, SGR, CGA1, Rbs1, SPLS, TYDC, SPIN1, SPL11, WRKY14, AP2/EREBP77, TET13, VP1, KO1, SPL32, JAR1, TET5, TET9, FON1, HD3A, PHYB, CYP703A3, MYB, GW8, CZOGT1, CZOGT2, CZOGT3, D1|D2|Os07g0558500, CCA1, RAC1, ABA8OX1, ATG7, D14, NCED1, NCED3, OsABA2, ZEP1, CP1, UDT1, SNAT1, AGO1C, NAS3, ALDH7, CHS1, GST, GRX6, SWEETS, GATA12, NAC58, APX2, ERF3, C3H35, NAM, LOX1, LOX11, LOG1, CKX1, DOS, SHL4, HOX33, NYC3, APX1, AHP1, ERF108, D17, PME1, GHD7, and GS2.

14. The method of claim 11 , wherein the nutrient is nitrogen, and each of the at least two genes is a gene that encodes a protein having at least 90% identity to a sequence selected from the group consisting of the sequences identified by SEQ ID NOs:1513-1533 or is a gene having a sequence selected from SEQ ID NOs:791-811 or is a gene selected from the group consisting of AMT1;1, AMT1;2, AMT1;3, GRX6, GS1;2, GS2, NADH-GOGAT, OsAMT3;1, OsARG, OsENOD93-1 (LOC_Os06g05010), OsGOGAT2, OsGS1;1, OsNRT1.1b, OsNRT2.1, OsNRT2.3b, OsPTR6, OsPTR9, IPT, and OsSPX1.

15. The method of claim 11 , wherein the nutrient is nitrogen, and the targeted modifications result in increased expression of at least two genes selected from the group consisting of OsPTR6, OsPTR9, OsNRT2.1, OsNRT2.3b, OsNRT1.1b, OsNPF6.5, OsGS1;1, GS1;2, GS2, NADH-GOGAT, NADH-GOGAT1, OsGOGAT2, AlaAT, AMT1;1, AMT1;2, AMT1;3, OsAMT3;1, IPT, and OsENOD93-1.

16. The method of claim 1 , wherein the insertion of the predetermined sequence consists of the enhancer OCS set forth in SEQ ID NO: 184.