Gene edited wheat plants with enhanced traits

Abstract

The disclosure relates to gene edited wheat plants, seeds, and compositions, as well as improvements to wheat plant breeding and methods for creating modifications in wheat plant genomes.

What is claimed is: 
     
         1 . A wheat plant cell having a modified genome in comparison to an unmodified wheat plant cell having a reference genome, wherein the modified genome differs from the reference genome by comprising at least one predetermined modification of a gene disclosed in Table 10, wherein the at least one predetermined modification is selected from the group consisting of:
 (a) heterologous integration of a nucleic acid sequence that is encoded by at least one donor polynucleotide molecule and that comprises a regulatory element, at a predetermined locus between 1-1000 nucleotides upstream of the start codon of the coding sequence of a gene of interest in the reference genome;   (b) heterologous integration of a nucleic acid sequence that is encoded by at least one donor polynucleotide molecule and that comprises a regulatory element at a predetermined locus within 1000 nucleotides downstream of the stop codon of a gene disclosed in Table 10;   (c) deletion, addition, or substitution of at least one nucleotide in a regulatory element that regulates expression of a gene disclosed in Table 10;   (d) deletion, addition, or substitution of at least one nucleotide in coding sequence of a gene disclosed in Table 10; and   (e) a combination of any of (a), (b), (c), and (d);   wherein the gene disclosed in Table 10 is selected from the group consisting of TsVP, ZmSEC14p, ACC synthase, D-myo-inositol-3-phosphate synthase (IPS), ZmbZIP72, ZmPLC1, ZmGOLS2, ZmPIS, ZmNF-YB, ZmPsbA, HB2, ZmPP2C2, ZmCIPK16, ZmSAPK8, OsABA8ox3, OsORAP1, OsDIS1, OsVPE3, OsRZFP34, ZFP185, DCA1, OsSRFP1, SQS, OsTPP1, SAPK6, JIOsPR10, OsClpD1, MSD1, OsWR1, OsTPS1, OsGS, OgTT1, OsFKBP20, OsANN1, OsSIK1, OsNHX1, OsMGD, OsDHODH1, Oshsp16.9, OsGME-2, OsChI1, OsCYP18-2, OsCNX, OsCBL8, OsCDPK13, OsRAN2, OsGGP, OVP1, ZFP177, RGG1, OsEm1, CTB4a, GS2, COLD1, OsACA6, OsRab7, OsTOP6A1, osHsp101, OsAMTR1, Rubisco activase, OsSPX1, OsGME-1, OsMPG1, SNAC3, OsSDIR1, OsPgk2a-P, glyoxalase II, OsPUB15, OsIMP, OsHBP1b, OsCYP2, OsPEX11 (Os03g0302000), OsCPK4, EG1, OsCBSX4, OsSIDP366, OsSUV3, GA2ox6, SAPK9, OsRbohA, OsCAS, OsRacB, OsECS, OsVTE1, SAPK4, OsCDPK7, NUS1, OsGL1-2, OsSce1, OsPsbR1, OsCYP21-4, OsPIP1;3, OsCIPK03, OsGRX8, OsMIOX, SLG, CKX3, HAP3A, CDPK9, JAR1, MFO1, LFY, ZMM4, HD3A, MADS24, BRD2, SK2(T)(SCL, FGR), SLR1, ILI5, GW2, ZmPTR1, GA2OX3, ETR2, EXPA4, D2, D61, PDR6, ACO4, Rab6a, OsSERK1, D11, FTL1, BC1, Strongculm2a, BrittleStalk2, SNAT1, AGO1A, AGO1B, AGO1C, DL, DEP3, CYP734A2, CYP734A4, CYP734A6, CEL9D, ZmPP2AA1, rth1 (root hair), CKX4, LSI1, CSLD1, CSLD3, EXPA7, EXPA10, EXPA8, PNH1, OSH15, QHB, LOG1, compact plant2 (ct2), SERK1, PIN, LPA1, MADS57, D14, AGR1, ric2, VAMP714, XA5, GST23, Zm NPR1, Zm LOX3, ALD1, RLCK185, LCB2A1, PhyB1, COP1, WRKY51, Os PLDbeta1, RAC5, OsCPK12, GF14e, Os SBP, OsHIR1, BWMKY1, AOS1, Os LOL2, GH3, GH3-8, XB3, GLP1, Os MAPK6, ACS2, OsLRR1, OsMPK3, Os SGT1, GAP1, Os RAC1, Os TPC1, GH3-2, OsBIANK1, CIPK14, OS BIDK1, OsMPK6, Os MKK4, Gns1, Os CCR1, Os MAPKY5, RACK1A, OsGI, OsphyB, Hd16, RCN1, SPL11, Spin1, PAL, PAL1, OsAGPS1, NRAMP3, OsMTP1, ATM3, OsYSL2, DMAS1, OsMRP5, OsSULTR3;3, AMT1;2, OsAMT3;1, OsNRT2.3b, GS1;2, OsARG, OsNRT2.1, AMT1;1, AlaAT, ABC1, NADH-GOGAT, RBCS, NLA1, PHF1, OsMYB2P-1, CASTOR, INO1, sedoheptulose-1,7-bisphosphatase (SBPase), Fbpase; fructose-1,6-bisphosphatase, OsDET1, Os02g0465900, OsHox32, OsBZR1, OsNAL1, AlaAT, ZmNRT2.2, esp1, ZmGW2-CHR5, Asn synthetase, AspAT, NAD(H)-dependent GOGAT 1, Gln1-3, obap1, ZmAAP4 (amino acid permease 4), crtRB1, ZmMRP1, ZmDA1, ZmDAR1, APS, 6-phospho-fructokinase, wx1, shrunken 1, sus1, brittle endosperm bt2, sugary 1, sbe1, MADS22, RT, GAMYB, HSP90, AOS2, SPS1, NYC1, D35, PIMT1, PIMT2, TYDC, TET9, CYP703A3, D1|D2|Os07g0558500, ABA80X1, OsABA2, NCED1, ZEP1, ALDH7, CHS1, APX2, DOS, HOX33, NYC3, and APX1, or is a gene encoding a protein having at least 90% identity to a sequence selected from the group consisting of SEQ ID NOs:693-975, and 976, or is a genomic sequence selected from the group consisting of SEQ ID NO:977-1259, and 1260.   
     
     
         2 . The wheat plant cell of  claim 1 , wherein the modified genome further differs from the reference genome by comprising (a) a predetermined modification in at least one homeoallele of a gene selected from the group consisting of pinBv1, pinBv2, LOC543302, LOC101290594, TaMOR-D, TaTFL1-2D, TB-A1, TB-B1, TB-D1, DEP1, Gasr7, PIN1, TaMOC1, TaPAP2-5A, TaVRS1-2B, WFZP-A, WFZP-B, WFZP-D, TaFT-B1, LOC542960, TaSnrk2.10-4A, TaSK5, TaOBF1a, TaPIMP1, TaWRKY2, TaWRKY19, LOC100415880, TaNAC2a, LEA3, TaUb2, NAC69-1, NAC2, TaMDC1, TaSC, Waox1a, ALMT1, SOD, CHP, TaAQP7, TaAQP8, TaWRKY10, CIPK14, TaWRKY1, TaWRKY33, TaGAPC1, UBA, Fhb1, Lr34, Lr67, Sr22, Sr33, Sr35, Sr45, Sr50, Tsn1, Yr36 (WKS1), Snn1, TaMLO-A1, TaMLO-B1, TaMLO-D1, FT, FKF1, PhyB, WCO1, ZenMFT-3D, MADS, TaGI1, WAP1, NFYB-A, NFYB-B, NFYB-D, NAC1, Skp1, TIF, WCBP1, WRKY, TaSAG6, TaSAG3, TaSAG1, FeSOD, CWINV2SM, CWINV1SM, SOD, APX, GS2, NAM, rbcL, IVR1, and a1 as disclosed in Table 9, or (b) a predetermined modification in a gene encoding a protein having at least 90% identity to a sequence selected from SEQ ID NOs:257-474 as disclosed in Table 9, or (c) a predetermined modification in a gene selected from the group consisting of genomic sequences identified as SEQ ID NOs:475-691, and 692 as disclosed in Table 9. 
     
     
         3 . The wheat plant cell of  claim 1 , wherein the modified genome is more than 99.9% identical to the reference genome. 
     
     
         4 . The wheat plant cell of  claim 1 , wherein the gene of interest is located on a chromosome in the wheat plant cell, and wherein the modified genome comprises:
 (a) a difference of DNA methylation in less than 0.01% of the portion of the genome that is contained within the chromosome containing the gene of interest, relative to the reference genome; or   (b) a difference of DNA methylation in less than 0.005% of the portion of the genome that is contained within the chromosome containing the gene of interest, relative to the reference genome; or   (c) a difference of DNA methylation in less than 0.001% of the portion of the genome that is contained within the chromosome containing the gene of interest, relative to the reference genome.   
     
     
         5 . The wheat plant cell of  claim 1 , wherein the predetermined modification of the gene disclosed in Table 10 comprises modification of only non-coding sequences of the reference genome, or of only coding sequences of the reference genome, or of a combination of coding and non-coding sequences of the reference genome. 
     
     
         6 . The wheat plant cell of  claim 1 , wherein the predetermined modification of the gene disclosed in Table 10 results in:
 increased expression of the gene of interest, relative to expression of the gene of interest in the reference genome, or   decreased expression of the gene of interest, relative to expression of the gene of interest in the reference genome.   
     
     
         7 . The wheat plant cell of  claim 1 , wherein the predetermined modification of the gene disclosed in Table 10 comprises multiple predetermined modifications of the gene in the reference genome. 
     
     
         8 . The wheat plant cell of  claim 1 , wherein the predetermined modification of the gene disclosed in Table 10 comprises a predetermined modification of multiple homeoalleles of the gene. 
     
     
         9 . The wheat plant cell of  claim 1 , wherein the wheat plant cell is a  Triticum  sp., an  Aegilops  sp., common or bread wheat ( Triticum aestivum ), spelt ( Triticum spelta ), emmer ( Triticum dicoccum ), einkorn ( Triticum monococcum ), durum wheat ( Triticum durum ), or synthetic hexaploid wheat. 
     
     
         10 . The wheat plant cell of  claim 1 , wherein the wheat plant cell is an allotetraploid, wherein the reference genome consists of an A genome and a B genome, and wherein the predetermined modification of the gene disclosed in Table 10 comprises: (a) a predetermined modification of both homeoalleles of the gene of interest in the A genome, (b) a predetermined modification of both homeoalleles of the gene of interest in the B genome, or (c) a predetermined modification of at least two homeoalleles of the gene of interest in the A genome and the B genome. 
     
     
         11 . The wheat plant cell of  claim 1 , wherein the wheat plant cell is an allohexaploid, wherein the reference genome consists of an A genome, a B genome, and a D genome, and wherein the predetermined modification of the gene disclosed in Table 10 comprises: a) a predetermined modification of both homeoalleles of the gene of interest in the A genome, (b) a predetermined modification of both homeoalleles of the gene of interest in the B genome, (c) a predetermined modification of both homeoalleles of the gene of interest in the D genome, or (d) a predetermined modification of at least two homeoalleles of the gene of interest in any combination of the A genome, the B genome, and the D genome. 
     
     
         12 . The wheat plant cell of  claim 1 , wherein the plant cell comprises a predetermined modification in each of two genes disclosed in Table 10. 
     
     
         13 . A wheat plant or plant part thereof comprising the wheat plant cell of  claim 1 , wherein the plant or plant part comprises the at least one predetermined modification. 
     
     
         14 . A progeny plant or progeny seed of the wheat plant of  claim 13 , wherein the progeny plant or progeny seed comprises the at least one predetermined modification. 
     
     
         15 . A method of manufacturing a processed wheat product, comprising processing the wheat plant or plant part thereof of  claim 13  into a processed wheat product, thereby manufacturing a processed wheat product.