Abstract:
Disclosed are chill- or cold-tolerant plants and methods of making the plants. Also disclosed are methods for identifying a plant that is tolerant to chill.

Description:
RELATED APPLICATION 
     This application claims priority of U.S. Provisional Application No. 61/370,351, filed on Aug. 3, 2010. The prior application is incorporated herein by reference in its entirety. 
    
    
     BACKGROUND 
     Various plants, including most important food crops, are not tolerant to cold. For example, rice seedlings are particularly sensitive to chilling in early spring in temperate and subtropical zones and in high elevation areas. Improvement of chilling tolerance in rice or other food crops may significantly increase their production. There is a need for cold-tolerant plants. 
     SUMMARY 
     This invention relates to using transgenic technology to generate cold-tolerant plants. 
     Accordingly, one aspect of this invention features a transgenic plant having a cell that has a MYBS3 gene expression level that is higher than a wild type MYBS3 protein level. Listed below is polypeptide sequence (SEQ ID NO: 1) and the nucleic acid sequence (SEQ ID NO: 2) of rice OsMybS3: 
     
       
         
               
               
               
               
             
           
               
                    1 
                 ATCGATCGATCGATCTCCATAGGTGGGGGAAGGGAAGCTTTGGAAGGTGGAGGGACGGAG 
                 *(SEQ ID NO: 1) 
                   
               
               
                   61 
                 GGGGGGATGACGAGGCGGTGCTCGCACTGCAGCCACAACGGGCACAACTCGCGGACGTGC 
                   
               
               
                   
                       M  T  R  R  C  S  H  C  S  H  N  G  H  N  S  R  T  C 
                   
               
               
                   
               
               
                  121 
                 CCCAACCGCGGGGTCAAGATCTTCGGGGTGCGCCTCACCGATGGCTCCATCCGCAAGAGC 
                   
               
               
                   
                 P  N  R  G  V  K  I  F  G  V  R  L  T  D  G  S  I  R  K  S 
                   
               
               
                   
               
               
                  181 
                 GCCAGCATGGGGAACCTCTCCCTCCTCTCCTCCGCCGCCGGATCCACCAGCGGCGGCGCC 
                   
               
               
                   
                 A  S  M  G  N  L  S  L  L  S  S  A  A  G  S  T  S  G  G  A 
                   
               
               
                   
               
               
                  241 
                 TCCCCCGCCGACGGCCCCGACGCCGCCCCCACCGCCGCCGACGGCTACGCCTCCGACGAC 
                   
               
               
                   
                 S  P  A  D  G  P  D  A  A  P  T  A  A  D  G  Y  A  S  D  D 
                   
               
               
                   
               
               
                  301 
                 TTCGTCCAGGGCTTCTCCTCCGCCACCCGCGACCGCAAGAAGGGTGTTCCTTGGACTGAA 
                   
               
               
                   
                 F  V  Q  G  F  S  S  A  T  R  D  R  K  K  G  V  P  W  T  E 
                   
               
               
                   
               
               
                  361 
                 GAAGAACACCGGAGGTTTTTGCTTGGATTGCAAAAGCTTGGCAAAGGTGATTGGCGAGGA 
                   
               
               
                   
                 E  E  H  R  R  F  L  L  G  L  Q  K  L  G  K  G  D  W  R  G 
                   
               
               
                   
               
               
                  421 
                 ATCTCTCGTAATTTCGTGGTCTCAAGAACACCTACTCAAGTAGCCAGTCATGCTCAGAAA 
                   
               
               
                   
                 I  S  R  N  F  V  V  S  R  T  P  T  Q  V  A  S  H  A  Q  K 
                   
               
               
                   
               
               
                  481 
                 TATTTTATACGCCAATCCAATATGACCAGAAGGAAAAGAAGGTCTAGCCTTTTTGACATG 
                   
               
               
                   
                 Y  F  I  R  Q  S  N  M  T  R  R  K  R  R  S  S  L  F  D  M 
                   
               
               
                   
               
               
                  541 
                 GTGCCAGATGAGTCTATGGACCTTCCACCACTTCCTGGAGGTCAAGAACCAGAGACCCAA 
                   
               
               
                   
                 V  P  D  E  S  M  D  L  P  P  L  P  G  G  Q  E  P  E  T  Q 
                   
               
               
                   
               
               
                  601 
                 GTATTAAATCAACCAGCACTACCTCCACCGAAGGAGGAAGAGGAGGTAGATTCTATGGAG 
                   
               
               
                   
                 V  L  N  Q  P  A  L  P  P  P  K  E  E  E  E  V  D  S  M  E 
                   
               
               
                   
               
               
                  661 
                 TCAGATACTTCTGCCGTTGCAGAGAGCTCTTCCGCTTCTGCTATCATGCCAGATAATTTG 
                   
               
               
                   
                 S  D  T  S  A  V  A  E  S  S  S  A  S  A  I  M  P  D  N  L 
                   
               
               
                   
               
               
                  721 
                 CAGTCGACCTATCCAGTGATTGTTCCAGCTTATTTCTCGCCCTTTTTGCAATTCTCGGTT 
                   
               
               
                   
                 Q  S  T  Y  P  V  I  V  P  A  Y  F  S  P  F  L  Q  F  S  V 
                   
               
               
                   
               
               
                  781 
                 CCTTTCTGGCAAAATCAGAAAGATGAAGATGGTCCTGTGCAAGAAACACATGAGATTGTC 
                   
               
               
                   
                 P  F  W  Q  N  Q  K  D  E  D  G  P  V  Q  E  T  H  E  I  V 
                   
               
               
                   
               
               
                  841 
                 AAGCCTGTTCCAGTTCATTCAAAGAGCCCAATCAACGTTGATGAGCTTGTTGGCATGTCG 
                   
               
               
                   
                 K  P  V  P  V  H  S  K  S  P  I  N  V  D  E  L  V  G  M  S 
                   
               
               
                   
               
               
                  901 
                 AAGCTCAGCATAGGAGAGTCCAATCAAGAGACAGAGTCTACTTCTCTTTCATTAAATCTG 
                   
               
               
                   
                 K  L  S  I  G  E  S  N  Q  E  T  E  S  T  S  L  S  L  N  L 
                   
               
               
                   
               
               
                  961 
                 GTAGGAGGTCAAAATAGACAATCAGCTTTCCATGCAAATCCACCAACAAGGGCACAGGCA 
                   
               
               
                   
                 V  G  G  Q  N  R  Q  S  A  F  H  A  N  P  P  T  R  A  Q  A 
                   
               
               
                   
               
               
                 1021 
                 TGATCTGGTTGTGCACACAACTGCATTTAGATGAATCCCAGGCAAAATAAGCTTTGCCTC 
                   
               
               
                   
               
               
                 1081 
                 CTTGTTTTTTTGTTTTTATTTTAAGATTAACCGTTCTCCGTAGTCTGTATCATGTGCTGT 
                 (SEQ ID NO: 2) 
               
               
                   
               
               
                 1141 
                 AAGTTATGCTATGTATGAATGTATCTGTTGTTTGTCTGGCACACATGATAAATCACTCTA 
                   
               
               
                   
               
               
                 1201 
                 TGTTAACAAAATCAGTAATGGTAGTGCTGATCTTCGTGGTTGTACTGTTGTAAACTCTTT 
                   
               
               
                   
               
               
                 1261 
                 TATAAGAAAAAAAAATATTAGTTAGTC 
                   
               
             
          
         
       
     
     In the above-described transgenic plant, the MYBS3 gene encodes a polypeptide that is at least 40%, e.g., 50, 60, 70, 80, 85, 90, 95, 98, 99, or 100% identical to rice MYBS3 protein (SEQ ID NO: 1). For example, the MYBS3 gene can be a rice MYBS3 gene or its homologues, such as those from other plants (e.g., maize, wheat, barley, sorghum, sugarcane, turf grass, Miscanthus, switchgrass, soybean, canola, potato, tomato, bean, pea, or jatropha). The exemplary homologues are listed below: 
     
       
         
               
               
             
           
               
                 &gt; At5g47390 (DNA) 
                   
               
               
                 (SEQ ID NO: 43) 
                   
               
               
                 ATGACTCGTCGATGTTCTCACTGCAATCACAATGGCCACAACTCTCGGACTTGTCCCAATCGCGG 
                   
               
               
                   
               
               
                 CGTGAAGCTCTTTGGTGTTCGGCTCACCGAAGGTTCGATCCGGAAAAGTGCAAGTATGGGTAATC 
               
               
                   
               
               
                 TTAGCCATTACACGGGTTCTGGATCGGGTGGGCATGGAACCGGGTCCAACACTCCGGGTTCTCCG 
               
               
                   
               
               
                 GGTGATGTCCCTGACCATGTCGCTGGTGATGGTTACGCTTCTGAGGATTTCGTTGCTGGCTCTTC 
               
               
                   
               
               
                 CTCTAGCCGCGAGAGAAAGAAAGGAACTCCATGGACAGAGGAAGAACACAGGATGTTCTTATTAG 
               
               
                   
               
               
                 GTTTACAGAAGCTGGGTAAAGGTGATTGGAGAGGTATCTCAAGAAACTATGTGACCACTAGGACA 
               
               
                   
               
               
                 CCTACACAAGTTGCTAGCCATGCTCAGAAGTATTTCATCAGACAATCCAATGTCTCTCGTCGCAA 
               
               
                   
               
               
                 AAGACGTTCTAGTCTCTTTGATATGGTTCCTGATGAGGTTGGAGATATTCCCATGGATTTGCAAG 
               
               
                   
               
               
                 AACCAGAGGAAGATAATATTCCTGTGGAAACTGAAATGCAAGGTGCTGACTCTATTCATCAGACA 
               
               
                   
               
               
                 CTTGCTCCTAGCTCACTTCACGCACCGTCAATCTTGGAAATCGAAGAATGTGAATCAATGGACTC 
               
               
                   
               
               
                 CACAAACTCTACCACCGGGGAACCAACCGCAACTGCCGCTGCTGCTTCTTCTTCTTCCAGACTAG 
               
               
                   
               
               
                 AAGAAACCACACAACTGCAATCACAACTGCAACCGCAGCCGCAACTACCTGGCTCATTCCCCATA 
               
               
                   
               
               
                 CTATATCCGACCTACTTTTCACCATATTACCCGTTTCCATTCCCAATATGGCCTGCTGGTTATGT 
               
               
                   
               
               
                 TCCTGAACCACCCAAGAAAGAGGAAACTCATGAAATTCTCAGACCAACTGCTGTGCACTCGAAAG 
               
               
                   
               
               
                 CTCCTATCAATGTTGACGAGCTTCTTGGTATGTCTAAGCTCAGCCTTGCAGAGTCCAACAAACAT 
               
               
                   
               
               
                 GGAGAATCCGATCAGTCTCTTTCATTGAAGCTAGGTGGCGGGTCATCTTCAAGACAATCAGCATT 
               
               
                   
               
               
                 TCACCCGAATCCTAGCTCTGATAGTTCAGACATCAAAAGCGTGATACACGCTTTATAAAAGACCT 
               
               
                   
               
               
                 GAGGAAGTGATGGTCTAAAATGGG 
               
               
                   
               
               
                 &gt;At5g47390 (Protein) 
               
               
                 (SEQ ID NO: 44) 
                   
               
               
                 MTRRCSHCNHNGHNSRTCPNRGVKLFGVRLTEGSIRKSASMGNLSHYTGSGSGGHGTGSNTPGSP 
                   
               
               
                   
               
               
                 GDVPDHVAGDGYASEDFVAGSSSSRERKKGTPWTEEEHRMFLLGLQKLGKGDWRGISRNYVTTRT 
               
               
                   
               
               
                 PTQVASHAQKYFIRQSNVSRRKRRSSLFDMVPDEVGDIPMDLQEPEEDNIPVETEMQGADSIHQT 
               
               
                   
               
               
                 LAPSSLHAPSILEIEECESMDSTNSTTGEPTATAAAASSSSRLEETTQLQSQLQPQPQLPGSFPI 
               
               
                   
               
               
                 LYPTYFSPYYPFPFPIWPAGYVPEPPKKEETHEILRPTAVHSKAPINVDELLGMSKLSLAESNKH 
               
               
                   
               
               
                 GESDQSLSLKLGGGSSSRQSAFHPNPSSDSSDIKSVIHAL 
               
               
                   
               
               
                 &gt; At3g16350 (DNA) 
               
               
                 (SEQ ID NO: 45) 
                   
               
               
                 ATGACTCGTCGGTGTTCGCATTGTAGCAACAATGGGCACAATTCACGCACGTGTCCAACGCGTGG 
                   
               
               
                   
               
               
                 TGGTGGCACGTGCGGTGGAAGTGGCGGAGGAGGAGGAGGTGGTGGTGGAGGAGGGTCTGGTTCCT 
               
               
                   
               
               
                 CCTCCGCCGTGAAGTTATTTGGTGTGAGGTTAACGGATGGCTCGATTATTAAAAAGAGTGCGAGT 
               
               
                   
               
               
                 ATGGGTAATCTCTCGGCATTGGCTGTTGCGGCGGCGGCGGCAACGCACCACCGTTTATCTCCGTC 
               
               
                   
               
               
                 GTCTCCTCTGGCGACGTCAAATCTTAATGATTCGCCGTTATCGGATCATGCCCGATACTCTAATT 
               
               
                   
               
               
                 TGCATCATAATGAAGGGTATTTATCTGATGATCCTGCTCATGGTTCTGGGTCTAGTCACCGTCGT 
               
               
                   
               
               
                 GGTGAGAGGAAGAGAGGTGTTCCTTGGACTGAAGAGGAACATAGACTATTCTTAGTCGGTCTTCA 
               
               
                   
               
               
                 GAAACTCGGGAAAGGAGATTGGCGCGGTATTTCGAGAAACTATGTAACGTCAAGAACTCCTACAC 
               
               
                   
               
               
                 AAGTGGCTAGTCATGCTCAAAAGTATTTTATTCGACATACTAGTTCAAGCCGCAGGAAAAGACGG 
               
               
                   
               
               
                 TCTAGCCTCTTCGACATGGTTACAGATGAGATGGTAACCGATTCATCGCCAACACAGGAAGAGCA 
               
               
                   
               
               
                 GACCTTAAACGGTTCCTCTCCAAGCAAGGAACCTGAAAAGAAAAGCTACCTTCCTTCACTTGAGC 
               
               
                   
               
               
                 TCTCACTCAATAATACCACAGAAGCTGAAGAGGTCGTAGCCACGGCGCCACGACAGGAAAAATCT 
               
               
                   
               
               
                 CAAGAAGCTATAGAACCATCAAATGGTGTTTCACCAATGCTAGTCCCGGGTGGCTTCTTTCCTCC 
               
               
                   
               
               
                 TTGTTTTCCAGTGACTTACACGATTTGGCTCCCTGCGTCACTTCACGGAACAGAACATGCCTTAA 
               
               
                   
               
               
                 ACGCTGAGACTTCTTCTCAGCAGCATCAGGTCCTAAAACCAAAACCTGGATTTGCTAAAGAACGT 
               
               
                   
               
               
                 GTGAACATGGACGAGTTGGTCGGTATGTCTCAGCTTAGCATAGGAATGGCGACAAGACACGAAAC 
               
               
                   
               
               
                 CGAAACTTCCCCTTCCCCGCTATCTTTGAGACTAGAGCCCTCAAGGCCATCAGCGTTTCACTCGA 
               
               
                   
               
               
                 ATGGCTCGGTTAATGGTGCAGATTTGAGTAAAGGCAACAGCGCGATTCAGGCTATCTAA 
               
               
                   
               
               
                 &gt;At3g1635 (Protein) 
               
               
                 (SEQ ID NO: 46) 
                   
               
               
                 MTRRCSHCSNNGHNSRTCPTRGGGTCGGSGGGGGGGGGGGSGSSSAVKLFGVRLTDGSIIKKSAS 
                   
               
               
                   
               
               
                 MGNLSALAVAAAAATHHRLSPSSPLATSNLNDSPLSDHARYSNLHHNEGYLSDDPAHGSGSSHRR 
               
               
                   
               
               
                 GERKRGVPWTEEEHRLFLVGLQKLGKGDWRGISRNYVTSRTPTQVASHAQKYFIRHTSSSRRKRR 
               
               
                   
               
               
                 SSLFDMVTDEMVTDSSPTQEEQTLNGSSPSKEPEKKSYLPSLELSLNNTTEAEEVVATAPRQEKS 
               
               
                   
               
               
                 QEAIEPSNGVSPMLVPGGFFPPCFPVTYTIWLPASLHGTEHALNAETSSQQHQVLKPKPGFAKER 
               
               
                   
               
               
                 VNMDELVGMSQLSIGMATRHETETSPSPLSLRLEPSRPSAFHSNGSVNGADLSKGNSAIQAI 
               
               
                   
               
               
                 &gt; GRMZM2G034110_T01 (DNA) 
               
               
                 (SEQ ID NO: 47) 
                   
               
               
                 ATGACGCGGCGGTGCTCGCACTGCAGCCACAACGGGCACAACTCGCGGACGTGCCCCAACCGCGG 
                   
               
               
                   
               
               
                 GGTCAAGATCTTCGGGGTGCACCTCACCGATGGCTCGGCCATCCGCAAGAGCGCGAGCATGGGGA 
               
               
                   
               
               
                 ACCTCTCCCTCCTCTCCGCGGGATCCACCAGCGGCGGCGCGTCCCCCGCCGACGGGCCCGACCTC 
               
               
                   
               
               
                 GCCGACGGCGGCGGGGGCTACGCCTCCGACGACTTCGTCCAGGGGTCGTCCTCCGCCAGCCGCGA 
               
               
                   
               
               
                 TCGAAAGAAAGGTGTTCCTTGGACTGAAGAAGAACACCGGAGGTTTTTGCTGGGATTACAAAAGC 
               
               
                   
               
               
                 TCGGGAAAGGGGATTGGCGAGGAATTTCTCGTAATTTTGTGGTCTCAAGAACACCTACTCAAGTA 
               
               
                   
               
               
                 GCAAGTCATGCTCAAAAGTATTTTATACGCCAATCAAATATGAGCAGAAGGAAGAGAAGGTCTAG 
               
               
                   
               
               
                 CCTTTTCGACATGGTTCCTGATGAGTCCATGGACCTTCCGCCCCTTCCTGGAAGTCAAGAACCAG 
               
               
                   
               
               
                 AGACCTCAATGTTAAATCAACCGCCACTGCCTCCTGCTGTGGAGGAGGAGGTGGAATCGATGGAG 
               
               
                   
               
               
                 TCAGATACTTCTGCTGTCGCAGAGAGTTCTGGAGCTTCTGCTCTCATGCCCGAGAGTTTACAGCC 
               
               
                   
               
               
                 TACCTATCCGATGATTGTTCCAGCTTATTTCTCGCCGTTCTTGCAATTCTCAGTTCCTTTCTGGC 
               
               
                   
               
               
                 CAAATCAGGAAGATGGAGGCGATCTTCCCCAAGAAACACACGAGATTGTCAAGCCTGTTGCAGTT 
               
               
                   
               
               
                 CATTCCCAGAATCCAATTAATGTTGATGAACTCGTGGGCATGTCAAAGCTAAGCATATGGGAGCA 
               
               
                   
               
               
                 TGGTCAGGAGACAGTGTCTACTTCTCTGTCGCTAAATCTGCTAGGGGGTCAAAATAGGCAGTCGG 
               
               
                   
               
               
                 CTTTCCATGCAAACCCTCAAACAAGAGCTCAAGCCTGA 
               
               
                   
               
               
                 &gt;GRMZM2G034110_T01 (Protein) 
               
               
                 (SEQ ID NO: 48) 
                   
               
               
                 MTRRCSHCSHNGHNSRTCPNRGVKIFGVHLTDGSAIRKSASMGNLSLLSAGSTSGGASPADGPDL 
                   
               
               
                   
               
               
                 ADGGGGYASDDFVQGSSSASRDRKKGVPWTEEEHRRFLLGLQKLGKGDWRGISRNFVVSRTPTQV 
               
               
                   
               
               
                 ASHAQKYFIRQSNMSRRKRRSSLFDMVPDESMDLPPLPGSQEPETSMLNQPPLPPAVEEEVESME 
               
               
                   
               
               
                 SDTSAVAESSGASALMPESLQPTYPMIVPAYFSPFLQFSVPFWPNQEDGGDLPQETHEIVKPVAV 
               
               
                   
               
               
                 HSQNPINVDELVGMSKLSIWEHGQETVSTSLSLNLLGGQNRQSAFHANPQTRAQA 
               
               
                   
               
               
                 &gt; GRMZM2G020934_T01 (DNA) 
               
               
                 (SEQ ID NO: 49) 
                   
               
               
                 ATGGCTCGGCCATCCGCAAGAGCGCAAGCATGGGGAACCTCTCCCTCCTCTCCGCGGGGTCAACC 
                   
               
               
                   
               
               
                 AGCGGCGGCGCGTCGCCCGCCGACGGGCCCGACCTCGCCGACGGCGGCGGGGGCTACGCCTCCGA 
               
               
                   
               
               
                 CGACTTCGTCCAGGGGTCGTCCTCCGCCAGCCGCGAGCGTAAGAAAGGTGTTCCTTGGACTGAAG 
               
               
                   
               
               
                 AAGAACACCGGAGGTTTTTTGCTGGGGATTACAAAAAGCTTGGGGAAAGGTGATTGGCGAGGGGA 
               
               
                   
               
               
                 TTTTCTCGTAATTTTCGTGGTCTCAAAGAACACCCTACTCAAAGTAGCAAAGTCATGCTCAAAAA 
               
               
                   
               
               
                 ATATTTTTATACGTCAAATCAAATATGAGCAGAAGGGAAGAGAAGGTCTAGCCTTTTTTGACATG 
               
               
                   
               
               
                 GTGCCTGATGAGTCCATGGACCTTCCACCCCTTCCTGGAAGTCAAGAGCCAGAGACCTCAGTGTT 
               
               
                   
               
               
                 AAATCAACCACCACTGCCTCCCCCTGTGGAGGAGGAGGAGGAGGTGGAATCGATGGAGTCAGATA 
               
               
                   
               
               
                 CTTCTGCTGTTGCGGAGAGTTCTGCAGCTTCAGCTCTTATGCCCGAGAGTTTACAGCCTACCTAT 
               
               
                   
               
               
                 CCGATGATTGTTCCAGCTTATTTCTCACCGTTCTTGCAATTCTCAGTTCCTTTCTGGCCAAATCA 
               
               
                   
               
               
                 GGAAGATGGAGGTGATCTGCCTCAAGAAACGCACGAGATTGTCAAGCCTGTTGCAGTTCATTCCA 
               
               
                   
               
               
                 AGAATCCAATTAATGTTGATGAACTTGTGAGCATGTCAAAGCTAAGCATAGGGGAGCCTGGTCAG 
               
               
                   
               
               
                 GAAACGGTGTCTACTTCTCTGTCGTTAAATCTGCTGGTGGGTCAAAATAGGCAGTCGGCCTTCCA 
               
               
                   
               
               
                 TGCAAATCCTCAAACGAGGGCTCAAGCTTGA 
               
               
                   
               
               
                 &gt;GRMZM2G020934_T01 (Protein) 
               
               
                 (SEQ ID NO: 50) 
                   
               
               
                 MARPSARAQAWGTSPSSPRGQPAAARRPPTGPTSPTAAGATPPTTSSRGRPPPAASVRKVFLGLK 
                   
               
               
                   
               
               
                 KNTGGFLLGITKSLGKGDWRGDFLVIFVVSKNTLLKVAKSCSKNIFIRQIKYEQKGREGLAFFDM 
               
               
                   
               
               
                 VPDESMDLPPLPGSQEPETSVLNQPPLPPPVEEEEEVESMESDTSAVAESSAASALMPESLQPTY 
               
               
                   
               
               
                 PMIVPAYFSPFLQFSVPFWPNQEDGGDLPQETHEIVKPVAVHSKNPINVDELVSMSKLSIGEPGQ 
               
               
                   
               
               
                 ETVSTSLSLNLLVGQNRQSAFHANPQTRAQA 
               
               
                   
               
               
                 &gt; Sb01g029020.1 (DNA) 
               
               
                 (SEQ ID NO: 51) 
                   
               
               
                 ATGACGCGGCGGTGCTCGCACTGCAGCCACAACGGGCACAACTCGCGGACGTGCCCCAACCGCGG 
                   
               
               
                   
               
               
                 GGTCAAGATCTTCGGGGTGCGCCTCACCGATGGCTCCGCCATCCGCAAGAGCGCCAGCATGGGGA 
               
               
                   
               
               
                 ACCTCTCCCTCCTCTCCGCGGGATCCACCAGCGGCGGCGCGTCCCCCGCCGACGGGCCCGACCTC 
               
               
                   
               
               
                 GCCGACGGCGGCGCCGGGGGATACGCCTCCGACGACTTCGTCCAGGGCTCCTCCTCCGCCAGCCG 
               
               
                   
               
               
                 CGAGCGCAAGAAAGGTGTTCCTTGGACTGAAGAAGAACACCGGAGGTTTTTGCTGGGATTACAAA 
               
               
                   
               
               
                 AGCTTGGGAAAGGTGATTGGCGAGGAATTTCTCGTAATTTCGTGGTCTCAAGAACACCTACTCAA 
               
               
                   
               
               
                 GTAGCAAGTCATGCTCAAAAATATTTTATACGTCAATCAAATATGAGCAGAAGGAAGAGAAGGTC 
               
               
                   
               
               
                 TAGCCTTTTTGACATGGTGCCTGATGAGTCCATGGACCTTCCACCCCTTCCTGGAAGTCAAGAAC 
               
               
                   
               
               
                 CAGAGACCTCAGTGTTAAATCAAGCACCACTGCCGCCTCCTGTGGAGGAGGAGGTGGAATCAATG 
               
               
                   
               
               
                 GAGTCAGATACTTCTGCTGTTGCAGAGAGTTCTACGGCTTCTGCTCTCATGCCCGAGAGTTTACA 
               
               
                   
               
               
                 ACCTAATTATCCGATGATTGTTCCAGCTTATTTCTCACCGTTCTTGCAATTCTCAGTTCCTTTCT 
               
               
                   
               
               
                 GGCCAAATCAGGAAGATGGAGGCGATCTGCCCCAAGAAACACACGAGATTGTCAAGCCTGTGGCA 
               
               
                   
               
               
                 GTTCATTCCAAGAATCCAATTAATGTTGATGAACTTGTGGGCATGTCAAAGCTAAGCATAGGGGA 
               
               
                   
               
               
                 GCCTGGTCAGGAGACAGTTTCTACTTCTCTGTCGCTAAATCTGCTAGGGGGTCAAAATAGGCAGT 
               
               
                   
               
               
                 CGGCTTTCCATGCAAATCCTCAAACGAGAGCTCAAGCCTGA 
               
               
                   
               
               
                 &gt;Sb01g029020.1 (Protein) 
               
               
                 (SEQ ID NO: 52) 
                   
               
               
                 MTRRCSHCSHNGHNSRTCPNRGVKIFGVRLTDGSAIRKSASMGNLSLLSAGSTSGGASPADGPDL 
                   
               
               
                   
               
               
                 ADGGAGGYASDDFVQGSSSASRERKKGVPWTEEEHRRFLLGLQKLGKGDWRGISRNFVVSRTPTQ 
               
               
                   
               
               
                 VASHAQKYFIRQSNMSRRKRRSSLFDMVPDESMDLPPLPGSQEPETSVLNQAPLPPPVEEEVESM 
               
               
                   
               
               
                 ESDTSAVAESSTASALMPESLQPNYPMIVPAYFSPFLQFSVPFWPNQEDGGDLPQETHEIVKPVA 
               
               
                   
               
               
                 VHSKNPINVDELVGMSKLSIGEPGQETVSTSLSLNLLGGQNRQSAFHANPQTRAQA 
               
               
                   
               
               
                 &gt;Sb03g003270.1 (DNA) 
               
               
                 (SEQ ID NO: 53) 
                   
               
               
                 ATGACGCGGAGGTGCTCGCACTGCAGCAACAACGGCCACAACTCGCGCACCTGCCCCGCCCGCTC 
                   
               
               
                   
               
               
                 CGGCGGCGGGGTGAGGCTATTTGGCGTGCGCCTCACAACGGCGCCGGCTCCGGCGGCGATGAAGA 
               
               
                   
               
               
                 AGAGCGCCAGCATGAGCTGCATCGCGTCCTCGCTCGGGGGCGGGTCCGGGGGCTCGTCGCCGCCG 
               
               
                   
               
               
                 GCGGGAGGAGTGGGTGGTGGCAGGGGAGGAGGAGACGGCGGGGCCGGCTACGTCTCCGATGATCC 
               
               
                   
               
               
                 CGGGCACGCCTCCTGCTCGACGAATGGCCGCGTCGAGCGGAAGAAAGGTACACCTTGGACTGAAG 
               
               
                   
               
               
                 AAGAGCATAGAATGTTTCTGATGGGTCTTCAGAAGCTTGGTAAGGGAGATTGGCGCGGGATATCT 
               
               
                   
               
               
                 CGAAACTTTGTTGTTTCCAGGACCCCGACTCAAGTGGCAAGCCATGCTCAAAAGTACTTTATTAG 
               
               
                   
               
               
                 ACAGACAAACTCATCAAGACGGAAGAGGCGGTCAAGCTTGTTTGACATGGTTGCAGAAATGCCAG 
               
               
                   
               
               
                 TAGACGAGTCCCTAGCTGCTGCGGAACAAATTACTATCCAAAATACTCAAGATGAAGCTGCAAGT 
               
               
                   
               
               
                 TCAAATCAACTGCCGACCTTACATCTTGGGCATCAGAAGGAAGCAGAGTTTGCTAAGCAAATGCC 
               
               
                   
               
               
                 AACTTTTCAGCTAAGGCAGCATGAGGAATCTGAATATGCAGAACCTTCATTGACATTACCAGATT 
               
               
                   
               
               
                 TAGAGATGAACTCCAGTGTACCATTCAATACCATAGCTGTTCCGACGATGCCAGCATTCTACCCT 
               
               
                   
               
               
                 GCGTTGGTCCCTGTTCCACTAACTCTTTGGCCTCCAAGTGTTGCCCATGTGGAGGACGCAGGCAC 
               
               
                   
               
               
                 AACCCATGAAATCCTAAAACCAACTCCTTTGAATGGTAAGGAGGTGATTAAAGCAGATGATGTTG 
               
               
                   
               
               
                 TTGGTATGTCTAAGCTCAGCATTGGTGAGGCCAGCTCTGGCTCCATGGAACCCACAGCTCTTTCC 
               
               
                   
               
               
                 CTTCAGCTTATTGGATCGACAGATACAAGGCAGTCAGCTTTTCATGTGAGTCCACCAATGAATAG 
               
               
                   
               
               
                 ACCTGAACTAAGCAAGAGAAACAGCAGTCCAATTCATGCCGTTTGA 
               
               
                   
               
               
                 &gt;Sb03g003270.1 (Protein) 
               
               
                 (SEQ ID NO: 54) 
                   
               
               
                 MTRRCSHCSNNGHNSRTCPARSGGGVRLFGVRLTTAPAPAAMKKSASMSCIASSLGGGSGGSSPP 
                   
               
               
                   
               
               
                 AGGVGGGRGGGDGGAGYVSDDPGHASCSTNGRVERKKGTPWTEEEHRMFLMGLQKLGKGDWRGIS 
               
               
                   
               
               
                 RNFVVSRTPTQVASHAQKYFIRQTNSSRRKRRSSLFDMVAEMPVDESLAAAEQITIQNTQDEAAS 
               
               
                   
               
               
                 SNQLPTLHLGHQKEAEFAKQMPTFQLRQHEESEYAEPSLTLPDLEMNSSVPFNTIAVPTMPAFYP 
               
               
                   
               
               
                 ALVPVPLTLWPPSVAHVEDAGTTHEILKPTPLNGKEVIKADDVVGMSKLSIGEASSGSMEPTALS 
               
               
                   
               
               
                 LQLIGSTDTRQSAFHVSPPMNRPELSKRNSSPIHAV 
               
               
                   
               
               
                 &gt; Glyma17g15330.1 (DNA) 
               
               
                 (SEQ ID NO: 55) 
                   
               
               
                 ATGACGCGGCGTTGCTCGCATTGCAGCCACAATGGGCACAACTCAAGAACTTGCCCTAACCGCGG 
                   
               
               
                   
               
               
                 GGTGAAGCTCTTCGGGGTCCGATTAACCGATGGGTCGATCCGGAAGAGTGCTAGCATGGGCAATC 
               
               
                   
               
               
                 TAACCCACTATGCCGGTTCCGGGTCGGGTCCACTCCATACCGGGTTGAATAACCCCGGTTCGCCC 
               
               
                   
               
               
                 GGGGAAACCCCCGATCATGCCGCCGCAGTCGCCGACGGTTACTTGTCCGAGGACTTCGTTCCCGG 
               
               
                   
               
               
                 GTCTTCTTCTAGCTCCCGTGAAAGAAAGAAGGGTGTTCCATGGACTGAGGAGGAACATAGAATGT 
               
               
                   
               
               
                 TTTTACTCGGATTGCAGAAGCTGGGCAAAGGTGATTGGCGTGGAATTGCAAGGACCTATGTTATA 
               
               
                   
               
               
                 TCAAGGACACCTACTCAAGTGGCTAGCCATGCTCAGAAATATTTCATCAGGCAGAGCAATGTGTC 
               
               
                   
               
               
                 CAGGCGGAAAAGACGGTCCAGCTTGTTTGATATTGTTGCAGATGAAGCAGCTGACACTGCAATGG 
               
               
                   
               
               
                 TACAGCAAGACTTCTTGTCTGCTAATCAGTTACCCACTGAAACAGAAGGCAATAACCCCTTGCCA 
               
               
                   
               
               
                 GCTCCTCCTCCCCTCGACGAAGAGTGCGAATCCATGGATTCCACAAACTCAAATGATGGAGAGCC 
               
               
                   
               
               
                 TGCCCCATCAAAGCCAGAAAACACACAGTCATCTTATCCAATGTTATATCCTGCATATTATTCTC 
               
               
                   
               
               
                 CGGTGTTCCCGTTTCCTCTGCCCTATTGGTCAGGATACAGTCCAGAGTCCACCAAGAAGGAGGAG 
               
               
                   
               
               
                 ACACATGAAGTACTGAAGCCAACTGCAGTTCATTCTAAAAGCCCTATCAATGTTGATGAACTGGT 
               
               
                   
               
               
                 TGGCATTTCAAAATTGAGTTTAGGGGAGTCTATTGGTGACTCTGGTCCCTCCTCTCTGTCTCGAA 
               
               
                   
               
               
                 AACTTATCGAAGAAGGACCCTCTAGACAGTCAGCTTTTCATGCAACACCGACATGTGGCAGTTCA 
               
               
                   
               
               
                 AATGGCAGTGCCATCCATGCAGTTTAA 
               
               
                   
               
               
                 &gt;Glyma17g15330.1 (Protein) 
               
               
                 (SEQ ID NO: 56) 
                   
               
               
                 MTRRCSHCSHNGHNSRTCPNRGVKLFGVRLTDGSIRKSASMGNLTHYAGSGSGPLHTGLNNPGSP 
                   
               
               
                   
               
               
                 GETPDHAAAVADGYLSEDFVPGSSSSSRERKKGVPWTEEEHRMFLLGLQKLGKGDWRGIARTYVI 
               
               
                   
               
               
                 SRTPTQVASHAQKYFIRQSNVSRRKRRSSLFDIVADEAADTAMVQQDFLSANQLPTETEGNNPLP 
               
               
                   
               
               
                 APPPLDEECESMDSTNSNDGEPAPSKPENTQSSYPMLYPAYYSPVFPFPLPYWSGYSPESTKKEE 
               
               
                   
               
               
                 THEVLKPTAVHSKSPINVDELVGISKLSLGESIGDSGPSSLSRKLIEEGPSRQSAFHATPTCGSS 
               
               
                   
               
               
                 NGSAIHAV 
               
               
                   
               
               
                 &gt; Glyma05g04950.1 (DNA) 
               
               
                 (SEQ ID NO: 57) 
                   
               
               
                 ATGACGCGGCGTTGCTCGCATTGCAGCCACAATGGGCACAACTCCAGAACCTGCCCTAACCGCGG 
                   
               
               
                   
               
               
                 GGTTAAGCTCTTCGGGGTCCGATTAACCGACGGGTCGATCCGGAAGAGCGCCAGCATGGGCAACC 
               
               
                   
               
               
                 TAACCCACTACGCTGGTTCCGGGTCGGCCCCGCTCCATGTCGGGTTGAATAACCCGGGTTCACCC 
               
               
                   
               
               
                 GGGGAGACGCCCGATCACGCCGCCGCCGCCGCCGACGGCTACGCCTCCGAGGACTTCGTTCCCGG 
               
               
                   
               
               
                 GTCTTCTTCTAGCTCCCGTGAAAGAAAGAAGGGTGTTCCATGGACTGAGGAGGAACATAGAATGT 
               
               
                   
               
               
                 TTTTGCTCGGATTGCAGAAGCTGGGCAAAGGTGATTGGCGTGGAATTGCAAGGAACTATGTTATA 
               
               
                   
               
               
                 TCAAGGACGCCTACTCAAGTGGCCAGCCATGCTCAGAAATATTTCATCAGGCAAAGCAATGTGTC 
               
               
                   
               
               
                 CAGGCGAAAAAGACGGTCCAGCTTGTTTGATATTGTTGCAGATGAAGCAGCTGACACTGCAATGG 
               
               
                   
               
               
                 TACAGCAAGACTTCTTGTCTGCTAATGAGTTACCAACTGAAACAGAAGGCAATAACCCCTTGCCT 
               
               
                   
               
               
                 GCTCCTCCTCCCCTCGATGAAGAGTGTGAATCAATGGATTCCACAAACTCAAATGATGGAGAGCC 
               
               
                   
               
               
                 TGCCCCATCAAAGCCAGAAAACACACATCCATCTTATCCTATGTTATATCCTGCGTATTATTCTC 
               
               
                   
               
               
                 CAGTGTTCCCGTTTCCTCTGCCCTATTGGTCAGGATACAGTCCAGAGCCCACCAAGAAGGAGGAA 
               
               
                   
               
               
                 ACACATGAAGTGCTGAAACCAACTGCAGTACATTCTAAAAGCCCTATCAATGTTGATGAACTGGT 
               
               
                   
               
               
                 TGGCATATCAAAACTGAGTTTAGGGGAGTCTATTGGTGACTCGGGTCCCTCCACCCTGTCTCGAA 
               
               
                   
               
               
                 AACTTATTGAAGAAGGACCCTCTAGACAATCAGCTTTTCATGCAACACCAACATGTGGTGATATG 
               
               
                   
               
               
                 AATGGCAGTGCCATCCATGCAGTTTAA 
               
               
                   
               
               
                 &gt;Glyma05g04950.1 (Protein) 
               
               
                 (SEQ ID NO: 58) 
                   
               
               
                 MTRRCSHCSHNGHNSRTCPNRGVKLFGVRLTDGSIRKSASMGNLTHYAGSGSAPLHVGLNNPGSP 
                   
               
               
                   
               
               
                 GETPDHAAAAADGYASEDFVPGSSSSSRERKKGVPWTEEEHRMFLLGLQKLGKGDWRGIARNYVI 
               
               
                   
               
               
                 SRTPTQVASHAQKYFIRQSNVSRRKRRSSLFDIVADEAADTAMVQQDFLSANELPTETEGNNPLP 
               
               
                   
               
               
                 APPPLDEECESMDSTNSNDGEPAPSKPENTHPSYPMLYPAYYSPVFPFPLPYWSGYSPEPTKKEE 
               
               
                   
               
               
                 THEVLKPTAVHSKSPINVDELVGISKLSLGESIGDSGPSTLSRKLIEEGPSRQSAFHATPTCGDM 
               
               
                   
               
               
                 NGSAIHAV 
               
               
                   
               
               
                 &gt; GSVIVT00013475001 (DNA) 
               
               
                 (SEQ ID NO: 59) 
                   
               
               
                 ATGACTCGCCGCTGCTCGCATTGCAGTCACAACGGGCACAATTCCAGGACATGCCCCAACCGCGG 
                   
               
               
                   
               
               
                 GGTCAAGATCTTCGGGGTTCGATTGACTGATGGGTTGATCCGTAAGAGTGCTAGTATGGGCAATC 
               
               
                   
               
               
                 TCAGCCACTACGCCGGGTCGACCTCTGGTCATCATCAGAACGGCGTTTCCGGTAACAATTCGGTC 
               
               
                   
               
               
                 TCTCCCGGAGAGACTCCAGAGCACGGCGCCGCGGCCGATGGATACGCCTCCGAGGGTTTCGTTCC 
               
               
                   
               
               
                 CGGTTCATCATCCAGCCGGGAGCGCAAGAAAGGCACTCCATGGACTGAAGAGGAACACAGAATGT 
               
               
                   
               
               
                 TTCTACTTGGACTGCAGAAGCTTGGAAAAGGGGATTGGCGTGGAATTTCACGTAATTATGTTATA 
               
               
                   
               
               
                 TCAAGGACACCTACTCAAGTCGCCAGCCATGCTCAGAAATATTTCATCAGGCAAACTAATGTGTC 
               
               
                   
               
               
                 TAGGAGAAAAAGACGGTCCAGCTTGTTTGATATTGTAGCTGATGAATCTGTCGACACTCCAATGG 
               
               
                   
               
               
                 TATCACGGGATTTCTTCTCCACCAACCCTTCGCAAGCTGAAACACTAAGCAATAACCCATTGCCT 
               
               
                   
               
               
                 GTTCCTCCGGCTCTGGATGAAGAATGTGAATCAATGGATTCTACCAACTCGAATGATGGAGAACC 
               
               
                   
               
               
                 GCCCATTCCAAAGCCGGATGGCTTACAAGGCTGTCCCCCAGTAATATATCCTACTTATTTCTCAC 
               
               
                   
               
               
                 CATTCTTCCCATTTTCTTTTCCATTCTGGCCGGGAAACAGTTCAGAGCCAACTAAAATGGAGACT 
               
               
                   
               
               
                 CATGAGGTGCTTAAGCCAACAGCTGTACATTCTAAGAGTCCAATCAATGTTGATGAGCTGGTTGG 
               
               
                   
               
               
                 CATGTCAAAACTGAGTTTAGGAGAATCCATCGGTCATGCTGGTCCCTCCTCTCTCACACTGAAAC 
               
               
                   
               
               
                 TGCTTGAAGGGTCAAGCAGGCAATCTGCTTTCCATGCTAATCCAGCCTCTGGCAGTTCAAGCATG 
               
               
                   
               
               
                 AACTCGAGCGGCAGTCCAATCCATGCAGTTTGA 
               
               
                   
               
               
                 &gt;GSVIVT00013475001 (Protein) 
               
               
                 (SEQ ID NO: 60) 
                   
               
               
                 MTRRCSHCSHNGHNSRTCPNRGVKIFGVRLTDGLIRKSASMGNLSHYAGSTSGHHQNGVSGNNSV 
                   
               
               
                   
               
               
                 SPGETPEHGAAADGYASEGFVPGSSSSRERKKGTPWTEEEHRMFLLGLQKLGKGDWRGISRNYVI 
               
               
                   
               
               
                 SRTPTQVASHAQKYFIRQTNVSRRKRRSSLFDIVADESVDTPMVSRDFFSTNPSQAETLSNNPLP 
               
               
                   
               
               
                 VPPALDEECESMDSTNSNDGEPPIPKPDGLQGCPPVIYPTYFSPFFPFSFPFWPGNSSEPTKMET 
               
               
                   
               
               
                 HEVLKPTAVHSKSPINVDELVGMSKLSLGESIGHAGPSSLTLKLLEGSSRQSAFHANPASGSSSM 
               
               
                   
               
               
                 NSSGSPIHAV 
               
               
                   
               
               
                 &gt; GSVIVT00012218001 (DNA) 
               
               
                 (SEQ ID NO: 61) 
                   
               
               
                 ATGACTCGCCGCTGCTCGCATTGCAGTCACAACGGGCACAATTCCAGGACATGCCCCAACCGCGG 
                   
               
               
                   
               
               
                 GGTCAAGATCTTCGGGGTTCGATTGACTGATGGGTTGATCCGTAAGAGTGCTAGTATGGGCAATC 
               
               
                   
               
               
                 TCAGCCACTACGCCGGGTCGACCTCTGGTCATCATCAGAACGGCGTTTCCGGTAACAATTCGGTC 
               
               
                   
               
               
                 TCTCCCGGAGAGACTCCAGAGCACGGCGCCGCGGCCGATGGATACGCCTCCGAGGGTTTCGTTCC 
               
               
                   
               
               
                 CGGTTCATCATCCAGCCGGGAGCGCAAGAAAGGCACTCCATGGACTGAAGAGGAACACAGAATGT 
               
               
                   
               
               
                 TTCTACTTGGACTGCAGAAGCTTGGAAAAGGGGATTGGCGTGGAATTTCACGTAATTATGTTATA 
               
               
                   
               
               
                 TCAAGGACACCTACTCAAGTCGCCAGCCATGCTCAGAAATATTTCATCAGGCAAACCAATGTGTC 
               
               
                   
               
               
                 TAGGAGAAAAAGACGGTCCAGCTTGTTTGATATTGTAGCTGATGAATCTGTTGACACTCCAATGG 
               
               
                   
               
               
                 TATCACGGGATTTCTTCTCCACCAACCCTTCGCAAGCTGAAACACTAAGCAATAACCCATTGCCT 
               
               
                   
               
               
                 GTTCCTCCGGCTCTGGATGAAGAATGTGAATCAATGGATTCTACCAACTCGAATGATGGAGAACC 
               
               
                   
               
               
                 ACCCATTCCAAAGCCGGATGGCTTACAAGGCTGTCCCCCAGTAATATATCCTACTTATTTCTCGC 
               
               
                   
               
               
                 CATTCTTCCCATTTTCTTTTCCATTCTGGCCGGGAAACAGTTCAGAGCCAACTAAAATGGAGACT 
               
               
                   
               
               
                 CATGAGGTGCTTAAGCCAACAGCTGTACATTCTAAGAGTCCAATCAATGTTGATGAGCTGGTTGG 
               
               
                   
               
               
                 CATGTCAAAACTGAGTTTAGGAGAATCCATCGGTCATGCTGGTCCCTCCTCTCTCACACTGAAAC 
               
               
                   
               
               
                 TGCTTGAAGGGTCAAGCAGGCAATCTGCTTTCCATGCTAATCCAGCCTCTGGCAGTTCAAGCATG 
               
               
                   
               
               
                 AACTCGAGCGGCAGTCCAATCCATGCACCCAATGGGAAGATTCTGCTGGTATGGAGATTGTAG 
               
               
                   
               
               
                 &gt;GSVIVT00012218001 (Protein) 
               
               
                 (SEQ ID NO: 62) 
                   
               
               
                 MTRRCSHCSHNGHNSRTCPNRGVKIFGVRLTDGLIRKSASMGNLSHYAGSTSGHHQNGVSGNNSV 
                   
               
               
                   
               
               
                 SPGETPEHGAAADGYASEGFVPGSSSSRERKKGTPWTEEEHRMFLLGLQKLGKGDWRGISRNYVI 
               
               
                   
               
               
                 SRTPTQVASHAQKYFIRQTNVSRRKRRSSLFDIVADESVDTPMVSRDFFSTNPSQAETLSNNPLP 
               
               
                   
               
               
                 VPPALDEECESMDSTNSNDGEPPIPKPDGLQGCPPVIYPTYFSPFFPFSFPFWPGNSSEPTKMET 
               
               
                   
               
               
                 HEVLKPTAVHSKSPINVDELVGMSKLSLGESIGHAGPSSLTLKLLEGSSRQSAFHANPASGSSSM 
               
               
                   
               
               
                 NSSGSPIHAPNGKILLVWRL 
               
               
                   
               
               
                 &gt; LjT37H17.80.nd (DNA) 
               
               
                 (SEQ ID NO: 63) 
                   
               
               
                 ATGACCCGGCGATGCTCGCATTGCAGCCATGGTGGCCACAACGCCAGGACCTGCCCCAACCGCGG 
                   
               
               
                   
               
               
                 AGTCAAGCTTTTCGGTGTCCGATTGACTGATGGCTCGATCCGGAAGAGTGCTAGTATGGGTAATC 
               
               
                   
               
               
                 TCACCCACTACACTGGCTCCGGGTCTGGACCTCTTCTTGGTGGGTCCAATAACCCTGATTCTCCC 
               
               
                   
               
               
                 GGTGAAACCCCTGATCACGCCGCCGCTGCTGACGGTTACGCCTCTGAGGATTTTGTTCCTGGCTC 
               
               
                   
               
               
                 TTCTTCTAGCTCCCGTGAAAGAAAAAAGGGCACTCCATGGACTGAGGAGGAACACAGAATGTTTT 
               
               
                   
               
               
                 TACTTGGATTGCAGAAACTGGGCAAAGGTGATTGGCGTGGAATTGCAAGGAACTATGTTATTTCA 
               
               
                   
               
               
                 AGGACACCTACTCAAGTGGCCAGTCATGCTCAGAAATATTTCATCAGGCAAAGCAATGTGTCTAG 
               
               
                   
               
               
                 GAGAAAGAGACGGTCCAGCTTGTTTGATATTGTTGCAGATGATGCGTCCGACACTCCAATGGTAG 
               
               
                   
               
               
                 AGCAAGACTTCTTGTCAGCTAATCAGCTACAGACTGAAACAGAAGGCAATAACCCTTTGCCTGCT 
               
               
                   
               
               
                 CCTCCTCCCATTGATGAAGAGTGTGAATCCATGGATTCCACAAACTCAATAGATGGAGACTCTGC 
               
               
                   
               
               
                 CCTGTTAAAGCCCGACACTCCAATACCGCCAACCTACCCGGTGTTATATCCTGCATATTATCCTC 
               
               
                   
               
               
                 CATTCTACCCGTATCCTCTGCCTTATTGGTCTGGATACAGTCCTGCAGAGCCCCCAAAGAAAGAG 
               
               
                   
               
               
                 GAGACACATGAAGTGGTGAAGCCAACTGCGGTGCTTTCCAAAAGCCCAATCAATGTGGATGAACT 
               
               
                   
               
               
                 TGTCGGCATGTCAAAACTGAGTTTGGGAGACTCCATTGGTGACTCTGGCCCCTCCTCTCTGTCTC 
               
               
                   
               
               
                 GAAAACTCGTCGAAGAAGGACCTTCCAGACAATCAGCTTTTCATGCTACTCCAGCATGTGGCAGT 
               
               
                   
               
               
                 TCAAATATAAATGGCAGTGTCATACATGCAGTTTAA 
               
               
                   
               
               
                 &gt;LjT37H17.80.nd (Protein) 
               
               
                 (SEQ ID NO: 64) 
                   
               
               
                 MTRRCSHCSHGGHNARTCPNRGVKLFGVRLTDGSIRKSASMGNLTHYTGSGSGPLLGGSNNPDSP 
                   
               
               
                   
               
               
                 GETPDHAAAADGYASEDFVPGSSSSSRERKKGTPWTEEEHRMFLLGLQKLGKGDWRGIARNYVIS 
               
               
                   
               
               
                 RTPTQVASHAQKYFIRQSNVSRRKRRSSLFDIVADDASDTPMVEQDFLSANQLQTETEGNNPLPA 
               
               
                   
               
               
                 PPPIDEECESMDSTNSIDGDSALLKPDTPIPPTYPVLYPAYYPPFYPYPLPYWSGYSPAEPPKKE 
               
               
                   
               
               
                 ETHEVVKPTAVLSKSPINVDELVGMSKLSLGDSIGDSGPSSLSRKLVEEGPSRQSAFHATPACGS 
               
               
                   
               
               
                 SNINGSVIHAV 
               
               
                   
               
               
                 &gt;chr2.CM0028.230.nd (DNA) 
               
               
                 (SEQ ID NO: 65) 
                   
               
               
                 ATGTCTCGCACGTGCTCACAGTGCGGCAACAACGGCCACAACTCCCGCACATGCACCGACACCGC 
                   
               
               
                   
               
               
                 CGCCGCTGGAGACAACGGCATCATGCTCTTCGGCGTGCGCCTCACCGAAGGCTCCACCTCCTCCT 
               
               
                   
               
               
                 CCGCCTTCATCAGGAAGAGCGCTAGCATGAACAACCTCTCCCAGTATAACGAACCCGAATCCAAC 
               
               
                   
               
               
                 CCCGCTGACGCAGCTGGCTACGCCTCCGACGACGTCGTTCATCCCTCCGCACGCGCCCGCGACCG 
               
               
                   
               
               
                 CAAGCGAGGTGTGCCTTGGACGGAAGAAGAACACAAACTGTTTCTGTTGGGATTGCATAAAGTGG 
               
               
                   
               
               
                 GGAAGGGAGATTGGAGAGGAATTTCTAGAAACTTCGTCAAAACTCGCACACCCACTCAGGTTGCT 
               
               
                   
               
               
                 AGTCATGCTCAGAAGTATTTCCTCCGCCGTCACAACCATAACCGCCGGCGCCGGAGATCTAGCCT 
               
               
                   
               
               
                 TTTCGACATCACCACCGATACGGTGATGGAATCTTCAACAATAATGGAGGAAGAACAAGATCAGC 
               
               
                   
               
               
                 AAGAAATGGTGCCGCCAGCTACCTCCGCCGTGTATCCGCCGTTACATTACGGTGGCTTCCACGGC 
               
               
                   
               
               
                 CCAGCGTTTCCAATGGCTCTGTCTCCGGTGGTATTGCCGGTGGCCGGAGGGGAAAGACCGGCAAG 
               
               
                   
               
               
                 GCCGATTAGGCCAACGCCGATTTTCCCTGTGCCTCCGTCTTCTAAGATGGCTAGTTTGAACTTGA 
               
               
                   
               
               
                 AAGAGAAAGCAGCTTCTCCTTCCCCTTCTTCTCCATTTGAGCCTCTACCGCTGTCGCTGAAGCTG 
               
               
                   
               
               
                 CAGCCATCTCCGCCGCCGTCCAAGGATCATTCTCCGGCAACCAGTAGCCACTCGTCGCCATCATC 
               
               
                   
               
               
                 GCCGTCTTCTTCATCATCTTTTCAGGCTATGTCTGCAGGGAAGTTCAGCGGTGGTGGAGATAGCA 
               
               
                   
               
               
                 TTATTAGTGTTGCTTGA 
               
               
                   
               
               
                 &gt;chr2.CM0028.230.nd (Protein) 
               
               
                 (SEQ ID NO: 66) 
                   
               
               
                 MSRTCSQCGNNGHNSRTCTDTAAAGDNGIMLFGVRLTEGSTSSSAFIRKSASMNNLSQYNEPESN 
                   
               
               
                   
               
               
                 PADAAGYASDDVVHPSARARDRKRGVPWTEEEHKLFLLGLHKVGKGDWRGISRNFVKTRTPTQVA 
               
               
                   
               
               
                 SHAQKYFLRRHNHNRRRRRSSLFDITTDTVMESSTIMEEEQDQQEMVPPATSAVYPPLHYGGFHG 
               
               
                   
               
               
                 PAFPMALSPVVLPVAGGERPARPIRPTPIFPVPPSSKMASLNLKEKAASPSPSSPFEPLPLSLKL 
               
               
                   
               
               
                 QPSPPPSKDHSPATSSHSSPSSPSSSSSFQAMSAGKFSGGGDSIISVA 
               
             
          
         
       
     
     As shown below, SEQ ID NOs: 44, 46, 48, . . . , and 66 share at least 44% homology with SEQ ID NO: 1. Also see  FIG. 5  for a multiple protein sequence alignment. 
     
       
         
               
               
               
               
               
             
               
               
               
               
               
             
           
               
                   
               
               
                   
                   
                   
                 Identities 
                 Positives 
               
               
                 No. 
                 Species 
                 Gene ID 
                 (%) 
                 (%) 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                 1 
                 
                   Arabidopsis 
                 
                 AT5G47390 
                 56 
                 66 
               
               
                   
                 
                   thaliana 
                 
               
               
                 2 
                 
                   Arabidopsis 
                 
                 AT3G16350 
                 45 
                 55 
               
               
                   
                 
                   thaliana 
                 
               
               
                 3 
                 
                   Zea May 
                 
                 GRMZM2G034110_T01 
                 86 
                 90 
               
               
                 4 
                 
                   Zea May 
                 
                 GRMZM2G020934_T01 
                 62 
                 69 
               
               
                 5 
                 
                   Sorghum 
                 
                 Sb01g029020.1 
                 87 
                 90 
               
               
                   
                 
                   bicolor 
                 
               
               
                   
                 ( Sorghum ) 
               
               
                 6 
                 
                   Sorghum 
                 
                 Sb03g003270.1 
                 44 
                 56 
               
               
                   
                 
                   bicolor 
                 
               
               
                   
                 ( Sorghum ) 
               
               
                 7 
                 
                   Glycine 
                 
                 Glyma17g15330.1 
                 61 
                 72 
               
               
                   
                 
                   max 
                 
               
               
                   
                 (Soybean) 
               
               
                 8 
                 
                   Glycine 
                 
                 Glyma05g04950.1 
                 58 
                 71 
               
               
                   
                 
                   max 
                 
               
               
                   
                 (Soybean) 
               
               
                 9 
                 
                   Vitis 
                 
                 GSVIVT00013475001 
                 62 
                 71 
               
               
                   
                 
                   vinifera 
                 
               
               
                   
                 (Wine 
               
               
                   
                 Grape) 
               
               
                 10 
                 
                   Vitis 
                 
                 GSVIVT00012218001 
                 62 
                 71 
               
               
                   
                 vinifera 
               
               
                   
                 (Wine 
               
               
                   
                 Grape) 
               
               
                 11 
                 
                   Lotus 
                 
                 LjT37H17.80.nd 
                 59 
                 71 
               
               
                   
                 
                   japonicus 
                 
               
               
                   
                 (Lotus) 
               
               
                 12 
                 
                   Lotus 
                 
                 chr2.CM0028.230.nd 
                 57 
                 68 
               
               
                   
                 
                   japonicus 
                 
               
               
                   
                 (Lotus) 
               
               
                   
               
             
          
         
       
     
     As used herein, “percent homology” of two sequences is determined using the algorithm described in Karlin and Attschul,  Proc, Natl. Acad. Sci. USA  87:2264-2268, 1990, modified as described in Karlin and Altschul,  Proc, Natl. Acad. Sci. USA  90:5873-5877, 1993. Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul et al.,  J Mol. Biol.  215:403-410, 1990. BLAST protein searches are performed with the XBLAST program, score=50, wordlength=3, to obtain amino acid sequences homologous to a reference polypeptide. To obtain gapped alignments for comparison purposes, Gapped BLAST is utilized as described in Altschul et al.,  Nucleic Acids Res.  25:3389-3402, 1997. When utilizing the BLAST and Gapped BLAST programs, the default parameters of the respective programs (e.g., XBLAST and NBLAST) are used. See the NCBI website at ncbi.nlm,nih.gov. 
     In a preferred embodiment, the cell also has a DREB1 gene expression level that is higher than a wild type DREB1 protein level so that the plant over-expresses both MYBS3 and DREB1. Listed below are cDNA and protein sequences of DREB1A, 1B, 1C, and 1D. 
     
       
         
               
               
             
           
               
                 OsDREB1A (dehydration-responsive element-binding protein 
                   
               
               
                 1A)LOC_Os09g35030 
               
               
                 CDS &gt;12009.m06503 
               
               
                 (SEQ ID NO: 3) 
                   
               
               
                 ATGTGCGGGATCAAGCAGGAGATGAGCGGCGAGTCGTCGGGGTCGCCGTGCAGCTCGGCG 
                   
               
               
                   
               
               
                 TCGGCGGAGCGGCAGCACCAGACGGTGTGGACGGCGCCGCCGAAGAGGCCGGCGGGGCGG 
               
               
                   
               
               
                 ACCAAGTTCAGGGAGACGAGGCACCCGGTGTTCCGCGGCGTGCGGCGGAGGGGCAATGCC 
               
               
                   
               
               
                 GGGAGGTGGGTGTGCGAGGTGCGGGTGCCCGGGCGGCGCGGCTGCAGGCTCTGGCTCGGC 
               
               
                   
               
               
                 ACGTTCGACACCGCCGAGGGCGCGGCGCGCGCGCACGACGCCGCCATGCTCGCCATCAAC 
               
               
                   
               
               
                 GCCGGCGGCGGCGGCGGCGGGGGAGCATGCTGCCTCAACTTCGCCGACTCCGCGTGGCTC 
               
               
                   
               
               
                 CTCGCCGTGCCGCGCTCCTACCGCACCCTCGCCGACGTCCGCCACGCCGTCGCCGAGGCC 
               
               
                   
               
               
                 GTCGAGGACTTCTTCCGGCGCCGCCTCGCCGACGACGCGCTGTCCGCCACGTCGTCGTCC 
               
               
                   
               
               
                 TCGACGACGCCGTCCACCCCACGCACCGACGACGACGAGGAGTCCGCCGCCACCGACGGC 
               
               
                   
               
               
                 GACGAGTCCTCCTCCCCGGCCAGCGACCTGGCGTTCGAACTGGACGTCCTGAGTGACATG 
               
               
                   
               
               
                 GGCTGGGACCTGTACTACGCGAGCTTGGCGCAGGGGATGCTCATGGAGCCACCATCGGCG 
               
               
                   
               
               
                 GCGCTCGGCGACGACGGTGACGCCATCCTCGCCGACGTCCCACTCTGGAGCTACTAG 
               
               
                   
               
               
                 Protein &gt;12009.m06503 
               
               
                 (SEQ ID NO: 4) 
                   
               
               
                 MCGIKQEMSGESSGSPCSSASAERQHQTVWTAPPKRPAGRTKFRETRHPVFRGVRRRGNA 
                   
               
               
                   
               
               
                 GRWVCEVRVPGRRGCRLWLGTFDTAEGAARAHDAAMLAINAGGGGGGGACCLNFADSAWL 
               
               
                   
               
               
                 LAVPRSYRTLADVRHAVAEAVEDFFRRRLADDALSATSSSSTTPSTPRTDDDEESAATDG 
               
               
                   
               
               
                 DESSSPASDLAFELDVLSDMGWDLYYASLAQGMLMEPPSAALGDDGDAILADVPLWSY* 
               
               
                   
               
               
                 OsDREB1B (dehydration-responsive element-binding protein 
               
               
                 1B)LOC_Os09g35010 
               
               
                 CDS &gt;12009.m06501 
               
               
                 (SEQ ID NO: 5) 
                   
               
               
                 ATGGAGGTGGAGGAGGCGGCGTACAGGACGGTGTGGTCGGAGCCGCCGAAGAGGCCGGCG 
                   
               
               
                   
               
               
                 GGAAGGACCAAGTTCAGGGAGACGAGGCACCCGGTGTACCGCGGCGTGCGGCGGCGCGGG 
               
               
                   
               
               
                 GGGCGGCCGGGCGCGGCGGGGAGGTGGGTGTGCGAGGTGCGGGTGCCCGGGGCGCGCGGC 
               
               
                   
               
               
                 TCCAGGCTGTGGCTCGGCACGTTCGCCACCGCCGAGGCGGCGGCGCGCGCGCACGACGCC 
               
               
                   
               
               
                 GCCGCGCTGGCGCTCCGCGGCAGGGCCGCCTGCCTCAACTTCGCCGACTCCGCGTGGCGG 
               
               
                   
               
               
                 ATGCCGCCCGTCCCCGCGTCCGCCGCGCTCGCCGGCGCGAGGGGGGTCAGGGACGCCGTC 
               
               
                   
               
               
                 GCCGTGGCCGTCGAGGCGTTCCAGCGCCAGTCGGCCGCGCCGTCGTCTCCGGCGGAGACC 
               
               
                   
               
               
                 TTCGCCAACGATGGCGACGAAGAAGAAGACAACAAGGACGTGTTGCCGGTGGCGGCGGCG 
               
               
                   
               
               
                 GAGGTGTTCGACGCGGGGGCGTTCGAGCTCGACGACGGGTTCAGGTTCGGCGGGATGGAC 
               
               
                   
               
               
                 GCCGGGTCGTACTACGCGAGCTTGGCGCAGGGGCTGCTCGTCGAGCCGCCGGCCGCCGGA 
               
               
                   
               
               
                 GCGTGGTGGGAGGACGGCGAGCTCGCCGGCTCCGACATGCCGCTCTGGAGCTACTAA 
               
               
                   
               
               
                 Protein &gt;12009.m06501 
               
               
                 (SEQ ID NO: 6) 
                   
               
               
                 MEVEEAAYRTVWSEPPKRPAGRTKFRETRHPVYRGVRRRGGRPGAAGRWVCEVRVPGARG 
                   
               
               
                   
               
               
                 SRLWLGTFATAEAAARAHDAAALALRGRAACLNFADSAWRMPPVPASAALAGARGVRDAV 
               
               
                   
               
               
                 AVAVEAFQRQSAAPSSPAETFANDGDEEEDNKDVLPVAAAEVFDAGAFELDDGFRFGGMD 
               
               
                   
               
               
                 AGSYYASLAQGLLVEPPAAGAWWEDGELAGSDMPLWSY* 
               
               
                   
               
               
                 OsDREB1C (dehydration-responsive element-binding protein 
               
               
                 1C)LOC_Os06g03670 
               
               
                 CDS &gt;13106.m00305 
               
               
                 (SEQ ID NO: 7) 
                   
               
               
                 ATGGAGTACTACGAGCAGGAGGAGTACGCGACGGTGACGTCGGCGCCGCCGAAGCGGCCG 
                   
               
               
                   
               
               
                 GCGGGGAGGACCAAGTTCAGGGAGACGAGGCACCCGGTGTACCGCGGCGTGCGGCGGCGG 
               
               
                   
               
               
                 GGGCCCGCGGGGCGGTGGGTGTGCGAGGTCAGGGAGCCCAACAAGAAGTCCCGCATCTGG 
               
               
                   
               
               
                 CTCGGCACCTTCGCCACCGCCGAGGCCGCCGCGCGCGCCCACGACGTCGCCGCGCTCGCC 
               
               
                   
               
               
                 CTCCGCGGCCGCGGCGCGTGCCTCAACTTCGCCGACTCGGCCCGCCTCCTCCGCGTCGAC 
               
               
                   
               
               
                 CCGGCCACCCTCGCCACCCCCGACGACATCCGCCGCGCCGCCATCGAGCTCGCCGAGTCA 
               
               
                   
               
               
                 TGCCCGCACGACGCCGCCGCCGCCGCCGCCTCCAGCTCCGCCGCCGCCGTCGAGGCCTCC 
               
               
                   
               
               
                 GCCGCCGCCGCGCCCGCCATGATGATGCAGTACCAGGACGACATGGCGGCGACGCCGTCC 
               
               
                   
               
               
                 AGCTACGACTACGCGTACTACGGCAACATGGACTTCGACCAGCCGTCCTACTACTACGAC 
               
               
                   
               
               
                 GGGATGGGCGGCGGCGGCGAGTACCAGAGCTGGCAGATGGACGGCGACGACGATGGTGGC 
               
               
                   
               
               
                 GCCGGCGGCTACGGCGGCGGCGACGTCACACTCTGGAGCTACTGA 
               
               
                   
               
               
                 Protein &gt;13106.m00305 
               
               
                 (SEQ ID NO: 8) 
                   
               
               
                 MEYYEQEEYATVTSAPPKRPAGRTKFRETRHPVYRGVRRRGPAGRWVCEVREPNKKSRIW 
                   
               
               
                   
               
               
                 LGTFATAEAAARAHDVAALALRGRGACLNFADSARLLRVDPATLATPDDIRRAAIELAES 
               
               
                   
               
               
                 CPHDAAAAAASSSAAAVEASAAAAPAMMMQYQDDMAATPSSYDYAYYGNMDFDQPSYYYD 
               
               
                   
               
               
                 GMGGGGEYQSWQMDGDDDGGAGGYGGGDVTLWSY* 
               
               
                   
               
               
                 OsDREB1D (dehydration-responsive element-binding protein 
               
               
                 1D)LOC_Os06g06970 
               
               
                 CDS &gt;13106.m00721 
               
               
                 (SEQ ID NO: 9) 
                   
               
               
                 ATGGAGAAGAACACCGCCGCCAGCGGGCAATTGATGACCTCCTCCGCGGAGGCGACGCCG 
                   
               
               
                   
               
               
                 TCGTCGCCGAAGCGGCCGGCGGGGCGAACCAAGTTCCAGGAGACGAGGCACCTAGTGTTC 
               
               
                   
               
               
                 CGTGGGGTGCGATGGCGTGGGTGCGCGGGGCGGTGGGTGTGCAAGGTGCGTGTCCCGGGC 
               
               
                   
               
               
                 AGCCGCGGTGACCGTTTCTGGATAGGCACGTCTGACACCGCCGAGGAGACCGCGCGCACG 
               
               
                   
               
               
                 CACGACGCCGCCATGCTCGCCTTGTGCGGGGCCTCCGCCAGCCTCAACTTCGCCGACTCT 
               
               
                   
               
               
                 GCCTGGCTGCTCCACGTCCCGCGCGCCCCCGTCGTCTCCGGACTCCGGCCACCAGCTGCC 
               
               
                   
               
               
                 CGATGTGCAACGCGCTGCCTGCAAGGCCATCGCCGAGTTCCAGCGCCGGGCCGGGGGAGC 
               
               
                   
               
               
                 ACCGCCACTGCCACTGCCACCTCCGGCGATGCTGCATCGACCGCTCCTCCGTCGGCACCC 
               
               
                   
               
               
                 GTTCTGTCAGCCAAACAATGCGAATTCATCTTTCTTTCTTCACTAGATTGTTGGATGTTA 
               
               
                   
               
               
                 ATGTCAAAGCTTATCAGCAGTAGCAGAGCAAAAGGATCGTTGTGCCTGCGAAAAAATCCC 
               
               
                   
               
               
                 ATTTCATTTTGCATGGTTACAAATTCTTACACTGCTCTTTTGCTCGAATACATTATATTG 
               
               
                   
               
               
                 CAGATGAATTCAATGATCGTTTTAATCCACGAATTATCAAAATATCAAGTCTTTCTGCTA 
               
               
                   
               
               
                 CTAACCATGATAACACACCACCTTTTTCAATGGAGGAGGTAG 
               
               
                   
               
               
                 Protein &gt;13106.m00721 
               
               
                 (SEQ ID NO: 10) 
                   
               
               
                 MEKNTAASGQLMTSSAEATPSSPKRPAGRTKFQETRHLVFRGVRWRGCAGRWVCKVRVPG 
                   
               
               
                   
               
               
                 SRGDRFWIGTSDTAEETARTHDAAMLALCGASASLNFADSAWLLHVPRAPVVSGLRPPAA 
               
               
                   
               
               
                 RCATRCLQGHRRVPAPGRGSTATATATSGDAASTAPPSAPVLSAKQCEFIFLSSLDCWML 
               
               
                   
               
               
                 MSKLISSSRAKGSLCLRKNPISFCMVTNSYTALLLEYIILQMNSMIVLIHELSKYQVFLL 
               
               
                   
               
               
                 LTMITHHLFQWRR* 
               
             
          
         
       
     
     The above-mentioned level of wild type MYBS3 or DREB1 protein can be the MYBS3 or DREB 1 gene expression level in a wild type cell of a wild type plant. To achieve this overexpression, the genes can be under the control of native, constitutive, tissue-specific, developmental stage-specific, or other inducible promoters. 
     The above-described transgenic plant can be rice, maize, wheat, barley, sorghum, sugarcane, turf grass, Miscanthus, switchgrass, soybean, canola, potato, tomato, bean, pea, or jatropha. The transgenic plant is more tolerant to chill than the wild type plant. 
     In a second aspect, the invention features a method of generating the above-described plant. The method includes steps of introducing into a cell of a plant a first nucleic acid that encodes a polypeptide containing the amino acid sequence of MYBS3 protein; and expressing the MYBS3 protein in the cell. The level of the MYBS3 protein in the cell is higher than a wild type MYBS3 protein level. In one embodiment, the method further includes introducing into the cell of the plant a second nucleic acid that encodes a second polypeptide containing the amino acid sequence of DREB1 protein; and expressing the DREB1 protein in the cell. The level of the DREB1 protein in the cell is higher than a wild type DREB1 protein level. 
     In a third aspect, the invention features a method of identifying a plant that is tolerant to chill. The method can be carried out by obtaining a sample from a candidate plant, and determining the MYBS3 gene expression level in the sample. The candidate plant is determined to be tolerant to chill if the expression level is above a predetermined level. The predetermined level is the level in a wild type plant. With this method, one can use MYBS3 as a marker for molecular breeding plants and selecting chill tolerant plants. 
     The details of one or more embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and drawings, and from the claims. 
    
    
     
       BRIEF DESCRIPTION OF DRAWINGS 
         FIG. 1  shows two constructs for respectively over-expressing and under-expressing MYBS3 in transgenic rice; namely, pSMY-MYBS3(Ox), an over-expression construct; and pSMY-MYBS3(Ri), an under-expression construct. P A1 , Hgh, T Nos , P Ubi , LB, and RB denote A1 promoter, hygromycin phosphotransferase, nopalin synthase terminator, Ubi promoter, left border of T-DNA, and right border of T-DNA, respectively. 
         FIG. 2  is a bar graph showing expression of MYBS3 and DREB1A in 10-day-old rice seedlings that were shifted from 28° C. to 4° C. and incubated for 72 h. Total RNAs were isolated from seedlings and subjected to quantitative real-time RT-PCR analysis. The highest mRNA level was assigned a value of 100, and the mRNA levels of other samples were calculated relative to this value. The error bars indicate the SE of three replicates. 
         FIG. 3  includes two photographs showing 10-day-old seedlings of wild type (WT) and lines S3(Ox)-110-1 and S3(Ri)-52-7 that were incubated at 4° C. for 8 h (A) or 24 h (B). 
         FIG. 4  is a schematic flow chart for a proposed role of MYBS3 in cold stress tolerance in rice. 
         FIG. 5  is a sequence alignment of thirteen MYB3 proteins, one from rice and two from each of  Arabidopsis thaliana, Zea May , sorghum, soybean, twine grape, and lotus. 
     
    
    
     DETAILED DESCRIPTION 
     This invention is based, at least in part, on the unexpected discoveries of that over-expression of MYBS3 in a plant increased the cold tolerance. 
     MYBS3 is a single DNA-binding repeat (1R) MYB transcription factor previously shown to mediate sugar signaling in rice. MYBS3 also plays a critical role in cold adaptation in rice. Gain- and loss-of-function analyses indicates that MYBS3 is sufficient and necessary for enhancing cold tolerance in rice. Transgenic rice constitutively over-expressing MYBS3 tolerates 4° C. for at least 1 week, and exhibits no yield penalty in normal field conditions. Transcription profiling of transgenic rice over- or under-expressing MYBS3 lead to identification of many genes in the MYBS3-mediated cold signaling pathway. Several genes activated by MYBS3 as well as inducible by cold have previously been implicated in various abiotic stress response and/or tolerance in rice and other plant species. Surprisingly, MYBS3 represses the well-known DREB1/CBF-dependent cold signaling pathway in rice, and the repression appears to act at the transcriptional level. DREB1 responds quickly and transiently while MYBS3 responds slowly to cold stress, which suggests distinct pathways act sequentially and complementarily for adapting short- and long-term cold stress in rice. This novel pathway, which controls cold adaptation in rice as well as other plants, forms the basis for this invention. 
     A transgenic plant described in the invention can be generated by introducing into the plant or a part thereof an expression construct comprising a DNA sequence encoding a MYB3 protein, a DREB1 protein, or both. Expression constructs are provided by the present invention for the stable transformation of plants with a gene encoding a MYB3 protein, a DREB1 protein, or both. These constructs comprise a DNA sequence encoding a MYB3 protein or a DREB1 protein which is operably linked to regulatory sequences which are capable of directing the expression of a MYB3 protein, a DREB1 protein, or both. These regulatory sequences may also include sequences capable of directing transcription in plants, either constitutively, or stage and/or tissue specific, depending on the use of the plant or parts thereof. The expression constructs provided may be inserted into a vector, preferably a plasmid, used in bacteria-mediated transformation of the selected plant host. The expression construct is then preferably integrated into the genome of the plant host. 
     A transgene is a nucleic acid sequence (encoding, e.g., one or more subject polypeptides), which is partly or entirely heterologous to a plant cell into which it is introduced, or, is homologous to an endogenous gene of the plant or cell into which it is introduced but is intended to be inserted into the plant genome in such a way as to alter the genome (e.g., it is inserted at a location which differs from that of the natural gene or its insertion results in a knockout). A transgene can include one or more operably linked transcriptional regulatory sequences (e.g., an enhancer sequence) and any other nucleic acid, such as an intron, that may be necessary for optimal expression of a nucleic acid of interest. 
     A “transformed” and “transgenic cell refer to a host cell or organism into which a heterologous nucleic acid molecule has been introduced. The nucleic acid molecule can be stably integrated into the genome generally known in the art. Accordingly, a transgenic cell is a cell containing a transgene. A transgenic plant is any plant in which one or more, or all, of the cells of the plant include a transgene. The transgene can be introduced into the cell by introduction into a precursor cell by way of deliberate genetic manipulation, such as by T-DNA mediated transfer, electroporation, or protoplast transformation. The transgene may be integrated within a chromosome, or it may be an extrachromosomally replicating DNA. 
     The term “heterologous” refers to portions of a nucleic acid and indicates that the nucleic acid comprises two or more subsequences that are not found in the same relationship to each other in nature. For instance, a nucleic acid that is recombinantly produced typically has two or more sequences from unrelated genes synthetically arranged to make a new functional nucleic acid, e.g., a promoter from one source and a coding region from another source. The two nucleic acids are thus heterologous to each other in this context. When added to a cell, the recombinant nucleic acids would also be heterologous to the endogenous genes of the cell. Thus, in a chromosome, a heterologous nucleic acid would include a non-native (non-naturally occurring) nucleic acid that has integrated into the chromosome, or a non-native (non-naturally occurring) extra-chromosomal nucleic acid. In contrast, a naturally translocated piece of chromosome would not be considered heterologous in the context of this patent application, as it comprises an endogenous nucleic acid sequence that is native to the mutated cell. A heterologous nucleic acid, gene, or protein can be one that originates from a foreign species, or, if from the same species, is substantially modified from its original form. For example, a maize ubiquitin (Ubi) promoter operably linked to a nucleic acid sequence encoding a rice MYB3 protein is one form of a sequence heterologous to rice. If a promoter and a coding sequence are from the same species, one or both of them can be substantially modified from their original forms. 
     Rice is one of the most important food crops in the world, and increases in rice yield could significantly ease the pressure on world food production. Rice is also a powerful model for functional genomics study for dissecting genetic networks of stress responses in cereal crops. Low temperatures are one of the major environmental stresses that adversely affect rice productivity in temperate and subtropical zones and in high elevation areas. Rice seedlings are particularly sensitive to chilling in early spring in these areas, leading to slow seedling development, yellowing, withering, reduced tillering and stunted growth (Andaya, et al., 2003, J Exp Bot 54: 2579-2585). Rice cannot be grown in approximately 7,000,000 hectares of land in south and south-east Asia due to cold stress (Sthapit, et al., 1998, Crop Sci 38: 660-665); in temperate regions such as California (USA), cold is an important stress that results in delayed heading and yield reduction due to spikelet sterility (Peterson, et al., 1974, California Agriculture, 28(7), 12-14). Thus, improvement of chilling tolerance may significantly increase rice production. 
     Plants respond and adapt to cold stress at the molecular and cellular levels as well as induce an array of biochemical and physiological alterations that enable them to survive (Bohnert et al., 1995, Cell 7: 1099-1111; and Browse, et al., 2001, Curr Opin Plant Biol 4: 241-246). Under cold stress, the expression of many genes is induced in various plant species (Hughes, et al., 1996, J Exp Bot 47: 291; and Thomashow, 1999, Annu Rev Plant Physiol Plant Mol Biol 50: 571-59), and the products of these genes function not only in adaptations promoting stress tolerance, e.g., biosynthesis of osmotica (Chen, et al., 2002, Curr Opin Plant Biol 5: 250-257; and Taji, et al., 2002, Plant J 29: 417-426), generation of antioxidants (Prasad, et al., 1994, Plant Cell 6: 65-74), and increased membrane fluidity (Murata and Los, 1997, Plant Physiol 115: 875-879; and Orvar, et al., 2000, Plant J 23: 785-794), but also in the regulation of gene expression and signaling transduction in stress responses, e.g., transcription factors and proteins involved in RNA processing and nuclear export (Yamaguchi-Shinozaki, et al., 2006, Annu Rev Plant Biol 57: 781-803; and Chinnusamy, et al., 2007, Trends Plant Sci 12: 444-451). Deciphering the mechanisms by which plants perceive and transmit cold signals to cellular machinery to activate adaptive responses is of critical importance for developing breeding strategies to enhance cold stress tolerance in crops. 
     In  Arabidopsis  and rice, the CBF/DREB1-dependent cold response pathway has been shown to play a predominant role in freezing-tolerance through the process of cold acclimation (Thomashow, 1999, Annu Rev Plant Physiol Plant Mol Biol 50: 571-59; Yamaguchi-Shinozaki, et al., 2006, Annu Rev Plant Biol 57: 781-803; and Chinnusamy, et al., 2007, Trends Plant Sci 12: 444-451). The DREB1/CBF family, including DREB1A/CBF3, DREB1B/CBF1, and DREB1C/CBF2, are able to bind to and activate the cis-acting elements DRE (dehydration-responsive element) (Yamaguchi-Shinozaki, et al., 1994, Plant Cell 6: 251-264; and Stockinger, et al., 1997, Proc Natl Acad Sci USA 94: 1035-104) or CRT (C-repeat) (Baker, et al., 1994, Plant Mol Biol 24: 701-713) on promoters of several cold-responsive genes (CORs) (Gilmour, et al., 1998, Plant J 16: 433-442; Jaglo-Ottosen, et al., 1998, Science 280: 104-106; Liu, et al., 1998, Plant Cell 10: 1391-1406; Medina, et al., 1999, Plant Physiol 119: 463-470). 
     Rice DREB1A and DREB1B are induced by cold stress, and constitutive over-expression of these genes leads to induction of stress-responsive genes, increased tolerance to high-salt and cold, and growth retardation under normal conditions in transgenic  Arabidopsis  and rice (Dubouzet, et al., 2003, Plant J 33: 751-763; and Ito, et al., 2006, Plant Cell Physiol 47: 141-153), indicating the evolutionary conservation of the DREB1/CBF cold-responsive pathway in monocots and dicots. However, in comparison to  Arabidopsis  and other cereals like wheat and barley that cold acclimate (Wen, et al., 2002, Plant Physiol 129: 1880-1891), rice does not undergo acclimation process and is more sensitive to low temperature exposures. Microarray analysis demonstrated the existence of 22 cold-regulated genes in rice, which have not been reported in  Arabidopsis  (Rabbani, et al., 2003, Plant Physiol 133: 1755-1767). These studies also indicate that plant species vary in their abilities to adapt to cold stress. 
     Other rice proteins have also been shown to be involved in cold tolerance. For example, a zinc-finger protein iSAP1 confers cold, dehydration, and salt tolerance in transgenic tobacco (Mukhopadhyay, et al., 2004, Proc Natl Acad Sci USA 101: 6309-6314); the rice MYB4 transcription factor confers chilling and freezing tolerances by enhancing the COR gene expression and proline accumulation in  Arabidopsis  (Vannini, et al., 2004, Plant J 37: 115-127), and improves cold and drought tolerances by accumulating osmolyte in transgenic apples (Pasquali, et al., 2008, Plant Cell Rep 27: 1677-1686). Overexpression of the rice cold-, drought, and salt-inducible MYB3R-2 (an R1R2R3 MYB) gene enhances cold, drought, and salt tolerance by regulating some stress-responsive genes involved in the CBF-dependent or CBF-independent pathways in  Arabidopsis  (Dai, et al., 2007, Plant Physiol 143: 1739-1751; and Ma, et al., 2009, Plant Physiol 150: 244-256). 
     The expression of DREB1 is subjected to regulation by several factors. For example, it is affected by members in the same DREB1 family. The  Arabidopsis  cbf2 mutant, in which CBF2/DREB 1 C is disrupted, shows higher freezing, dehydration and salt tolerance than the wild-type plant, indicating that DREB1C/CBF2 acts as a repressor of CBF1/DREB1B and CBF3/DREB1A expression (Novillo, et al., 2004, Proc Natl Acad Sci USA 101: 3985-3990). The expression of DREB1/CBF is activated by Inducer of CBF Expression 1, ICE1 (a MYC-like basic helix-loop-helix-type transcription factor) (Chinnusamy, et al., 2003, Genes Dev 17: 1043-1054), CAX1 (a Ca 2+ /H +  transporter) (Catala, et al., 2003, Plant Cell 15: 2940-2951), CBL1 (a Ca 2+  sensor) (Albrecht, et al, 2003, Plant J 36: 457-470), and LOS4 (a DEAD-box RNA helicase) (Gong, et al., 2002, Proc Natl Acad Sci USA 99: 11507-11512), and repressed by FRY2 (a transcription factor) (Xiong, et al., 2002, Proc Natl Acad Sci USA 99: 10899-1090), HOS1 (a putative RING finger E3 ligase) (Lee, et al., 2001, Genes Dev 15: 912-924), and ZAT12 (a C 2 H 2  zinc finger transcription factor) (Vogel, et al., 2005, Plant J 41: 195-211), during cold acclimation in  Arabidopsis . The mechanism by which these factors affect the expression of CBF/DREB1 is not clear. 
     Previously, three MYB transcription factors, MYBS1, MYBS2, and MYBS3 each with a single DNA binding domain (1R MYB), were identified in rice and shown to bind specifically to the TA box (TATCCA) in the sugar response complex (SRC) of α-amylase gene (αAmy3) promoter (Lu, et al., 2002, Plant Cell 14: 1963-1980). MYBS1 and MYBS2 transactivate, while MYBS3 represses, the sugar starvation-inducible αAmy3 SRC activity in rice (Lu, et al., 2002, Plant Cell 14: 1963-1980). The rice MYBS3 homologue in  Arabidopsis  (AGI code: At5g47390) is activated by ABA, CdCl 2  and NaCl (Yanhui, et al., 2006, Plant Mol Biol 60: 107-124). It is unexpected that the expression of MYBS3 is induced by cold. By both gain- and loss-of-function analyses, MYBS3 is shown essential for cold stress tolerance in rice. Transcription profiling of transgenic rice over- or under-expressing MYBS3 led to identification of genes that are activated or repressed by MYBS3 and play diverse functions. The DREB1-dependent cold response signaling pathway is among those repressed by MYBS3 in rice. This finding suggests that the DREB1- and MYBS3-dependent pathways may complement each other and act sequentially to adapt to immediate and persistent cold stress in rice. 
     The specific examples below are to be construed as merely illustrative, and not limitative of the remainder of the disclosure in any way whatsoever. Without further elaboration, it is believed that one skilled in the art can, based on the description herein, utilize the present invention to its fullest extent. All publications cited herein are hereby incorporated by reference in their entirety. Further, any mechanism proposed below does not in any way restrict the scope of the claimed invention. 
     EXAMPLE 
     Materials and Methods 
     Plant Materials 
     The rice cultivar  Oryza sativa  L. cv. Tainung 67 was used in this study. Induction of rice calli was performed as described (Yu, et al., 1991, J Biol Chem 266: 21131-21137). For hydroponic culture of rice seedlings, seeds were sterilized with 3% NaOCl for 30 min, washed extensively with distilled water, and germinated in Petri dishes with wetted filter papers at 37° C. in the dark. After 48 h incubation, germinated seeds were cultivated in a half-strength Kimura B solution containing the following macronutrients: (NH4) 2 SO 4  (0.18 mM), KNO 3  (0.09 mM), MgSO 4  (0.27 mM), KH 2 PO 4  (0.09 mM), and Ca(NO 3 ) 2  (0.18 mM), and micronutrients: Fe-citrate (0.03 μM), H 3 BO 3  (2.5 μM), MnSO 4 .H 2 O (0.2 μM), ZnSO 4 .7H 2 O (0.2 μM), CuSO 4 .5H 2 O (0.05 μM), and H 2 MoO 4  (0.05 μM). The pH of the solution was adjusted to 4.7-4.8 using 0.5 N HCl. The culture solution was replaced with fresh solution every 2 days. Seedlings were grown under a 14-h light/10-h dark cycle for 10 days in a 28° C. chamber before treatments. 
     Primers 
     All primers used for the cloning of cDNAs or plasmid constructions and quantitative RT-PCR are listed in Table 1 below. 
                                                         TABLE 1                   Primers                    Annealing   Fragment       Target       temperature   size       gene   Primer   (° C.)   (bp)                    MYBS3   S3F1: 5′-CCT TTCTGGCAA AATCAG AAAGA-3′ (SEQ ID NO: 11)   60   78           S3R1: 5′-ATG AACTGG AACAGGCTTGACA-3′ (SEQ ID NO: 12)                       MYBS3   S3PF: GCGGATCCCCTTTTGACTTGCAGGTTAATTACTTCAGG   68   2500       promoter   (SEQ ID NO: 13)                   S3PR: CATGCCATGGTTTAAACCCCCCCTCCGTCCCTCCACCTTCC                   (SEQ ID NO: 14)                       DREB1A   1AF: 5′-GGACCTGTACTACGCGAGCTT-3′ (SEQ ID NO: 15)   60   138           1AR: 5′-GGCAAAATTGTACAGTTGATTGA-3′ (SEQ ID NO: 16)                       DREB1A   1APro: 5′-TTGACCGGGATACCGAATTA-3′ (SEQ ID NO: 17)   60   1054       promoter   1APro: 5-GTAATGGCGATGGGAGAAGA-3′ (SEQ ID NO: 18)                       DREB1B   1BF: 5′-AGCTCGCCGGCTCCGACA-3′ (SEQ ID NO: 19)   60   194           1BR: 5′-GGGAGAAATCTGGCACATTCC-3′ (SEQ ID NO: 20)                       DREB1B   1BPro: 5′-AGGTAAGCCATTAGCGCATG-3′ (SEQ ID NO: 21)   60   747       promoter   1BPro: 5′-GGATGACTCTCTCTGGTTCA-3′ (SEQ ID NO: 22)                       DREB1C   1CF: 5′-GAGTTGGAGCTAGCAGTTTTGAG-3′ (SEQ ID NO: 23)   60   54           1CR: 5′-TAGCTGTATAGGAGGAGCAAAGC-3′ (SEQ ID NO: 24)                       Amy3   Amy3F: 5′-GTAGGCAGGCTCTCTAGCCTCTAGG-3′ (SEQ ID NO: 25)   60   112           Amy3R: 5′-GTAGGCAGGCTCTCTAGCCTCTAGG-3′ (SEQ ID NO: 26)                       Cytochrome   CytF: 5′-GTCATCCAGGAGACGATGAGG-3′ (SEQ ID NO: 27)   60   129       P450   CytR: 5′-GATGTTGCGGAACAGAGGTAG-3′ (SEQ ID NO: 28)                       18S rRNA   18SF: 5′-CCTATCAACTTTCGATGGTAGGATA-3′ (SEQ ID NO: 29)   60   229           18SR: 5′-CGTTAAGGGATTTAGATTGTACTCATT-3′ (SEQ ID NO: 30)                       Trehalose-6-   T6PP1 F: 5′-GGAGTTCCTCAATTTCTTGGTG-3′ (SEQ ID NO: 31)   60   116       phosphate   T6PP1 R: 5′-CGCCTCGGAAACTACAGTTATT-3′ (SEQ ID NO: 32)               phosphatase 1                   gene                   (Os02g44230)                           Trehalose-6-   T6PP F: 5′-AGGATGCATTCAAGGTTCTGA-3′ (SEQ ID NO: 33)   60   139       phosphate   T6PP R: 5′-CAAGATGCCAGTTTCTTCAGG-3′ (SEQ ID NO: 34)               phosphatase 2                   gene                   (Os10g40550)                           GFP   GFP_F: 5′-CCTGTCCTTTTACCAGACAACC-3′ (SEQ ID NO: 35)   60   85           GFP_R: 5′-GGACCATGTGGTCTCTCTTTTC-3′ (SEQ ID NO: 36)                       Multidrug-   MRT_F: 5′-CAGGCAGAGGAACAGGTGAT-3′ (SEQ ID NO: 37)   60   108       resistantce   MRT_R: 5′-CGTACCGGAACAAGCTGAAC-3′ (SEQ ID NO: 38)               (Os01g50100)                           Glutamate   GD_F: 5′ AAGACGCTGCTGATTGATATGAT-3′ (SEQ ID NO: 39)   60   50       decarboxylase   GD_R: 5′-TGGTAGCTCACACCATGAATGTA-3′ (SEQ ID NO: 40)               (Os03g13300)                           WRKY77   WRKY77_F: 5′-GGAATGGACAATTAGTTTGTCTCC-3′ (SEQ ID NO:   60   73       (Os01g40260)   41)                   WRKY77_R: 5′-ATATATCGATGGGCCGTAATTTT-3′ (SEQ ID NO: 42)                    
Plasmid Construction
 
     The GATEWAY gene cloning system (Invitrogen, Carlsbad, CA) was used to construct the MYBS3-GFP fusion gene. Briefly, the full-length cDNA of MYBS3 was inserted between the attL1 and attL2 sites in pENTR/D-TOPO, generating the entry vector pENT-MYBS3. The CaMV35S promoter upstream of GFP in pCAMBIA1302 (see the website at cambia.org.au/daisy/cambia/585.html) was replaced with the maize ubiquitin (Ubi) promoter, and the ccdB DNA fragment flanked by attR1 and attR2 sties was inserted between the Ubi promoter and GFP, generating the destination vector pDEST-GFP. MYBS3 in pENT-MYBS3 was then inserted upstream of GFP in pDEST-GFP through the GATEWAY lambda recombination system, generating p1302-MYBS3-GFP. The 2.5-kb MYBS3 promoter fragment (upstream of ATG) was PCR synthesized and used for replacement of the Ubi promoter in pDEST-GFP, generating the Ubi::MYBS3-GFP construct. 
     For generating constructs used for the embryo transient expression assay, the 1054-bp DREB1A and 747-bp DREB1B promoters (upstream of ATG) were PCR-synthesized and fused upstream of Luc cDNA in pLuc (Lu, et al., 1998, J Biol Chem 273: 10120-10131). Plasmid p3Luc.18 contains αAmy3 SRC (−186 to −82 upstream of the transcription start site) fused to the CaMV35S minimal promoter-Adh intron-Luc fusion gene (Lu, et al., 1998, J Biol Chem 273: 10120-10131). 
     For generating constructs used for rice transformation, plasmid pBS-MYBS3 (Lu, et al., 2002, Plant Cell 14: 1963-1980) containing the Ubi promoter fused upstream of MYBS3 cDNA was linearized with EcoRI and inserted into the binary vector pSMY1H (Ho, et al., 2000, Plant Physiol 122: 57-66), generating pSMY-MYBS3 ( FIG. 1 ). To make the MYBS3 RNA interference construct, a 227-bp sequence derived from the 3′UTR of MYBS3 cDNA was synthesized by PCR, fused in antisense and sense orientations flanking the 750-bp GFP cDNA. This MYBS3 RNAi fragment was used to replace the MYBS3 cDNA in pUbi-MYBS3, generating pUbi-MYBS3(Ri). pUbi-MYBS3(Ri) was linearized with EcoRI and inserted into the binary vector pSMY1H, generating pSMY-MYBS3(Ri) ( FIG. 1 ). 
     Rice Transformation 
     Plasmids p1302-MYBS3-GFP, pSMY-MYBS3, pSMY-MYBS3(Ri) as constructed above were introduced into  Agrobacterium tumefaciens  strain EHA101, and rice transformation was performed as described elsewhere (Ho, et al., 2000, Plant Physiol 122: 57-66). 
     RNA Extraction and Real-Time Quantitative RT-PCR Analysis 
     Total RNA was extracted from leaves of rice seedlings with Trizol reagent (Invitrogen) and treated with RNase-free DNase I (Promega, Madison, Wis.). Four μg of RNA was used for cDNA preparation with reverse transcriptase (Applied Biosystems, Foster City, Calif.), and cDNA was then diluted to 10 ng/μl. Five μl of cDNA was mixed with primers and the 2× Power SYBR Green PCR Master Mix reagent, and applied to an ABI 7500 Fast Real-Time PCR System (Applied Biosystems). The quantitative variation between different samples was evaluated by the delta-delta CT method, and the amplification of 18S ribosomal RNA was used as an internal control to normalize all data. 
     Subcellular Localization of MYBS3-GFP Fusion Protein 
     Protoplasts were isolated from transformed calli as described (Lu, et al., 1998, J Biol Chem 273: 10120-10131). GFP expression was detected under a LSM510 confocal laser scanning microscope (Carl Zeiss) using a 40× objective lens and the confocal microscopy software Release 2.8 (Carl Zeiss). 
     Stress Treatments 
     Ten-day-old seedlings cultured in the half-strength Kimura B solution at 28° C. and with 16-h light and 8-h dark cycle in a growth chamber were used for all stress treatments. Stress treatments are as follows: ABA, seedlings were transferred to a culture solution containing 20 μM ABA; drought, seedlings were air-dried until 10% or 30% of fresh weight was lost; cold, seedlings were transferred to 4° C.; salt, seedlings were transferred to a culture solution containing 200 mM NaCl; heat, seedlings were transferred to 45° C. 
     Microarray Analysis 
     Total RNA was extracted from leaves of rice seedlings using the Qiagen RNeasy Plant Mini Kits (Qiagen, Valencia, Calif.) according to the Qiagen manual. RNA quality was examined by the Agilent 2100 bioanalyzer (Affymetrix, Palo Alto, Calif.), and biotinylated target RNA was prepared from total RNA. Samples were hybridized to the Affymetrix Rice GeneChip (Affymetrix, Santa Clara, Calif.) as described in the GeneChip Expression Analysis Technical Manual. Two biological replicates were performed for cold treated samples per time point. 
     The hybridization signals were scanned with an Affymetrix GeneChip scanner 3000 7G, and the cell intensity (CEL) files were obtained from software Affymetrix GCOS version 1.4 (Affymetrix). CEL files were loaded into GeneSpring GX 9.0 (Agilent Technologies, Palo Alto, Calif.). Filtering tools in the GeneSpring software were used to identify genes significantly up-regulated and down-regulated between different chips. All genes up-regulated or down-regulated by over-expression or under-expression of MYBS3 or by cold are listed in Tables S7-S11 of Su, et al, Plant Physiol. 2010; 153(1):145-58. 
     Accession Number 
     DREB1A (Os09g35030); DREB1B (Os09g35010); DREB1C (Os06g03670); αAmy3/RAmy3D (Os08g36910); Cytochrome P450 gene (Os02g47470); Glutamate decarboxylase gene (Os03g13300); WRKY77 (Os01g40260); Multidrug resistance protein 4 gene (Os01g50100); Trehalose-6-phosphate phosphatase 1 gene (Os02g44230); and Trehalose-6-phosphate phosphatase 2 gene (Os10g40550). 
     Results 
     Expression of MYBS3 is Ubiquitous and Activated by Cold Stress 
     Expression of MYBS3 was found to be ubiquitous in all tissues in 7-day-old seedlings and 3-month-old mature plants (including spike, stem, sheath, leaf, senescent leaf, leaf in light, root in light, leaf in dark, and root in dark) and in suspension cells of rice cultured in media with or without sucrose for 2 days. The regulation of MYBS3 expression by various stresses was investigated by subjecting 10-day-old rice seedlings to ABA (20 μM), drought (air dry), cold (4° C.), salt (200 mM NaCl), and heat (45° C.) treatments. The accumulation of MYBS3 mRNA was induced by cold in roots and by cold and salt in shoots, but reduced by ABA in shoots. In 10-day-old rice seedlings, the expression pattern of MYBS3 and DREB1A under cold stress was further compared. The amount of MYBS3 mRNA was detectable at 28° C., and increased 5-fold at 4° C. after 72 h; in contrast, the accumulation of DREB1A mRNA was barely detectable at 28° C., increased drastically after shifting to 4° C. and peaked at 6 h, but declined to one fifth after 72 h ( FIG. 2 ). 
     To determine whether MYBS3 is regulated by cold at the transcriptional level, the 2.5-kb MYBS3 promoter was fused to the reporter gene GFP encoding a green fluorescence protein and introduced into the rice genome. Ubi promoter fused to GFP was used as a control. Transgenic rice seedlings were grown at 4° C. Under the control of MYBS3 promoter, the accumulation of GFP mRNA was 2.5 times higher at 12 h and stayed high up to 24 h. In contrast, under the control of Ubi promoter, the accumulation of GFP mRNA decreased by nearly 50% at 6 h, and then stayed at similar levels up to 24 h. This result indicates that the MYBS3 promoter is activated by cold. 
     MYBS3 is a transcriptional repressor of αAmy3 SRC in rice suspension cells (Lu, et al., 2002, Plant Cell 14: 1963-1980). To determine whether MYBS3 is localized in nucleus, the Ubi promoter was fused to the MYBS3-GFP fusion DNA. The Ubi::MYBS3-GFP and Ubi::GFP constructs were introduced into the rice genome. Protoplasts were isolated from transformed calli, incubated at 4° C. or 28° C., and examined. Accumulation of MYBS3-GFP was detected mainly in the nucleus, whereas GFP alone was distributed throughout the cell except the vacuole, at both 4° C. and 28° C., suggesting that MYBS3 is constitutively localized in the nucleus. 
     MYBS3 is Sufficient and Necessary for Cold Tolerance in Rice 
     Since MYBS3 was induced by cold, its role in cold tolerance in rice was explored by gain- and loss-of-function approaches. Constructs Ubi::MYBS3 and Ubi::MYBS3(RNAi) (RNA interference) ( FIG. 1 ) were introduced into the rice genome, and several transgenic lines were obtained. Compared to the untransformed wild type (WT) rice, the accumulation of MYBS3 mRNA was 62.5 and 19.4 times that of WT in MYBS3-overexpression [MYBS3(Ox)] lines S3(Ox)-110-1 and S3(Ox)-112-7, and 0.19 and 0.16 times that of WT in MYBS3-underexpression [MYBS3(Ri)] lines S3(Ri)-42-10 and S3(Ri)-52-7. Each of these lines contained only one copy of inserted DNA. 
     To test the cold tolerance of transgenic rice, seedlings were shifted from 28° C. to 4° C. MYBS3(Ox) lines and WT remained normal while MYBS3(Ri) lines started to show leaf rolling at 4° C. after 8 h ( FIG. 3A ), and both WT and MYBS3(Ri) lines showed leaf rolling and wilting at 4° C. after 24 h in hydroponic culture ( FIG. 3B ) or 1 week in soil. Seedlings seemed to be more sensitive to cold in hydroponic culture, probably due to weaker growth in hydroponic culture than in soil. Line S3(Ox)-110-1, which accumulated three times more MYBS3 mRNA than S3(Ox)-112-7, conferred higher cold tolerance than line S3(Ox)-112-7. Quantitative analysis also indicated that MYBS3(Ox) lines were more cold tolerant than WT and MYBS3(Ri) lines, and WTs were more cold tolerant than MYBS3(Ri) lines (Table 2). These observations suggest that MYBS3 is sufficient and necessary for cold tolerance in rice, and the degree of cold tolerance correlates with the MYBS3 expression level. 
     
       
         
               
             
               
               
               
               
             
               
               
               
               
             
           
               
                 TABLE 2 
               
             
             
               
                   
               
               
                 MYBS3(Ox) lines are more cold tolerant. 
               
             
          
           
               
                   
                 No. of plants 
                 Total no. of 
                   
               
               
                 Line 
                 survived* 
                 plants tested 
                 Survival rate (%) 
               
               
                   
               
             
          
           
               
                 Wild type 
                 3 
                 30 
                 10.0 ± 0.0  
               
               
                 S3(Ox)-110-1 
                 18 
                 21 
                 85.7 ± 10.5 
               
               
                 S3(Ox)-112-7 
                 26 
                 32 
                 81.3 ± 11.1 
               
               
                 S3(Ri)-42-10 
                 0 
                 20 
                 0.0 ± 0.0 
               
               
                 S3(Ri)-52-7 
                 0 
                 21 
                 0.0 ± 0.0 
               
               
                   
               
               
                 *Number of plants survived after exposure to 4° C. for 24 h. Experiments were repeated 4 times. Five to eight plants per line were tested in each experiment. The survival rate is a mean ± SD. 
               
             
          
         
       
     
     The morphology of transgenic rice was similar to the WT, except under greenhouse growth conditions, where plants of the MYBS3(Ox) lines were 20% shorter, had 30% lower tiller numbers, and headed 1 week later than the WT and MYBS3(Ri) line. However, in field conditions, most agronomic traits and yield of MYBS3(Ox) lines were similar to those of the WT (Table 3). 
                                       TABLE 3                   Comparison of agronomic traits of a MYBS3(Ox) line with       wild type grown in field.                Trait   WT   S3(Ox)-110-1                       Plant height (cm)   101.6 ± 3.7*   95.5 ± 5.4           Tiller number   12.3 ± 2.5   19.5 ± 6.8           Panicle number/plant   12.9 ± 2.9   19.0 ± 6.1           Panicle length (cm)   18.9 ± 1.3   18.4 ± 0.1           Grain number/panicle   118.0 ± 14.5   103.5 ± 8.8            Fertility (%)   95.7 ± 1.2   93.8 ± 1.7           Grain yield (g/plant)    41.7 ± 11.0    45.4 ± 15.9           1000 Grains weight (g)   26.3 ± 0.5   24.3 ± 0.4                        
Twenty plants each of WT and line S3(Ox)-110-1 per replicate, and with total of 3 replicates, were grown during February to July, 2008. The value is a mean±SD.
 
MYBS3 Regulates the Expression of Genes with Diverse Functions
 
     To identify downstream genes regulated by MYBS3 under cold stress, seedlings of S3(Ox)-110-1, S3(Ri)-52-7 and WT were grown at 4 and 28° C. for 24 h. Total RNAs were isolated for microarray analysis using the Affymetrix rice gene chip array containing 55,515 probe sets. Relative change was calculated by comparing the data for MYBS3(Ox) line or MYBS3(Ri) line against those for WT grown at 4° C. and 28° C., generating six comparisons. Only relative changes of 3-fold or more were taken to be significantly different. Based on a Venn diagram analysis, 89 genes were up-regulated in the MYBS3(Ox) line (compared with WT) at either 4 or 28° C., and 1466 genes were up-regulated in WT at 4° C. (compared with 28° C.). Among these genes, 17 genes were up-regulated by over-expression of MYBS3 as well as up-regulated by cold in WT (Table S1 of Su, et al, Plant Physiol. 2010; 153(1):145-58). On the other hand, 291 genes were down-regulated in the MYBS3(Ox) line (compared with WT) at either 4 or 28° C., and 871 genes were down-regulated in WT at 4° C. (compared with 28° C.). Among these genes, 53 genes were down-regulated by over-expression of MYBS3 as well as down-regulated by cold in WT (Table S1 of Su, et al, Plant Physiol. 2010; 153(1):145-58). 
     Another analysis revealed that 389 genes were up-regulated in the MYBS3(Ri) line (compared with WT) at either 4 or 28° C. Among these genes, 17 genes were up-regulated by under-expression of MYBS3 as well as up-regulated by cold in WT (Table S2 of Su, et al, Plant Physiol. 2010; 153(1):145-58). On the other hand, 124 genes were down-regulated in the MYBS3(Ri) line (compared with WT) at either 4 or 28° C. Among these genes, 37 genes were down-regulated by over-expression of MYBS3 as well as by cold in WT (Table S2 of Su, et al, Plant Physiol. 2010; 153(1):145-58). 
     The cold- and MYBS3-regulated genes seem to be involved in diverse functions, and many of them have also been shown to be regulated by drought and salt stresses (Tables S1 and S2 of Su, et al, Plant Physiol. 2010; 153(1):145-58). Among the 17 genes up-regulated by over-expression of MYBS3 as well as up-regulated by cold in WT, five genes that have also been shown to be up-regulated by drought (Table Si of Su, et al, Plant Physiol. 2010; 153(1):145-58) and cold (Jain, et al., 2007, Plant Physiol 143: 1467-1483), such as genes encoding glutamate decarboxylase, WRKY77, multidrug resistance protein 4, and trehalose-6-phosphate phosphatases (TPP1 and TPP2), were selected for further quantitative real-time RT-PCR analysis. The accumulation of mRNA of all five genes was significantly increased in WT and further increased in the MYBS3(Ox) line but reduced in the MYBS3(Ri) line at 4° C. (Table S3 of Su, et al, Plant Physiol. 2010; 153(1):145-58), indicating that these genes are downstream of the MYBS3-mediated cold signaling pathway. 
     MYBS3 Suppresses the DREB1-Dependent Pathway Under Prolonged Cold Stress 
     We noticed that in the microarray analysis, the DREB1 family, including DREB1A, DREB1B and DREB1C, and another two DREB1-like genes (ERF#025 and ERF#104) were up-regulated in WT at 4° C., but the induction was surprisingly reduced or abolished in the MYBS3(Ox) line at 4° C. To investigate how MYBS3 regulates DREB1 gene expression, the accumulation of mRNAs of three DREB1 genes was further analyzed with the quantitative real-time RT-PCR analysis. Compared with WT, accumulation of MYBS3 mRNA increased significantly at 28° C. and was further induced 2-fold at 4° C. in the MYBS3(Ox) line. The accumulation of MYBS3 mRNA was reduced in the MYBS3(Ri) line at both 4 and 28° C. In contrast, the cold-induced DREB1A, DREB1B and DREB1C expression was significantly suppressed in the MYBS3(Ox) line at 4° C. Furthermore, the cold inducibility of αAmy3/RAmy3D and a cytochrome P450 gene, both members of the cold-inducible DREB1A regulon (Ito, et al., 2006, Plant Cell Physiol 47: 141-153), were also significantly reduced in the MYBS3(Ox) line at 4° C. The accumulation of DREB1, αAmy3/RAmy3D and cytochrome P450 mRNAs were significantly higher in the MYBS3(Ri) line than in the MYBS3(Ox) line at 4° C., although levels did not reach to that in WT at 4° C. 
     MYBS3 has been shown to repress αAmy3 SRC through the TA box (Lu, et al., 2002, Plant Cell 14: 1963-1980). Examination of promoter regions within 1 kb upstream of the translation start codon (ATG) revealed the presence of TA box and/or its variants in DREB1 genes. To determine whether MYBS3 represses DREB1 promoters, a rice embryo transient expression assay was performed. Rice embryos were cotransfected with the effector construct containing Ubi promoter fused to MYBS3 cDNA and the reporter construct containing DREB1A (1054 bp), DREB1B (747 bp) or αAmy3 SRC (105 bp) promoter sequence fused to luciferase cDNA (Luc). Both DREB1 promoters were significantly induced at 4° C., but only the DREB1B promoter was repressed by over-expression of MYBS3 at 4° C. The αAmy3 SRC was repressed by over-expression of MYBS3 at both 4 and 28° C., consistent with the role of MYBS3 as a repressor of αAmy3 SRC (Lu, et al., 2002, Plant Cell 14: 1963-1980). These results indicate that MYBS3 could repress DREB1B promoter and αAmy3 SRC at 4° C. 
     Discussion 
     A Novel MYBS3-Mediated Cold Signaling Pathway 
     Both gain- and loss-of-function analyses demonstrated that the MYBS3-mediated pathway was essential for cold stress tolerance in rice. DREB1A responded early and transiently, which is consistent with previous reports in  Arabidopsis  and rice (Liu, et al., 1998, Plant Cell 10: 1391-1406; Shinwari, et al., 1998, Biochem Biophys Res Commun 250: 161-170; Dubouzet, et al., 2003, Plant J 33: 751-763; and Vogel, et al., 2005, Plant J 41: 195-211), whereas MYBS3 responded relatively slowly, to cold stress in rice ( FIG. 4 ). The DREB1-mediated process is most likely crucial in responding to short term cold stress (cold shock), and the MYBS3-mediated system is more important for long-term adaptation to persistent cold stress. 
     Transcriptome profiling analyses suggest that multiple cold response pathways exist in  Arabidopsis  and rice (Fowler, et al., 2002, Plant Cell 14: 1675-1690; Vogel, et al., 2005, Plant J 41: 195-211; Cheng, et al., 2007, BMC Genomics 8: 175; and Chinnusamy, et al., 2007, Trends Plant Sci 12: 444-451). However, the MYBS3-mediated cold signaling pathway has never been observed previously. MYBS3 acts as a transcriptional repressor of αAmy3 SRC in the sugar signaling pathway in rice (Lu, et al., 2002, Plant Cell 14: 1963-1980), and is constitutively localized in the nucleus in cultured rice suspension cells. These studies indicate that MYBS3 may play multiple regulatory roles in plant growth in addition to cold response in rice. Consequently, gene expression in MYBS3(Ox) or MYBS3(Ri) line altered at 28° C. may not, whereas that altered at 4° C. may, be involved in cold response. 
     The MYBS3-regulated genes encompass a wide range of functions. In the microarray analysis, among the 17 genes up-regulated for at least 3-fold by over-expression of MYBS3 as well as by cold in WT, several of them have previously been implicated in stress responses and/or tolerance in plants (Table S1 of Su, et al, Plant Physiol. 2010; 153(1):145-58), such as glutamate decarboxylase, which catalyzes the conversion of glutamate to γ-aminobutyrate (GABA) and is activated in response to heat in  Arabidopsis  roots (Bouche et al., 2004, Plant Mol Biol 55: 315-325) and to anoxia in rice roots (Aurisano, et al., 1995, Plant Cell Physiol. 36: 1525-1529); WRKY77, which activates the ABA-inducible HVA22 promoter in cereal grains (Xie, et al., 2005, Plant Physiol 137: 176-189) and several WRKYs have been shown to confer biotic and abiotic stress tolerance in  Arabidopsis  (Ross, et al., 2007, J Integr Plant Biol 49: 827-842; Lai et al., 2008, BMC Plant Biol 8: 68; and Zhou et al., 2008, Plant Biotechnol J 6: 486-503); multidrug resistance protein 4, whose expression is activated by arsenate and arsenite stresses in rice seedlings (Chakrabarty, et al., 2009, Chemosphere 74: 688-702) and its homologous genes confer salt tolerance (Lee, et al., 2004, Plant Physiol 134: 528-538) and oxidative stress tolerance against pathogens (Sun, et al., 2006, Plant Cell 18: 3686-3705) in various plant species. 
     TPPs are a group of genes worthwhile noting. Trehalose is a disaccharide sugar widely distributed in bacteria, fungi, plants and invertebrate animals, and is produced from glucose by trehalose-6-phosphate synthase (TPS) and TPP, and serves as sugar storage, metabolic regulator, and protectant again abiotic stresses (Strom, et al., 1993, Mol Microbiol 8: 205-210; and Elbein, et al., 2003, Glycobiology 13: 17R-27R). Trehalose has been shown to stabilize dehydrated enzymes, proteins, and lipid membranes, as well as to protect biological structures from damage during desiccation (Elbein, et al., 2003, Glycobiology 13: 17R-27R). TPP1 and TPP2 are two major TPP genes expressed in rice seedlings (Shima, et al., 2007, Febs J 274: 1192-1201). Their expression is induced by cold and other abiotic stresses (Pramanik, et al., 2005, Plant Mol Biol 58: 751-762; Shima, et al., 2007, Febs J 274: 1192-1201; Ge, et al., 2008, Planta 228: 191-201). Trehalose accumulates rapidly and transiently, which follows the transient induction of TPP activity, in rice tissues during chilling stress (Pramanik, et al., 2005, Plant Mol Biol 58: 751-762). Over-expression of TPS and TPP enhances accumulation of trehalose and tolerance to cold stress in transgenic tobacco and rice (Garg, et al., 2002, Proc Natl Acad Sci USA 99: 15898-15903; Jang, et al., 2003 Plant Physiol 131: 516-524; Ge, et al., 2008, Planta 228: 191-201; and Iordachescu, et al., 2008, J Integr Plant Biol 50: 1223-1229). However, the regulatory mechanism of TPPs by cold or other stresses is unclear. 
     The accumulation of these MYBS3-activated genes were significantly increased in the MYBS3(Ox) line and decreased in the MYBS3(Ri) line at 4° C. MYBS3 confers stress tolerance to transgenic rice through the activation of these genes whose products are involved either in the regulation of gene expression for cold adaptation or for protection of cells from chilling injury. 
     Complexity in Cold Regulation 
     The temporal expression patterns and magnitudes of activation of DREB1A and MYBS3 expression by cold are quite different ( FIG. 2 ). Several factors have been found to regulate the expression of DREB1/CBF as mentioned in the introduction, but the detailed information about the cold signaling pathways upstream of DREB1/CBF is rather limited. Recently, a calmodulin binding transcription factor (CAMTA) was found to bind to the conserved motif 2 (CM2) present in promoters (within 200 by upstream of ATG), and function as a positive regulator, of the rapidly cold-inducible CBF2 and ZAT12 transcription factors in  Arabidopsis  (Doherty, et al., 2009, Plant Cell 21: 972-984). CM2 is present in one copy in the MYBS3 promoter (−117 to −112 upstream of ATG) (Table S4 of Su, et al, Plant Physiol. 2010; 153(1):145-58). For cold up-regulated but MYBS3 down-regulated genes, CM2 is present in two copies each in DREB1B (−134 to −129 and −80 to −75) and αAmy3 (−158 to −153 and −149 to −144) promoters; for cold up-regulated and MYBS3 up-regulated genes, CM2 is present in the glutamate decarboxylase (−54 to −49) and WRKY77 promoters (−96 to −91) (Table S4 of Su, et al, Plant Physiol. 2010; 153(1):145-58). Some of other CMs shared by the  Arabidopsis  CBF2 and ZAT12 promoters (Doherty, et al., 2009, Plant Cell 21: 972-984) could also be found in DREB1B, DREB1C, αAmy3 and cytochrome P450 promoters (Table S4 of Su, et al, Plant Physiol. 2010; 153(1):145-58), but the function of these cis-acting elements and the identify of their interacting transcription factors in cold signaling have not been determined (Doherty, et al., 2009, Plant Cell 21: 972-984). 
     CMs 1-7 have been found in the  Arabidopsis  CBF2 promoter (within 200 by upstream of ATG) (Doherty, et al., 2009, Plant Cell 21: 972-984), however, only CM4 is present in the 1-kb promoter region of DREB1C (the rice CBF2 homolog), suggesting that the mechanism of cold regulation on the DREB1/CBF family might have diverged throughout evolution. No CM is present in the 1-kb promoter region of DREB1A, indicating unidentified cis-acting element(s) could be responsible for cold induction of DREB1A. It appears that combinations of various cis-acting elements and interacting transcription factors constitute the quantitative and temporal regulation of the DREB1- and MYBS3-dependent cold signaling cascades. 
     It is also noticed that the DREB1A target sequence DRE (Ito, et al., 2006, Plant Cell Physiol 47: 141-153), is present in αAmy3 (−153 to −148) and cytochrome P450 (−605 to −600) promoters, and interestingly, it overlaps with the two CM2s in αAmy3 promoter. None of the 1-kb promoter regions of MYBS3-activated genes further characterized in this study contains DRE. 
     How MYBS3 represses the expression of the DREB1 regulon is unclear. The TA box has been shown to function in both sense and antisense orientations (Lu, et al., 1998, J Biol Chem 273: 10120-10131). Promoters of the cold inducible but MYBS3 repressible genes, except cytochrome P450, contain TA box or its variants (Yu, 1999, Regulation of alpha-amylase gene expression. In K Shimamoto, ed, Molecular Biology of Rice, Springer-Verlag, Tokyo, pp 161-178; and Wang, et al., 2007, Plant Mol Biol 63: 441-463) in sense or antisense orientation (Table S5 of Su, et al, Plant Physiol. 2010; 153(1):145-58), which could be the target of repression by MYBS3. However, in the transient expression assay, the 747-bp DREB1B promoter and 105-bp αAmy3 SRC, but not the 1054-bp DREB1A promoter, were repressed by over-expression of MYBS3 at 4° C. One explanation is that the TA3 box (−625 to −620) in the 1054-bp DREB1A promoter did not function as well as the TA2 box (−85 to −80) in the 747-bp DREB1B promoter and the TA1 box (the canonical TA box) (2 copies between −116 to −105) in the 105-bp αAmy3 SRC in the rice embryo transient expression assay. 
     How MYBS3 activates the expression of downstream genes in the cold signaling pathway, by serving as a transcriptional activator or repressing a transcriptional repressor, is unclear. However, except TPP2, other MYBS3 up-regulated genes also contain TA box or its variants (Table S5 of Su, et al, Plant Physiol. 2010; 153(1):145-58). Both MYBS1 and MYBS3 bind specifically to the TA box, however, MYBS1 activates and MYBS3 represses αAmy3 SRC under sugar starvation (Lu, et al., 2002, Plant Cell 14: 1963-1980). MYBs with one single DNA binding domain (1R MYB) have been proposed to bind DNA as a dimer, and MYBS1 does whereas MYBS3 doesn&#39;t form a homodimer (Lu, et al., 2002, Plant Cell 14: 1963-1980). Whether MYBS3 could be converted into an activator, by interacting with other 1R MYB and forming a heterodimer or with other transcription factor(s), remains for further study. 
     Taken together, above studies suggest the complexity of cold regulation in plants, which involves multiple cis-acting elements and transcription factors. Additionally, the regulation of the MYBS3-dependent pathway differs from that of the DREB1- or ROS-mediated pathways in response to cold stress (Ito, et al., 2006, Plant Cell Physiol 47: 141-153; Cheng, et al., 2007, BMC Genomics 8: 175), which suggests that MYBS3 defines a new signaling pathway mediating cold adaptation in rice. It appears that distinct regulatory pathways function in fine tuning the qualitative and quantitative gene expressions for short- and long-term cold adaptation in rice ( FIG. 4 ). 
     MYBS3 as a Tool for Improving Cold Stress Tolerance in Crops 
     Compared with microbial TPP, the rice TPP has been shown to be rather unstable, which leads to low level accumulation of trehalose in rice under normal growth conditions (Shima, et al., 2007, Febs J 274: 1192-1201). Although in WT plant, the expression of two rice TPPs is induced by cold, it peaks around 24 h and declined afterward at 4-6° C. (Pramanik, et al., 2005, Plant Mol Biol 58: 751-762; and Ge, et al., 2008, Planta 228: 191-201). The significant activation of TPP expression in the MYBS3(Ox) line may increase the accumulation of trehalose to levels high enough to confer cold tolerance in rice. 
     In the MYBS3(Ri) line, the expression of three DREB1 genes were 50-94% of the WT at 4° C., probably due to weaker growth and reduced cellular activities of plants under cold stress, as mentioned above that MYBS3 may play multiple regulatory roles in plant growth in addition to cold response in rice. However, it suggests that high-level DREB1 expression is insufficient to sustain cold tolerance if the level of MYBS3 expression is too low to efficiently activate the TPP-mediated cold response pathway. Consequently, the sequential expression of DREB1 and MYBS3 provides rice two complementary mechanisms for conferring cold tolerance in rice, with the DREB1-mediated process mediates the immediate cold shock response and the MYBS3-mediated system adjusts the long-term cold adaptation in rice. The antithetical regulation of αAmy3 in rice seedlings by two different pathways is physiologically meaningful: the transient activation of αAmy3 expression by DREB1 allows hydrolysis of reserved starch for providing immediate need of carbon source and energy to combat the cold shock, while the subsequent suppression of αAmy3 expression by MYBS3 allows rice to conserve carbohydrates until re-growth is allowed at elevated temperatures. It would be interesting to test whether stacking of these two systems, by over-expression of both DREB1 and MYBS3, could further enhance the cold tolerance in rice. 
     Overexpression of proteins or enzymes associated with stress responses has been a common practice in improving stress tolerance of crop plants. However, constitutive overexpression of these proteins frequently leads to impaired plant growth or yield penalty. For example, though transgenic  Arabidopsis  and rice constitutively overexpressing CBF/DREB1 and a NAC6 transcription factor are highly tolerant to freezing, the growth rates of these transgenic plants, however, are severely retarded under normal growth conditions (Jaglo-Ottosen, et al., 1998, Science 280: 104-106; Liu, et al., 1998, Plant Cell 10: 1391-1406; Kasuga, et al., 1999, Nat Biotechnol 17: 287-291; Gilmour, et al., 2000, Plant Physiol 124: 1854-1865; Ito, et al., 2006, Plant Cell Physiol 47: 141-153; and Nakashima et al., 2007, Plant J 51: 617-630). Using stress-inducible promoters for the expression of these transcription factors minimize their negative effects on plant growth (Kasuga, et al., 1999, Nat Biotechnol 17: 287-291; and Nakashima, et al., 2007, Plant J 51: 617-630). Transgenic seedlings were able to withstand 4° C. for at least 1 week after shifting from 28° C., which could significantly protect seedlings from chilling injury in rice fields in areas where are easily prone to transient temperature drops in early spring. Although the growth of MYBS3(Ox) lines was affected to certain extent in the greenhouse, the growth and yield of line S3(Ox)-110-1 was normal in field (Table 3). In conclusion, MYBS3 can be used for the improvement of cold tolerance in rice and possibly other crop plants. 
     Other Embodiments 
     All of the features disclosed in this specification may be combined in any combination. Each feature disclosed in this specification may be replaced by an alternative feature serving the same, equivalent, or similar purpose. Thus, unless expressly stated otherwise, each feature disclosed is only an example of a generic series of equivalent or similar features. 
     A number of embodiments of the invention have been described. Nevertheless, it will be understood that various modifications may be made without departing from the spirit and scope of the invention. Accordingly, other embodiments are within the scope of the following claims.