Acc414 (i, India) TTGGACCTTGAAGATAATAAGGATATACAGGATTCTCATCTGCAGGGCATATGTGAA---Acc420 (i, India) TTGGACCTTGAAGATAATAAGGATATACAGGATTCTCATCTGCAGGGCATATGTGAA---Acc761 (i, Hai-Nan-Tao) TTGGACCTTGAAGATAATAAGGATATACAGGATTCTCATCTGCAGGGCATATGTGAA---Acc108 (i, Taiwan) TTGGACCTTGAAGATAATAAGGATATACAGGATTCTCATCTGCAGGGCATATGTGAA---Acc130 (i, Taiwan) TTGGACCTTGAAGATAATAAGGATATACAGGATTCTCATCTGCAGGGCATATGTGAA---Acc504 (j, Taiwan) TTGGACCTTGAAGATAATAAGGATATACAGGATTCTCATCTGCAGGGCATATGTGAA---Acc563 (j, Japan) TTGGACCTTGAAGATAATAAGGATATACAGGATTCTCATCTGCAGGGCATATGTGAA---Acc709 (j, Central China) TTGGACCTTGAAGATAATAAGGATATACAGGATTCTCATCTGCAGGGCATATGTGAA---Acc710 (i, Central China) TTGGACCTTGAAGATAATAAGGATATACAGGATTCTCATCTGCAGGGCATATGTGAA---Acc719 (i, Central China) TTGGACCTTGAAGATAATAAGGATATACAGGATTCTCATCTGCAGGGCATATGTGAA---Acc729 (i, South China) TTGGACCTTGAAGATAATAAGGATATACAGGATTCTCATCTGCAGGGCATATGTGAA---Acc757 (j, Hai-Nan-Tao) TTGGACCTTGAAGATAATAAGGATATACAGGATTCTCATCTGCAGGGCATATGTGAA---Acc848 (j, Mountains of Taiwan) TTGGACCTTGAAGATAATAAGGATATACAGGATTCTCATCTGCAGGGCATATGTGAA---AccUp1 (j, Japan) TTGGACCTTGAAGATAATATCGGTATAGAGGACTCCCACCTGAAGAAGATATGTGAG---AccUp3 (j, Japan) TTGGACCTTGAAGATAATATCGGTATAGAGGACTCCCACCTGAAGAAGATATGTGAG---Acc201 (j, Philippines) TTGGACCTTGAAGATAATATCGGTATAGAGGACTCCCACCTGAAGAAGATATGTGAG---Acc220 (j, Philippines) TTGGACCTTGAAGATAATATCGGTATAGAGGACTCCCACCTGAAGAAGATATGTGAG---Acc224 (j, Philippines) TTGGACCTTGAAGATAATATCGGTATAGAGGACTCCCACCTGAAGAAGATATGTGAG---Acc206 (j, Philippines) TTGGACCTTGAAGATAATATCGGTATAGAGGACTCCCACCTGAAGAAGATATGTGAG---Acc1 (i, Vietnam) TTGGACCTTGAAGATAATATCGGTATAGAGGACTCCCACCTGAAGAAGATATGTGAG---Acc718 (j, Central China) TTGGACCTTGAAGATAATATCGGTATAGAGGACTCCCACCTGAAGAAGATATGTGAG---Acc101 (i, Taiwan) TTGGACCTTGAAGATAATATCGGTATAGAGGACTCCCACCTGAAGAAGATATGTGAG---Acc440 (i, India) TTGGACCTTGAAGATAATATCGGTATAGAGGACTCCCACCTGAAGAAGATATGTGAG---Acc868 (i, Mountains of Taiwan) TTGGACCTTGAAGATAATATCGGTATAGAGGACTCCCACCTGAAGAAGATATGTGAG---Acc715 (i, Central China) TTGGACCTTGAAGACAATCTCGATATAGATGACTCTCACCTGAAGAAGATATGTGAG---Acc724 (i, South China) TTGGACCTTGAAGACAATCTCGATATAGATGACTCTCACCTGAAGAAGATATGTGAG---Acc706 (i, North China) TTGGACCTTGAAGACAATCTCGATATAGATGACTCTCACCTGAAGAAGATATGTGAG---Acc624 (j, Celebes Is.) TTGGACCTTGAAGACAATCTCGATATAGATGACTCTCACCTGAAGAAGATATGTGAG---Acc421 (i, India) TTGGATCTTGAAGGAAATAAGGATATACTGAACTCTCACCTGCAGGATATATGTGAATGTAcc642 (j, Celebes Is.) TTGGATCTTGAAGGAAATAAGGATATACTGAACTCTCACCTGCAGGATATATGTGAATGTAccUp4 (j, Japan) TTGGATCTTGAAGGAAATAAGGATATACTGAACTCTCACCTGCAGGATATATGTGAATGTAcc708 (j, North China) TTGGATCTTGAAGGAAATAAGGATATACTGAACTCTCACCTGCAGGATATATGTGAATGT ***** ******* *** * **** * ** ** *** ** ********

Acc414 ---CAGTTA---AGCCTCAGAGTG---AGGTACCTTGGTCTCAAGGGAACGCGGATCCGAAcc420 ---CAGTTA---AGCCTCAGAGTG---AGGTACCTTGGTCTCAAGGGAACGCGGATCCGAAcc761 ---CAGTTA---AGCCTCAGAGTG---AGGTACCTTGGTCTCAAGGGAACGCGGATCCGAAcc108 ---CAGTTA---AGCCTCAGAGTG---AGGTACCTTGGTCTCAAGGGAACGCGGATCCGAAcc130 ---CAGTTA---AGCCTCAGAGTG---AGGTACCTTGGTCTCAAGGGAACGCGGATCCGAAcc504 ---CAGTTA---AGCCTCAGAGTG---AGGTACCTTGGTCTCAAGGGAACGCGGATCCGAAcc563 ---CAGTTA---AGCCTCAGAGTG---AGGTACCTTGGTCTCAAGGGAACGCGGATCCGAAcc709 ---CAGTTA---AGCCTCAGAGTG---AGGTACCTTGGTCTCAAGGGAACGCGGATCCGAAcc710 ---CAGTTA---AGCCTCAGAGTG---AGGTACCTTGGTCTCAAGGGAACGCGGATCCGAAcc719 ---CAGTTA---AGCCTCAGAGTG---AGGTACCTTGGTCTCAAGGGAACGCGGATCCGAAcc729 ---CAGTTA---AGCCTCAGAGTG---AGGTACCTTGGTCTCAAGGGAACGCGGATCCGAAcc757 ---CAGTTA---AGCCTCAGAGTG---AGGTACCTTGGTCTCAAGGGAACGCGGATCCGAAcc848 ---CAGTTA---AGCCTCAGAGTG---AGGTACCTTGGTCTCAAGGGAACGCGGATCCGAAccUp1 ---CAGCTAGAGAGCCTCAGGCTGCTCAAGTACCTAGGTCTCAAGGGTACGCGAATCACTAccUp3 ---CAGCTAGAGAGCCTCAGGCTGCTCAAGTACCTAGGTCTCAAGGGTACGCGAATCACTAcc201 ---CAGCTAGAGAGCCTCAGGCTGCTCAAGTACCTAGGTCTCAAGGGTACGCGAATCACTAcc220 ---CAGCTAGAGAGCCTCAGGCTGCTCAAGTACCTAGGTCTCAAGGGTACGCGAATCACTAcc224 ---CAGCTAGAGAGCCTCAGGCTGCTCAAGTACCTAGGTCTCAAGGGTACGCGAATCACTAcc206 ---CAGCTAGAGAGCCTCAGGCTGCTCAAGTACCTAGGTCTCAAGGGTACGCGAATCACTAcc1 ---CAGCTAGAGAGCCTCAGGCTGCTCAAGTACCTAGGTCTCAAGGGTACGCGAATCACTAcc718 ---CAGCTAGAGAGCCTCAGGCTGCTCAAGTACCTAGGTCTCAAGGGTACGCGAATCACTAcc101 ---CAGCTAGAGAGCCTCAGGCTGCTCAAGTACCTAGGTCTCAAGGGTACGCGAATCACTAcc440 ---CAGCTAGAGAGCCTCAGGCTGCTCAAGTACCTAGGTCTCAAGGGTACGCGAATCACTAcc868 ---CAGCTAGAGAGCCTCAGGCTGCTCAAGTACCTAGGTCTCAAGGGTACGCGAATCACTAcc715 ---CAGCTAGAGAGCCTCAGGCTGCTCAAGTACCTGGGTATCAAGGGTACACGGATCACTAcc724 ---CAGCTAGAGAGCCTCAGGCTGCTCAAGTACCTGGGTATCAAGGGTACACGGATCACTAcc706 ---CAGCTAGAGAGCCTCAGGCTGCTCAAGTACCTGGGTATCAAGGGTACACGGATCACTAcc624 ---CAGCTAGAGAGCCTCAGGCTGCTCAAGTACCTGGGTATCAAGGGTACACGGATCACTAcc421 GAGCAGTTA---AGCTTCAGGCTG---AGCTACCTGTGTCTAAAGGGGACTGGGATCACTAcc642 GAGCAGTTA---AGCTTCAGGCTG---AGCTACCTGTGTCTAAAGGGGACTGGGATCACTAccUp4 GAGCAGTTA---AGCTTCAGGCTG---AGCTACCTGTGTCTAAAGGGGACTGGGATCACTAcc708 GAGCAGTTA---AGCTTCAGGCTG---AGCTACCTGTGTCTAAAGGGGACTGGGATCACT *** ** *** **** ** * ***** ** * ***** ** * ***

Fig. S2a. DNA sequence alignment of the Pikm1-TS LRR region in set 2 lines. In parentheses, indica (i) and japonica (j) origins are followed by geographic origin of line. Alleles classed into clades 1, 2, and 3 are depicted in green, blue, and red, respectively.

Ashikawa et al. Supplementary figure S2a (1/5)

Acc414 AAGCTCCCTCAGGAGATGAGGAAGCTGAAGCATTTGGAGATTTTGTATGTGGGGAGCACTAcc420 AAGCTCCCTCAGGAGATGAGGAAGCTGAAGCATTTGGAGATTTTGTATGTGGGGAGCACTAcc761 AAGCTCCCTCAGGAGATGAGGAAGCTGAAGCATTTGGAGATTTTGTATGTGGGGAGCACTAcc108 AAGCTCCCTCAGGAGATGAGGAAGCTGAAGCATTTGGAGATTTTGTATGTGGGGAGCACTAcc130 AAGCTCCCTCAGGAGATGAGGAAGCTGAAGCATTTGGAGATTTTGTATGTGGGGAGCACTAcc504 AAGCTCCCTCAGGAGATGAGGAAGCTGAAGCATTTGGAGATTTTGTATGTGGGGAGCACTAcc563 AAGCTCCCTCAGGAGATGAGGAAGCTGAAGCATTTGGAGATTTTGTATGTGGGGAGCACTAcc709 AAGCTCCCTCAGGAGATGAGGAAGCTGAAGCATTTGGAGATTTTGTATGTGGGGAGCACTAcc710 AAGCTCCCTCAGGAGATGAGGAAGCTGAAGCATTTGGAGATTTTGTATGTGGGGAGCACTAcc719 AAGCTCCCTCAGGAGATGAGGAAGCTGAAGCATTTGGAGATTTTGTATGTGGGGAGCACTAcc729 AAGCTCCCTCAGGAGATGAGGAAGCTGAAGCATTTGGAGATTTTGTATGTGGGGAGCACTAcc757 AAGCTCCCTCAGGAGATGAGGAAGCTGAAGCATTTGGAGATTTTGTATGTGGGGAGCACTAcc848 AAGCTCCCTCAGGAGATGAGGAAGCTGAAGCATTTGGAGATTTTGTATGTGGGGAGCACTAccUp1 AAGCTCCCACAGGAGATACAGAAGCTGAAGCAACTGGAGATTTTGTACGTGAGGAGCACAAccUp3 AAGCTCCCACAGGAGATACAGAAGCTGAAGCAACTGGAGATTTTGTACGTGAGGAGCACAAcc201 AAGCTCCCACAGGAGATACAGAAGCTGAAGCAACTGGAGATTTTGTACGTGAGGAGCACAAcc220 AAGCTCCCACAGGAGATACAGAAGCTGAAGCAACTGGAGATTTTGTACGTGAGGAGCACAAcc224 AAGCTCCCACAGGAGATACAGAAGCTGAAGCAACTGGAGATTTTGTACGTGAGGAGCACAAcc206 AAGCTCCCACAGGAGATACAGAAGCTGAAGCAACTGGAGATTTTGTACGTGAGGAGCACAAcc1 AAGCTCCCACAGGAGATACAGAAGCTGAAGCAACTGGAGATTTTGTACGTGAGGAGCACAAcc718 AAGCTCCCACAGGAGATACAGAAGCTGAAGCAACTGGAGATTTTGTACGTGAGGAGCACAAcc101 AAGCTCCCACAGGAGATACAGAAGCTGAAGCAACTGGAGATTTTGTACGTGAGGAGCACAAcc440 AAGCTCCCACAGGAGATACAGAAGCTGAAGCAACTAGAGATTTTGTACGTGAGGAGCACAAcc868 AAGCTCCCACAGGAGATACAGAAGCTGAAGCAACTAGAGATTTTGTACGTGAGGAGCACAAcc715 AAGCTCCCACAGGAGATACAGAAGCTGAAGCATCTGGAGATTTTGTACGTGAGGAGCACAAcc724 AAGCTCCCACAGGAGATACAGAAGCTGAAGCATCTGGAGATTTTGTACGTGAGGAGCACAAcc706 AAGCTCCCACAGGAGATACAGAAGCTGAAGCATCTGGAGATTTTGTACGTGAGGAGCACAAcc624 AAGCTCCCACAGGAGATACAGAAGCTGAAGCATCTGGAGATTTTGTACGTGAGGAGCACAAcc421 AAGCTCCCACGAGAGATCGGGAAGCTCAAGCATCTGGAGATTTTGTACGTGGGGAACACAAcc642 AAGCTCCCACGAGAGATCGGGAAGCTCAAGCATCTGGAGATTTTGTACGTGGGGAACACAAccUp4 AAGCTCCCACGAGAGATCGGGAAGCTCAAGCATCTGGAGATTTTGTACGTGGGGAACACAAcc708 AAGCTCCCACGAGAGATCGGGAAGCTCAAGCATCTGGAGATTTTGTACGTGGGGAACACA ******** * ***** ****** ***** * *********** *** *** ***

Acc414 CGGATCAGTGAACTTCCGCAAGAGATTGGAGAGCTGAAGCATCTGCGGATTCTGGACGTGAcc420 CGGATCAGTGAACTTCCGCAAGAGATTGGAGAGCTGAAGCATCTGCGGATTCTGGACGTGAcc761 CGGATCAGTGAACTTCCGCAAGAGATTGGAGAGCTGAAGCATCTGCGGATTCTGGACGTGAcc108 CGGATCAGTGAACTTCCGCAAGAGATTGGAGAGCTGAAGCATCTGCGGATTCTGGACGTGAcc130 CGGATCAGTGAACTTCCGCAAGAGATTGGAGAGCTGAAGCATCTGCGGATTCTGGACGTGAcc504 CGGATCAGTGAACTTCCGCAAGAGATTGGAGAGCTGAAGCATCTGCGGATTCTGGACGTGAcc563 CGGATCAGTGAACTTCCGCAAGAGATTGGAGAGCTGAAGCATCTGCGGATTCTGGACGTGAcc709 CGGATCAGTGAACTTCCGCAAGAGATTGGAGAGCTGAAGCATCTGCGGATTCTGGACGTGAcc710 CGGATCAGTGAACTTCCGCAAGAGATTGGAGAGCTGAAGCATCTGCGGATTCTGGACGTGAcc719 CGGATCAGTGAACTTCCGCAAGAGATTGGAGAGCTGAAGCATCTGCGGATTCTGGACGTGAcc729 CGGATCAGTGAACTTCCGCAAGAGATTGGAGAGCTGAAGCATCTGCGGATTCTGGACGTGAcc757 CGGATCAGTGAACTTCCGCAAGAGATTGGAGAGCTGAAGCATCTGCGGATTCTGGACGTGAcc848 CGGATCAGTGAACTTCCGCAAGAGATTGGAGAGCTGAAGCATCTGCGGATTCTGGACGTGAccUp1 GGCATCGAAGAGCTCCCATGGGAGATCGGGGAATTGAAACAACTGCGGACTCTGGACGTGAccUp3 GGCATCGAAGAGCTCCCATGGGAGATCGGGGAATTGAAACAACTGCGGACTCTGGACGTGAcc201 GGCATCGAAGAGCTCCCATGGGAGATCGGGGAATTGAAACAACTGCGGACTCTGGACGTGAcc220 GGCATCGAAGAGCTCCCATGGGAGATCGGGGAATTGAAACAACTGCGGACTCTGGACGTGAcc224 GGCATCGAAGAGCTCCCATGGGAGATCGGGGAATTGAAACAACTGCGGACTCTGGACGTGAcc206 GGCATCGAAGAGCTCCCATGGGAGATCGGGGAATTGAAACAACTGCGGACTCTGGACGTGAcc1 GGCATCAAAGAGCTCCCACGGGAGATCGGGGAATTGAAACAACTGCGGACTCTGGACGTGAcc718 GGCATCGAAGAGCTCCCACAGGAGATCGGGGAATTGAAACAACTGCGGACTCTGGACGTGAcc101 GGCATCGAAGAGCTCCCACAGGAGATCGGGGAATTGAAACAACTGCGGACTCTGGACGTGAcc440 GGCATCAAAGAGCTCCCACGGGAGATCGGGGAATTGAAACAACTGCGGACTCTGGACGTGAcc868 GGCATCAAAGAGCTCCCACGGGAGATCGGGGAATTGAAACAACTGCGGACTCTGGACGTGAcc715 GGCATCAAAGAGCTCCCACGGGAGATCGGGGAATTGAAACAACTGCGGACTCTGGACATGAcc724 GGCATCAAAGAGCTCCCACGGGAGATCGGGGAATTGAAACAACTGCGGACTCTGGACATGAcc706 GGCATCAAAGAGCTCCCACGGGAGATCGGGGAATTGAAACAACTGCGGACTCTGGACATGAcc624 GGCATCAAAGAGCTCCCACGGGAGATCGGGGAATTGAAACAACTGCGGACTCTGGACATGAcc421 AAGATCAGTGACCTTCCACAGGAGATCGGGGAGCTCAAACATCTGCAGACTTTGGACGTGAcc642 AAGATCAGTGACCTTCCACAGGAGATCGGGGAGCTCAAACATCTGCAGACTTTGGACGTGAccUp4 AAGATCAGTGACCTTCCACAGGAGATCGGGGAGCTCAAACATCTGCAGACTTTGGACGTGAcc708 AAGATCAGTGACCTTCCACAGGAGATCGGGGAGCTCAAACATCTGCAGACTTTGGACGTG *** ** ** ** ***** ** ** * ** ** **** ** * ***** **

Fig. S2a. DNA sequence alignment of the Pikm1-TS LRR region in set 2 lines. Alleles classed into clades 1, 2, and 3 are depicted in green, blue, and red, respectively.

Ashikawa et al. Supplementary figure S2a (2/5)

Acc414 AGAAACACGGACATCACTGAGCTCCCACTGCAGATACGGGAGCTGCAGCATCTGCACACTAcc420 AGAAACACGGACATCACTGAGCTCCCACTGCAGATACGGGAGCTGCAGCATCTGCACACTAcc761 AGAAACACGGACATCACTGAGCTCCCACTGCAGATACGGGAGCTGCAGCATCTGCACACTAcc108 AGAAACACGGACATCACTGAGCTCCCACTGCAGATACGGGAGCTGCAGCATCTGCACACTAcc130 AGAAACACGGACATCACTGAGCTCCCACTGCAGATACGGGAGCTGCAGCATCTGCACACTAcc504 AGAAACACGGACATCACTGAGCTCCCACTGCAGATACGGGAGCTGCAGCATCTGCACACTAcc563 AGAAACACGGACATCACTGAGCTCCCACTGCAGATACGGGAGCTGCAGCATCTGCACACTAcc709 AGAAACACGGACATCACTGAGCTCCCACTGCAGATACGGGAGCTGCAGCATCTGCACACTAcc710 AGAAACACGGACATCACTGAGCTCCCACTGCAGATACGGGAGCTGCAGCATCTGCACACTAcc719 AGAAACACGGACATCACTGAGCTCCCACTGCAGATACGGGAGCTGCAGCATCTGCACACTAcc729 AGAAACACGGACATCACTGAGCTCCCACTGCAGATACGGGAGCTGCAGCATCTGCACACTAcc757 AGAAACACGGACATCACTGAGCTCCCACTGCAGATACGGGAGCTGCAGCATCTGCACACTAcc848 AGAAACACGGACATCACTGAGCTCCCACTGCAGATACGGGAGCTGCAGCATCTGCACACTAccUp1 AGGAACACGCGGATCAGCGAGCTCCCGTCGCAGATCGGGGAGCTCAAACATCTGCGGACTAccUp3 AGGAACACGCGGATCAGCGAGCTCCCGTCGCAGATCGGGGAGCTCAAACATCTGCGGACTAcc201 AGGAACACGCGGATCAGCGAGCTCCCGTCGCAGATCGGGGAGCTCAAACATCTGCGGACTAcc220 AGGAACACGCGGATCAGCGAGCTCCCGTCGCAGATCGGGGAGCTCAAACATCTGCGGACTAcc224 AGGAACACGCGGATCAGCGAGCTCCCGTCGCAGATCGGGGAGCTCAAACATCTGCGGACTAcc206 AGGAACACGCGGATCAGCGAGCTCCCGTCGCAGATCGGGGAGCTCAAACATCTGCGGACTAcc1 AGGAACACGCGGATCAGCGAGCTCCCGTCGCAGATCGGGGAGCTCAAACATCTGCGGACTAcc718 AGGAACACGCAGATCAGCGAGCTCCCGTCGCAGATCGGGGAGCTCAAACATCTGCGGACTAcc101 AGGAACACGCAGATCAGCGAGCTCCCGTCGCAGATCGGGGAGCTCAAACATCTGCGGACTAcc440 AGGAACACGCGGATCAGTGAGCTCCCGTCGCAGATCGGGGAGCTCAAACATCTGCGGACTAcc868 AGGAACACGCGGATCAGTGAGCTCCCGTCGCAGATCGGGGAGCTCAAACATCTGCGGACTAcc715 AGGAACACGCGGATCAGCGAGCTCCCGTCGCAGATCGGGGAGCTCAAACATCTGCGGACTAcc724 AGGAACACGCGGATCAGCGAGCTCCCGTCGCAGATCGGGGAGCTCAAACATCTGCGGACTAcc706 AGGAACACGCGGATCAGCGAGCTCCCGTCGCAGATCGGGGAGCTCAAACATCTGCGGACTAcc624 AGGAACACGCGGATCAGCGAGCTCCCGTCGCAGATCGGGGAGCTCAAACATCTGCGGACTAcc421 GGTGGCACGGATATCCGCGAGCTCCCACCACAGATAGGGGAGCTGAACAATCTGCGGACTAcc642 GGTGGCACGGATATCCGCGAGCTCCCACCACAGATAGGGGAGCTGAACAATCTGCGGACTAccUp4 GGTGGCACGGATATCCGCGAGCTCCCACCACAGATAGGGGAGCTGAACAATCTGCGGACTAcc708 GGTGGCACGGATATCCGCGAGCTCCCACCACAGATAGGGGAGCTGAACAATCTGCGGACT * **** *** ******** ***** ******* * ****** ***

Acc414 CTGGACGTGAGGAACA------CGCCAATCAGTGAGCTCCCGCCGCAGGTTGG-CAAGCTAcc420 CTGGACGTGAGGAACA------CGCCAATCAGTGAGCTCCCGCCGCAGGTTGG-CAAGCTAcc761 CTGGACGTGAGGAACA------CGCCAATCAGTGAGCTCCCGCCGCAGGTTGG-CAAGCTAcc108 CTGGACGTGAGGAACA------CTCCAATCAGTGAGCTCCCGCCGCAGGTTGG-CAAGCTAcc130 CTGGACGTGAGGAACA------CTCCAATCAGTGAGCTCCCGCCGCAGGTTGG-CAAGCTAcc504 CTGGACGTGAGGAACA------CTCCAATCAGTGAGCTCCCGCCGCAGGTTGG-CAAGCTAcc563 CTGGACGTGAGGAACA------CTCCAATCAGTGAGCTCCCGCCGCAGGTTGG-CAAGCTAcc709 CTGGACGTGAGGAACA------CTCCAATCAGTGAGCTCCCGCCGCAGGTTGG-CAAGCTAcc710 CTGGACGTGAGGAACA------CTCCAATCAGTGAGCTCCCGCCGCAGGTTGG-CAAGCTAcc719 CTGGACGTGAGGAACA------CTCCAATCAGTGAGCTCCCGCCGCAGGTTGG-CAAGCTAcc729 CTGGACGTGAGGAACA------CTCCAATCAGTGAGCTCCCGCCGCAGGTTGG-CAAGCTAcc757 CTGGACGTGAGGAACA------CTCCAATCAGTGAGCTCCCGCCGCAGGTTGG-CAAGCTAcc848 CTGGACGTGAGGAACA------CTCCAATCAGTGAGCTCCCGCCGCAGGTTGG-CAAGCTAccUp1 CTGGACGTGAGTAACA---TGTGGAATATCAGCGAGCTGCCGTCGCAAATCGG-GGAGCTAccUp3 CTGGACGTGAGTAACA---TGTGGAATATCAGCGAGCTGCCGTCGCAAATCGG-GGAGCTAcc201 CTGGACGTGAGTAACA---TGTGGAATATCAGCGAGCTGCCGTCGCAAATCGG-GGAGCTAcc220 CTGGACGTGAGTAACA---TGTGGAATATCAGCGAGCTGCCGTCGCAAATCGG-GGAGCTAcc224 CTGGACGTGAGTAACA---TGTGGAATATCAGCGAGCTGCCGTCGCAAATCGG-GGAGCTAcc206 CTGGACGTGAGTAACA---TGTGGAATATCAGCGAGCTGCCGTCGCAAATCGG-GGAGCTAcc1 CTGGACGTGAGTAACA---TGTGGAATATCAGCGAGCTGCCGTTGCAAATCGG-GGAGCTAcc718 CTGGACGTGAGTAACA---TGTGGAATATCAGCGAGCTGCCGTCGCAAATCGG-GGAGCTAcc101 CTGGACGTGAGTAACA---TGTGGAATATCAGCGAGCTGCCGTCGCAAATCGG-GGAGCTAcc440 CTGGACGTGAGTAACA---TGTGGAATATCAGCAAGCTGCCGTCGCAAATCGG-GGAGCTAcc868 CTGGACGTGAGTAACA---TGTGGAATATCAGCAAGCTGCCGTCGCAAATCGG-GGAGCTAcc715 CTGGACGTGAGTAACAACATGTGGAATATCAGCGAGCTGCCGTCGCAAATCGG-GGAGCTAcc724 CTGGACGTGAGTAACAACATGTGGAATATCAGCGAGCTGCCGTCGCAAATCGG-GGAGCTAcc706 CTGGACGTGAGTAACAACATGTGGAATATCAGCGAGCTGCCGTCGCAAATCGG-GGAGCTAcc624 CTGGACGTGAGTAACAACATGTGGAATATCAGCGAGCTGCCGTCGCAAATCGG-GGAGCTAcc421 TTGGACGTGAGGAACA------CGAGGGTGAGAGAGCTGCCATGGCAAGCTGGACAGATCAcc642 TTGGACGTGAGGAACA------CGAGGGTGAGAGAGCTGCCATGGCAAGCTGGACAGATCAccUp4 TTGGACGTGAGGAACA------CGAGGGTGAGAGAGCTGCCATGGCAAGCTGGACAGATCAcc708 TTGGACGTGAGGAACA------CGAGGGTGAGAGAGCTGCCATGGCAAGCTGGACAGATC ********** **** * ** **** ** *** **

Fig. S2a. DNA sequence alignment of the Pikm1-TS LRR region in set 2 lines.Alleles classed into clades 1, 2, and 3 are depicted in green, blue, and red, respectively.

Ashikawa et al. Supplementary figure S2a (3/5)

Acc414 GCAGAATCTCAAGATTATGTGCGTGAGGAGCACTGGGGTTAGGGAGCTCCCAAAGGAGATAcc420 GCAGAATCTCAAGATTATGTGCGTGAGGAGCACTGGGGTTAGGGAGCTCCCAAAGGAGATAcc761 GCAGAATCTCAAGATTATGTGCGTGAGGAGCACTGGGGTTAGGGAGCTCCCAAAGGAGATAcc108 GCAGAATCTCAAGATTATGTGCGTGAGGAGCACTGGGGTTAGGGAGCTCCCAAAGGAGATAcc130 GCAGAATCTCAAGATTATGTGCGTGAGGAGCACTGGGGTTAGGGAGCTCCCAAAGGAGATAcc504 GCAGAATCTCAAGATTATGTGCGTGAGGAGCACTGGGGTTAGGGAGCTCCCAAAGGAGATAcc563 GCAGAATCTCAAGATTATGTGCGTGAGGAGCACTGGGGTTAGGGAGCTCCCAAAGGAGATAcc709 GCAGAATCTCAAGATTATGTGCGTGAGGAGCACTGGGGTTAGGGAGCTCCCAAAGGAGATAcc710 GCAGAATCTCAAGATTATGTGCGTGAGGAGCACTGGGGTTAGGGAGCTCCCAAAGGAGATAcc719 GCAGAATCTCAAGATTATGTGCGTGAGGAGCACTGGGGTTAGGGAGCTCCCAAAGGAGATAcc729 GCAGAATCTCAAGATTATGTGCGTGAGGAGCACTGGGGTTAGGGAGCTCCCAAAGGAGATAcc757 GCAGAATCTCAAGATTATGTGCGTGAGGAGCACTGGGGTTAGGGAGCTCCCAAAGGAGATAcc848 GCAGAATCTCAAGATTATGTGCGTGAGGAGCACTGGGGTTAGGGAGCTCCCAAAGGAGATAccUp1 GAAGCATCTACAAACTCTGGATGTGAGGAACACGTCAGTGAGAGAGCTGCCATCGCAAATAccUp3 GAAGCATCTACAAACTCTGGATGTGAGGAACACGTCAGTGAGAGAGCTGCCATCGCAAATAcc201 GAAGCATCT---------------------------------------------------Acc220 GAAGCATCTACAAACTCTGGATGTGAGGAACACGTCAGTGAGAGAGCTGCCATCGCAAATAcc224 GAAGCATCT---------------------------------------------------Acc206 GAAGCATCT---------------------------------------------------Acc1 GAAGCATCTACAAACTCTGGATGTGAGGAACACGTCAGTGAGAGAGCTGCCATCGCAAATAcc718 GAAGCATCTACAAACTCTGGATGTGAGGAACACGTCAGTGAGAGAGCTGCCATCGCAAATAcc101 GAAGCATCT---------------------------------------------------Acc440 AAAGCATCT---------------------------------------------------Acc868 AAAGCATCT---------------------------------------------------Acc715 GAAGCATCTACAAACTCTGGATGTGAGGAATACGTCGGTGAGAGAGCTGCCATCGCAAATAcc724 GAAGCATCTACAAACTCTGGATGTGAGGAATACGTCGGTGAGAGAGCTGCCATCGCAAATAcc706 GAAGCATCT---------------------------------------------------Acc624 GAAGCATCT---------------------------------------------------Acc421 TCCGAATCACTGCGC-GTGCTTTTAGGCGACAAATCAGATAGCGTGCAGGTGCAGGTGCCAcc642 TCCGAATCACTGCGC-GTGCTTTTAGGCGACAAATCAGATAGCGTGCAGGTGCAGGTGCCAccUp4 TCCGAATCACTGCGC-GTGCTTTTAGGCGACAAATCAGATAGCGTGCAGGTGCAGGTGCCAcc708 TCCGAATCACTGCGC-GTGCTTTTAGGCGACAAATCAGATAGCGTGCAGGTGCAGGTGCC * ***

Acc414 TGGGGAGCTGAATCATCTACAGATTCTGGACGTGAGAAACACGAGGGTGAGAGAGCTGCCAcc420 TGGGGAGCTGAATCATCTACAGATTCTGGACGTGAGAAACACGAGGGTGAGAGAGCTGCCAcc761 TGGGGAGCTGAATCATCTACAGATTCTGGACGTGAGAAACACGAGGGTGAGAGAGCTGCCAcc108 TGGGGAGCTGAATCATCTACAGACTCTGGACGTGAGAAACACGAGGGTGAGAGAGCTGCCAcc130 TGGGGAGCTGAATCATCTACAGACTCTGGACGTGAGAAACACGAGGGTGAGAGAGCTGCCAcc504 TGGGGAGCTGAATCATCTACAGACTCTGGACGTGAGAAACACGAGGGTGAGAGAGCTGCCAcc563 TGGGGAGCTGAATCATCTACAGACTCTGGACGTGAGAAACACGAGGGTGAGAGAGCTGCCAcc709 TGGGGAGCTGAATCATCTACAGACTCTGGACGTGAGAAACACGAGGGTGAGAGAGCTGCCAcc710 TGGGGAGCTGAATCATCTACAGACTCTGGACGTGAGAAACACGAGGGTGAGAGAGCTGCCAcc719 TGGGGAGCTGAATCATCTACAGACTCTGGACGTGAGAAACACGAGGGTGAGAGAGCTGCCAcc729 TGGGGAGCTGAATCATCTACAGACTCTGGACGTGAGAAACACGAGGGTGAGAGAGCTGCCAcc757 TGGGGAGCTGAATCATCTACAGACTCTGGACGTGAGAAACACGAGGGTGAGAGAGCTGCCAcc848 TGGGGAGCTGAATCATCTACAGACTCTGGACGTGAGAAACACGAGGGTGAGAGAGCTGCCAccUp1 CGGGGAGCTGAAGCATCTGCGGTCTCTGGATGTGAGGAACACGGGGGTGAGAGAGCTGCCAccUp3 CGGGGAGCTGAAGCATCTGCGGTCTCTGGATGTGAGGAACACGGGGGTGAGAGAGCTGCCAcc201 ------------------GCGGACTCTGGATGTGAGGAACACGGGGGTGAGAGAGCTGCCAcc220 CGGGGAGCTGAAGCATCTGCGGACTCTGGATGTGAGGAACACGGGGGTGAGAGAGCTGCCAcc224 ------------------GCGGACTCTGGATGTGAGGAACACGGGGGTGAGAGAGCTGCCAcc206 ------------------GCGGACTCTGGATGTGAGGAACACGGGGGTGAGAGAGCTGCCAcc1 CGGGGAGCTGAAGCATCTGCGGACTCTGGATGTGAGGAACACGGGGGTGAGAGAGCTGCCAcc718 CGGGGAGCTGAAGCATCTGCGGACTCTGGATGTGAGGAACACGGGGGTGAGAGAGCTGCCAcc101 ------------------GCGGACTCTGGATGTGAGGAACACGGGGGTGAGAGAGCTGCCAcc440 ------------------GCGGACTCTGGATGTGAGGAACACGAGGGTGAGAGAGCTGCCAcc868 ------------------GCGGACTCTGGATGTGAGGAACACGAGGGTGAGAGAGCTGCCAcc715 CGGGGAGCTGAAGCATCTGCGGACTCTGGATGTGAGGAACACGGGGGTGAGAGAGCTGCCAcc724 CGGGGAGCTGAAGCATCTGCGGACTCTGGATGTGAGGAACACGGGGGTGAGAGAGCTGCCAcc706 ------------------GCGGACTCTGGATGTGAGGAACACGGGGGTGAGAGAGCTGCCAcc624 ------------------GCGGACTCTGGATGTGAGGAACACGGGGGTGAGAGAGCTGCCAcc421 TGAGGG-------CGTCAACAAA-----GATCTGGTAAA-ACATATTCCAGAGCATT-T-Acc642 TGAGGG-------CGTCAACAAA-----GATCTGGTAAA-ACATA----GGAGTATT-CCAccUp4 TGAGGG-------CGTCAACAAA-----GATCTGGTAAA-ACATA----GGAGTATT-CCAcc708 TGAGGG-------CGTCAACAAA-----GATCTGGTAAA-ACATA----GGAGTATT-CC * ** ** ** ** *** *

Fig. S2a. DNA sequence alignment of the Pikm1-TS LRR region in set 2 lines.Alleles classed into clades 1, 2, and 3 are depicted in green, blue, and red, respectively.

Ashikawa et al. Supplementary figure S2a (4/5)

Acc414 ATGGCAAGCTGGCCAGATCTCCCAATCGTTGCGCGTGCTTGCCGGTGACAGTGGCGATGGAcc420 ATGGCAAGCTGGCCAGATCTCCCAATCGTTGCGCGTGCTTGCCGGTGACAGTGGCGATGGAcc761 ATGGCAAGCTGGCCAGATCTCCCAATCGTTGCGCGTGCTTGCCGGTGACAGTGGCGATGGAcc108 ATGGCAAGCTGGCCAGATCTCCCAATCGTTGCGCGTGCTTGCCGGTGACAGTGGCGATGGAcc130 ATGGCAAGCTGGCCAGATCTCCCAATCGTTGCGCGTGCTTGCCGGTGACAGTGGCGATGGAcc504 ATGGCAAGCTGGCCAGATCTCCCAATCGTTGCGCGTGCTTGCCGGTGACAGTGGCGATGGAcc563 ATGGCAAGCTGGCCAGATCTCCCAATCGTTGCGCGTGCTTGCCGGTGACAGTGGCGATGGAcc709 ATGGCAAGCTGGCCAGATCTCCCAATCGTTGCGCGTGCTTGCCGGTGACAGTGGCGATGGAcc710 ATGGCAAGCTGGCCAGATCTCCCAATCGTTGCGCGTGCTTGCCGGTGACAGTGGCGATGGAcc719 ATGGCAAGCTGGCCAGATCTCCCAATCGTTGCGCGTGCTTGCCGGTGACAGTGGCGATGGAcc729 ATGGCAAGCTGGCCAGATCTCCCAATCGTTGCGCGTGCTTGCCGGTGACAGTGGCGATGGAcc757 ATGGCAAGCTGGCCAGATCTCCCAATCGTTGCGCGTGCTTGCCGGTGACAGTGGCGATGGAcc848 ATGGCAAGCTGGCCAGATCTCCCAATCGTTGCGCGTGCTTGCCGGTGACAGTGGCGATGGAccUp1 ATGGCAAGCTGGCCAGATCTCGGGATCGCTGCACGTGCATACAGATGACAGTGACGAGGGAccUp3 ATGGCAAGCTGGCCAGATCTCGGGATCGCTGCACGTGCATACAGATGACAGTGACGAGGGAcc201 ATGGCAAGCTGGCCAGATCTCGGGATCGCTGCACGTGCATACAGATGACAGTGACGAGGGAcc220 ATGGCAAGCTGGCCAGATCTCGGGATCGCTGCACGTGCATACAGATGACAGTGACGAGGGAcc224 ATGGCAAGCTGGCCAGATCTCGGGATCGCTGCACGTGCATACAGATGACAGTGACGAGGGAcc206 ATGGCAAGCTGGCCAGATCTCGGGATCGCTGCACGTGCATACAGATGACAGTGACGAGGGAcc1 ATGGCAAGCTGGCCAGATCTCGGGATCGCTGCACGTGCATACAGATGACAGTGACGAGGGAcc718 ATGGCAAGCTGGCCAGATCTCGGGATCGCTGCACGTGCATACAGATGACAGTGACGAGGGAcc101 ATGGCAAGCTGGCCAGATCTCGGGATCGCTGCACGTGCATACAGATGACAGTGACGAGGGAcc440 ATGGCAAGCTGGCCAGATCTCGGGATCGCTGCACGTGCATACAGATGACAGTGACGAGGGAcc868 ATGGCAAGCTGGCCAGATCTCGGGATCGCTGCACGTGCATACAGATGACAGTGACGAGGGAcc715 ATGGCAAGCTGGCCAGATCTCGGGATCGCTGCACGTGCATACAGATGACAGTGACGAGGGAcc724 ATGGCAAGCTGGCCAGATCTCGGGATCGCTGCACGTGCATACAGATGACAGTGACGAGGGAcc706 ATGGCAAGCTGGCCAGATCTCGGGATCGCTGCACGTGCATACAGATGACAGTGACGAGGGAcc624 ATGGCAAGCTGGCCAGATCTCGGGATCGCTGCACGTGCATACAGATGACAGTGACGAGGGAcc421 ---GCTTGCAAACTCAAC--CCTATCCATCGCG-AT---TCTCGATCGTTTTG-----GAAcc642 AGAGCTTGCAAACTCAAC--CCTATCCATCGCG-AT---TCTCGATGGTTTTG-----GAAccUp4 AGAGCTTGCAAACTCAAC--CCTATCCATCGCG-AT---TCTCGATGGTTTTG-----GAAcc708 AGAGCTTGCAAACTCAAC--CCTATCCATCGCG-AT---TCTCGATGGTTTTG-----GA ** ** * * * * ** * * * * ** *

Acc414 CGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTCTGATCAACGGTATTCCA-----------Acc420 CGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTCTGATCAACGGTATTCCA-----------Acc761 CGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTCTGATCAACGGTATTCCA-----------Acc108 CGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTCTGATCAACGGTATTCCA-----------Acc130 CGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTCTGATCAACGGTATTCCA-----------Acc504 CGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTCTGATCAACGGTATTCCA-----------Acc563 CGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTCTGATCAACGGTATTCCA-----------Acc709 CGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTCTGATCAACGGTATTCCA-----------Acc710 CGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTCTGATCAACGGTATTCCA-----------Acc719 CGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTCTGATCAACGGTATTCCA-----------Acc729 CGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTCTGATCAACGGTATTCCA-----------Acc757 CGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTCTGATCAACGGTATTCCA-----------Acc848 CGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTCTGATCAACGGTATTCCA-----------AccUp1 CATGCGGCTGCCAGAAGGCGTATGCGAAGATCTGATCAAGGGTATTCCC-----------AccUp3 CATGCGGCTGCCAGAAGGCGTATGCGAAGATCTGATCAAGGGTATTCCC-----------Acc201 CATGCGGCTGCCAGAAGGCGTATGCGAAGATCTGATCAAGGGTATTCCA-----------Acc220 CATGCGGCTGCCAGAAGGCGTATGCGAAGATCTGATCAAGGGTATTCCA-----------Acc224 CATGCGGCTGCCAGAAGGCGTATGCGAAGATCTGATCAAGGGTATTCCC-----------Acc206 CATGCGGCTGCCAGAAGGCGTATGCGAAGATCTGATCAAGGGTATTCCC-----------Acc1 CATGCGGCTGCCAGAAGGCGTATGCGAAGATCTGATCAAGGGTATTCCC-----------Acc718 CATGCGGCTGCCAGAAGGCGTATGCGAAGATCTGATCAAGGGTATTCCC-----------Acc101 CATGCGGCTGCCAGAAGGCGTATGCGAAGATCTGATCAAGGGTATTCCC-----------Acc440 CATGCGGCTGCCAGAAGGCGTATGCGAAGATCTGATCAAGGGTATTCCC-----------Acc868 CATGCGGCTGCCAGAAGGCGTATGCGAAGATCTGATCAAGGGTATTCCC-----------Acc715 CATGCGGCTGCCAGAAGGCGTATGCGAAGATCTGATCAAGGGTATTCCC-----------Acc724 CATGCGGCTGCCAGAAGGCGTATGCGAAGATCTGATCAAGGGTATTCCC-----------Acc706 CATGCGGCTGCCAGAAGGCGTATGCGAAGATCTGATCAAGGGTATTCCC-----------Acc624 CATGCGGCTGCCAGAAGGCGTATGCGAAGATCTGATCAAGGGTATTCCC-----------Acc421 CCTCCCCTTGTTGGGA----TATTCAAGGTTCTAGGCAGGAACGTACGT-----------Acc642 CCTCCCCTTGTTGGGA----CATTCAAGGTTCTAGGCAGGAACGTACGT-----------AccUp4 CCTCCCCTTGTTGGGA----CATTCAAGGTTCTAGGCAGGAACGTACGT-----------Acc708 CCTCCCCTTGTTGGGA----TATTCAAGGTTCTAGGCAGGAACGTACGT----------- * * * ** * * * * * * *** ** * *

Fig. S2a. DNA sequence alignment of the Pikm1-TS LRR region in set 2 lines.Alleles classed into clades 1, 2, and 3 are depicted in green, blue, and red, respectively.

Ashikawa et al. Supplementary figure S2a (5/5)

Acc440 (i, India) CTAAAACGGATCAATAGTATACTTGGAGGGAACAAAAAAACACGGGAGGGGCTGAGGTTGAcc868 (i, Mountains of Taiwan) CTAAAACGGATCAATAGTATACTTGGAGGGAACAAAAAAACACGGGAGGGGCTGAGGTTGAcc101 (i, Taiwan) CTAAAACGGATCAATAGCATACTTGGGGGGAACAAAAATACACGGAAGGGGTTGAGGTTGAcc706 (i, North China) CTAAAACGGATCAATAGCATACTTGGGGGGAACAAAAATACACGGAAGGGGTTGAGGTTGAcc715 (i, Central China) CTAAAACGGATCAATAGCATACTTGGGGGGAACAAAAATACACGGAAGGGGTTGAGGTTGAcc1 (i, Vietnam) CTAAAACGGATCAATAGCATACTTGGGGGGAACAAAAATACACGGAAGGGGTTGAGGTTGAcc624 (j, Celebes Is.) CTAAAACGGATCAGTAGCATACTTGGGGGGAACAAAAATACACGGAAGGGGTTGAGGTTGAcc415 (i, India) CTAAAACGGATCAGTAGCATACTTGGGGGGAACAAAAATACACGGAAGGGGCTGAGGTTGAcc417 (i, India) CTAAAACGGATCAGTAGCATACTTGGGGGGAACAAAAATACACGGAAGGGGCTGAGGTTGAcc435 (i, Ceylon) CTAAAACGGATCAGTAGCATACTTGGGGGGAACAAAAATACACGGAAGGGGCTGAGGTTGAcc712 (j, Central China) CTAAAACGGATCAGTAGCATACTTGCCGGGAACAAAAATACACGGAAGGGGCTGAGGTTGAcc201 (j, Philippines) CTAAAACGGATCAGTAGCATACTTGGGGGGAACAAAAATACACGGAAGGGGCTGAGGTTGAcc206 (j, Philippines) CTAAAACGGATCAGTAGCATACTTGGGGGGAACAAAAATACACGGAAGGGGCTGAGGTTGAcc724 (i, South China) CTAAAACGGATCAGTAGCATACTTGGGGGGAACAAAAATACACGGAAGGGGCTGAGGTTGAcc224 (j, Philippines) CTAAAACGGATCAGTAGCATACTTGGGGGGAACAAAAATACACGGAAGGGGCTGAGGTTGAcc220 (j,Philippines) CTAAAACGGATCAGTAGCATACTTGGGGGGAACAAAAATACACGGAAGGGGCTGAGGTTGAccUp3 (j, Japan) CTAAAACGGATCAGTAGCATACTTGGGGGGAACAAAAATACACGGAAGGGGCTGAGGTTGAccUp1 (j, Japan) CTAAAACGGATCAGTAGCATACTTGGGGGGAACAAAAATACACGGAAGGGGCTGAGGTTGAcc563 (j, Japan) CTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGAAGGGGCTGAGGTTGAcc709 (j, Central China) CTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGAAGGGGCTGAGGTTGAcc848 (j, Mountains of Taiwan) CTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGAAGGGGCTGAGGTTGAcc504 (j, Taiwan) CTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGAAGGGGCTGAGGTTGAcc757 (j, Hai-Nan-Tao) CTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGAAGGGGCTGAGGTTGAcc108 (i, Taiwan) CTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGAAGGGGCTGAGGTTGAcc130 (i, Taiwan) CTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGAAGGGGCTGAGGTTGAcc414 (i, India) CTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGAAGGGGCTGAGGTTGAcc710 (i, Central China) CTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGAAGGGGCTGAGGTTGAcc719 (i, Central China) CTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGAAGGGGCTGAGGTTGAcc729 (i, South China) CTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGAAGGGGCTGAGGTTGAcc761 (i, Hai-Nan-Tao) CTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGAAGGGGCTGAGGTTGAcc420 (i, India) CTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGAAGGGGCTGAGGTTGAccUp4 (j, Japan) CTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACAAGGAAGGGGCTGAGGTTGAcc642 (j, Celebes Is.) CTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACAAGGAAGGGGCTGAGGTTGAcc708 (j, North China) CTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACAAGGAAGGGGCTGAGGTTGAcc421 (i, India) CTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACAAGGAAGGGGCTGAGGTTG ************* *** ******* ***** ***** *** ** ***** ********

Acc440 CCTCAAGAAAAAGGAAATAAGACAATTAAAAACCCGTTGCCTCAAGGTAAAACAAAGGAGAcc868 CCTCAAGAAAAAGGAAATAAGACAATTAAAAACCCGTTGCCTCAAGGTAAAACAAAGGAGAcc101 CCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAGGTAAAACAAAGGAGAcc706 CCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAGGTAAAACAAAGGAGAcc715 CCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAGGTAAAACAAAGGAGAcc1 CCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAGGTAAAACAAAGGAGAcc624 CCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAGGTAAAACAAAGGAGAcc415 CCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAGGTAAAACAAAGGAGAcc417 CCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAGGTAAAACAAAGGAGAcc435 CCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAGGTAAAACAAAGGAGAcc712 CCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAGGTAAAACAAAGGAGAcc201 CCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAGGTAAAACAAAGGAGAcc206 CCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAGGTAAAACAAAGGAGAcc724 CCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAGGTAAAACAAAGGAGAcc224 CCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAGGTAAAACAAAGGAGAcc220 CCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAGGTAAAACAAAGGAGAccUp3 CCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAGGTAAAACAAAGGAGAccUp1 CCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAGGTAAAACAAAGGAGAcc563 CCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAGGAAAAACAAAGGAGAcc709 CCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAGGAAAAACAAAGGAGAcc848 CCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAGGAAAAACAAAGGAGAcc504 CCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAGGAAAAACAAAGGAGAcc757 CCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAGGAAAAACAAAGGAGAcc108 CCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAGGAAAAACAAAGGAGAcc130 CCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAGGAAAAACAAAGGAGAcc414 CCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAGGAAAAACAAAGGAGAcc710 CCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAGGAAAAACAAAGGAGAcc719 CCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAGGAAAAACAAAGGAGAcc729 CCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAGGAAAAACAAAGGAGAcc761 CCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAGGAAAAACAAAGGAGAcc420 CCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAGGAAAAACAAAGGAGAccUp4 CCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAGGAAAAACAAAGAAGAcc642 CCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAGGAAAAACAAAGAAG Acc421 CCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAGGAAAAACAAAGAAG ************ * ** *** **** ********** ******** ********* **

Fig. S2b. DNA sequence alignment of the Pikm2-TS LRR region in set 2 lines.In parentheses, indica (i) and japonica (j) origins are followed by geographic origin ofline. Alleles classed into clades 1, 2, and 3 are depicted in green, blue, and red, respectively.

Ashikawa et al. Supplementary figure S2b(1/5)

Acc440 CCTGCAAAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAATGAAGTCACTCCGTAcc868 CCTGCAAAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAATGAAGTCACTCCGTAcc101 CCTGCAAAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAATGAAGTCACTCCGTAcc706 CCTGCAAAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAATGAAGTCACTCCGTAcc715 CCTGCAAAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAATGAAGTCACTCCGTAcc1 CCTGCAAAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAATGAAGTCACTCCGTAcc624 CCTGCAAAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAATGAAGTCACTCCGTAcc415 CCTGCAGAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAATGAAGTCACTCCGTAcc417 CCTGCAGAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAATGAAGTCACTCCGTAcc435 CCTGCAGAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAATGAAGTCACTCCGTAcc712 CCTGCAGAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAATGAAGTCACTCCGTAcc201 CCTGCAGAGAAAGGATCCTTGTCCCAAGAAAAAGCTAAAGGCACAATGAAGTCACTCCGTAcc206 CCTGCAGAGAAAGGATCCTTGTCCCAAGAAAAAGCTAAAGGCACAATGAAGTCACTCCGTAcc724 CCTGCAGAGAAAGGATCCTTGTCCCAAGAAAAAGCTAAAGGCACAATGAAGTCACTCCGTAcc224 CCTGCAGAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAATGAAGTCACTCCGTAcc220 CCTGCAGAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAATGAAGTCACTCCGTAccUp3 CCTGCAGAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAATGAAGTCACTCCGTAccUp1 CCTGCAGAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAATGAAGTCACTCCGTAcc563 CCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAATGAAAGCACTCCGTAcc709 CCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAATGAAAGCACTCCGTAcc848 CCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAATGAAAGCACTCCGTAcc504 CCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAATGAAAGCACTCCGTAcc757 CCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAATGAAAGCACTCCGTAcc108 CCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAATGAAAGCACTCCGTAcc130 CCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAATGAAAGCACTCCGTAcc414 CCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAATGAAAGCACTCCGTAcc710 CCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAATGAAAGCACTCCGTAcc719 CCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAATGAAAGCACTCCGTAcc729 CCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAATGAAAGCACTCCGTAcc761 CCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAATGAAAGCACTCCGTAcc420 CCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAATGAAAGCACTCCGTAccUp4 CCCACAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAATGAAAGCACTCCGTAcc642 CCCACAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAATGAAAGCACTCCGTAcc708 CCCACAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAATGAAAGCACTCCGTAcc421 CCCACAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAATGAAAGCACTCCGT ** ** ********* *** ************* ******* ******* ********

Acc440 GTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTGCAAGCCTTCATCAGAcc868 GTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTGCAAGCCTTCATCAGAcc101 GTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTGCAAGCCTTCATCAGAcc706 GTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTGCAAGCCTTCATCAGAcc715 GTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTGCAAGCCTTCATCAGAcc1 GTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTGCAAGCCTTCATCAGAcc624 GTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTGCAAGCCTTCATCAGAcc415 GTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTGCAAGCCTTCATCAGAcc417 GTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTGCAAGCCTTCATCAGAcc435 GTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTGCAAGCCTTCATCAGAcc712 GTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTGCAAGCCTTCATCAGAcc201 GTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTGCAAGCCTTCATCAGAcc206 GTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTGCAAGCCTTCATCAGAcc724 GTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTGCAAGCCTTCATCAGAcc224 GTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTGCAAGCCTTCATCAGAcc220 GTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTGCAAGCCTTCATCAGAccUp3 GTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTGCAAGCCTTCATCAGAccUp1 GTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTGCAAGCCTTCATCAGAcc563 GTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTGCAGGCCTTCATCAGAcc709 GTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTGCAGGCCTTCATCAGAcc848 GTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTGCAGGCCTTCATCAGAcc504 GTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTGCAGGCCTTCATCAGAcc757 GTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTGCAGGCCTTCATCAGAcc108 GTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTGCAGGCCTTCATCAGAcc130 GTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTGCAGGCCTTCATCAGAcc414 GTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTGCAGGCCTTCATCAGAcc710 GTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTGCAGGCCTTCATCAGAcc719 GTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTGCAGGCCTTCATCAGAcc729 GTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTGCAGGCCTTCATCAGAcc761 GTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTGCAGGCCTTCATCAGAcc420 GTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTGCAGGCCTTCATCAGAccUp4 GTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTGCAGGCCTTCATCAGAcc642 GTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTGCAGGCCTTCATCAGAcc708 GTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTGCAGGCCTTCATCAGAcc421 GTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTGCAGGCCTTCATCAG ******************** ***** ****** *** ********** ***********

Fig. S2b. DNA sequence alignment of the Pikm2-TS LRR region in set 2 rice lines.Alleles classed into clades 1, 2, and 3 are depicted in green, blue, and red, respectively.

Ashikawa et al. Supplementary figure S2b (2/5)

Acc440 TTGACAGGATTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCGAGGAAAATGATACAAcc868 TTGACAGGATTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCGAGGAAAATGATACAAcc101 TTGACAGGATTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCGAGGAAAATGATACAAcc706 TTGACAGGATTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCGAGGAAAATGATACAAcc715 TTGACAGGATTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCGAGGAAAATGATACAAcc1 TTGACAGGATTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCGAGGAAAATGATACAAcc624 TTGACAGGATTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCGAGGAAAATGATACAAcc415 TTGACAGGACTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCGAGGAAAATGATACAAcc417 TTGACAGGACTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCGAGGAAAATGATACAAcc435 TTGACAGGACTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCGAGGAAAATGATACAAcc712 TTGACAGGACTAAGGAAGCTTGCCNTTTACAAGCTCAAAATAAGCGAGGAAAATGATACAAcc201 TTGACAGGACTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCGAGGAAAATGATACAAcc206 TTGACAGGACTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCGAGGAAAATGATACAAcc724 TTGACAGGACTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCGAGGAAAATGATACAAcc224 TTGACAGGACTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCGAGGAAAATGATACAAcc220 TTGACAGGACTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCGAGGAAAATGATACAAccUp3 TTGACAGGACTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCGAGGAAAATGATACAAccUp1 TTGACAGGACTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCGAGGAAAATGATACAAcc563 TTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAAAGGGTGGTGATACCAcc709 TTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAAAGGGTGGTGATACCAcc848 TTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAAAGGGTGGTGATACCAcc504 TTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAAAGGGTGGTGATACCAcc757 TTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAAAGGGTGGTGATACCAcc108 TTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAAAGGGTGGTGATACCAcc130 TTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAAAGGGTGGTGATACCAcc414 TTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAAAGGGTGGTGATACCAcc710 TTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAAAGGGTGGTGATACCAcc719 TTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAAAGGGTGGTGATACCAcc729 TTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAAAGGGTGGTGATACCAcc761 TTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAAAGGGTGGTGATACCAcc420 TTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAAAGGGTGGTGATACCAccUp4 TTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAAAGGGTGGTGATACCAcc642 TTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAAAGGGTGGTGATACCAcc708 TTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAAAGGGTGGTGATACCAcc421 TTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAAAGGGTGGTGATACC ******** ************** * *********** **** *** ******

Acc440 TTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCATCTGCGGCCTGCAGACTCTGGCCAcc868 TTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCATCTGCGGCCTGCAGACTCTGGCCAcc101 TTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCCTGCAGACTCTGGCCAcc706 TTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCCTGCAGACTCTGGCCAcc715 TTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCCTGCAGACTCTGGCCAcc1 TTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCCTGCAGACTCTGGCCAcc624 TTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCCTGCAGACTCTGGCCAcc415 TTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCCTGCAGACTCTGGCCAcc417 TTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCCTGCAGACTCTGGCCAcc435 TTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCCTGCAGACTCTGGCCAcc712 TTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCCTGCAGACTCTGGCCAcc201 TTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCCTGCAGACTCTGGCCAcc206 TTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCCTGCAGACTCTGGCCAcc724 TTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCCTGCAGACTCTGGCCAcc224 TTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCCTGCAGACTCTGGCCAcc220 TTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCCTGCAGACTCTGGCCAccUp3 TTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCCTGCAGACTCTGGCCAccUp1 TTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCCTGCAGACTCTGGCCAcc563 TTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTCTGCAGACTCTGGCCAcc709 TTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTCTGCAGACTCTGGCCAcc848 TTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTCTGCAGACTCTGGCCAcc504 TTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTCTGCAGACTCTGGCCAcc757 TTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTCTGCAGACTCTGGCCAcc108 TTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTCTGCAGACTCTGGCCAcc130 TTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTCTGCAGACTCTGGCCAcc414 TTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTCTGCAGACTCTGGCCAcc710 TTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTCTGCAGACTCTGGCCAcc719 TTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTCTGCAGACTCTGGCCAcc729 TTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTCTGCAGACTCTGGCCAcc761 TTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTCTGCAGACTCTGGCCAcc420 TTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTCTGCAGACTCTGGCCAccUp4 TTCAAACAATTACAGTCCTCCATTGAATACCTTGGCAGCTGTGGTCTGCAGACTCTGGCCAcc642 TTCAAACAATTACAGTCCTCCATTGAATACCTTGGCAGCTGTGGTCTGCAGACTCTGGCCAcc708 TTCAAACAATTACAGTCCTCCATTGAATACCTTGGCAGCTGTGGTCTGCAGACTCTGGCCAcc421 TTCAAACAATTACAGTCCTCCATTGAATACCTTGGCAGCTGTGGTCTGCAGACTCTGGCC ****** ****** ***** ***** ********** *** ** ***************

Fig. S2b. DNA sequence alignment of the Pikm2-TS LRR region in set 2 lines.Alleles classed into clades 1, 2, and 3 are depicted in green, blue, and red, respectively.

Ashikawa et al. Supplementary figure S2b (3/5)

Acc440 ATCAATGATGAGAATTCTAAATTTATCAACTCATCGCACCTGCACTACATGTCTGCACCTAcc868 ATCAATGATGAGAATTCTAAATTTATCAACTCATCGCACCTGCACTACATGTCTGCACCTAcc101 ATCAATGATGAGAATTCTAAATTTATCAACTCACTGCCCCTGCACTACATGTCTGCACCTAcc706 ATCAATGATGAGAATTCTAAATTTATCAACTCACTGCCCCTGCACTACATGTCTGCACCTAcc715 ATCAATGATGAGAATTCTAAATTTATCAACTCACTGCCCCTGCACTACATGTCTGCACCTAcc1 ATCAATGATGAGAATTCTAAATTTATCAACTCACTGCACCTGCACTACATGTCTGCACCTAcc624 ATCAATGATGAGAATTCTAAATTTATCAACTCACTGCCCCTGCACTACATGTCTGCACCTAcc415 ATCAATGATGAGAATTCTAAATTTATCAACTCACTAT------ACAACATGTCTGCACCTAcc417 ATCAATGATGAGAATTCTAAATTTATCAACTCACTAT------ACAACATGTCTGCACCTAcc435 ATCAATGATGAGAATTCTAAATTTATCAACTCACTAT------ACAACATGTCTGCACCTAcc712 ATCAATGATGAGAATTCTAAATTTATCAACTCACTAT------ACAACATGTCTGCACCTAcc201 ATCAATGATGAGAATTCTAAATTTATCAACTCACTAT------ACAACATGTCTGCACCTAcc206 ATCAATGATGAGAATTCTAAATTTATCAACTCACTAT------ACAACATGTCTGCACCTAcc724 ATCAATGATGAGAATTCTAAATTTATCAACTCACTAT------ACAACATGTCTGCACCTAcc224 ATCAATGATGAGAATTCTAAATTTATCAACTCACTAT------ACAACATGTCTGCACCTAcc220 ATCAATGATGAGAATTCTAAATTTATCAACTCACTAT------ACAACATGTCTGCACCTAccUp3 ATCAATGATGAGAATTCTAAATTTATCAACTCACTAT------ACAACATGTCTGCACCTAccUp1 ATCAATGATGAGAATTCTAAATTTATCAACTCACTAT------ACAACATGTCTGCACCTAcc563 ATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCGACATGCCCGCGCCTAcc709 ATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCGACATGCCCGCGCCTAcc848 ATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCGACATGCCCGCGCCTAcc504 ATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCGACATGCCCGCGCCTAcc757 ATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCGACATGCCCGCGCCTAcc108 ATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCGACATGCCCGCGCCTAcc130 ATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCGACATGCCCGCGCCTAcc414 ATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCGACATGCCCGCGCCTAcc710 ATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCGACATGCCCGCGCCTAcc719 ATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCGACATGCCCGCGCCTAcc729 ATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCGACATGCCCGCGCCTAcc761 ATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCGACATGCCCGCGCCTAcc420 ATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCGACATGCCCGCGCCTAccUp4 ATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCGACATGCCCGCGCCTAcc642 ATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCGACATGCCCGCGCCTAcc708 ATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCGACATGCCCGCGCCTAcc421 ATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCGACATGCCCGCGCCT ****************** ************** * ***** * ** ***

Acc440 CCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGGACTGGCTACCTGTGTGGATCAcc868 CCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGGACTGGCTACCTGTGTGGATCAcc101 CCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGGACTGGCTACCTGTGTGGATCAcc706 CCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGGACTGGCTACCTGTGTGGATCAcc715 CCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGGACTGGCTACCTGTGTGGATCAcc1 CCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGGACTGGCTACCTGTGTGGATCAcc624 CCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGGACTGGCTACCTGTGTGGATCAcc415 CCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGAAATGGCTACCTGGGTGGATCAcc417 CCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGAAATGGCTACCTGGGTGGATCAcc435 CCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGAAATGGCTACCTGGGTGGATCAcc712 CCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGAAATGGCTACCTGGGTGGATCAcc201 CCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGAAATGGCTACCTGAGTGGATCAcc206 CCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGAAATGGCTACCTGAGTGGATCAcc724 CCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGAAATGGCTACCTGAGTGGATCAcc224 CCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGAAATGGCTACCTGAGTGGATCAcc220 CCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGAAATGGCTACCTGAGTGGATCAccUp3 CCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGAAATGGCTACCTGAGTGGATCAccUp1 CCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGAAATGGCTACCTGAGTGGATCAcc563 CCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGCTACCCAAGTGGATCAcc709 CCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGCTACCCAAGTGGATCAcc848 CCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGCTACCCAAGTGGATCAcc504 CCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGCTACCCAAGTGGATCAcc757 CCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGCTACCCAAGTGGATCAcc108 CCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGCTACCCAAGTGGATCAcc130 CCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGCTACCCAAGTGGATCAcc414 CCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGCTACCCAAGTGGATCAcc710 CCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGCTACCCAAGTGGATCAcc719 CCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGCTACCCAAGTGGATCAcc729 CCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGCTACCCAAGTGGATCAcc761 CCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGCTACCCAAGTGGATCAcc420 CCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGCTACCCAAGTGGATCAccUp4 CCAAGATATCTTATCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGCTACCCAAGTGGATCAcc642 CCAAGATATCTTATCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGCTACCCAAGTGGATCAcc708 CCAAGATATCTTATCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGCTACCCAAGTGGATCAcc421 CCAAGATATCTTATCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGCTACCCAAGTGGATC *********** ** ************* ********* * ****** *******

Fig. S2b. DNA sequence alignment of the Pikm2-TS LRR region in set 2 rice lines.Alleles classed into clades 1, 2, and 3 are depicted in green, blue, and red, respectively.

Ashikawa et al. Supplementary figure S2b (4/5)

Acc440 ACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTCTTAcc868 ACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTCTTAcc101 ACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTCTTAcc706 ACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTCTTAcc715 ACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTCTTAcc1 ACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTCTTAcc624 ACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTCTTAcc415 ACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTCTTAcc417 ACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTCTTAcc435 ACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTCTTAcc712 ACCAGCATTACTACTCTCAACAGGTTAACCATATCTATAACAGTTCTTAcc201 ACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTCTTAcc206 ACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTCTTAcc724 ACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTCTTAcc224 ACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTCTTAcc220 ACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTCTTAccUp3 ACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTCTTAccUp1 ACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTCTTAcc563 ACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTCTTAcc709 ACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTCTTAcc848 ACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTCTTAcc504 ACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTCTTAcc757 ACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTCTTAcc108 ACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTCTTAcc130 ACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTCTTAcc414 ACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTCTTAcc710 ACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTCTTAcc719 ACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTCTTAcc729 ACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTCTTAcc761 ACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTCTTAcc420 ACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTCTTAccUp4 ACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTCTTAcc642 ACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTCTTAcc708 ACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTCTTAcc421 ACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTCTT ******** ************* * *********** ***********

Figure S2b. DNA sequence alignment of the Pikm2-TS LRR region in set 2 lines.Alleles classed into clades 1, 2, and 3 are depicted in green, blue, and red, respectively.

Ashikawa et al. Supplementary figure S2b (5/5)