Acc414 ATGGAGTTGGTGGTAGGTGTTTCCGAAGCCACCATGAAATCTCTCTTGGGCAAGCTGGGC 60Acc420 ATGGAGTTGGTGGTAGGTGTTTCCGAAGCCACCATGAAATCTCTCTTGGGCAAGCTGGGC 60Acc761 ATGGAGTTGGTGGTAGGTGTTTCCGAAGCCACCATGAAATCTCTCTTGGGCAAGCTGGGC 60Acc504 ATGGAGTTGGTGGTAGGTGCTTCCGAAGCCACCATGAAATCTCTCTTGGGCAAGCTGGGC 60Acc563 ATGGAGTTGGTGGTAGGTGCTTCCGAAGCCACCATGAAATCTCTCTTGGGCAAGCTGGGC 60Acc757 ATGGAGTTGGTGGTAGGTGCTTCCGAAGCCACCATGAAATCTCTCTTGGGCAAGCTGGGC 60Acc848 ATGGAGTTGGTGGTAGGTGCTTCCGAAGCCACCATGAAATCTCTCTTGGGCAAGCTGGGC 60Tsuyuake_Pikm ATGGAGTTGGTGGTAGGTGCTTCCGAAGCCACCATGAAATCTCTCTTGGGCAAGCTGGGC 60Kusabue_Pik ATGGAGTTGGTGGTAGGTGCTTCCGAAGCCACCATGAAATCTCTCTTGGGCAAGCTGGGC 60Kanto51_Pik ATGGAGTTGGTGGTAGGTGCTTCCGAAGCCACCATGAAATCTCTCTTGGGCAAGCTGGGC 60K60_Pikp ATGGAGTTGGTGGTAGGTGCTTCCGAAGCCACCATGAAATCTCTCTTGGGCAAGCTGGGC 60Acc108 ATGGAGTTGGTGGTAGGTGCTTCCGAAGCCACCATGAAATCTCTCTTGGGCAAGCTGGGC 60Acc130 ATGGAGTTGGTGGTAGGTGCTTCCGAAGCCACCATGAAATCTCTCTTGGGCAAGCTGGGC 60Acc719 ATGGAGTTGGTGGTAGGTGCTTCCGAAGCCACCATGAAATCTCTCTTGGGCAAGCTGGGC 60Acc729 ATGGAGTTGGTGGTAGGTGCTTCCGAAGCCACCATGAAATCTCTCTTGGGCAAGCTGGGC 60Acc710 ATGGAGTTGGTGGTAGGTGCTTCCGAAGCCACCATGAAATCTCTCTTGGGCAAGCTGGGC 60Acc709 ATGGAGTTGGTGGTAGGTGCTTCCGAAGCCACCATGAAATCTCTCTTGGGCAAGCTGGGC 60Acc220 ATGGAGTTGGCGGTAGGTGCTTCGGAAGCCACCATGAGATCTCTCCTGGGCAAGCTGGGC 60Nipponbare ATGGAGTTGGCGGTAGGTGCTTCGGAAGCCACCATGAGATCTCTCCTGGGCAAGCTGGGC 60Acc224 ATGGAGTTGGCGGTAGGTGCTTCGGAAGCCACCATGAGATCTCTCCTGGGCAAGCTGGGC 60AccUP3 ATGGAGTTGGCGGTAGGTGCTTCGGAAGCCACCATGAGATCTCTCCTGGGCAAGCTGGGC 60AccUP1 ATGGAGTTGGCGGTAGGTGCTTCGGAAGCCACCATGAGATCTCTCCTGGGCAAGCTGGGC 60Acc206 ATGGAGTTGGCGGTAGGTGCTTCGGAAGCCACCATGAGATCTCTCCTGGGCAAGCTGGGC 60Acc201 ATGGAGTTGGCGGTAGGTGCTTCGGAAGCCACCATGAGATCTCTCCTGGGCAAGCTGGGC 60Acc724 ATGGAGTTGGCGGTAGGTGCTTCGGAAGCCACCATGAGATCTCTCCTGGGCAAGCTGGGC 60Acc415 ATGGAGTTGGCGGTAGGTGCTTCGGAAGCCACCATGAGATCTCTCCTGGGCAAGCTGGGC 60Acc417 ATGGAGTTGGCGGTAGGTGCTTCGGAAGCCACCATGAGATCTCTCCTGGGCAAGCTGGGC 60Acc435 ATGGAGTTGGCGGTAGGTGCTTCGGAAGCCACCATGAGATCTCTCCTGGGCAAGCTGGGC 60Acc712 ATGGAGTTGGCGGTAGGTGCTTCGGAAGCCACCATGAGATCTCTCCTGGGCAAGCTGGGC 60Acc101 ATGGAGTTGGTGGTAGGTGCTTCGGAAGCCACCATGAGATCTCTCCTGGGCAAGCTGGGC 60Acc715 ATGGAGTTGGTGGTAGGTGCTTCGGAAGCCACCATGAGATCTCTCCTGGGCAAGCTGGGC 60Acc706 ATGGAGTTGGTGGTAGGTGCTTCGGAAGCCACCATGAGATCTCTCCTGGGCAAGCTGGGC 60Acc624 ATGGAGTTGGTGGTAGGTGCTTCGGAAGCCACCATGAGATCTCTCCTGGGCAAGCTGGGC 60Acc1 ATGGAGTTGGTGGTAGGTGCTTCGGAAGCCACCATGAGATCTCTCCTGGGCAAGCTGGGC 60Acc440 ATGGAGTTGGTGGTAGGTGCTTCGGAAGCCACCATGAGATCTCTCCTGGGCAAGCTGGGC 60Acc868 ATGGAGTTGGTGGTAGGTGCTTCGGAAGCCACCATGAGATCTCTCCTGGGCAAGCTGGGC 60Acc718 ATGGAGTTGGTGGTAGGTGCTTCGGAAGCCACCATGAGATCTCTCCTGGGCAAGCTGGGC 60 ********** ******** *** ************* ******* ************** Acc414 AATCTTCTAGCCCAGGAGTATGCTCTCATCAGCGGTATCCGTGGTGACATCCAGTACATC 120Acc420 AATCTTCTAGCCCAGGAGTATGCTCTCATCAGCGGTATCCGTGGTGACATCCAGTACATC 120Acc761 AATCTTCTAGCCCAGGAGTATGCTCTCATCAGCGGTATCCGTGGTGACATCCAGTACATC 120Acc504 AATCTTCTAGCCCAGGAGTATGCTCTCATCAGCGGTATCCGTGGTGACATCCAGTACATC 120Acc563 AATCTTCTAGCCCAGGAGTATGCTCTCATCAGCGGTATCCGTGGTGACATCCAGTACATC 120Acc757 AATCTTCTAGCCCAGGAGTATGCTCTCATCAGCGGTATCCGTGGTGACATCCAGTACATC 120Acc848 AATCTTCTAGCCCAGGAGTATGCTCTCATCAGCGGTATCCGTGGTGACATCCAGTACATC 120Tsuyuake_Pikm AATCTTCTAGCCCAGGAGTATGCTCTCATCAGCGGTATCCGTGGTGACATCCAGTACATC 120Kusabue_Pik AATCTTCTAGCCCAGGAGTATGCTCTCATCAGCGGTATCCGTGGTGACATCCAGTACATC 120Kanto51_Pik AATCTTCTAGCCCAGGAGTATGCTCTCATCAGCGGTATCCGTGGTGACATCCAGTACATC 120K60_Pikp AATCTTCTAGCCCAGGAGTATGCTCTCATCAGCGGTATCCGTGGTGACATCCAGTACATC 120Acc108 AATCTTCTAGCCCAGGAGTATGCTCTCATCAGCGGTATCCGTGGTGACATCCAGTACATC 120Acc130 AATCTTCTAGCCCAGGAGTATGCTCTCATCAGCGGTATCCGTGGTGACATCCAGTACATC 120Acc719 AATCTTCTAGCCCAGGAGTATGCTCTCATCAGCGGTATCCGTGGTGACATCCAGTACATC 120Acc729 AATCTTCTAGCCCAGGAGTATGCTCTCATCAGCGGTATCCGTGGTGACATCCAGTACATC 120Acc710 AATCTTCTAGCCCAGGAGTATGCTCTCATCAGCGGTATCCGTGGTGACATCCAGTACATC 120Acc709 AATCTTCTAGCCCAGGAGTATGCTCTCATCAGCGGTATCCGTGGTGACATCCAGTACATC 120Acc220 AACCTTCTTGCCCAGGAGTATTCTCTGGTCAGCGGCGTCCGTGGTGACATCCAGTACATC 120Nipponbare AACCTTCTTGCCCAGGAGTATTCTCTGGTCAGCGGCGTCCGTGGTGACATCCAGTACATC 120Acc224 AACCTTCTTGCCCAGGAGTATTCTCTGGTCAGCGGCGTCCGTGGTGACATCCAGTACATC 120AccUP3 AACCTTCTTGCCCAGGAGTATTCTCTGGTCAGCGGCGTCCGTGGTGACATCCAGTACATC 120AccUP1 AACCTTCTTGCCCAGGAGTATTCTCTGGTCAGCGGCGTCCGTGGTGACATCCAGTACATC 120Acc206 AACCTTCTTGCCCAGGAGTATTCTCTGGTCAGCGGCGTCCGTGGTGACATCCAGTACATC 120Acc201 AACCTTCTTGCCCAGGAGTATTCTCTGGTCAGCGGCGTCCGTGGTGACATCCAGTACATC 120Acc724 AACCTTCTTGCCCAGGAGTATTCTCTGGTCAGCGGCGTCCGTGGTGACATCCAGTACATC 120Acc415 AACCTTCTTGCCCAGGAGTATTCTCTGGTCAGCGGCGTCCGTGGTGACATCCAGTACATC 120Acc417 AACCTTCTTGCCCAGGAGTATTCTCTGGTCAGCGGCGTCCGTGGTGACATCCAGTACATC 120Acc435 AACCTTCTTGCCCAGGAGTATTCTCTGGTCAGCGGCGTCCGTGGTGACATCCAGTACATC 120Acc712 AACCTTCTTGCCCAGGAGTATTCTCTGGTCAGCGGCGTCCGTGGTGACATCCAGTACATC 120Acc101 AACCTTCTTGCCCAGGAGTATGCTCTCATCAGCGGCGTCCGTGGTGACATCCAGTACATC 120Acc715 AACCTTCTTGCCCAGGAGTATGCTCTCATCAGCGGCGTCCGTGGTGACATCCAGTACATC 120Acc706 AACCTTCTTGCCCAGGAGTATGCTCTCATCAGCGGCGTCCGTGGTGACATCCAGTACATC 120Acc624 AACCTTCTTGCCCAGGAGTATGCTCTCATCAGCGGCGTCCGTGGTGACATCCAGTACATC 120Acc1 AACCTTCTTGCCCAGGAGTATGCTCTCATCAGCGGCGTCCGTGGTGACATCCAGTACATC 120Acc440 AACCTTCTTGCCCAGGAGTATTCTCTGGTCAGCGGCGTCCGTGGTGACATCCAGTACATC 120Acc868 AACCTTCTTGCCCAGGAGTATTCTCTGGTCAGCGGCGTCCGTGGTGACATCCAGTACATC 120Acc718 AACCTTCTTGCCCAGGAGTATTCTCTGGTCAGCGGCGTCCGTGGTGACATCCAGTACATC 120 ** ***** ************ **** ******* ***********************

Fig. S2. Multiple alignment of the second-gene sequences of the 32 rice lines, cultivars showing Pik-family-specific blast resistance (Kusabue, Kanto 51, Tsuyuake, and K60) and the susceptible Nipponbare. Sequences grouped clade 1 are black, and those in clade 2 are red.

Ashikawa et al. Supplementary Fig. S2 (1/28)

Acc414 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGATCTCAGCAACGTGCCAGAGGGT 180Acc420 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGATCTCAGCAACGTGCCAGAGGGT 180Acc761 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGATCTCAGCAACGTGCCAGAGGGT 180Acc504 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGATCTCAGCAACGTGCCAGAGGGT 180Acc563 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGATCTCAGCAACGTGCCAGAGGGT 180Acc757 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGATCTCAGCAACGTGCCAGAGGGT 180Acc848 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGATCTCAGCAACGTGCCAGAGGGT 180Tsuyuake_Pikm AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGATCTCAGCAACGTGCCAGAGGGT 180Kusabue_Pik AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGATCTCAGCAACGTGCCAGAGGGT 180Kanto51_Pik AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGATCTCAGCAACGTGCCAGAGGGT 180K60_Pikp AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGATCTCAGCAACGTGCCAGAGGGT 180Acc108 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGATCTCAGCAACGTGCCAGAGGGT 180Acc130 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGATCTCAGCAACGTGCCAGAGGGT 180Acc719 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGATCTCAGCAACGTGCCAGAGGGT 180Acc729 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGATCTCAGCAACGTGCCAGAGGGT 180Acc710 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGATCTCAGCAACGTGCCAGAGGGT 180Acc709 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGATCTCAGCAACGTGCCAGAGGGT 180Acc220 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGACCTTAGCGTTGTGACGGAGGGT 180Nipponbare AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGACCTTAGCGTTGTGACGGAGGGT 180Acc224 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGACCTTAGCGTTGTGACGGAGGGT 180AccUP3 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGACCTTAGCGTTGTGACGGAGGGT 180AccUP1 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGACCTTAGCGTTGTGACGGAGGGT 180Acc206 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGACCTTAGCGTTGTGACGGAGGGT 180Acc201 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGACCTTAGCGTTGTGACGGAGGGT 180Acc724 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGACCTTAGCGTTGTGACGGAGGGT 180Acc415 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGACCTTAGCGTTGTGACGGAGGGT 180Acc417 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGACCTTAGCGTTGTGACGGAGGGT 180Acc435 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGACCTTAGCGTTGTGACGGAGGGT 180Acc712 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGACCTTAGCGTTGTGACGGAGGGT 180Acc101 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGACCTCAGCGTTTTGCCGGAGGGT 180Acc715 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGACCTCAGCGTTTTGCCGGAGGGT 180Acc706 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGACCTCAGCGTTTTGCCGGAGGGT 180Acc624 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGACCTCAGCGTTTTGCCGGAGGGT 180Acc1 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGACCTCAGCGTTTTGCCGGAGGGT 180Acc440 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGACCTCAGCGTTTTGCCGGAGGGT 180Acc868 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGACCTCAGCGTTTTGCCGGAGGGT 180Acc718 AATGACGAGCTTGCCAGCATGCAGGCCTTCCTCCGTGACCTCAGCGTTTTGCCGGAGGGT 180 ************************************** ** *** ** * ****** Acc414 CACAGTCATGGCCACCGGATGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAT 240Acc420 CACAGTCATGGCCACCGGATGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAT 240Acc761 CACAGTCATGGCCACCGGATGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAT 240Acc504 CACAGTCATGGCCACCGGATGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAT 240Acc563 CACAGTCATGGCCACCGGATGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAT 240Acc757 CACAGTCATGGCCACCGGATGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAT 240Acc848 CACAGTCATGGCCACCGGATGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAT 240Tsuyuake_Pikm CACAGTCATGGCCACCGGATGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAT 240Kusabue_Pik CACAGTCATGGCCACCGGATGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAT 240Kanto51_Pik CACAGTCATGGCCACCGGATGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAT 240K60_Pikp CACAGTCATGGCCACCGGATGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAT 240Acc108 CACAGTCATGGCCACCGGATGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAT 240Acc130 CACAGTCATGGCCACCGGATGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAT 240Acc719 CACAGTCATGGCCACCGGATGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAT 240Acc729 CACAGTCATGGCCACCGGATGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAT 240Acc710 CACAGTCATGGCCACCGGATGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAT 240Acc709 CACAGTCATGGCCACCGGATGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAT 240Acc220 CACAACCATGACAACCGGAGGAAGGACTGGATGAAGCAGATCCGAGACGTCGCCTATGAC 240Nipponbare CACAACCATGACAACCGGAGGAAGGACTGGATGAAGCAGATCCGAGACGTCGCCTATGAC 240Acc224 CACAACCATGACAACCGGAGGAAGGACTGGATGAAGCAGATCCGAGACGTCGCCTATGAC 240AccUP3 CACAACCATGACAACCGGAGGAAGGACTGGATGAAGCAGATCCGAGACGTCGCCTATGAC 240AccUP1 CACAACCATGACAACCGGAGGAAGGACTGGATGAAGCAGATCCGAGACGTCGCCTATGAC 240Acc206 CACAACCATGACAACCGGAGGAAGGACTGGATGAAGCAGATCCGAGACGTCGCCTATGAC 240Acc201 CACAACCATGACAACCGGAGGAAGGACTGGATGAAGCAGATCCGAGACGTCGCCTATGAC 240Acc724 CACAACCATGACAACCGGAGGAAGGACTGGATGAAGCAGATCCGAGACGTCGCCTATGAT 240Acc415 CACAACCATGACAACCGGAGGAAGGACTGGATGAAGCAGATCCGAGACGTCGCCTATGAC 240Acc417 CACAACCATGACAACCGGAGGAAGGACTGGATGAAGCAGATCCGAGACGTCGCCTATGAC 240Acc435 CACAACCATGACAACCGGAGGAAGGACTGGATGAAGCAGATCCGAGACGTCGCCTATGAC 240Acc712 CACAACCATGACAACCGGAGGAAGGACTGGATGAAGCAGATCCGAGACGTCGCCTATGAT 240Acc101 CACTACCATGACAACCGGAGGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAC 240Acc715 CACTACCATGACAACCGGAGGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAC 240Acc706 CACTACCATGACAACCGGAGGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAC 240Acc624 CACTACCATGACAACCGGAGGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAC 240Acc1 CACTACCATGACAACCGGAGGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAC 240Acc440 CACTACCATGACAACCGGAGGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAC 240Acc868 CACTACCATGACAACCGGAGGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAC 240Acc718 CACTACCATGACAACCGGAGGAAGGACTGGATGAAGCAGATCCGAGACATCGCCTATGAC 240 *** **** * ****** **************************** **********

Ashikawa et al. Supplementary Fig. S2 (2/28)

Acc414 GTTGAGGACTGTATCGATGACTTTGCCCACCGCCTCCCTCAGGATTCCATCAGCGATGCC 300Acc420 GTTGAGGACTGTATCGATGACTTTGCCCACCGCCTCCCTCAGGATTCCATCAGCGATGCC 300Acc761 GTTGAGGACTGTATCGATGACTTTGCCCACCGCCTCCCTCAGGATTCCATCAGCGATGCC 300Acc504 GTTGAGGACTGTATCGATGACTTTGCCCACCGCCTCCCTCAGGATTCCATCAGCGATGCC 300Acc563 GTTGAGGACTGTATCGATGACTTTGCCCACCGCCTCCCTCAGGATTCCATCAGCGATGCC 300Acc757 GTTGAGGACTGTATCGATGACTTTGCCCACCGCCTCCCTCAGGATTCCATCAGCGATGCC 300Acc848 GTTGAGGACTGTATCGATGACTTTGCCCACCGCCTCCCTCAGGATTCCATCAGCGATGCC 300Tsuyuake_Pikm GTTGAGGACTGTATCGATGACTTTGCCCACCGCCTCCCTCAGGATTCCATCAGCGATGCC 300Kusabue_Pik GTTGAGGACTGTATCGATGACTTTGCCCACCGCCTCCCTCAGGATTCCATCAGCGATGCC 300Kanto51_Pik GTTGAGGACTGTATCGATGACTTTGCCCACCGCCTCCCTCAGGATTCCATCAGCGATGCC 300K60_Pikp GTTGAGGACTGTATCGATGACTTTGCCCACCGCCTCCCTCAGGATTCCATCAGCGATGCC 300Acc108 GTTGAGGACTGTATCGATGACTTTGCCCACCGCCTCCCTCAGGATTCCATCAGCGATGCC 300Acc130 GTTGAGGACTGTATCGATGACTTTGCCCACCGCCTCCCTCAGGATTCCATCAGCGATGCC 300Acc719 GTTGAGGACTGTATCGATGACTTTGCCCACCGCCTCCCTCAGGATTCCATCAGCGATGCC 300Acc729 GTTGAGGACTGTATCGATGACTTTGCCCACCGCCTCCCTCAGGATTCCATCAGCGATGCC 300Acc710 GTTGAGGACTGTATCGATGACTTTGCCCACCGCCTCCCTCAGGATTCCATCAGCGATGCC 300Acc709 GTTGAGGACTGTATCGATGACTTTGCCCACCGCCTCCCTCAGGATTCCATCAGCGATGCC 300Acc220 GTTGAGGACTGCATCGATGACTTTGCGCACCGGCTCCCCCAGGATTCAATCAGCGATGCC 300Nipponbare GTTGAGGACTGCATCGATGACTTTGCGCACCGGCTCCCCCAGGATTCAATCAGCGATGCC 300Acc224 GTTGAGGACTGCATCGATGACTTTGCGCACCGGCTCCCCCAGGATTCAATCAGCGATGCC 300AccUP3 GTTGAGGACTGCATCGATGACTTTGCGCACCGGCTCCCCCAGGATTCAATCAGCGATGCC 300AccUP1 GTTGAGGACTGCATCGATGACTTTGCGCACCGGCTCCCCCAGGATTCAATCAGCGATGCC 300Acc206 GTTGAGGACTGCATCGATGACTTTGCGCACCGGCTCCCCCAGGATTCAATCAGCGATGCC 300Acc201 GTTGAGGACTGCATCGATGACTTTGCGCACCGGCTCCCCCAGGATTCAATCAGCGATGCC 300Acc724 GTTGAGGACTGCATCGATGACTTTGCGCACCGGCTCCCCCAGGATTCAATCAGCGATGCC 300Acc415 GTTGAGGACTGCATCGATGACTTTGCGCACCGGCTCCCCCAGGATTCAATCAGCGATGCC 300Acc417 GTTGAGGACTGCATCGATGACTTTGCGCACCGGCTCCCCCAGGATTCAATCAGCGATGCC 300Acc435 GTTGAGGACTGCATCGATGACTTTGCGCACCGGCTCCCCCAGGATTCAATCAGCGATGCC 300Acc712 GTTGAGGACTGCATCGATGACTTTGCGCACCGGCTCCCCCAGGATTCAATCAGCGATGCC 300Acc101 GTTGAGGACTGCATCGATGACTTTGCCCACCGGCTCCCCCAGGACTCAATCAGCGACGCC 300Acc715 GTTGAGGACTGCATCGATGACTTTGCCCACCGGCTCCCCCAGGACTCAATCAGCGACGCC 300Acc706 GTTGAGGACTGCATCGATGACTTTGCCCACCGGCTCCCCCAGGACTCAATCAGCGACGCC 300Acc624 GTTGAGGACTGCATCGATGACTTTGCCCACCGGCTCCCCCAGGACTCAATCAGCGACGCC 300Acc1 GTTGAGGACTGCATCGATGACTTTGCCCACCGGCTCCCCCAGGATTCAATCAGCGACGCC 300Acc440 GTTGAGGACTGCATCGATGACTTTGCCCACCGGCTCCCCCAGGATTCAATCAGCGACGCC 300Acc868 GTTGAGGACTGCATCGATGACTTTGCCCACCGGCTCCCCCAGGATTCAATCAGCGACGCC 300Acc718 GTTGAGGACTGCATCGATGACTTTGCCCACCGGCTCCCCCAGGATTCAATCAGCGACGCC 300 *********** ************** ***** ***** ***** ** ******** *** Acc414 AAATGGTCCTTCCTACTCACAAAAATCTATGAACTATGGACATGGTGGCCACGTCGTGTG 360Acc420 AAATGGTCCTTCCTACTCACAAAAATCTATGAACTATGGACATGGTGGCCACGTCGTGTG 360Acc761 AAATGGTCCTTCCTACTCACAAAAATCTATGAACTATGGACATGGTGGCCACGTCGTGTG 360Acc504 AAATGGTCCTTCCTACTCACAAAAATCTATGAACTATGGACATGGTGGCCACGTCGTGTG 360Acc563 AAATGGTCCTTCCTACTCACAAAAATCTATGAACTATGGACATGGTGGCCACGTCGTGTG 360Acc757 AAATGGTCCTTCCTACTCACAAAAATCTATGAACTATGGACATGGTGGCCACGTCGTGTG 360Acc848 AAATGGTCCTTCCTACTCACAAAAATCTATGAACTATGGACATGGTGGCCACGTCGTGTG 360Tsuyuake_Pikm AAATGGTCCTTCCTACTCACAAAAATCTATGAACTATGGACATGGTGGCCACGTCGTGTG 360Kusabue_Pik AAATGGTCCTTCCTACTCACAAAAATCTATGAACTATGGACATGGTGGCCACGTCGTGTG 360Kanto51_Pik AAATGGTCCTTCCTACTCACAAAAATCTATGAACTATGGACATGGTGGCCACGTCGTGTG 360K60_Pikp AAATGGTCCTTCCTACTCACAAAAATCTATGAACTATGGACATGGTGGCCACGTCGTGTG 360Acc108 AAATGGTCCTTCCTACTCACAAAAATCTATGAACTATGGACATGGTGGCCACGTCGTGTG 360Acc130 AAATGGTCCTTCCTACTCACAAAAATCTATGAACTATGGACATGGTGGCCACGTCGTGTG 360Acc719 AAATGGTCCTTCCTACTCACAAAAATCTATGAACTATGGACATGGTGGCCACGTCGTGTG 360Acc729 AAATGGTCCTTCCTACTCACAAAAATCTATGAACTATGGACATGGTGGCCACGTCGTGTG 360Acc710 AAATGGTCCTTCCTACTCACAAAAATCTATGAACTATGGACATGGTGGCCACGTCGTGTG 360Acc709 AAATGGTCCTTCCTACTCACAAAAATCTATGAACTATGGACATGGTGGCCACGTCGTGTG 360Acc220 AAATGCTCCTTCATACTCACAAAAATGTATGAACTCTTGACATGGTGGCCTCGTCGCGAT 360Nipponbare AAATGCTCCTTCATACTCACAAAAATGTATGAACTCTTGACATGGTGGCCTCGTCGCGAT 360Acc224 AAATGCTCCTTCATACTCACAAAAATGTATGAACTCTTGACATGGTGGCCTCGTCGCGAT 360AccUP3 AAATGCTCCTTCATACTCACAAAAATGTATGAACTCTTGACATGGTGGCCTCGTCGCGAT 360AccUP1 AAATGCTCCTTCATACTCACAAAAATGTATGAACTCTTGACATGGTGGCCTCGTCGCGAT 360Acc206 AAATGCTCCTTCATACTCACAAAAATGTATGAACTCTTGACATGGTGGCCTCGTCGCGAT 360Acc201 AAATGCTCCTTCATACTCACAAAAATGTATGAACTCTTGACATGGTGGCCTCGTCGCGAT 360Acc724 AAATGCTCCTTCATACTCACAAAAATGTATGAACTCTTGACATGGTGGCCTCGTCGCGAT 360Acc415 AAATGCTCCTTCATACTCACAAAAATGTATGAACTCTTGACATGGTGGCCTCGTCGCGAT 360Acc417 AAATGCTCCTTCATACTCACAAAAATGTATGAACTCTTGACATGGTGGCCTCGTCGCGAT 360Acc435 AAATGCTCCTTCATACTCACAAAAATGTATGAACTCTTGACATGGTGGCCTCGTCGCGAT 360Acc712 AAATGCTCCTTCATACTCACAAAAATGTATGAACTCTTGACATGGTGGCCTCGTCGCGAT 360Acc101 AAATGCTCCTTCCTAGTCACGAAAATGTATGAACTCTTGACATGGTGGCCTCGTCGTGAT 360Acc715 AAATGCTCCTTCCTAGTCACGAAAATGTATGAACTCTTGACATGGTGGCCTCGTCGTGAT 360Acc706 AAATGCTCCTTCCTAGTCACGAAAATGTATGAACTCTTGACATGGTGGCCTCGTCGTGAT 360Acc624 AAATGCTCCTTCCTAGTCACGAAAATGTATGAACTCTTGACATGGTGGCCTCGTCGTGAT 360Acc1 AAATGCTCCTTCCTAGTCACGAAAATGTATGAACTCTTGACATGGTGGCCTCGTCGTGAT 360Acc440 AAATGCTCCTTCCTAGTCACGAAAATGTATGAACTCTTGACATGGTGGCCTCGTCGTGAT 360Acc868 AAATGCTCCTTCCTAGTCACGAAAATGTATGAACTCTTGACATGGTGGCCTCGTCGTGAT 360Acc718 AAATGCTCCTTCCTAGTCACGAAAATGTATGAACTCTTGACATGGTGGCCTCGTCGTGAT 360 ***** ****** ** **** ***** ******** * ************ ***** *

Ashikawa et al. Supplementary Fig. S2 (3/28)

Acc414 ATTGCTTCCAACATTGCCCAACTCAAGGTACGGGCACAACAGATCG-------------- 406Acc420 ATTGCTTCCAACATTGCCCAACTCAAGGTACGGGCACAACAGATCG-------------- 406Acc761 ATTGCTTCCAACATTGCCCAACTCAAGGTACGGGCACAACAGATCG-------------- 406Acc504 ATTGCTTCCAACATTGCCCAACTCAAGGTACGGGCACAACAGATCG-------------- 406Acc563 ATTGCTTCCAACATTGCCCAACTCAAGGTACGGGCACAACAGATCG-------------- 406Acc757 ATTGCTTCCAACATTGCCCAACTCAAGGTACGGGCACAACAGATCG-------------- 406Acc848 ATTGCTTCCAACATTGCCCAACTCAAGGTACGGGCACAACAGATCG-------------- 406Tsuyuake_Pikm ATTGCTTCCAACATTGCCCAACTCAAGGTACGGGCACAACAGATCG-------------- 406Kusabue_Pik ATTGCTTCCAACATTGCCCAACTCAAGGTACGGGCACAACAGATCG-------------- 406Kanto51_Pik ATTGCTTCCAACATTGCCCAACTCAAGGTACGGGCACAACAGATCG-------------- 406K60_Pikp ATTGCTTCCAACATTGCCCAACTCAAGGTACGGGCACAACAGATCG-------------- 406Acc108 ATTGCTTCCAACATTGCCCAACTCAAGGTACGGGCACAACAGATCG-------------- 406Acc130 ATTGCTTCCAACATTGCCCAACTCAAGGTACGGGCACAACAGATCG-------------- 406Acc719 ATTGCTTCCAACATTGCCCAACTCAAGGTACGGGCACAACAGATCG-------------- 406Acc729 ATTGCTTCCAACATTGCCCAACTCAAGGTACGGGCACAACAGATCG-------------- 406Acc710 ATTGCTTCCAACATTGCCCAACTCAAGGTACGGGCACAACAGATCG-------------- 406Acc709 ATTGCTTCCAACATTGCCCAACTCAAGGTACGGGCACAACAGATCG-------------- 406Acc220 ATTGCTTCGAGAATTGCTGAACTCAAGGTACGGGCGCAACAGATCG-------------- 406Nipponbare ATTGCTTCGAGAATTGCTGAACTCAAGGTACGGGCGCAACAGATCG-------------- 406Acc224 ATTGCTTCGAGAATTGCTGAACTCAAGGTACGGGCGCAACAGATCG-------------- 406AccUP3 ATTGCTTCGAGAATTGCTGAACTCAAGGTACGGGCGCAACAGATCG-------------- 406AccUP1 ATTGCTTCGAGAATTGCTGAACTCAAGGTACGGGCGCAACAGATCG-------------- 406Acc206 ATTGCTTCGAGAATTGCTGAACTCAAGGTACGGGCGCAACAGATCG-------------- 406Acc201 ATTGCTTCGAGAATTGCTGAACTCAAGGTACGGGCGCAACAGATCG-------------- 406Acc724 ATTGCTTCGAGAATTGCTGAACTCAAGGTACGGGCGCAACAGATCG-------------- 406Acc415 ATTGCTTCGAGAATTGCTGAACTCAAGGTACGGGCGCAACAGATCG-------------- 406Acc417 ATTGCTTCGAGAATTGCTGAACTCAAGGTACGGGCGCAACAGATCG-------------- 406Acc435 ATTGCTTCGAGAATTGCTGAACTCAAGGTACGGGCGCAACAGATCG-------------- 406Acc712 ATTGCTTCGAGAATTGCTGAACTCAAGGTACGGGCGCAACAGATCG-------------- 406Acc101 ATTGCTTCGAGAATTGCTGAACTCAAGGTACGGGCGCAACAGATCG-------------- 406Acc715 ATTGCTTCGAGAATTGCTGAACTCAAGGTACGGGCGCAACAGATCG-------------- 406Acc706 ATTGCTTCGAGAATTGCTGAACTCAAGGTACGGGCGCAACAGATCG-------------- 406Acc624 ATTGCTTCGAGAATTGCTGAACTCAAGGTACGGGCGCAACAGATCG-------------- 406Acc1 ATTGCTTCGAGAATTGCTGAACTCAAGGTACGGGCGCAACAGATCG-------------- 406Acc440 ATTGCTTCGAGAATTGCTGAACTCAAGGTACGGGCGCAACAGATCG-------------- 406Acc868 ATTGCTTCGAGAATTGCTGAACTCAAGGTACGGGCGCAACAGATCGGGCGCAACAGATCG 420Acc718 ATTGCTTCGAGAATTGCTGAACTCAAGGTACGGGCGCAACAGATCG-------------- 406 ******** * ***** **************** **********  Acc414 CAGATCGACGTAGTAGATACGGAGTGAACAACCCAGAAC---ACCTTGACAGTAGCAGCA 463Acc420 CAGATCGACGTAGTAGATACGGAGTGAACAACCCAGAAC---ACCTTGACAGTAGCAGCA 463Acc761 CAGATCGACGTAGTAGATACGGAGTGAACAACCCAGAAC---ACCTTGACAGTAGCAGCA 463Acc504 CAGATCGACGTAGTAGATACGGAGTGAACAACCCAGAAC---ACCTTGACAGTAGCAGCA 463Acc563 CAGATCGACGTAGTAGATACGGAGTGAACAACCCAGAAC---ACCTTGACAGTAGCAGCA 463Acc757 CAGATCGACGTAGTAGATACGGAGTGAACAACCCAGAAC---ACCTTGACAGTAGCAGCA 463Acc848 CAGATCGACGTAGTAGATACGGAGTGAACAACCCAGAAC---ACCTTGACAGTAGCAGCA 463Tsuyuake_Pikm CAGATCGACGTAGTAGATACGGAGTGAACAACCCAGAAC---ACCTTGACAGTAGCAGCA 463Kusabue_Pik CAGATCGACGTAGTAGATACGGAGTGAACAACCCAGAAC---ACCTTGACAGTAGCAGCA 463Kanto51_Pik CAGATCGACGTAGTAGATACGGAGTGAACAACCCAGAAC---ACCTTGACAGTAGCAGCA 463K60_Pikp CAGATCGACGTAGTAGATACGGAGTGAACAACCCAGAAC---ACCTTGACAGTAGCAGCA 463Acc108 CAGATCGACGTAGTAGATACGGAGTGAACAACCCAGAAC---ACCTTGACAGTAGCAGCA 463Acc130 CAGATCGACGTAGTAGATACGGAGTGAACAACCCAGAAC---ACCTTGACAGTAGCAGCA 463Acc719 CAGATCGACGTAGTAGATACGGAGTGAACAACCCAGAAC---ACCTTGACAGTAGCAGCA 463Acc729 CAGATCGACGTAGTAGATACGGAGTGAACAACCCAGAAC---ACCTTGACAGTAGCAGCA 463Acc710 CAGATCGACGTAGTAGATACGGAGTGAACAACCCAGAAC---ACCTTGACAGTAGCAGCA 463Acc709 CAGATCGACGTAGTAGATACGGAGTGAACAACCCAGAAC---ACCTTGACAGTAGCAGCA 463Acc220 CGGATCGGCGCAACAGATATGGAGTGAACAACCCAGAAC---ACTGTGACAGCAGCAACA 463Nipponbare CGGATCGGCGCAACAGATATGGAGTGAACAACCCAGAAC---ACTGTGACAGCAGCAACA 463Acc224 CGGATCGGCGCAACAGATATGGAGTGAACAACCCAGAAC---ACTGTGACAGCAGCAACA 463AccUP3 CGGATCGGCGCAACAGATATGGAGTGAACAACCCAGAAC---ACTGTGACAGCAGCAACA 463AccUP1 CGGATCGGCGCAACAGATATGGAGTGAACAACCCAGAAC---ACTGTGACAGCAGCAACA 463Acc206 CGGATCGGCGCAACAGATATGGAGTGAACAACCCAGAAC---ACTGTGACAGCAGCAACA 463Acc201 CGGATCGGCGCAACAGATATGGAGTGAACAACCCAGAAC---ACTGTGACAGCAGCAACA 463Acc724 CGGATCGGCGCAACAGATATGGAGTGAACAACCCAGAAC---ACTGTGACAGCAGCAACA 463Acc415 CGGATCGGCGCAACAGATATGGAGTGAACAACCCAGAAC---ACTGTGACAGCAGCAACA 463Acc417 CGGATCGGCGCAACAGATATGGAGTGAACAACCCAGAAC---ACTGTGACAGCAGCAACA 463Acc435 CGGATCGGCGCAACAGATATGGAGTGAACAACCCAGAAC---ACTGTGACAGCAGCAACA 463Acc712 CGGATCGGCGCAACAGATATGGAGTGAACAACCCAGAAC---ACTGTGACAGCAGCAACA 463Acc101 CGGATCGGCGCAACAGATATGGAGTGAACAACCCAGAACTGCACTGTGACAGCAGCAACA 466Acc715 CGGATCGGCGCAACAGATATGGAGTGAACAACCCAGAACTGCACTGTGACAGCAGCAACA 466Acc706 CGGATCGGCGCAACAGATATGGAGTGAACAACCCAGAACTGCACTGTGACAGCAGCAACA 466Acc624 CGGATCGGCGCAACAGATATGGAGTGAACAACCCAGAACTGCACTGTGACAGCAGCAACA 466Acc1 CGGATCGGCGCAACAGATATGGAGTGAACAACCCAGAACTGCACTGTGACAGCAGCAACA 466Acc440 CGGATCGGCGCAACAGATATGGAGTGAACAACCCAGAACTGCACTGTGACAGCAGCAACA 466Acc868 CGGATCGGCGCAACAGATATGGAGTGAACAACCCAGAACTGCACTGTGACAGCAGCAACA 480Acc718 CGGATCGGCGCAACAGATATGGAGTGAACAACCCAGAACTGCACTGTGACAGCAGCAACA 466 * ***** ** * ***** ******************* ** ****** **** **

Ashikawa et al. Supplementary Fig. S2 (4/28)

Acc414 GT------GCCAGGACCCGTGCTGTCAATTACGAAATTGCTGAGTATCAGGTCACAAGCC 517Acc420 GT------GCCAGGACCCGTGCTGTCAATTACGAAATTGCTGAGTATCAGGTCACAAGCC 517Acc761 GT------GCCAGGACCCGTGCTGTCAATTACGAAATTGCTGAGTATCAGGTCACAAGCC 517Acc504 GT------GCCAGGACCCGTGCTGTCAATTACGAAATTGCTGAGTATCAGGTCACAAGCC 517Acc563 GT------GCCAGGACCCGTGCTGTCAATTACGAAATTGCTGAGTATCAGGTCACAAGCC 517Acc757 GT------GCCAGGACCCGTGCTGTCAATTACGAAATTGCTGAGTATCAGGTCACAAGCC 517Acc848 GT------GCCAGGACCCGTGCTGTCAATTACGAAATTGCTGAGTATCAGGTCACAAGCC 517Tsuyuake_Pikm GT------GCCAGGACCCGTGCTGTCAATTACGAAATTGCTGAGTATCAGGTCACAAGCC 517Kusabue_Pik GT------GCCAGGACCCGTGCTGTCAATTACGAAATTGCTGAGTATCAGGTCACAAGCC 517Kanto51_Pik GT------GCCAGGACCCGTGCTGTCAATTACGAAATTGCTGAGTATCAGGTCACAAGCC 517K60_Pikp GT------GCCAGGACCCGTGCTGTCAATTACGAAATTGCTGAGTATCAGGTCACAAGCC 517Acc108 GT------GCCAGGACCCGTGCTGTCAATTACGAAATTGCTGAGTATCAGGTCACAAGCC 517Acc130 GT------GCCAGGACCCGTGCTGTCAATTACGAAATTGCTGAGTATCAGGTCACAAGCC 517Acc719 GT------GCCAGGACCCGTGCTGTCAATTACGAAATTGCTGAGTATCAGGTCACAAGCC 517Acc729 GT------GCCAGGACCCGTGCTGTCAATTACGAAATTGCTGAGTATCAGGTCACAAGCC 517Acc710 GT------GCCAGGACCCGTGCTGTCAATTACGAAATTGCTGAGTATCAGGTCACAAGCC 517Acc709 GT------GCCAGGACCCGTGCTGTCAATTACGAAATTGCTGAGTATCAGGTCACAAGCC 517Acc220 GTCCCAGACCCAGAGCCCATGCTGCGGCTCAAGACATTGCTGAGTATCAGGACACAAAAC 523Nipponbare GTCCCAGACCCAGAGCCCATGCTGCGGCTCAAGACATTGCTGAGTATCAGGACACAAAAC 523Acc224 GTCCCAGACCCAGAGCCCATGCTGCGGCTCAAGACATTGCTGAGTATCAGGACACAAAAC 523AccUP3 GTCCCAGACCCAGAGCCCATGCTGCGGCTCAAGACATTGCTGAGTATCAGGACACAAAAC 523AccUP1 GTCCCAGACCCAGAGCCCATGCTGCGGCTCAAGACATTGCTGAGTATCAGGACACAAAAC 523Acc206 GTCCCAGACCCAGAGCCCATGCTGCGGCTCAAGACATTGCTGAGTATCAGGACACAAAAC 523Acc201 GTCCCAGACCCAGAGCCCATGCTGCGGCTCAAGACATTGCTGAGTATCAGGACACAAAAC 523Acc724 GTCCCAGACCCAGAGCCCATGCTGCGGCTCAAGACATTGCTGAGTATCAGGACACAAAAC 523Acc415 GTCCCAGACCCAGAGCCCATGCTGCGGCTCAAGACATTGCTGAGTATCAGGACACAAAAC 523Acc417 GTCCCAGACCCAGAGCCCATGCTGCGGCTCAAGACATTGCTGAGTATCAGGACACAAAAC 523Acc435 GTCCCAGACCCAGAGCCCATGCTGCGGCTCAAGACATTGCTGAGTATCAGGACACAAAAC 523Acc712 GTCCCAGACCCAGAGCCCATGCTGCGGCTCAAGACATTGCTGAGTATCAGGACACAAAAC 523Acc101 G------GCCCAGAGCCCGTTCTGCGGCTCAAGACATTGCTGAGTATCAGGTCACAAAAC 520Acc715 G------GCCCAGAGCCCGTTCTGCGGCTCAAGACATTGCTGAGTATCAGGTCACAAAAC 520Acc706 G------GCCCAGAGCCCGTTCTGCGGCTCAAGACATTGCTGAGTATCAGGTCACAAAAC 520Acc624 G------GCCCAGAGCCCGTTCTGCGGCTCAAGACATTGCTGAGTATCAGGTCACAAAAC 520Acc1 G------GCCCAGAGCCCGTTCTGCGGCTCAAGACATTGCTGAGTATCAGGTCACAAAAC 520Acc440 G------GCCCAGAGCCCGTTCTGCGGCTCAAGACATTGCTGAGTATCAGGTCACAAAAC 520Acc868 G------GCCCAGAGCCCGTTCTGCGGCTCAAGACATTGCTGAGTATCAGGTCACAAAAC 534Acc718 G------GCCCAGAGCCCGTTCTGCGGCTCAAGACATTGCTGAGTATCAGGTCACAAAAC 520 * **** *** * *** * * ** **************** ***** * Acc414 CTCAGATCATTGGTATAAAGGAGCCTGTGGGGATGAAGACGGTCATGGAGGAGCTTGAGG 577Acc420 CTCAGATCATTGGTATAAAGGAGCCTGTGGGGATGAAGACGGTCATGGAGGAGCTTGAGG 577Acc761 CTCAGATCATTGGTATAAAGGAGCCTGTGGGGATGAAGACGGTCATGGAGGAGCTTGAGG 577Acc504 CTCAGATCATTGGTATAAAGGAGCCTGTGGGGATGAAGACGGTCATGGAGGAGCTTGAGG 577Acc563 CTCAGATCATTGGTATAAAGGAGCCTGTGGGGATGAAGACGGTCATGGAGGAGCTTGAGG 577Acc757 CTCAGATCATTGGTATAAAGGAGCCTGTGGGGATGAAGACGGTCATGGAGGAGCTTGAGG 577Acc848 CTCAGATCATTGGTATAAAGGAGCCTGTGGGGATGAAGACGGTCATGGAGGAGCTTGAGG 577Tsuyuake_Pikm CTCAGATCATTGGTATAAAGGAGCCTGTGGGGATGAAGACGGTCATGGAGGAGCTTGAGG 577Kusabue_Pik CTCAGATCATTGGTATAAAGGAGCCTGTGGGGATGAAGACGGTCATGGAGGAGCTTGAGG 577Kanto51_Pik CTCAGATCATTGGTATAAAGGAGCCTGTGGGGATGAAGACGGTCATGGAGGAGCTTGAGG 577K60_Pikp CTCAGATCATTGGTATAAAGGAGCCTGTGGGGATGAAGACGGTCATGGAGGAGCTTGAGG 577Acc108 CTCAGATCATTGGTATAAAGGAGCCTGTGGGGATGAAGACGGTCATGGAGGAGCTTGAGG 577Acc130 CTCAGATCATTGGTATAAAGGAGCCTGTGGGGATGAAGACGGTCATGGAGGAGCTTGAGG 577Acc719 CTCAGATCATTGGTATAAAGGAGCCTGTGGGGATGAAGACGGTCATGGAGGAGCTTGAGG 577Acc729 CTCAGATCATTGGTATAAAGGAGCCTGTGGGGATGAAGACGGTCATGGAGGAGCTTGAGG 577Acc710 CTCAGATCATTGGTATAAAGGAGCCTGTGGGGATGAAGACGGTCATGGAGGAGCTTGAGG 577Acc709 CTCAGATCATTGGTATAAAGGAGCCTGTGGGGATGAAGACGGTCATGGAGGAGCTTGAGG 577Acc220 CTCAGATCGTCAGTATAAAGGAGCCTGTGGGGATGAAGACTGTCATGGAAAACCTTGAGA 583Nipponbare CTCAGATCGTCAGTATAAAGGAGCCTGTGGGGATGAAGACTGTCATGGAAAACCTTGAGA 583Acc224 CTCAGATCGTCAGTATAAAGGAGCCTGTGGGGATGAAGACTGTCATGGAAAACCTTGAGA 583AccUP3 CTCAGATCGTCAGTATAAAGGAGCCTGTGGGGATGAAGACTGTCATGGAAAACCTTGAGA 583AccUP1 CTCAGATCGTCAGTATAAAGGAGCCTGTGGGGATGAAGACTGTCATGGAAAACCTTGAGA 583Acc206 CTCAGATCGTCAGTATAAAGGAGCCTGTGGGGATGAAGACTGTCATGGAAAACCTTGAGA 583Acc201 CTCAGATCGTCAGTATAAAGGAGCCTGTGGGGATGAAGACTGTCATGGAAAACCTTGAGA 583Acc724 CTCAGATCGTCAGTATAAAGGAGCCTGTGGGGATGAAGACTGTCATGGAAAACCTTGAGA 583Acc415 CTCAGATCGTCAGTATAAAGGAGCCTGTGGGGATGAAGACTGTCATGGAAAACCTTGAGA 583Acc417 CTCAGATCGTCAGTATAAAGGAGCCTGTGGGGATGAAGACTGTCATGGAAAACCTTGAGA 583Acc435 CTCAGATCGTCAGTATAAAGGAGCCTGTGGGGATGAAGACTGTCATGGAAAACCTTGAGA 583Acc712 CTCAGATCGTCAGTATAAAGGAGCCTGTGGGGATGAAGACTGTCATGGAAAACCTTGAGA 583Acc101 TTCAGATCATCGGTATAAAGGAGCCTGTGGGGATGAAGACTGTCATGGAAGACCTTGAGA 580Acc715 TTCAGATCATCGGTATAAAGGAGCCTGTGGGGATGAAGACTGTCATGGAAGACCTTGAGA 580Acc706 TTCAGATCATCGGTATAAAGGAGCCTGTGGGGATGAAGACTGTCATGGAAGACCTTGAGA 580Acc624 TTCAGATCATCGGTATAAAGGAGCCTGTGGGGATGAAGACTGTCATGGAAGACCTTGAGA 580Acc1 TTCAGATCATCGGTATAAAGGAGCCTGTGGGGATGAAGACTGTCATGGAAGACCTTGAGA 580Acc440 TTCAGATCATCGGTATAAAGGAGCCTGTGGGGATGAAGACTGTCATGGAAGACCTTGAGA 580Acc868 TTCAGATCATCGGTATAAAGGAGCCTGTGGGGATGAAGACTGTCATGGAAGACCTTGAGA 594Acc718 TTCAGATCATCGGTATAAAGGAGCCTGTGGGGATGAAGACTGTCATGGAAGACCTTGAGA 580 ******* * **************************** ******** * ******

Ashikawa et al. Supplementary Fig. S2 (5/28)

Acc414 TTTGGTTAACTAATCCTCAAGCTGAAAATGGGCAAGCTGTTCTGTCCATAGTCGGTTTTG 637Acc420 TTTGGTTAACTAATCCTCAAGCTGAAAATGGGCAAGCTGTTCTGTCCATAGTCGGTTTTG 637Acc761 TTTGGTTAACTAATCCTCAAGCTGAAAATGGGCAAGCTGTTCTGTCCATAGTCGGTTTTG 637Acc504 TTTGGTTAACTAATCCTCAAGCTGAAAATGGGCAAGCTGTTCTGTCCATAGTCGGTTTTG 637Acc563 TTTGGTTAACTAATCCTCAAGCTGAAAATGGGCAAGCTGTTCTGTCCATAGTCGGTTTTG 637Acc757 TTTGGTTAACTAATCCTCAAGCTGAAAATGGGCAAGCTGTTCTGTCCATAGTCGGTTTTG 637Acc848 TTTGGTTAACTAATCCTCAAGCTGAAAATGGGCAAGCTGTTCTGTCCATAGTCGGTTTTG 637Tsuyuake_Pikm TTTGGTTAACTAATCCTCAAGCTGAAAATGGGCAAGCTGTTCTGTCCATAGTCGGTTTTG 637Kusabue_Pik TTTGGTTAACTAATCCTCAAGCTGAAAATGGGCAAGCTGTTCTGTCCATAGTCGGTTTTG 637Kanto51_Pik TTTGGTTAACTAATCCTCAAGCTGAAAATGGGCAAGCTGTTCTGTCCATAGTCGGTTTTG 637K60_Pikp TTTGGTTAACTAATCCTCAAGCTGAAAATGGGCAAGCTGTTCTGTCCATAGTCGGTTTTG 637Acc108 TTTGGTTAACTAATCCTCAAGCTGAAAATGGGCAAGCTGTTCTGTCCATAGTCGGTTTTG 637Acc130 TTTGGTTAACTAATCCTCAAGCTGAAAATGGGCAAGCTGTTCTGTCCATAGTCGGTTTTG 637Acc719 TTTGGTTAACTAATCCTCAAGCTGAAAATGGGCAAGCTGTTCTGTCCATAGTCGGTTTTG 637Acc729 TTTGGTTAACTAATCCTCAAGCTGAAAATGGGCAAGCTGTTCTGTCCATAGTCGGTTTTG 637Acc710 TTTGGTTAACTAATCCTCAAGCTGAAAATGGGCAAGCTGTTCTGTCCATAGTCGGTTTTG 637Acc709 TTTGGTTAACTAATCCTCAAGCTGAAAATGGGCAAGCTGTTCTGTCCATAGTCGGTTTTG 637Acc220 AGTGGCTAACCGAACCTCAACCTGATAAGGGGCGAGCTGTTCTGTCCATTGTCGGTTTCG 643Nipponbare AGTGGCTAACCGAACCTCAACCTGATAAGGGGCGAGCTGTTCTGTCCATTGTCGGTTTCG 643Acc224 AGTGGCTAACCGAACCTCAACCTGATAAGGGGCGAGCTGTTCTGTCCATTGTCGGTTTCG 643AccUP3 AGTGGCTAACCGAACCTCAACCTGATAAGGGGCGAGCTGTTCTGTCCATTGTCGGTTTCG 643AccUP1 AGTGGCTAACCGAACCTCAACCTGATAAGGGGCGAGCTGTTCTGTCCATTGTCGGTTTCG 643Acc206 AGTGGCTAACCGAACCTCAACCTGATAAGGGGCGAGCTGTTCTGTCCATTGTCGGTTTCG 643Acc201 AGTGGCTAACCGAACCTCAACCTGATAAGGGGCGAGCTGTTCTGTCCATTGTCGGTTTCG 643Acc724 AGTGGCTAACCGAACCTCAACCTGATAAGGGGCGAGCTGTTCTGTCCATTGTCGGTTTCG 643Acc415 AGTGGCTAACCGAACCTCAACCTGATAAGGGGCGAGCTGTTCTGTCCATTGTCGGTTTCG 643Acc417 AGTGGCTAACCGAACCTCAACCTGATAAGGGGCGAGCTGTTCTGTCCATTGTCGGTTTCG 643Acc435 AGTGGCTAACCGAACCTCAACCTGATAAGGGGCGAGCTGTTCTGTCCATTGTCGGTTTCG 643Acc712 AGTGGCTAACCGAACCTCAACCTGATAAGGGGCGAGCTGTTCTGTCCATTGTCGGTTTCG 643Acc101 AGTGGTTAACCGAACCTCAACCTGATAACGGGCGAGCTGTTCTGTCCATTGTCGGTTTCG 640Acc715 AGTGGTTAACCGAACCTCAACCTGATAACGGGCGAGCTGTTCTGTCCATTGTCGGTTTCG 640Acc706 AGTGGTTAACCGAACCTCAACCTGATAACGGGCGAGCTGTTCTGTCCATTGTCGGTTTCG 640Acc624 AGTGGTTAACCGAACCTCAACCTGATAACGGGCGAGCTGTTCTGTCCATTGTCGGTTTCG 640Acc1 AGTGGTTAACCGAACCTCAACCTGATAACGGGCGAGCTGTTCTGTCCATTGTCGGTTTCG 640Acc440 AGTGGTTAACCGAACCTCAACCTGATAACGGGCGAGCTGTTCTGTCCATTGTCGGTTTCG 640Acc868 AGTGGTTAACCGAACCTCAACCTGATAACGGGCGAGCTGTTCTGTCCATTGTCGGTTTCG 654Acc718 AGTGGTTAACCGAACCTCAACCTGATAACGGGCGAGCTGTTCTGTCCATTGTCGGTTTCG 640 *** **** * ****** **** ** **** *************** ******** * Acc414 GAGGTGTGGGAAAGACTACCATTGCCACAGCATTGTACAGAAAAGTCAGTGATAAATTTC 697Acc420 GAGGTGTGGGAAAGACTACCATTGCCACAGCATTGTACAGAAAAGTCAGTGATAAATTTC 697Acc761 GAGGTGTGGGAAAGACTACCATTGCCACAGCATTGTACAGAAAAGTCAGTGATAAATTTC 697Acc504 GAGGTGTGGGAAAGACTACCATTGCCACAGCATTGTACAGAAAAGTCAGTGAAAAATTTC 697Acc563 GAGGTGTGGGAAAGACTACCATTGCCACAGCATTGTACAGAAAAGTCAGTGAAAAATTTC 697Acc757 GAGGTGTGGGAAAGACTACCATTGCCACAGCATTGTACAGAAAAGTCAGTGAAAAATTTC 697Acc848 GAGGTGTGGGAAAGACTACCATTGCCACAGCATTGTACAGAAAAGTCAGTGAAAAATTTC 697Tsuyuake_Pikm GAGGTGTGGGAAAGACTACCATTGCCACAGCATTGTACAGAAAAGTCAGTGAAAAATTTC 697Kusabue_Pik GAGGTGTGGGAAAGACTACCATTGCCACAGCATTGTACAGAAAAGTCAGTGAAAAATTTC 697Kanto51_Pik GAGGTGTGGGAAAGACTACCATTGCCACAGCATTGTACAGAAAAGTCAGTGAAAAATTTC 697K60_Pikp GAGGTGTGGGAAAGACTACCATTGCCACAGCATTGTACAGAAAAGTCAGTGATAAATTTC 697Acc108 GAGGTGTGGGAAAGACTACCATTGCCACAGCATTGTACAGAAAAGTCAGTGATAAATTTC 697Acc130 GAGGTGTGGGAAAGACTACCATTGCCACAGCATTGTACAGAAAAGTCAGTGATAAATTTC 697Acc719 GAGGTGTGGGAAAGACTACCATTGCCACAGCATTGTACAGAAAAGTCAGTGATAAATTTC 697Acc729 GAGGTGTGGGAAAGACTACCATTGCCACAGCATTGTACAGAAAAGTCAGTGATAAATTTC 697Acc710 GAGGTGTGGGAAAGACTACCATTGCCACAGCATTGTACAGAAAAGTCAGTGATAAATTTC 697Acc709 GAGGTGTGGGAAAGACTACCATTGCCACAGCATTGTACAGAAAAGTCAGTGATAAATTTC 697Acc220 GTGGTGTGGGGAAGACCACCATTGCCATGGCATTGTACAGAAAAGTCAGTGGTAAATTTG 703Nipponbare GTGGTGTGGGGAAGACCACCATTGCCATGGCATTGTACAGAAAAGTCAGTGGTAAATTTG 703Acc224 GTGGTGTGGGGAAGACCACCATTGCCATGGCATTGTACAGAAAAGTCAGTGGTAAATTTG 703AccUP3 GTGGTGTGGGGAAGACCACCATTGCCATGGCATTGTACAGAAAAGTCAGTGGTAAATTTG 703AccUP1 GTGGTGTGGGGAAGACCACCATTGCCATGGCATTGTACAGAAAAGTCAGTGGTAAATTTG 703Acc206 GTGGTGTGGGGAAGACCACCATTGCCATGGCATTGTACAGAAAAGTCAGTGGTAAATTTG 703Acc201 GTGGTGTGGGGAAGACCACCATTGCCATGGCATTGTACAGAAAAGTCAGTGGTAAATTTG 703Acc724 GTGGTGTGGGGAAGACCACCATTGCCATGGCATTGTACAGAAAAGTCAGTGGTAAATTTG 703Acc415 GTGGTGTGGGGAAGACCACCATTGCCATGGCATTGTACAGAAAAGTCAGTGGTAAATTTG 703Acc417 GTGGTGTGGGGAAGACCACCATTGCCATGGCATTGTACAGAAAAGTCAGTGGTAAATTTG 703Acc435 GTGGTGTGGGGAAGACCACCATTGCCATGGCATTGTACAGAAAAGTCAGTGGTAAATTTG 703Acc712 GTGGTGTGGGGAAGACCACCATTGCCATGGCATTGTACAGAAAAGTCAGTGGTAAATTTG 703Acc101 GTGGTGTGGGGAAGACCACCATTGCCATGGCTTTGTACAGAAAAGTCAGTGGTAAATTTG 700Acc715 GTGGTGTGGGGAAGACCACCATTGCCATGGCTTTGTACAGAAAAGTCAGTGGTAAATTTG 700Acc706 GTGGTGTGGGGAAGACCACCATTGCCATGGCTTTGTACAGAAAAGTCAGTGGTAAATTTG 700Acc624 GTGGTGTGGGGAAGACCACCATTGCCATGGCTTTGTACAGAAAAGTCAGTGGTAAATTTG 700Acc1 GTGGTGTGGGGAAGACCACCATTGCCATGGCTTTGTACAGAAAAGTCAGTGGTAAATTTG 700Acc440 GTGGTGTGGGGAAGACCACCATTGCCATGGCTTTGTACAGAAAAGTCAGTGGTAAATTTG 700Acc868 GTGGTGTGGGGAAGACCACCATTGCCATGGCTTTGTACAGAAAAGTCAGTGGTAAATTTG 714Acc718 GTGGTGTGGGGAAGACCACCATTGCCATGGCTTTGTACAGAAAAGTCAGTGGTAAATTTG 700 * ******** ***** ********** ** ******************* ******

Ashikawa et al. Supplementary Fig. S2 (6/28)

Acc414 AGTGCCGGGCATCAGTAGCTGTGTCTCAGAACTATGACCAAGGCAAAGTCCTCAATAGTA 757Acc420 AGTGCCGGGCATCAGTAGCTGTGTCTCAGAACTATGACCAAGGCAAAGTCCTCAATAGTA 757Acc761 AGTGCCGGGCATCAGTAGCTGTGTCTCAGAACTATGACCAAGGCAAAGTCCTCAATAGTA 757Acc504 AGTGCCGGGCATCAGTAGCTGTGTCTCAGAACTATGACCAAGGCAAAGTCCTCAATAGTA 757Acc563 AGTGCCGGGCATCAGTAGCTGTGTCTCAGAACTATGACCAAGGCAAAGTCCTCAATAGTA 757Acc757 AGTGCCGGGCATCAGTAGCTGTGTCTCAGAACTATGACCAAGGCAAAGTCCTCAATAGTA 757Acc848 AGTGCCGGGCATCAGTAGCTGTGTCTCAGAACTATGACCAAGGCAAAGTCCTCAATAGTA 757Tsuyuake_Pikm AGTGCCGGGCATCAGTAGCTGTGTCTCAGAACTATGACCAAGGCAAAGTCCTCAATAGTA 757Kusabue_Pik AGTGCCGGGCATCAGTAGCTGTGTCTCAGAACTATGACCAAGGCAAAGTCCTCAATAGTA 757Kanto51_Pik AGTGCCGGGCATCAGTAGCTGTGTCTCAGAACTATGACCAAGGCAAAGTCCTCAATAGTA 757K60_Pikp AGTGCCGGGCATCAGTAGCTGTGTCTCAGAACTATGACCAAGGCAAAGTCCTCAATAGTA 757Acc108 AGTGCCGGGCATCAGTAGCTGTGTCTCAGAACTATGACCAAGGCAAAGTCCTCAATAGTA 757Acc130 AGTGCCGGGCATCAGTAGCTGTGTCTCAGAACTATGACCAAGGCAAAGTCCTCAATAGTA 757Acc719 AGTGCCGGGCATCAGTAGCTGTGTCTCAGAACTATGACCAAGGCAAAGTCCTCAATAGTA 757Acc729 AGTGCCGGGCATCAGTAGCTGTGTCTCAGAACTATGACCAAGGCAAAGTCCTCAATAGTA 757Acc710 AGTGCCGGGCATCAGTAGCTGTGTCTCAGAACTATGACCAAGGCAAAGTCCTCAATAGTA 757Acc709 AGTGCCGGGCATCAGTAGCTGTGTCTCAGAACTATGACCAAGGCAAAGTCCTCAATAGTA 757Acc220 ACTGCCAGGCGTCAGTCGCTGTGTCTCAGAACTATGATGAAGACGAAGTCCTCAGGAGTA 763Nipponbare ACTGCCAGGCGTCAGTCGCTGTGTCTCAGAACTATGATGAAGACGAAGTCCTCAGGAGTA 763Acc224 ACTGCCAGGCGTCAGTCGCTGTGTCTCAGAACTATGATGAAGACGAAGTCCTCAGGAGTA 763AccUP3 ACTGCCAGGCGTCAGTCGCTGTGTCTCAGAACTATGATGAAGACGAAGTCCTCAGGAGTA 763AccUP1 ACTGCCAGGCGTCAGTCGCTGTGTCTCAGAACTATGATGAAGACGAAGTCCTCAGGAGTA 763Acc206 ACTGCCAGGCGTCAGTCGCTGTGTCTCAGAACTATGATGAAGACGAAGTCCTCAGGAGTA 763Acc201 ACTGCCAGGCGTCAGTCGCTGTGTCTCAGAACTATGATGAAGACGAAGTCCTCAGGAGTA 763Acc724 ACTGCCAGGCGTCAGTCGCTGTGTCTCAGAACTATGATGAAGACGAAGTCCTCAGGAGTA 763Acc415 ACTGCCAGGCGTCAGTCGGCGTGTCTCAGAACTATGATGAAGACGAAGTCCTCAGGAGTA 763Acc417 ACTGCCAGGCGTCAGTCGCTGTGTCTCAGAACTATGATGAAGACGAAGTCCTCAGGAGTA 763Acc435 ACTGCCAGGCGTCAGTCGCTGTGTCTCAGAACTATGATGAAGACGAAGTCCTCAGGAGTA 763Acc712 ACTGCCAGGCGTCAGTCGCTGTGTCTCAGAACTATGATGAAGACGAAGTCCTCAGGAGTA 763Acc101 GCTGCCGGGCGTCAGTAGCTGTGTCTCAGAACTATGACCAAGATGCAGTCCTCAGGAGTA 760Acc715 GCTGCCGGGCGTCAGTAGCTGTGTCTCAGAACTATGACCAAGATGCAGTCCTCAGGAGTA 760Acc706 GCTGCCGGGCGTCAGTAGCTGTGTCTCAGAACTATGACCAAGATGCAGTCCTCAGGAGTA 760Acc624 GCTGCCGGGCGTCAGTAGCTGTGTCTCAGAACTATGACCAAGATGCAGTCCTCAGGAGTA 760Acc1 GCTGCCGGGCGTCAGTAGCTGTGTCTCAGAACTATGACCAAGATGCAGTCCTCAGGAGTA 760Acc440 GCTGCCGGGCGTCAGTAGCTGTGTCTCAGAACTATGACCAAGATGCAGTCCTCAGGAGTA 760Acc868 GCTGCCGGGCGTCAGTAGCTGTGTCTCAGAACTATGACCAAGATGCAGTCCTCAGGAGTA 774Acc718 GCTGCCGGGCGTCAGTAGCTGTGTCTCAGAACTATGACCAAGATGCAGTCCTCAGGAGTA 760 **** *** ***** * ***************** *** ******** **** Acc414 TTCTGAGTCAAGTCAGCAATCAGGAGCAGG---GCAGCAGCACAACAATTAGT----GAG 810Acc420 TTCTGAGTCAAGTCAGCAATCAGGAGCAGG---GCAGCAGCACAACAATTAGT----GAG 810Acc761 TTCTGAGTCAAGTCAGCAATCAGGAGCAGG---GCAGCAGCACAACAATTAGT----GAG 810Acc504 TTCTGAGTCAAGTCAGCAATCAGGAGCAGG---GCAGCAGCACAACAATTAGT----GAG 810Acc563 TTCTGAGTCAAGTCAGCAATCAGGAGCAGG---GCAGCAGCACAACAATTAGT----GAG 810Acc757 TTCTGAGTCAAGTCAGCAATCAGGAGCAGG---GCAGCAGCACAACAATTAGT----GAG 810Acc848 TTCTGAGTCAAGTCAGCAATCAGGAGCAGG---GCAGCAGCACAACAATTAGT----GAG 810Tsuyuake_Pikm TTCTGAGTCAAGTCAGCAATCAGGAGCAGG---GCAGCAGCACAACAATTAGT----GAG 810Kusabue_Pik TTCTGAGTCAAGTCAGCAATCAGGAGCAGG---GCAGCAGCACAACAATTAGT----GAG 810Kanto51_Pik TTCTGAGTCAAGTCAGCAATCAGGAGCAGG---GCAGCAGCACAACAATTAGT----GAG 810K60_Pikp TTCTGAGTCAAGTCAGCAATCAGGAGCAGG---GCAGCAGCACAACAATTAGT----GAG 810Acc108 TTCTGAGTCAAGTCAGCAATCAGGAGCAGG---GCAGCAGCACAACAATTAGT----GAG 810Acc130 TTCTGAGTCAAGTCAGCAATCAGGAGCAGG---GCAGCAGCACAACAATTAGT----GAG 810Acc719 TTCTGAGTCAAGTCAGCAATCAGGAGCAGG---GCAGCAGCACAACAATTAGT----GAG 810Acc729 TTCTGAGTCAAGTCAGCAATCAGGAGCAGG---GCAGCAGCACAACAATTAGT----GAG 810Acc710 TTCTGAGTCAAGTCAGCAATCAGGAGCAGG---GCAGCAGCACAACAATTAGT----GAG 810Acc709 TTCTGAGTCAAGTCAGCAATCAGGAGCAGG---GCAGCAGCACAACAATTAGT----GAG 810Acc220 TTCTGAATCAAGTCAGCAAACAGGAGGAGGCCGGTGGCAGCACAGAAAGTAGTAGTAGAG 823Nipponbare TTCTGAATCAAGTCAGCAAACAGGAGGAGGCCGGTGGCAGCACAGAAAGTAGTAGTAGAG 823Acc224 TTCTGAATCAAGTCAGCAAACAGGAGGAGGCCGGTGGCAGCACAGAAAGTAGTAGTAGAG 823AccUP3 TTCTGAATCAAGTCAGCAAACAGGAGGAGGCCGGTGGCAGCACAGAAAGTAGTAGTAGAG 823AccUP1 TTCTGAATCAAGTCAGCAAACAGGAGGAGGCCGGTGGCAGCACAGAAAGTAGTAGTAGAG 823Acc206 TTCTGAATCAAGTCAGCAAACAGGAGGAGGCCGGTGGCAGCACAGAAAGTAGTAGTAGAG 823Acc201 TTCTGAATCAAGTCAGCAAACAGGAGGAGGCCGGTGGCAGCACAGAAAGTAGTAGTAGAG 823Acc724 TTCTGAATCAAGTCAGCAAACAGGAGGAGGCCGGTGGCAGCACAGAAAGTAGTAGTAGAG 823Acc415 TTCTGAATCAAGTCAGCAAACAGGAGGAGGCCGGTGGCAGCACAGAAAGTAGTAGTAGAG 823Acc417 TTCTGAATCAAGTCAGCAAACAGGAGGAGGCCGGTGGCAGCACAGAAAGTAGTAGTAGAG 823Acc435 TTCTGAATCAAGTCAGCAAACAGGAGGAGGCCGGTGGCAGCACAGAAAGTAGTAGTAGAG 823Acc712 TTCTGAATCAAGTCAGCAAACAGGAGGAGGCCGGTGGCAGCACAGAAAGTAGTAGTAGAG 823Acc101 TTCTGAATCAAGTCAGCAACCAGGAGGAGGCCGGTAGCAGCACAGAAAGTAGT---AGAG 817Acc715 TTCTGAATCAAGTCAGCAACCAGGAGGAGGCCGGTAGCAGCACAGAAAGTAGT---AGAG 817Acc706 TTCTGAATCAAGTCAGCAACCAGGAGGAGGCCGGTAGCAGCACAGAAAGTAGT---AGAG 817Acc624 TTCTGAATCAAGTCAGCAACCAGGAGGAGGCCGGTAGCAGCACAGAAAGTAGT---AGAG 817Acc1 TTCTGAATCAAGTCAGCAACCAGGAGGAGGCCGGTAGCAGCACAGAAAGTAGT---AGAG 817Acc440 TTCTGAATCAAGTCAGCAACCAGGAGGAGGCCGGTAGCAGCACAGAAAGTAGT---AGAG 817Acc868 TTCTGAATCAAGTCAGCAACCAGGAGGAGGCCGGTAGCAGCACAGAAAGTAGT---AGAG 831Acc718 TTCTGAATCAAGTCAGCAACCAGGAGGAGGCCGGTAGCAGCACAGAAAGTAGT---AGAG 817 ****** ************ ****** *** * ******** ** **** ***

Ashikawa et al. Supplementary Fig. S2 (7/28)

Acc414 A-----------------------------------------------AAAAGAACCTCA 823Acc420 A-----------------------------------------------AAAAGAACCTCA 823Acc761 A-----------------------------------------------AAAAGAACCTCA 823Acc504 A-----------------------------------------------AAAAGAACCTCA 823Acc563 A-----------------------------------------------AAAAGAACCTCA 823Acc757 A-----------------------------------------------AAAAGAACCTCA 823Acc848 A-----------------------------------------------AAAAGAACCTCA 823Tsuyuake_Pikm A-----------------------------------------------AAAAGAACCTCA 823Kusabue_Pik A-----------------------------------------------AAAAGAACCTCA 823Kanto51_Pik A-----------------------------------------------AAAAGAACCTCA 823K60_Pikp A-----------------------------------------------AAAAGAACCTCA 823Acc108 A-----------------------------------------------AAAAGAACCTCA 823Acc130 A-----------------------------------------------AAAAGAACCTCA 823Acc719 A-----------------------------------------------AAAAGAACCTCA 823Acc729 A-----------------------------------------------AAAAGAACCTCA 823Acc710 A-----------------------------------------------AAAAGAACCTCA 823Acc709 A-----------------------------------------------AAAAGAACCTCA 823Acc220 ATGAGAACACCAGGGAACCCCAGGGCAGCAGTAGCACATCAAGTAGAGAGGAGAACACTG 883Nipponbare ATGAGAACACCAGGGAACCCCAGGGCAGCAGTAGCACATCAAGTAGAGAGGAGAACACTG 883Acc224 ATGAGAACACCAGGGAACCCCAGGGCAGCAGTAGCACATCAAGTAGAGAGGAGAACACTG 883AccUP3 ATGAGAACACCAGGGAACCCCAGGGCAGCAGTAGCACATCAAGTAGAGAGGAGAACACTG 883AccUP1 ATGAGAACACCAGGGAACCCCAGGGCAGCAGTAGCACATCAAGTAGAGAGGAGAACACTG 883Acc206 ATGAGAACACCAGGGAACCCCAGGGCAGCAGTAGCACATCAAGTAGAGAGGAGAACACTG 883Acc201 ATGAGAACACCAGGGAACCCCAGGGCAGCAGTAGCACATCAAGTAGAGAGGAGAACACTG 883Acc724 ATGAGAACACCAGGGAACCCCAGGGCAGCAGTAGCACATCAAGTAGAGAGGAGAACACTG 883Acc415 ATGAGAACACCAGGGAACCCCAGGGCAGCAGTAGCACATCAAGTAGAGAGGAGAACACTG 883Acc417 ATGAGAACACCAGGGAACCCCAGGGCAGCAGTAGCACATCAAGTAGAGAGGAGAACACTG 883Acc435 ATGAGAACACCAGGGAACCCCAGGGCAGCAGTAGCACATCAAGTAGAGAGGAGAACACTG 883Acc712 ATGAGAACACCAGGGAACCCCAGGGCAGCAGTAGCACATCAAGTAGAGAGGAGAACACTG 883Acc101 AT------------------------------ACCACAGCAAGTAGAGAGGAGAACACTG 847Acc715 AT------------------------------ACCACAGCAAGTAGAGAGGAGAACACTG 847Acc706 AT------------------------------ACCACAGCAAGTAGAGAGGAGAACACTG 847Acc624 AT------------------------------ACCACAGCAAGTAGAGAGGAGAACACTG 847Acc1 AT------------------------------ACCACAGCAAGTAGAGAGGAGAACACTG 847Acc440 AT------------------------------ACCACAGCAAGTAGAGAGGAGAACACTG 847Acc868 AT------------------------------ACCACAGCAAGTAGAGAGGAGAACACTG 861Acc718 AT------------------------------ACCACAGCAAGTAGAGAGGAGAACACTG 847 * * *****  Acc414 CC---TCAGGCGCTAAGAGCATGTT---------GAAGACAGCCCTGTCACTGCTCAGAG 871Acc420 CC---TCAGGCGCTAAGAGCATGTT---------GAAGACAGCCCTGTCACTGCTCAGAG 871Acc761 CC---TCAGGCGCTAAGAGCATGTT---------GAAGACAGCCCTGTCACTGCTCAGAG 871Acc504 CC---TCAGGCGCTAAGAGCATGTT---------GAAGACAGCCCTGTCACTGCTCAGAG 871Acc563 CC---TCAGGCGCTAAGAGCATGTT---------GAAGACAGCCCTGTCACTGCTCAGAG 871Acc757 CC---TCAGGCGCTAAGAGCATGTT---------GAAGACAGCCCTGTCACTGCTCAGAG 871Acc848 CC---TCAGGCGCTAAGAGCATGTT---------GAAGACAGCCCTGTCACTGCTCAGAG 871Tsuyuake_Pikm CC---TCAGGCGCTAAGAGCATGTT---------GAAGACAGCCCTGTCACTGCTCAGAG 871Kusabue_Pik CC---TCAGGCGCTAAGAGCATGTT---------GAAGACAGCCCTGTCACTGCTCAGAG 871Kanto51_Pik CC---TCAGGCGCTAAGAGCATGTT---------GAAGACAGCCCTGTCACTGCTCAGAG 871K60_Pikp CC---TCAGGCGCTAAGAGCATGTT---------GAAGACAGCCCTGTCACTGCTCAGAG 871Acc108 CC---TCAGGCGCTAAGAGCATGTT---------GAAGACAGCCCTGTCACTGCTCAGAG 871Acc130 CC---TCAGGCGCTAAGAGCATGTT---------GAAGACAGCCCTGTCACTGCTCAGAG 871Acc719 CC---TCAGGCGCTAAGAGCATGTT---------GAAGACAGCCCTGTCACTGCTCAGAG 871Acc729 CC---TCAGGCGCTAAGAGCATGTT---------GAAGACAGCCCTGTCACTGCTCAGAG 871Acc710 CC---TCAGGCGCTAAGAGCATGTT---------GAAGACAGCCCTGTCACTGCTCAGAG 871Acc709 CC---TCAGGCGCTAAGAGCATGTT---------GAAGACAGCCCTGTCACTGCTCAGAG 871Acc220 CCGAGTCAGGCACTAAAAGGATGTTGAACAAGTTGAAGAAAGCCCTACCACTGTC----- 938Nipponbare CCGAGTCAGGCACTAAAAGGATGTTGAACAAGTTGAAGAAAGCCCTACCACTGTC----- 938Acc224 CCGAGTCAGGCACTAAAAGGATGTTGAACAAGTTGAAGAAAGCCCTACCACTGTC----- 938AccUP3 CCGAGTCAGGCACTAAAAGGATGTTGAACAAGTTGAAGAAAGCCCTACCACTGTC----- 938AccUP1 CCGAGTCAGGCACTAAAAGGATGTTGAACAAGTTGAAGAAAGCCCTACCACTGTC----- 938Acc206 CCGAGTCAGGCACTAAAAGGATGTTGAACAAGTTGAAGAAAGCCCTACCACTGTC----- 938Acc201 CCGAGTCAGGCACTAAAAGGATGTTGAACAAGTTGAAGAAAGCCCTACCACTGTC----- 938Acc724 CCGAGTCAGGCACTAAAAGGATGTTGAACAAGTTGAAGAAAGCCCTACCACTGTC----- 938Acc415 CCGAGTCAGGCACTAAAAGGATGTTGAACAAGTTGAAGAAAGCCCTACCACTGTC----- 938Acc417 CCGAGTCAGGCACTAAAAGGATGTTGAACAAGTTGAAGAAAGCCCTACCACTGTC----- 938Acc435 CCGAGTCAGGCACTAAAAGGATGTTGAACAAGTTGAAGAAAGCCCTACCACTGTC----- 938Acc712 CCGAGTCAGGCACTAAAAGGATGTTGAACAAGTTGAAGAAAGCCCTACCACTGTC----- 938Acc101 CTGAGCCAGGCACTAAAAGCACGTTTATCAAATTGAAGAAAGCCCCATCACTGTC----- 902Acc715 CTGAGCCAGGCACTAAAAGCACGTTTATCAAATTGAAGAAAGCCCCATCACTGTC----- 902Acc706 CTGAGCCAGGCACTAAAAGCACGTTTATCAAATTGAAGAAAGCCCCATCACTGTC----- 902Acc624 CTGAGCCAGGCACTAAAAGCACGTTTATCAAATTGAAGAAAGCCCCATCACTGTC----- 902Acc1 CTGAGCCAGGCACTAAAAGCACGTTTATCAAATTGAAGAAAGCCCCATCACTGTC----- 902Acc440 CTGAGCCAGGCACTAAAAGCACGTTTATCAAATTGAAGAAAGCCCCATCACTGTC----- 902Acc868 CTGAGCCAGGCACTAAAAGCACGTTTATCAAATTGAAGAAAGCCCCATCACTGTC----- 916Acc718 CTGAGCCAGGCACTAAAAGCACGTTTATCAAATTGAAGAAAGCCCCATCACTGTC----- 902 * ***** **** ** * *** ***** ***** *****

Ashikawa et al. Supplementary Fig. S2 (8/28)

Acc414 GTAATTGTATATGTCAGCCAGAAAATGATGGAAACCCTGATAATACACCAATCAGGCTGC 931Acc420 GTAATTGTATATGTCAGCCAGAAAATGATGGAAACCCTGATAATACACCAATCAGGCTGC 931Acc761 GTAATTGTATATGTCAGCCAGAAAATGATGGAAACCCTGATAATACACCAATCAGGCTGC 931Acc504 GTAATTGTATATGTCAGCCAGAAAATGATGGAAACCCTGATAATACACCAATCAGGCTGC 931Acc563 GTAATTGTATATGTCAGCCAGAAAATGATGGAAACCCTGATAATACACCAATCAGGCTGC 931Acc757 GTAATTGTATATGTCAGCCAGAAAATGATGGAAACCCTGATAATACACCAATCAGGCTGC 931Acc848 GTAATTGTATATGTCAGCCAGAAAATGATGGAAACCCTGATAATACACCAATCAGGCTGC 931Tsuyuake_Pikm GTAATTGTATATGTCAGCCAGAAAATGATGGAAACCCTGATAATACACCAATCAGGCTGC 931Kusabue_Pik GTAATTGTATATGTCAGCCAGAAAATGATGGAAACCCTGATAATACACCAATCAGGCTGC 931Kanto51_Pik GTAATTGTATATGTCAGCCAGAAAATGATGGAAACCCTGATAATACACCAATCAGGCTGC 931K60_Pikp GTAATTGTATATGTCAGCCAGAAAATGATGGAAACCCTGATAATACACCAATCAGGCTGC 931Acc108 GTAATTGTATATGTCAGCCAGAAAATGATGGAAACCCTGATAATACACCAATCAGGCTGC 931Acc130 GTAATTGTATATGTCAGCCAGAAAATGATGGAAACCCTGATAATACACCAATCAGGCTGC 931Acc719 GTAATTGTATATGTCAGCCAGAAAATGATGGAAACCCTGATAATACACCAATCAGGCTGC 931Acc729 GTAATTGTATATGTCAGCCAGAAAATGATGGAAACCCTGATAATACACCAATCAGGCTGC 931Acc710 GTAATTGTATATGTCAGCCAGAAAATGATGGAAACCCTGATAATACACCAATCAGGCTGC 931Acc709 GTAATTGTATATGTCAGCCAGAAAATGATGGAAACCCTGATAATACACCAATCAGGCTGC 931Acc220 ---ACTAC-----TCGG--AGGGAATGATG---------ATAAGACATCGGTCAGGCAGC 979Nipponbare ---ACTAC-----TCGG--AGGGAATGATG---------ATAAGACATCGGTCAGGCAGC 979Acc224 ---ACTAC-----TCGG--AGGGAATGATG---------ATAAGACATCGGTCAGGCAGC 979AccUP3 ---ACTAC-----TCGG--AGGGAATGATG---------ATAAGACATCGGTCAGGCAGC 979AccUP1 ---ACTAC-----TCGG--AGGGAATGATG---------ATAAGACATCGGTCAGGCAGC 979Acc206 ---ACTAC-----TCGG--AGGGAATGATG---------ATAAGACATCGGTCAGGCAGC 979Acc201 ---ACTAC-----TCGG--AGGGAATGATG---------ATAAGACATCGGTCAGGCAGC 979Acc724 ---ACTAC-----TCGG--AGGGAATGATG---------ATAAGACATCGGTCAGGCAGC 979Acc415 ---ACTAC-----TCGG--AGGGAATGATG---------ATAAGACATCGGTCAGGCAGC 979Acc417 ---ACTAC-----TCGG--AGGGAATGATG---------ATAAGACATCGGTCAGGCAGC 979Acc435 ---ACTAC-----TCGG--AGGGAATGATG---------ATAAGACATCGGTCAGGCAGC 979Acc712 ---ACTAC-----TCGG--AGGGAATGATG---------ATAAGACATCGGTCAGGCAGC 979Acc101 ---ACTGC-----TCGG--AAGAAATGATG---------ATAAGACACCGGTCAGCCAGC 943Acc715 ---ACTGC-----TCGG--AAGAAATGATG---------ATAAGACACCGGTCAGCCAGC 943Acc706 ---ACTGC-----TCGG--AAGAAATGATG---------ATAAGACACCGGTCAGCCAGC 943Acc624 ---ACTGC-----TCGG--AAGAAATGATG---------ATAAGACACCGGTCAGCCAGC 943Acc1 ---ACTGC-----TCGG--AAGAAATGATG---------ATAAGACACCGGTCAGCCAGC 943Acc440 ---ACTGC-----TCGG--AAGAAATGATG---------ATAAGACACCGGTCAGCCAGC 943Acc868 ---ACTGC-----TCGG--AAGAAATGATG---------ATAAGACACCGGTCAGCCAGC 957Acc718 ---ACTGC-----TCGG--AAGAAATGATG---------ATAAGACACCGGTCAGCCAGC 943 * * ** * * ******* **** *** * **** * ** Acc414 AGGAAACAACGGACGATGATCAAAACCCCAGAAAACTGGAACAGCTCCTGGCCGAAAAGA 991Acc420 AGGAAACAACGGACGATGATCAAAACCCCAGAAAACTGGAACAGCTCCTGGCCGAAAAGA 991Acc761 AGGAAACAACGGACGATGATCAAAACCCCAGAAAACTGGAACAGCTCCTGGCCGAAAAGA 991Acc504 AGGAAACAACGGACGATGATCAAAACCCCAGAAAACTGGAACAGCTCCTGGCCGAAAAGA 991Acc563 AGGAAACAACGGACGATGATCAAAACCCCAGAAAACTGGAACAGCTCCTGGCCGAAAAGA 991Acc757 AGGAAACAACGGACGATGATCAAAACCCCAGAAAACTGGAACAGCTCCTGGCCGAAAAGA 991Acc848 AGGAAACAACGGACGATGATCAAAACCCCAGAAAACTGGAACAGCTCCTGGCCGAAAAGA 991Tsuyuake_Pikm AGGAAACAACGGACGATGATCAAAACCCCAGAAAACTGGAACAGCTCCTGGCCGAAAAGA 991Kusabue_Pik AGGAAACAACGGACGATGATCAAAACCCCAGAAAACTGGAACAGCTCCTGGCCGAAAAGA 991Kanto51_Pik AGGAAACAACGGACGATGATCAAAACCCCAGAAAACTGGAACAGCTCCTGGCCGAAAAGA 991K60_Pikp AGGAAACAACGGACGATGATCAAAACCCCAGAAAACTGGAACAGCTCCTGGCCGAAAAGA 991Acc108 AGGAAACAACGGACGATGATCAAAACCCCAGAAAACTGGAACAGCTCCTGGCCGAAAAGA 991Acc130 AGGAAACAACGGACGATGATCAAAACCCCAGAAAACTGGAACAGCTCCTGGCCGAAAAGA 991Acc719 AGGAAACAACGGACGATGATCAAAACCCCAGAAAACTGGAACAGCTCCTGGCCGAAAAGA 991Acc729 AGGAAACAACGGACGATGATCAAAACCCCAGAAAACTGGAACAGCTCCTGGCCGAAAAGA 991Acc710 AGGAAACAACGGACGATGATCAAAACCCCAGAAAACTGGAACAGCTCCTGGCCGAAAAGA 991Acc709 AGGAAACAACGGACGATGATCAAAACCCCAGAAAACTGGAACAGCTCCTGGCCGAAAAGA 991Acc220 AGGAAACAATGGGCTCTCTTCAGCTCCGCGAAGAACTGAAACGGCGCCTGGCCGAAAAGA 1039Nipponbare AGGAAACAATGGGCTCTCTTCAGCTCCGCGAAGAACTGAAACGGCGCCTGGCCGAAAAGA 1039Acc224 AGGAAACAATGGGCTCTCTTCAGCTCCGCGAAGAACTGAAACGGCGCCTGGCCGAAAAGA 1039AccUP3 AGGAAACAATGGGCTCTCTTCAGCTCCGCGAAGAACTGAAACGGCGCCTGGCCGAAAAGA 1039AccUP1 AGGAAACAATGGGCTCTCTTCAGCTCCGCGAAGAACTGAAACGGCGCCTGGCCGAAAAGA 1039Acc206 AGGAAACAATGGGCTCTCTTCAGCTCCGCGAAGAACTGAAACGGCGCCTGGCCGAAAAGA 1039Acc201 AGGAAACAATGGGCTCTCTTCAGCTCCGCGAAGAACTGAAACGGCGCCTGGCCGAAAAGA 1039Acc724 AGGAAACAATGGGCTCTCTTCAGCTCCGCGAAGAACTGAAACGGCGCCTGGCCGAAAAGA 1039Acc415 AGGAAACAATGGGCTCTCTTCAGCTCCGCGAAGAACTGAAACGGCGCCTGGCCGAAAAGA 1039Acc417 AGGAAACAATGGGCTCTCTTCAGCTCCGCGAAGAACTGAAACGGCGCCTGGCCGAAAAGA 1039Acc435 AGGAAACAATGGGCTCTCTTCAGCTCCGCGAAGAACTGAAACGGCGCCTGGCCGAAAAGA 1039Acc712 AGGAAACAATGGGCTCTCTTCAGCTCCGCGAAGAACTGAAACGGCGCCTGGCCGAAAAGA 1039Acc101 AGGAAACAATGGGCTATGTTCAGCTTCGCCAAGAACTGAAACGGCGCCTGGGCGAAAAGA 1003Acc715 AGGAAACAATGGGCTATGTTCAGCTTCGCCAAGAACTGAAACGGCGCCTGGGCGAAAAGA 1003Acc706 AGGAAACAATGGGCTATGTTCAGCTTCGCCAAGAACTGAAACGGCGCCTGGGCGAAAAGA 1003Acc624 AGGAAACAATGGGCTATGTTCAGCTTCGCCAAGAACTGAAACGGCGCCTGGGCGAAAAGA 1003Acc1 AGGAAACAATGGGCTATGTTCAGCTTCGCCAAGAACTGAAACGGCGCCTGGGCGAAAAGA 1003Acc440 AGGAAACAATGGGCTATGTTCAGCTTCGCCAAGAACTGAAACGGCGCCTGGGCGAAAAGA 1003Acc868 AGGAAACAATGGGCTATGTTCAGCTTCGCCAAGAACTGAAACGGCGCCTGGGCGAAAAGA 1017Acc718 AGGAAACAATGGGCTATGTTCAGCTTCGCCAAGAACTGAAACGGCGCCTGGGCGAAAAGA 1003 ********* ** * * *** * * * ***** *** ** ***** ******** 

Ashikawa et al. Supplementary Fig. S2 (9/28)

Acc414 GTTATATCCTCTTGATTGATGACATTTGGTCTGCCGAAACATGGGAGAGTAT---CAGAT 1048Acc420 GTTATATCCTCTTGATTGATGACATTTGGTCTGCCGAAACATGGGAGAGTAT---CAGAT 1048Acc761 GTTATATCCTCTTGATTGATGACATTTGGTCTGCCGAAACATGGGAGAGTAT---CAGAT 1048Acc504 GTTATATCCTCTTGATTGATGACATTTGGTCTGCCGAAACATGGGAGAGTAT---CAGAT 1048Acc563 GTTATATCCTCTTGATTGATGACATTTGGTCTGCCGAAACATGGGAGAGTAT---CAGAT 1048Acc757 GTTATATCCTCTTGATTGATGACATTTGGTCTGCCGAAACATGGGAGAGTAT---CAGAT 1048Acc848 GTTATATCCTCTTGATTGATGACATTTGGTCTGCCGAAACATGGGAGAGTAT---CAGAT 1048Tsuyuake_Pikm GTTATATCCTCTTGATTGATGACATTTGGTCTGCCGAAACATGGGAGAGTAT---CAGAT 1048Kusabue_Pik GTTATATCCTCTTGATTGATGACATTTGGTCTGCCGAAACATGGGAGAGTAT---CAGAT 1048Kanto51_Pik GTTATATCCTCTTGATTGATGACATTTGGTCTGCCGAAACATGGGAGAGTAT---CAGAT 1048K60_Pikp GTTATATCCTCTTGATTGATGACATTTGGTCTGCCGAAACATGGGAGAGTAT---CAGAT 1048Acc108 GTTATATCCTCTTGATTGATGACATTTGGTCTGCCGAAACATGGGAGAGTAT---CAGAT 1048Acc130 GTTATATCCTCTTGATTGATGACATTTGGTCTGCCGAAACATGGGAGAGTAT---CAGAT 1048Acc719 GTTATATCCTCTTGATTGATGACATTTGGTCTGCCGAAACATGGGAGAGTAT---CAGAT 1048Acc729 GTTATATCCTCTTGATTGATGACATTTGGTCTGCCGAAACATGGGAGAGTAT---CAGAT 1048Acc710 GTTATATCCTCTTGATTGATGACATTTGGTCTGCCGAAACATGGGAGAGTAT---CAGAT 1048Acc709 GTTATATCCTCTTGATTGATGACATTTGGTCTGCCGAAACATGGGAGAGTAT---CAGAT 1048Acc220 GATATATCCTCTTGATTGATGATATTTGGTCTGCCAAGACATGGAACAGTATCATCATAC 1099Nipponbare GATATATCCTCTTGATTGATGATATTTGGTCTGCCAAGACATGGAACAGTATCATCATAC 1099Acc224 GATATATCCTCTTGATTGATGATATTTGGTCTGCCAAGACATGGAACAGTATCATCATAC 1099AccUP3 GATATATCCTCTTGATTGATGATATTTGGTCTGCCAAGACATGGAACAGTATCATCATAC 1099AccUP1 GATATATCCTCTTGATTGATGATATTTGGTCTGCCAAGACATGGAACAGTATCATCATAC 1099Acc206 GATATATCCTCTTGATTGATGATATTTGGTCTGCCAAGACATGGAACAGTATCATCATAC 1099Acc201 GATATATCCTCTTGATTGATGATATTTGGTCTGCCAAGACATGGAACAGTATCATCATAC 1099Acc724 GATATATCCTCTTGATTGATGATATTTGGTCTGCCAAGACATGGAACAGTATCATCATAC 1099Acc415 GATATATCCTCTTGATTGATGATATTTGGTCTGCCAAGACATGGAACAGTATCATCATAC 1099Acc417 GATATATCCTCTTGATTGATGATATTTGGTCTGCCAAGACATGGAACAGTATCATCATAC 1099Acc435 GATATATCCTCTTGATTGATGATATTTGGTCTGCCAAGACATGGAACAGTATCATCATAC 1099Acc712 GATATATCCTCTTGATTGATGATATTTGGTCTGCCAAGACATGGAACAGTATCATCATAC 1099Acc101 GATATATCCTCTTGATTGATGACATTTGGTCTGCCAAGACATGGTTGGATGTCGTCATAC 1063Acc715 GATATATCCTCTTGATTGATGACATTTGGTCTGCCAAGACATGGTTGGATGTCGTCATAC 1063Acc706 GATATATCCTCTTGATTGATGACATTTGGTCTGCCAAGACATGGTTGGATGTCGTCATAC 1063Acc624 GATATATCCTCTTGATTGATGACATTTGGTCTGCCAAGACATGGTTGGATGTCGTCATAC 1063Acc1 GATATATCCTCTTGATTGATGACATTTGGTCTGCCAAGACATGGTTGGATGTCGTCATAC 1063Acc440 GATATATCCTCTTGATTGATGACATTTGGTCTGCCAAGACATGGTTGGATGTCGTCATAC 1063Acc868 GATATATCCTCTTGATTGATGACATTTGGTCTGCCAAGACATGGTTGGATGTCGTCATAC 1077Acc718 GATATATCCTCTTGATTGATGACATTTGGTCTGCCAAGACATGGTTGGATGTCGTCATAC 1063 * ******************** ************ * ****** * * ** *  Acc414 CGATTTTGCC---TAAAAATAATAAAGGCGGTAGAATAATAGTGACTACAAGATTTCAAG 1105Acc420 CGATTTTGCC---TAAAAATAATAAAGGCGGTAGAATAATAGTGACTACAAGATTTCAAG 1105Acc761 CGATTTTGCC---TAAAAATAATAAAGGCGGTAGAATAATAGTGACTACAAGATTTCAAG 1105Acc504 CGATTTTGCC---TAAAAATAATAAAGGCGGTAGAATAATAGTGACTACAAGATTTCAAG 1105Acc563 CGATTTTGCC---TAAAAATAATAAAGGCGGTAGAATAATAGTGACTACAAGATTTCAAG 1105Acc757 CGATTTTGCC---TAAAAATAATAAAGGCGGTAGAATAATAGTGACTACAAGATTTCAAG 1105Acc848 CGATTTTGCC---TAAAAATAATAAAGGCGGTAGAATAATAGTGACTACAAGATTTCAAG 1105Tsuyuake_Pikm CGATTTTGCC---TAAAAATAATAAAGGCGGTAGAATAATAGTGACTACAAGATTTCAAG 1105Kusabue_Pik CGATTTTGCC---TAAAAATAATAAAGGCGGTAGAATAATAGTGACTACAAGATTTCAAG 1105Kanto51_Pik CGATTTTGCC---TAAAAATAATAAAGGCGGTAGAATAATAGTGACTACAAGATTTCAAG 1105K60_Pikp CGATTTTGCC---TAAAAATAATAAAGGCGGTAGAATAATAGTGACTACAAGATTTCAAG 1105Acc108 CGATTTTGCC---TAAAAATAATAAAGGCGGTAGAATAATAGTGACTACAAGATTTCAAG 1105Acc130 CGATTTTGCC---TAAAAATAATAAAGGCGGTAGAATAATAGTGACTACAAGATTTCAAG 1105Acc719 CGATTTTGCC---TAAAAATAATAAAGGCGGTAGAATAATAGTGACTACAAGATTTCAAG 1105Acc729 CGATTTTGCC---TAAAAATAATAAAGGCGGTAGAATAATAGTGACTACAAGATTTCAAG 1105Acc710 CGATTTTGCC---TAAAAATAATAAAGGCGGTAGAATAATAGTGACTACAAGATTTCAAG 1105Acc709 CGATTTTGCC---TAAAAATAATAAAGGCGGTAGAATAATAGTGACTACAAGATTTCAAG 1105Acc220 CGTTTCTGCCTTCTGAAAATGATAAAGACAGCAGAATAATAGTGACTACAAGATTTCATG 1159Nipponbare CGTTTCTGCCTTCTGAAAATGATAAAGACAGCAGAATAATAGTGACTACAAGATTTCATG 1159Acc224 CGTTTCTGCCTTCTGAAAATGATAAAGACAGCAGAATAATAGTGACTACAAGATTTCATG 1159AccUP3 CGTTTCTGCCTTCTGAAAATGATAAAGACAGCAGAATAATAGTGACTACAAGATTTCATG 1159AccUP1 CGTTTCTGCCTTCTGAAAATGATAAAGACAGCAGAATAATAGTGACTACAAGATTTCATG 1159Acc206 CGTTTCTGCCTTCTGAAAATGATAAACACAGCAGAATAATAGTGACTACAAGATTTCATG 1159Acc201 CGTTTCTGCCTTCTGAAAATGATAAACACAGCAGAATAATAGTGACTACAAGATTTCATG 1159Acc724 CGTTTCTGCCTTCTGAAAATGATAAAGACAGCAGAATAATAGTGACTACAAGATTTCATG 1159Acc415 CGTTTCTGCCTTCTGAAAATGATAAAGACAGCAGAATAATAGTGACTACAAGATTTCATG 1159Acc417 CGTTTCTGCCTTCTGAAAATGATAAAGACAGCAGAATAATAGTGACTACAAGATTTCATG 1159Acc435 CGTTTCTGCCTTCTGAAAATGATAAAGACAGCAGAATAATAGTGACTACAAGATTTCATG 1159Acc712 CGTTTCTGCCTTCTGAAAATGATAAAGACAGCAGAATAATAGTGACTACAAGATTTCATG 1159Acc101 CGTTTTTGCCGGATGAAGCTAATAACAACAGCAGAATAATAGTGACTACAAGATTTCATG 1123Acc715 CGTTTTTGCCGGATGAAGCTAATAACAACAGCAGAATAATAGTGACTACAAGATTTCATG 1123Acc706 CGTTTTTGCCGGATGAAGCTAATAACAACAGCAGAATAATAGTGACTACAAGATTTCATG 1123Acc624 CGTTTTTGCCGGATGAAGCTAATAACAACAGCAGAATAATAGTGACTACAAGATTTCATG 1123Acc1 CGTTTTTGCCGGATGAAGCTAATAACAACAGCAGAATAATAGTGACTACAAGATTTCATG 1123Acc440 CGTTTTTGCCGGATGAAGATAATAACAGCAGCAGAATAATAGTGACTACAAGATTTCATG 1123Acc868 CGTTTTTGCCGGATGAAGATAATAACAGCAGCAGAATAATAGTGACTACAAGATTTCATG 1137Acc718 CGTTTTTGCCGGATGAAGATAATAACAGCAGCAGAATAATAGTGACTACAAGATTTCATG 1123 ** ** **** * ** * **** * * ************************** *

Ashikawa et al. Supplementary Fig. S2 (10/28)

Acc414 CTGTTGGTTCAACATGCTCCCCT------------------------------------C 1129Acc420 CTGTTGGTTCAACATGCTCCCCT------------------------------------C 1129Acc761 CTGTTGGTTCAACATGCTCCCCT------------------------------------C 1129Acc504 CTGTTGGTTCAACATGCTCCCCT------------------------------------C 1129Acc563 CTGTTGGTTCAACATGCTCCCCT------------------------------------C 1129Acc757 CTGTTGGTTCAACATGCTCCCCT------------------------------------C 1129Acc848 CTGTTGGTTCAACATGCTCCCCT------------------------------------C 1129Tsuyuake_Pikm CTGTTGGTTCAACATGCTCCCCT------------------------------------C 1129Kusabue_Pik CTGTTGGTTCAACATGCTCCCCT------------------------------------C 1129Kanto51_Pik CTGTTGGTTCAACATGCTCCCCT------------------------------------C 1129K60_Pikp CTGTTGGTTCAACATGCTCCCCT------------------------------------C 1129Acc108 CTGTTGGTTCAACATGCTCCCCT------------------------------------C 1129Acc130 CTGTTGGTTCAACATGCTCCCCT------------------------------------C 1129Acc719 CTGTTGGTTCAACATGCTCCCCT------------------------------------C 1129Acc729 CTGTTGGTTCAACATGCTCCCCT------------------------------------C 1129Acc710 CTGTTGGTTCAACATGCTCCCCT------------------------------------C 1129Acc709 CTGTTGGTTCAACATGCTCCCCT------------------------------------C 1129Acc220 CTGTTGGTTCCACATGCTCCCCTAGACATAAAAATGATGAGGCCACATCCTCCCCTGGAC 1219Nipponbare CTGTTGGTTCCACATGCTCCCCTAGACATAAAAATGATGAGGCCACATCCTCCCCTGGAC 1219Acc224 CTGTTGGTTCCACATGCTCCCCTAGACATAAAAATGATGAGGCCACATCCTCCCCTGGAC 1219AccUP3 CTGTTGGTTCCACATGCTCCCCTAGACATAAAAATGATGAGGCCACATCCTCCCCTGGAC 1219AccUP1 CTGTTGGTTCCACATGCTCCCCTAGACATAAAAATGATGAGGCCACATCCTCCCCTGGAC 1219Acc206 CTGTTGGTTCCACATGCTCCCCTAGACATAAAAATGATGAGGCCACATCCTCCCCTGGAC 1219Acc201 CTGTTGGTTCCACATGCTCCCCTAGACATAAAAATGATGAGGCCACATCCTCCCCTGGAC 1219Acc724 CTGTTGGTTCCACATGCTCCCCTAGACATAAAAATGATGAGGCCACATCCTCCCCTGGAC 1219Acc415 CTGTTGGTTCCACATGCTCCCCTAGACATAAAAATGATGAGGCCACATCCTCCCCTGGAC 1219Acc417 CTGTTGGTTCCACATGCTCCCCTAGACATAAAAATGATGAGGCCACATCCTCCCCTGGAC 1219Acc435 CTGTTGGTTCCACATGCTCCCCTAGACATAAAAATGATGAGGCCACATCCTCCCCTGGAC 1219Acc712 CTGTTGGTTCCACATGCTCCCCTAGACATAAAAATGATGAGGCCACATCCTCCCCTGGAC 1219Acc101 CTGTTGGTTCCACATGCTCCCCTGGACATAAAAATGTTGAGGCCACATCCTCCCCTAGAC 1183Acc715 CTGTTGGTTCCACATGCTCCCCTGGACATAAAAATGTTGAGGCCACATCCTCCCCTAGAC 1183Acc706 CTGTTGGTTCCACATGCTCCCCTGGACATAAAAATGTTGAGGCCACATCCTCCCCTAGAC 1183Acc624 CTGTTGGTTCCACATGCTCCCCTGGACATAAAAATGTTGAGGCCACATCCTCCCCTAGAC 1183Acc1 CTGTTGGTTCCACATGCTCCCCTGGACATAAAAATGTTGAGGCCACATCCTCCCCTAGAC 1183Acc440 CTGTTGGTTCCACATGCTCCCCTGGACATAAAAATGTTGAGGCCACATCCTCCCCTAGAC 1183Acc868 CTGTTGGTTCCACATGCTCCCCTGGACATAAAAATGTTGAGGCCACATCCTCCCCTAGAC 1197Acc718 CTGTTGGTTCCACATGCTCCCCTGGACATAAAAATGTTGAGGCCACATCCTCCCCTAGAC 1183 ********** ************ * Acc414 TTGAAACT---------------------------------------------------G 1138Acc420 TTGAAACT---------------------------------------------------G 1138Acc761 TTGAAACT---------------------------------------------------G 1138Acc504 TTGAAACT---------------------------------------------------G 1138Acc563 TTGAAACT---------------------------------------------------G 1138Acc757 TTGAAACT---------------------------------------------------G 1138Acc848 TTGAAACT---------------------------------------------------G 1138Tsuyuake_Pikm TTGAAACT---------------------------------------------------G 1138Kusabue_Pik TTGAAACT---------------------------------------------------G 1138Kanto51_Pik TTGAAACT---------------------------------------------------G 1138K60_Pikp TTGAAACT---------------------------------------------------G 1138Acc108 TTGAAACT---------------------------------------------------G 1138Acc130 TTGAAACT---------------------------------------------------G 1138Acc719 TTGAAACT---------------------------------------------------G 1138Acc729 TTGAAACT---------------------------------------------------G 1138Acc710 TTGAAACT---------------------------------------------------G 1138Acc709 TTGAAACT---------------------------------------------------G 1138Acc220 ATGGAAAG---------------------------------------------------G 1228Nipponbare ATGGAAAG---------------------------------------------------G 1228Acc224 ATGGAAAG---------------------------------------------------G 1228AccUP3 ATGGAAAG---------------------------------------------------G 1228AccUP1 ATGGAAAG---------------------------------------------------G 1228Acc206 ATGGAAAG---------------------------------------------------G 1228Acc201 ATGGAAAG---------------------------------------------------G 1228Acc724 ATGGAAAG---------------------------------------------------G 1228Acc415 ATGGAAAG---------------------------------------------------G 1228Acc417 ATGGAAAG---------------------------------------------------G 1228Acc435 ATGGAAAG---------------------------------------------------G 1228Acc712 ATGGAAAG---------------------------------------------------G 1228Acc101 CTGGAAATGATCGTGTGCATAAAAATGTTGAGGCCACATCCTCCCCTAGACCTGGAAATA 1243Acc715 CTGGAAATGATCGTGTGCATAAAAATGTTGAGGCCACATCCTCCCCTAGACCTGGAAATA 1243Acc706 CTGGAAATGATCGTGTGCATAAAAATGTTGAGGCCACATCCTCCCCTAGACCTGGAAATA 1243Acc624 CTGGAAATGATCGTGTGCATAAAAATGTTGAGGCCACATCCTCCCCTAGACCTGGAAATA 1243Acc1 CTGGAAAT---------------------------------------------------A 1192Acc440 CTGGAAAT---------------------------------------------------G 1192Acc868 CTGGAAAT---------------------------------------------------G 1206Acc718 CTGGAAAT---------------------------------------------------G 1192 ** **  

Ashikawa et al. Supplementary Fig. S2 (11/28)

Acc414 ATCGTTTGCATACAGTTGATTTTCTCACCGATGACGAGTCCCAAAACTTATTCAATACAA 1198Acc420 ATCGTTTGCATACAGTTGATTTTCTCACCGATGACGAGTCCCAAAACTTATTCAATACAA 1198Acc761 ATCGTTTGCATACAGTTGATTTTCTCACCGATGACGAGTCCCAAAACTTATTCAATACAA 1198Acc504 ATCGTTTGCATACAGTTGATTTTCTCACCGATGACGAGTCCCAAAACTTATTCAATACAA 1198Acc563 ATCGTTTGCATACAGTTGATTTTCTCACCGATGACGAGTCCCAAAACTTATTCAATACAA 1198Acc757 ATCGTTTGCATACAGTTGATTTTCTCACCGATGACGAGTCCCAAAACTTATTCAATACAA 1198Acc848 ATCGTTTGCATACAGTTGATTTTCTCACCGATGACGAGTCCCAAAACTTATTCAATACAA 1198Tsuyuake_Pikm ATCGTTTGCATACAGTTGATTTTCTCACCGATGACGAGTCCCAAAACTTATTCAATACAA 1198Kusabue_Pik ATCGTTTGCATACAGTTGATTTTCTCACCGATGACGAGTCCCAAAACTTATTCAATACAA 1198Kanto51_Pik ATCGTTTGCATACAGTTGATTTTCTCACCGATGACGAGTCCCAAAACTTATTCAATACAA 1198K60_Pikp ATCGTTTGCATACAGTTGATTTTCTCACCGATGACGAGTCCCAAAACTTATTCAATACAA 1198Acc108 ATCGTTTGCATACAGTTGATTTTCTCACCGATGACGAGTCCCAAAACTTATTCAATACAA 1198Acc130 ATCGTTTGCATACAGTTGATTTTCTCACCGATGACGAGTCCCAAAACTTATTCAATACAA 1198Acc719 ATCGTTTGCATACAGTTGATTTTCTCACCGATGACGAGTCCCAAAACTTATTCAATACAA 1198Acc729 ATCGTTTGCATACAGTTGATTTTCTCACCGATGACGAGTCCCAAAACTTATTCAATACAA 1198Acc710 ATCGTTTGCATACAGTTGATTTTCTCACCGATGACGAGTCCCAAAACTTATTCAATACAA 1198Acc709 ATCGTTTGCATACAGTTGATTTTCTCACCGATGACGAGTCCCAAAACTTATTCAATACAA 1198Acc220 ATCTTTTGCATAAAGTTGATTTTCTCACAGGTGACAAGCCCCTAGATTTATTTAATGCAA 1288Nipponbare ATCTTTTGCATAAAGTTGATTTTCTCACAGGTGACAAGCCCCTAGATTTATTTAATGCAA 1288Acc224 ATCTTTTGCATAAAGTTGATTTTCTCACAGGTGACAAGCCCCTAGATTTATTTAATGCAA 1288AccUP3 ATCTTTTGCATAAAGTTGATTTTCTCACAGGTGACAAGCCCCTAGATTTATTTAATGCAA 1288AccUP1 ATCTTTTGCATAAAGTTGATTTTCTCACAGGTGACAAGCCCCTAGATTTATTTAATGCAA 1288Acc206 ATCTTTTGCATAAAGTTGATTTTCTCACAGGTGACAAGCCCCTAGATTTATTTAATGCAA 1288Acc201 ATCTTTTGCATAAAGTTGATTTTCTCACAGGTGACAAGCCCCTAGATTTATTTAATGCAA 1288Acc724 ATCTTTTGCATAAAGTTGATTTTCTCACAGGTGACAAGCCCCTAGATTTATTTAATGCAA 1288Acc415 ATCTTTTGCATAAAGTTGATTTTCTCACAGGTGACAAGCCCCTAGATTTATTTAATGCAA 1288Acc417 ATCTTTTGCATAAAGTTGATTTTCTCACAGGTGACAAGCCCCTAGATTTATTTAATGCAA 1288Acc435 ATCTTTTGCATAAAGTTGATTTTCTCACAGGTGACAAGCCCCTAGATTTATTTAATGCAA 1288Acc712 ATCTTTTGCATAAAGTTGATTTTCTCACAGGTGACAAGCCCCTAGATTTATTTAATGCAA 1288Acc101 ATCGTGTGCATACTGTTGATTTTCTCAGCGATGACGAGTCCCAAAACTTATTTAATGCAA 1303Acc715 ATCGTGTGCATACTGTTGATTTTCTCAGCGATGACGAGTCCCAAAACTTATTTAATGCAA 1303Acc706 ATCGTGTGCATACTGTTGATTTTCTCAGCGATGACGAGTCCCAAAACTTATTTAATGCAA 1303Acc624 ATCGTGTGCATACTGTTGATTTTCTCAGCGATGACGAGTCCCAAAACTTATTTAATGCAA 1303Acc1 ATCGTGTGCATACTGTTGATTTTCTCAGCGATGACGAGTCCCAAAACTTATTTAATGCAA 1252Acc440 ATCTTGTGCATACTGTTCATTTTCTCAGCGATGACGAGTCCCAAAACTTATTTAATGCAA 1252Acc868 ATCTTGTGCATACTGTTCATTTTCTCAGCGATGACGAGTCCCAAAACTTATTTAATGCAA 1266Acc718 ATCTTGTGCATACTGTTCATTTTCTCAGCGATGACGAGTCCCAAAACTTATTTAATGCAA 1252 *** * ****** *** ********* * **** ** *** * * ***** *** *** Acc414 GTATTTGTGAATCAAAGATAAGAAAAGATAGCAACAAAGTAGACGAGCAAGTCCCTGAGG 1258Acc420 GTATTTGTGAATCAAAGATAAGAAAAGATAGCAACAAAGTAGACGAGCAAGTCCCTGAGG 1258Acc761 GTATTTGTGAATCAAAGATAAGAAAAGATAGCAACAAAGTAGACGAGCAAGTCCCTGAGG 1258Acc504 GTATTTGTGAATCAAAGATAAGAAAAGATAGCAACAAAGTAGACGAGCAAGTCCCTGAGG 1258Acc563 GTATTTGTGAATCAAAGATAAGAAAAGATAGCAACAAAGTAGACGAGCAAGTCCCTGAGG 1258Acc757 GTATTTGTGAATCAAAGATAAGAAAAGATAGCAACAAAGTAGACGAGCAAGTCCCTGAGG 1258Acc848 GTATTTGTGAATCAAAGATAAGAAAAGATAGCAACAAAGTAGACGAGCAAGTCCCTGAGG 1258Tsuyuake_Pikm GTATTTGTGAATCAAAGATAAGAAAAGATAGCAACAAAGTAGACGAGCAAGTCCCTGAGG 1258Kusabue_Pik GTATTTGTGAATCAAAGATAAGAAAAGATAGCAACAAAGTAGACGAGCAAGTCCCTGAGG 1258Kanto51_Pik GTATTTGTGAATCAAAGATAAGAAAAGATAGCAACAAAGTAGACGAGCAAGTCCCTGAGG 1258K60_Pikp GTATTTGTGAATCAAAGATAAGAAAAGATAGCAACAAAGTAGACGAGCAAGTCCCTGAGG 1258Acc108 GTATTTGTGAATCAAAGATAAGAAAAGATAGCAACAAAGTAGACGAGCAAGTCCCTGAGG 1258Acc130 GTATTTGTGAATCAAAGATAAGAAAAGATAGCAACAAAGTAGACGAGCAAGTCCCTGAGG 1258Acc719 GTATTTGTGAATCAAAGATAAGAAAAGATAGCAACAAAGTAGACGAGCAAGTCCCTGAGG 1258Acc729 GTATTTGTGAATCAAAGATAAGAAAAGATAGCAACAAAGTAGACGAGCAAGTCCCTGAGG 1258Acc710 GTATTTGTGAATCAAAGATAAGAAAAGATAGCAACAAAGTAGACGAGCAAGTCCCTGAGG 1258Acc709 GTATTTGTGAATCAAAGATAAGAAAAGATAGCAACAAAGTAGACGAGCAAGTCCCTGAGG 1258Acc220 GCATTCCTGACCCAATGAAAAGAACAGATAGAGACAA---------------------GA 1327Nipponbare GCATTCCTGACCCAATGAAAAGAACAGATAGAGACAA---------------------GA 1327Acc224 GCATTCCTGACCCAATGAAAAGAACAGATAGAGACAA---------------------GA 1327AccUP3 GCATTCCTGACCCAATGAAAAGAACAGATAGAGACAA---------------------GA 1327AccUP1 GCATTCCTGACCCAATGAAAAGAACAGATAGAGACAA---------------------GA 1327Acc206 GCATTCCTGACCCAATGAAAAGAACAGATAGAGACAA---------------------CA 1327Acc201 GCATTCCTGACCCAATGAAAAGAACAGATAGAGACAA---------------------CA 1327Acc724 GCATTCCTGACCCAATGAAAAGAACAGATAGAGACAA---------------------GA 1327Acc415 GCATTCCTGACCCAATGAAAAGAACAGATAGAGACAA---------------------CA 1327Acc417 GCATTCCTGACCCAATGAAAAGAACAGATAGAGACAA---------------------CA 1327Acc435 GCATTCCTGACCCAATGAAAAGAACAGATAGAGACAA---------------------CA 1327Acc712 GCATTCCTGACCCAATGAAAAGAACAGATAGAGACAA---------------------CA 1327Acc101 GCATTCCTGATTCAATGAAAAGTGCAGATAGAGACAA---------------------GG 1342Acc715 GCATTCCTGATTCAATGAAAAGTGCAGATAGAGACAA---------------------GG 1342Acc706 GCATTCCTGATTCAATGAAAAGTGCAGATAGAGACAA---------------------GG 1342Acc624 GCATTCCTGATTCAATGAAAAGTGCAGATAGAGACAA---------------------GG 1342Acc1 GCATTCCTGATTCAATGAAAAGTGCAGATAGAGACAA---------------------GG 1291Acc440 GCATTCCTGATTCAATGAAAAGTGCAGATAGAGACAA---------------------GG 1291Acc868 GCATTCCTGATTCAATGAAAAGTGCAGATAGAGACAA---------------------GG 1305Acc718 GCATTCCTGATTCAATGAAAAGTGCAGATAGAGACAA---------------------GG 1291 * *** *** *** ** *** ****** ****

Ashikawa et al. Supplementary Fig. S2 (12/28)

Acc414 AAATATGGAAAATATGTGGGGGATTGCCTTTGGCCATAGTCACCATGGCTGGTCTTGTCG 1318Acc420 AAATATGGAAAATATGTGGGGGATTGCCTTTGGCCATAGTCACCATGGCTGGTCTTGTCG 1318Acc761 AAATATGGAAAATATGTGGGGGATTGCCTTTGGCCATAGTCACCATGGCTGGTCTTGTCG 1318Acc504 AAATATGGAAAATATGTGGGGGATTGCCTTTGGCCATAGTCAGCATGGCTGGTCTTGTCG 1318Acc563 AAATATGGAAAATATGTGGGGGATTGCCTTTGGCCATAGTCAGCATGGCTGGTCTTGTCG 1318Acc757 AAATATGGAAAATATGTGGGGGATTGCCTTTGGCCATAGTCAGCATGGCTGGTCTTGTCG 1318Acc848 AAATATGGAAAATATGTGGGGGATTGCCTTTGGCCATAGTCAGCATGGCTGGTCTTGTCG 1318Tsuyuake_Pikm AAATATGGAAAATATGTGGGGGATTGCCTTTGGCCATAGTCAGCATGGCTGGTCTTGTCG 1318Kusabue_Pik AAATATGGAAAATATGTGGGGGATTGCCTTTGGCCATAGTCAGCATGGCTGGTCTTGTCG 1318Kanto51_Pik AAATATGGAAAATATGTGGGGGATTGCCTTTGGCCATAGTCAGCATGGCTGGTCTTGTCG 1318K60_Pikp AAATATGGAAAATATGTGGGGGATTGCCTTTGGCCATAGTCACCATGGCTGGTCTTGTCG 1318Acc108 AAATATGGAAAATATGTGGGGGATTGCCTTTGGCCATAGTCACCATGGCTGGTCTTGTCG 1318Acc130 AAATATGGAAAATATGTGGGGGATTGCCTTTGGCCATAGTCACCATGGCTGGTCTTGTCG 1318Acc719 AAATATGGAAAATATGTGGGGGATTGCCTTTGGCCATAGTCACCATGGCTGGTCTTGTCG 1318Acc729 AAATATGGAAAATATGTGGGGGATTGCCTTTGGCCATAGTCACCATGGCTGGTCTTGTCG 1318Acc710 AAATATGGAAAATATGTGGGGGATTGCCTTTGGCCATAGTCACCATGGCTGGTCTTGTCG 1318Acc709 AAATATGGAAAATATGTGGGGGATTGCCTTTGGCCATAGTCACCATGGCTGGTCTTGTCG 1318Acc220 AGTTATCAAAGATATGTGGGGGATTGCCTTTGGCCATTGTCACCATGGCTGGTCTTGTAG 1387Nipponbare AGTTATCAAAGATATGTGGGGGATTGCCTTTGGCCATTGTCACCATGGCTGGTCTTGTAG 1387Acc224 AGTTATCAAAGATATGTGGGGGATTGCCTTTGGCCATTGTCACCATGGCTGGTCTTGTAG 1387AccUP3 AGTTATCAAAGATATGTGGGGGATTGCCTTTGGCCATTGTCACCATGGCTGGTCTTGTAG 1387AccUP1 AGTTATCAAAGATATGTGGGGGATTGCCTTTGGCCATTGTCACCATGGCTGGTCTTGTAG 1387Acc206 AGTTATCAAAGATATGTGGGGGATTGCCTTTGGCCATTGTCACCATGGCTGGTCTTGTAG 1387Acc201 AGTTATCAAAGATATGTGGGGGATTGCCTTTGGCCATTGTCACCATGGCTGGTCTTGTAG 1387Acc724 AGTTATCAAAGATATGTGGGGGATTGCCTTTGGCCATTGTCACCATGGCTGGTCTTGTAG 1387Acc415 AGTTATCAAAGATATGTGGGGGATTGCCTTTGGCCATTGTCACCATGGCTGGTCTTGTAG 1387Acc417 AGTTATCAAAGATATGTGGGGGATTGCCTTTGGCCATTGTCACCATGGCTGGTCTTGTAG 1387Acc435 AGTTATCAAAGATATGTGGGGGATTGCCTTTGGCCATTGTCACCATGGCTGGTCTTGTAG 1387Acc712 AGTTATCAAAGATATGTGGGGGATTGCCTTTGGCCATTGTCACCATGGCTGGTCTTGTAG 1387Acc101 AGTTATCGAGCATATGTGGGGGATTACCTTTGACCATTGTCACCATGGCTGGTCTTGTCG 1402Acc715 AGTTATCGAGCATATGTGGGGGATTACCTTTGACCATTGTCACCATGGCTGGTCTTGTCG 1402Acc706 AGTTATCGAGCATATGTGGGGGATTACCTTTGACCATTGTCACCATGGCTGGTCTTGTCG 1402Acc624 AGTTATCGAGCATATGTGGGGGATTACCTTTGACCATTGTCACCATGGCTGGTCTTGTCG 1402Acc1 AGTTATCGAGCATATGTGGGGGATTACCTTTGACCATTGTCACCATGGCTGGTCTTGTCG 1351Acc440 AGTTATCGAGCATATGTGGGGGATTACCTTTGACCATTGTCACCATGGCTGGTCTTGTCG 1351Acc868 AGTTATCGAGCATATGTGGGGGATTACCTTTGACCATTGTCACCATGGCTGGTCTTGTCG 1365Acc718 AGTTATCGAGCATATGTGGGGGATTACCTTTGACCATTGTCACCATGGCTGGTCTTGTCG 1351 * *** * ************** ****** **** **** *************** * Acc414 CCTGCAACCCAAGGAAAGCCTGCTGCGATTGGAGTAAACTTTGCAAATCATTATTTCCAG 1378Acc420 CCTGCAACCCAAGGAAAGCCTGCTGCGATTGGAGTAAACTTTGCAAATCATTATTTCCAG 1378Acc761 CCTGCAACCCAAGGAAAGCCTGCTGCGATTGGAGTAAACTTTGCAAATCATTATTTCCAG 1378Acc504 CCTGCAACCCAAGGAAAGCCTGCTGCGATTGGAGTAAACTTTGCAAATCATTATTTCCAG 1378Acc563 CCTGCAACCCAAGGAAAGCCTGCTGCGATTGGAGTAAACTTTGCAAATCATTATTTCCAG 1378Acc757 CCTGCAACCCAAGGAAAGCCTGCTGCGATTGGAGTAAACTTTGCAAATCATTATTTCCAG 1378Acc848 CCTGCAACCCAAGGAAAGCCTGCTGCGATTGGAGTAAACTTTGCAAATCATTATTTCCAG 1378Tsuyuake_Pikm CCTGCAACCCAAGGAAAGCCTGCTGCGATTGGAGTAAACTTTGCAAATCATTATTTCCAG 1378Kusabue_Pik CCTGCAACCCAAGGAAAGCCTGCTGCGATTGGAGTAAACTTTGCAAATCATTATTTCCAG 1378Kanto51_Pik CCTGCAACCCAAGGAAAGCCTGCTGCGATTGGAGTAAACTTTGCAAATCATTATTTCCAG 1378K60_Pikp CCTGCAACCCAAGGAAAGCCTGCTGCGATTGGAGTAAACTTTGCAAATCATTATTTCCAG 1378Acc108 CCTGCAACCCAAGGAAAGCCTGCTGCGATTGGAGTAAACTTTGCAAATCATTATTTCCAG 1378Acc130 CCTGCAACCCAAGGAAAGCCTGCTGCGATTGGAGTAAACTTTGCAAATCATTATTTCCAG 1378Acc719 CCTGCAACCCAAGGAAAGCCTGCTGCGATTGGAGTAAACTTTGCAAATCATTATTTCCAG 1378Acc729 CCTGCAACCCAAGGAAAGCCTGCTGCGATTGGAGTAAACTTTGCAAATCATTATTTCCAG 1378Acc710 CCTGCAACCCAAGGAAAGCCTGCTGCGATTGGAGTAAACTTTGCAAATCATTATTTCCAG 1378Acc709 CCTGCAACCCAAGGAAAGCCTGCTGCGATTGGAGTAAACTTTGCAAATCATTATTTCCAG 1378Acc220 CCTGCAACCCAAACAAAGCCAACTCCGATTGGAGTAAACTTTGCGAATCATTATTTCCAT 1447Nipponbare CCTGCAACCCAAACAAAGCCAACTCCGATTGGAGTAAACTTTGCGAATCATTATTTCCAT 1447Acc224 CCTGCAACCCAAACAAAGCCAACTCCGATTGGAGTAAACTTTGCGAATCATTATTTCCAT 1447AccUP3 CCTGCAACCCAAACAAAGCCAACTCCGATTGGAGTAAACTTTGCGAATCATTATTTCCAT 1447AccUP1 CCTGCAACCCAAACAAAGCCAACTCCGATTGGAGTAAACTTTGCGAATCATTATTTCCAT 1447Acc206 CCTGCAACCCAAACAAAGCCAACTCCGATTGGAGTAAACTTTGCGAATCATTATTTCCAT 1447Acc201 CCTGCAACCCAAACAAAGCCAACTCCGATTGGAGTAAACTTTGCGAATCATTATTTCCAT 1447Acc724 CCTGCAACCCAAACAAAGCCAACTCCGATTGGAGTAAACTTTGCGAATCATTATTTCCAT 1447Acc415 CCTGCAACCCAAACAAAGCCAACTCCGATTGGAGTAAACTTTGCGAATCATTATTTCCAT 1447Acc417 CCTGCAACCCAAACAAAGCCAACTCCGATTGGAGTAAACTTTGCGAATCATTATTTCCAT 1447Acc435 CCTGCAACCCAAACAAAGCCAACTCCGATTGGAGTAAACTTTGCGAATCATTATTTCCAT 1447Acc712 CCTGCAACCCAAACAAAGCCAACTCCGATTGGAGTAAACTTTGCGAATCATTATTTCCAT 1447Acc101 CCTGCAACCCAAACAAGACCGACTGCGATTGGCGTAAACTTTGCGAATCATTATTTCCAG 1462Acc715 CCTGCAACCCAAACAAGACCGACTGCGATTGGCGTAAACTTTGCGAATCATTATTTCCAG 1462Acc706 CCTGCAACCCAAACAAGACCGACTGCGATTGGCGTAAACTTTGCGAATCATTATTTCCAG 1462Acc624 CCTGCAACCCAAACAAGACCGACTGCGATTGGCGTAAACTTTGCGAATCATTATTTCCAG 1462Acc1 CCTGCAACCCAAACAAGACCGACTGCGATTGGCGTAAACTTTGCGAATCATTATTTCCAG 1411Acc440 CCTGCAACCCAAACAAGACCGACTGCGATTGGCGTAAACTTTGCAAATCATTATTTCCAG 1411Acc868 CCTGCAACCCAAACAAGACCGACTGCGATTGGCGTAAACTTTGCAAATCATTATTTCCAG 1425Acc718 CCTGCAACCCAAACAAGACCGACTGCGATTGGCGTAAACTTTGCAAATCATTATTTCCAG 1411 ************ ** ** ** ******* *********** **************

Ashikawa et al. Supplementary Fig. S2 (13/28)

Acc414 AGCAAGAAACTCCTCTTACCCTCGATGGTGTTACAAGGATACTGGATTGTTGTTACAATG 1438Acc420 AGCAAGAAACTCCTCTTACCCTCGATGGTGTTACAAGGATACTGGATTGTTGTTACAATG 1438Acc761 AGCAAGAAACTCCTCTTACCCTCGATGGTGTTACAAGGATACTGGATTGTTGTTACAATG 1438Acc504 AGCAAGAAACTCCTCTTACCCTCGATGGTGTTACAAGGATACTGGATTGTTGTTACAATG 1438Acc563 AGCAAGAAACTCCTCTTACCCTCGATGGTGTTACAAGGATACTGGATTGTTGTTACAATG 1438Acc757 AGCAAGAAACTCCTCTTACCCTCGATGGTGTTACAAGGATACTGGATTGTTGTTACAATG 1438Acc848 AGCAAGAAACTCCTCTTACCCTCGATGGTGTTACAAGGATACTGGATTGTTGTTACAATG 1438Tsuyuake_Pikm AGCAAGAAACTCCTCTTACCCTCGATGGTGTTACAAGGATACTGGATTGTTGTTACAATG 1438Kusabue_Pik AGCAAGAAACTCCTCTTACCCTCGATGGTGTTACAAGGATACTGGATTGTTGTTACAATG 1438Kanto51_Pik AGCAAGAAACTCCTCTTACCCTCGATGGTGTTACAAGGATACTGGATTGTTGTTACAATG 1438K60_Pikp AGCAAGAAACTCCTCTTACCCTCGATGGTGTTACAAGGATACTGGATTGTTGTTACAATG 1438Acc108 AGCAAGAAACTCCTCTTACCCTCGATGGTGTTACAAGGATACTGGATTGTTGTTACAATG 1438Acc130 AGCAAGAAACTCCTCTTACCCTCGATGGTGTTACAAGGATACTGGATTGTTGTTACAATG 1438Acc719 AGCAAGAAACTCCTCTTACCCTCGATGGTGTTACAAGGATACTGGATTGTTGTTACAATG 1438Acc729 AGCAAGAAACTCCTCTTACCCTCGATGGTGTTACAAGGATACTGGATTGTTGTTACAATG 1438Acc710 AGCAAGAAACTCCTCTTACCCTCGATGGTGTTACAAGGATACTGGATTGTTGTTACAATG 1438Acc709 AGCAAGAAACTCCTCTTACCCTCGATGGTGTTACAAGGATACTGGATTGTTGTTACAATG 1438Acc220 ATCCAGTAACTACTCTTAACCTGGATGGGGTTACGAGGATACTGGATTGTTGTTACAATG 1507Nipponbare ATCCAGTAACTACTCTTAACCTGGATGGGGTTACGAGGATACTGGATTGTTGTTACAATG 1507Acc224 ATCCAGTAACTACTCTTAACCTGGATGGGGTTACGAGGATACTGGATTGTTGTTACAATG 1507AccUP3 ATCCAGTAACTACTCTTAACCTGGATGGGGTTACGAGGATACTGGATTGTTGTTACAATG 1507AccUP1 ATCCAGTAACTACTCTTAACCTGGATGGGGTTACGAGGATACTGGATTGTTGTTACAATG 1507Acc206 ATCCAGTAACTACTCTTAACCTGGATGGGGTTACGAGGATACTGGATTGTTGTTACAATG 1507Acc201 ATCCAGTAACTACTCTTAACCTGGATGGGGTTACGAGGATACTGGATTGTTGTTACAATG 1507Acc724 ATCCAGTAACTACTCTTAACCTGGATGGGGTTACGAGGATACTGGATTGTTGTTACAATG 1507Acc415 ATCCAGTAACTACTCTTAACCTGGATGGGGTTACGAGGATACTGGATTGTTGTTACAATG 1507Acc417 ATCCAGTAACTACTCTTAACCTGGATGGGGTTACGAGGATACTGGATTGTTGTTACAATG 1507Acc435 ATCCAGTAACTACTCTTAACCTGGATGGGGTTACGAGGATACTGGATTGTTGTTACAATG 1507Acc712 ATCCAGTAACTACTCTTAACCTGGATGGGGTTACGAGGATACTGGATTGTTGTTACAATG 1507Acc101 ATCCAGTAACTACTCTTAACCTGGATGGGGTTACGAGGATACTGGATTGTTGTTACAATG 1522Acc715 ATCCAGTAACTACTCTTAACCTGGATGGGGTTACGAGGATACTGGATTGTTGTTACAATG 1522Acc706 ATCCAGTAACTACTCTTAACCTGGATGGGGTTACGAGGATACTGGATTGTTGTTACAATG 1522Acc624 ATCCAGTAACTACTCTTAACCTGGATGGGGTTACGAGGATACTGGATTGTTGTTACAATG 1522Acc1 ATCCAGTAACTACTCTTAACCTGGATGGGGTTACGAGGATACTGGATTGTTGTTACAATG 1471Acc440 ATCCAGTAACTACTCTTAACCTGGATGGGGTTACGAGGATACTGGATTGTTGTTACAATG 1471Acc868 ATCCAGTAACTACTCTTAACCTGGATGGGGTTACGAGGATACTGGATTGTTGTTACAATG 1485Acc718 ATCCAGTAACTACTCTTAACCTGGATGGGGTTACGAGGATACTGGATTGTTGTTACAATG 1471 * * ** **** ****** *** ***** ***** ************************* Acc414 ATTTGCCTGCGGATCTGAAGACTTGCTTATTGTACTTGAGTATATTTCCGAAGGGTTGGA 1498Acc420 ATTTGCCTGCGGATCTGAAGACTTGCTTATTGTACTTGAGTATATTTCCGAAGGGTTGGA 1498Acc761 ATTTGCCTGCGGATCTGAAGACTTGCTTATTGTACTTGAGTATATTTCCGAAGGGTTGGA 1498Acc504 ATTTGCCTGCGGATCTGAAGACTTGCTTATTGTACTTGAGTATATTTCCGAAGGGTTGGA 1498Acc563 ATTTGCCTGCGGATCTGAAGACTTGCTTATTGTACTTGAGTATATTTCCGAAGGGTTGGA 1498Acc757 ATTTGCCTGCGGATCTGAAGACTTGCTTATTGTACTTGAGTATATTTCCGAAGGGTTGGA 1498Acc848 ATTTGCCTGCGGATCTGAAGACTTGCTTATTGTACTTGAGTATATTTCCGAAGGGTTGGA 1498Tsuyuake_Pikm ATTTGCCTGCGGATCTGAAGACTTGCTTATTGTACTTGAGTATATTTCCGAAGGGTTGGA 1498Kusabue_Pik ATTTGCCTGCGGATCTGAAGACTTGCTTATTGTACTTGAGTATATTTCCGAAGGGTTGGA 1498Kanto51_Pik ATTTGCCTGCGGATCTGAAGACTTGCTTATTGTACTTGAGTATATTTCCGAAGGGTTGGA 1498K60_Pikp ATTTGCCTGCGGATCTGAAGACTTGCTTATTGTACTTGAGTATATTTCCGAAGGGTTGGA 1498Acc108 ATTTGCCTGCGGATCTGAAGACTTGCTTATTGTACTTGAGTATATTTCCGAAGGGTTGGA 1498Acc130 ATTTGCCTGCGGATCTGAAGACTTGCTTATTGTACTTGAGTATATTTCCGAAGGGTTGGA 1498Acc719 ATTTGCCTGCGGATCTGAAGACTTGCTTATTGTACTTGAGTATATTTCCGAAGGGTTGGA 1498Acc729 ATTTGCCTGCGGATCTGAAGACTTGCTTATTGTACTTGAGTATATTTCCGAAGGGTTGGA 1498Acc710 ATTTGCCTGCGGATCTGAAGACTTGCTTATTGTACTTGAGTATATTTCCGAAGGGTTGGA 1498Acc709 ATTTGCCTGCGGATCTGAAGACTTGCTTATTGTACTTGAGTATATTTCCGAAGGGTTGGA 1498Acc220 ATTTGCCTGCAGATCTCAAGACCTGCTTATTGTACTTGAGTATATTTCCAAAGGGTTGGA 1567Nipponbare ATTTGCCTGCAGATCTCAAGACCTGCTTATTGTACTTGAGTATATTTCCAAAGGGTTGGA 1567Acc224 ATTTGCCTGCAGATCTCAAGACCTGCTTATTGTACTTGAGTATATTTCCAAAGGGTTGGA 1567AccUP3 ATTTGCCTGCAGATCTCAAGACCTGCTTATTGTACTTGAGTATATTTCCAAAGGGTTGGA 1567AccUP1 ATTTGCCTGCAGATCTCAAGACCTGCTTATTGTACTTGAGTATATTTCCAAAGGGTTGGA 1567Acc206 ATTTGCCTGCAGATCTCAAGACCTGCTTATTGTACTTGAGTATATTTCCAAAGGGTTGGA 1567Acc201 ATTTGCCTGCAGATCTCAAGACCTGCTTATTGTACTTGAGTATATTTCCAAAGGGTTGGA 1567Acc724 ATTTGCCTGCAGATCTCAAGACCTGCTTATTGTACTTGAGTATATTTCCAAAGGGTTGGA 1567Acc415 ATTTGCCTGCAGATCTCAAGACCTGCTTATTGTACTTGAGTATATTTCCAAAGGGTTGGA 1567Acc417 ATTTGCCTGCAGATCTCAAGACCTGCTTATTGTACTTGAGTATATTTCCAAAGGGTTGGA 1567Acc435 ATTTGCCTGCAGATCTCAAGACCTGCTTATTGTACTTGAGTATATTTCCAAAGGGTTGGA 1567Acc712 ATTTGCCTGCAGATCTCAAGACCTGCTTATTGTACTTGAGTATATTTCCAAAGGGTTGGA 1567Acc101 ATTTGCCTGCAGATCTCAAGACCTGCTTATTGTACTTGAGTATATTTCCAAAGGGTTGGA 1582Acc715 ATTTGCCTGCAGATCTCAAGACCTGCTTATTGTACTTGAGTATATTTCCAAAGGGTTGGA 1582Acc706 ATTTGCCTGCAGATCTCAAGACCTGCTTATTGTACTTGAGTATATTTCCAAAGGGTTGGA 1582Acc624 ATTTGCCTGCAGATCTCAAGACCTGCTTATTGTACTTGAGTATATTTCCAAAGGGTTGGA 1582Acc1 ATTTGCCTGCAGATCTCAAGACCTGCTTATTGTACTTGAGTATATTTCCAAAGGGTTGGA 1531Acc440 ATTTGCCTGCAGATATCAAGACCTGCTTATTGTACTTGAGTATATTTCCAAAGGGTTGGA 1531Acc868 ATTTGCCTGCAGATATCAAGACCTGCTTATTGTACTTGAGTATATTTCCAAAGGGTTGGA 1545Acc718 ATTTGCCTGCAGATATCAAGACCTGCTTATTGTACTTGAGTATATTTCCAAAGGGTTGGA 1531 ********** *** * ***** ************************** ********** 

Ashikawa et al. Supplementary Fig. S2 (14/28)

Acc414 AAATTAGTAGGAAACGTTTGTCCCGGCGATGGATAGCTGAAGGTTTTGCTAATGAGAAGC 1558Acc420 AAATTAGTAGGAAACGTTTGTCCCGGCGATGGATAGCTGAAGGTTTTGCTAATGAGAAGC 1558Acc761 AAATTAGTAGGAAACGTTTGTCCCGGCGATGGATAGCTGAAGGTTTTGCTAATGAGAAGC 1558Acc504 AAATTAGTAGGAAACGTTTGTCCCGGCGATGGATAGCTGAAGGTTTTGCTAATGAGAAGC 1558Acc563 AAATTAGTAGGAAACGTTTGTCCCGGCGATGGATAGCTGAAGGTTTTGCTAATGAGAAGC 1558Acc757 AAATTAGTAGGAAACGTTTGTCCCGGCGATGGATAGCTGAAGGTTTTGCTAATGAGAAGC 1558Acc848 AAATTAGTAGGAAACGTTTGTCCCGGCGATGGATAGCTGAAGGTTTTGCTAATGAGAAGC 1558Tsuyuake_Pikm AAATTAGTAGGAAACGTTTGTCCCGGCGATGGATAGCTGAAGGTTTTGCTAATGAGAAGC 1558Kusabue_Pik AAATTAGTAGGAAACGTTTGTCCCGGCGATGGATAGCTGAAGGTTTTGCTAATGAGAAGC 1558Kanto51_Pik AAATTAGTAGGAAACGTTTGTCCCGGCGATGGATAGCTGAAGGTTTTGCTAATGAGAAGC 1558K60_Pikp AAATTAGTAGGAAACGTTTGTCCCGGCGATGGATAGCTGAAGGTTTTGCTAATGAGAAGC 1558Acc108 AAATTAGTAGGAAACGTTTGTCCCGGCGATGGATAGCTGAAGGTTTTGCTAATGAGAAGC 1558Acc130 AAATTAGTAGGAAACGTTTGTCCCGGCGATGGATAGCTGAAGGTTTTGCTAATGAGAAGC 1558Acc719 AAATTAGTAGGAAACGTTTGTCCCGGCGATGGATAGCTGAAGGTTTTGCTAATGAGAAGC 1558Acc729 AAATTAGTAGGAAACGTTTGTCCCGGCGATGGATAGCTGAAGGTTTTGCTAATGAGAAGC 1558Acc710 AAATTAGTAGGAAACGTTTGTCCCGGCGATGGATAGCTGAAGGTTTTGCTAATGAGAAGC 1558Acc709 AAATTAGTAGGAAACGTTTGTCCCGGCGATGGATAGCTGAAGGTTTTGCTAATGAGAAGC 1558Acc220 AAATTAGTAGGAAGCGGTTGGCCCGACGATGGATTGCTGAAGGTTTTGCTACTGAGAAGC 1627Nipponbare AAATTAGTAGGAAGCGGTTGGCCCGACGATGGATTGCTGAAGGTTTTGCTACTGAGAAGC 1627Acc224 AAATTAGTAGGAAGCGGTTGGCCCGACGATGGATTGCTGAAGGTTTTGCTACTGAGAAGC 1627AccUP3 AAATTAGTAGGAAGCGGTTGGCCCGACGATGGATTGCTGAAGGTTTTGCTACTGAGAAGC 1627AccUP1 AAATTAGTAGGAAGCGGTTGGCCCGACGATGGATTGCTGAAGGTTTTGCTACTGAGAAGC 1627Acc206 AAATTAGTAGGAAGCGGTTGGCCCGACGATGGATTGCTGAAGGTTTTGCTACTGAGAAGC 1627Acc201 AAATTAGTAGGAAGCGGTTGGCCCGACGATGGATTGCTGAAGGTTTTGCTACTGAGAAGC 1627Acc724 AAATTAGTAGGAAGCGGTTGGCCCGACGATGGATTGCTGAAGGTTTTGCTACTGAGAAGC 1627Acc415 AAATTAGTAGGAAGCGGTTGGCCCGGCGATGGATTGCTGAAGGTTTTGCTACTGAGAAGC 1627Acc417 AAATTAGTAGGAAGCGGTTGGCCCGGCGATGGATTGCTGAAGGTTTTGCTACTGAGAAGC 1627Acc435 AAATTAGTAGGAAGCGGTTGGCCCGGCGATGGATTGCTGAAGGTTTTGCTACTGAGAAGC 1627Acc712 AAATTAGTAGGAAGCGGTTGGCCCGGCGATGGATTGCTGAAGGTTTTGCTACTGAGAAGC 1627Acc101 AAATTAGTAGGAAGCGTTTGGCCCGGCGATGGATTGCTGAAGGTTTTGCTACTGAGAAGC 1642Acc715 AAATTAGTAGGAAGCGTTTGGCCCGGCGATGGATTGCTGAAGGTTTTGCTACTGAGAAGC 1642Acc706 AAATTAGTAGGAAGCGTTTGGCCCGGCGATGGATTGCTGAAGGTTTTGCTACTGAGAAGC 1642Acc624 AAATTAGTAGGAAGCGTTTGGCCCGGCGATGGATTGCTGAAGGTTTTGCTACTGAGAAGC 1642Acc1 AAATTAGTAGGAAGCGTTTGGCCCGGCGATGGATTGCTGAAGGTTTTGCTACTGAGAAGC 1591Acc440 AAATTAGTAGAAAGCGTTTGGCCCGGCGATGGATTGCTGAAGGTTTTGCTACTGAGAAGC 1591Acc868 AAATTAGTAGAAAGCGTTTGGCCCGGCGATGGATTGCTGAAGGTTTTGCTACTGAGAAGC 1605Acc718 AAATTAGTAGAAAGCGTTTGGCCCGGCGATGGATTGCTGAAGGTTTTGCTACTGAGAAGC 1591 ********** ** ** *** **** ******** **************** ******** Acc414 AAGGGTTAACCCAGGAAAGAGTTGCAGAGGCATACTTTAATCAACTCACAAGAAGGAACT 1618Acc420 AAGGGTTAACCCAGGAAAGAGTTGCAGAGGCATACTTTAATCAACTCACAAGAAGGAACT 1618Acc761 AAGGGTTAACCCAGGAAAGAGTTGCAGAGGCATACTTTAATCAACTCACAAGAAGGAACT 1618Acc504 AAGGGTTAACCCAGGAAAGAGTTGCAGAGGCATACTTTAATCAACTCACAAGAAGGAACT 1618Acc563 AAGGGTTAACCCAGGAAAGAGTTGCAGAGGCATACTTTAATCAACTCACAAGAAGGAACT 1618Acc757 AAGGGTTAACCCAGGAAAGAGTTGCAGAGGCATACTTTAATCAACTCACAAGAAGGAACT 1618Acc848 AAGGGTTAACCCAGGAAAGAGTTGCAGAGGCATACTTTAATCAACTCACAAGAAGGAACT 1618Tsuyuake_Pikm AAGGGTTAACCCAGGAAAGAGTTGCAGAGGCATACTTTAATCAACTCACAAGAAGGAACT 1618Kusabue_Pik AAGGGTTAACCCAGGAAAGAGTTGCAGAGGCATACTTTAATCAACTCACAAGAAGGAACT 1618Kanto51_Pik AAGGGTTAACCCAGGAAAGAGTTGCAGAGGCATACTTTAATCAACTCACAAGAAGGAACT 1618K60_Pikp AAGGGTTAACCCAGGAAAGAGTTGCAGAGGCATACTTTAATCAACTCACAAGAAGGAACT 1618Acc108 AAGGGTTAACCCAGGAAAGAGTTGCAGAGGCATACTTTAATCAACTCACAAGAAGGAACT 1618Acc130 AAGGGTTAACCCAGGAAAGAGTTGCAGAGGCATACTTTAATCAACTCACAAGAAGGAACT 1618Acc719 AAGGGTTAACCCAGGAAAGAGTTGCAGAGGCATACTTTAATCAACTCACAAGAAGGAACT 1618Acc729 AAGGGTTAACCCAGGAAAGAGTTGCAGAGGCATACTTTAATCAACTCACAAGAAGGAACT 1618Acc710 AAGGGTTAACCCAGGAAAGAGTTGCAGAGGCATACTTTAATCAACTCACAAGAAGGAACT 1618Acc709 AAGGGTTAACCCAGGAAAGAGTTGCAGAGGCATACTTTAATCAACTCACAAGAAGGAACT 1618Acc220 AAGGGCTAACCGAAGAGGAAGTTGCAGAGGCATACTTTAATCAGCTCGCAAGAAGGAACT 1687Nipponbare AAGGGCTAACCGAAGAGGAAGTTGCAGAGGCATACTTTAATCAGCTCGCAAGAAGGAACT 1687Acc224 AAGGGCTAACCGAAGAGGAAGTTGCAGAGGCATACTTTAATCAGCTCGCAAGAAGGAACT 1687AccUP3 AAGGGCTAACCGAAGAGGAAGTTGCAGAGGCATACTTTAATCAGCTCGCAAGAAGGAACT 1687AccUP1 AAGGGCTAACCGAAGAGGAAGTTGCAGAGGCATACTTTAATCAGCTCGCAAGAAGGAACT 1687Acc206 AAGGGCTAACCGAAGAGGAAGTTGCAGAGGCATACTTTAATCAGCTCGCAAGAAGGAACT 1687Acc201 AAGGGCTAACCGAAGAGGAAGTTGCAGAGGCATACTTTAATCAGCTCGCAAGAAGGAACT 1687Acc724 AAGGGCTAACCGAAGAGGAAGTTGCAGAGGCATACTTTAATCAGCTCGCAAGAAGGAACT 1687Acc415 AAGGGCTAACCGAAGAGGAAGTTGCAGAGGCATACTTTAATCAGCTCGCAAGAAGGAACT 1687Acc417 AAGGGCTAACCGAAGAGGAAGTTGCAGAGGCATACTTTAATCAGCTCGCAAGAAGGAACT 1687Acc435 AAGGGCTAACCGAAGAGGAAGTTGCAGAGGCATACTTTAATCAGCTCGCAAGAAGGAACT 1687Acc712 AAGGGCTAACCGAAGAGGAAGTTGCAGAGGCATACTTTAATCAGCTCGCAAGAAGGAACT 1687Acc101 AAGGGCTAACCGAGGAGGAAGTTGCAGAGACATACTTTAATCAGCTCACAAGAAGGAACT 1702Acc715 AAGGGCTAACCGAGGAGGAAGTTGCAGAGACATACTTTAATCAGCTCACAAGAAGGAACT 1702Acc706 AAGGGCTAACCGAGGAGGAAGTTGCAGAGACATACTTTAATCAGCTCACAAGAAGGAACT 1702Acc624 AAGGGCTAACCGAGGAGGAAGTTGCAGAGACATACTTTAATCAGCTCACAAGAAGGAACT 1702Acc1 AAGGGCTAACCGAGGAGGAAGTTGCAGAGACATACTTTAATCAGCTCACAAGAAGGAACT 1651Acc440 AAGGGCTAACCGAGGAGGAAGTTGCAGAGACATACTTTAATCAGCTCACAAGAAGGAACT 1651Acc868 AAGGGCTAACCGAGGAGGAAGTTGCAGAGACATACTTTAATCAGCTCACAAGAAGGAACT 1665Acc718 AAGGGCTAACCGAGGAGGAAGTTGCAGAGACATACTTTAATCAGCTCACAAGAAGGAACT 1651 ***** ***** * ** ********** ************* *** ************

Ashikawa et al. Supplementary Fig. S2 (15/28)

Acc414 TAGTACGTCCCATGGAGCATGGCAGCAATGGGAAGGTAAAAACGTTTCAAGTTCATGACA 1678Acc420 TAGTACGTCCCATGGAGCATGGCAGCAATGGGAAGGTAAAAACGTTTCAAGTTCATGACA 1678Acc761 TAGTACGTCCCATGGAGCATGGCAGCAATGGGAAGGTAAAAACGTTTCAAGTTCATGACA 1678Acc504 TAGTACGTCCCATGGAGCATGGCAGCAATGGGAAGGTAAAAACGTTTCAAGTTCATGACA 1678Acc563 TAGTACGTCCCATGGAGCATGGCAGCAATGGGAAGGTAAAAACGTTTCAAGTTCATGACA 1678Acc757 TAGTACGTCCCATGGAGCATGGCAGCAATGGGAAGGTAAAAACGTTTCAAGTTCATGACA 1678Acc848 TAGTACGTCCCATGGAGCATGGCAGCAATGGGAAGGTAAAAACGTTTCAAGTTCATGACA 1678Tsuyuake_Pikm TAGTACGTCCCATGGAGCATGGCAGCAATGGGAAGGTAAAAACGTTTCAAGTTCATGACA 1678Kusabue_Pik TAGTACGTCCCATGGAGCATGGCAGCAATGGGAAGGTAAAAACGTTTCAAGTTCATGACA 1678Kanto51_Pik TAGTACGTCCCATGGAGCATGGCAGCAATGGGAAGGTAAAAACGTTTCAAGTTCATGACA 1678K60_Pikp TAGTACGTCCCATGGAGCATGGCAGCAATGGGAAGGTAAAAACGTTTCAAGTTCATGACA 1678Acc108 TAGTACGTCCCATGGAGCATGGCAGCAATGGGAAGGTAAAAACGTTTCAAGTTCATGACA 1678Acc130 TAGTACGTCCCATGGAGCATGGCAGCAATGGGAAGGTAAAAACGTTTCAAGTTCATGACA 1678Acc719 TAGTACGTCCCATGGAGCATGGCAGCAATGGGAAGGTAAAAACGTTTCAAGTTCATGACA 1678Acc729 TAGTACGTCCCATGGAGCATGGCAGCAATGGGAAGGTAAAAACGTTTCAAGTTCATGACA 1678Acc710 TAGTACGTCCCATGGAGCATGGCAGCAATGGGAAGGTAAAAACGTTTCAAGTTCATGACA 1678Acc709 TAGTACGTCCCATGGAGCATGGCAGCAATGGGAAGGTAAAAACGTTTCAAGTTCATGACA 1678Acc220 TAATACGCCCTGTGGAGCATGGCAGCAATGGGAAGGTAAAAGCCTTTCAAGTTCATGACA 1747Nipponbare TAATACGCCCTGTGGAGCATGGCAGCAATGGGAAGGTAAAAGCCTTTCAAGTTCATGACA 1747Acc224 TAATACGCCCTGTGGAGCATGGCAGCAATGGGAAGGTAAAAGCCTTTCAAGTTCATGACA 1747AccUP3 TAATACGCCCTGTGGAGCATGGCAGCAATGGGAAGGTAAAAGCCTTTCAAGTTCATGACA 1747AccUP1 TAATACGCCCTGTGGAGCATGGCAGCAATGGGAAGGTAAAAGCCTTTCAAGTTCATGACA 1747Acc206 TAATACGCCCTGTGGAGCATGGCAGCAATGGGAAGGTAAAAGCCTTTCAAGTTCATGACA 1747Acc201 TAATACGCCCTGTGGAGCATGGCAGCAATGGGAAGGTAAAAGCCTTTCAAGTTCATGACA 1747Acc724 TAATACGCCCTGTGGAGCATGGCAGCAATGGGAAGGTAAAAGCCTTTCAAGTTCATGACA 1747Acc415 TAATACGCCCTGTGGAGCATGGCAGCAATGGGAAGGTAAAAGCCTTTCAAGTTCATGACA 1747Acc417 TAATACACCCTGTGGAGCATGGCAGCAATGGGAAGGTAAAAGCCTTTCAAGTTCATGACA 1747Acc435 TAATACGCCCTGTGGAGCATGGCAGCAATGGGAAGGTAAAAGCCTTTCAAGTTCATGACA 1747Acc712 TAATACGCCCTGTGGAGCATGGCAGCAATGGGAAGGTAAAAGCCTTTCAAGTTCATGACA 1747Acc101 TAATACGTCCTGTGGAGCATGGCAGCAATGGGAAGGTAAAATCCTTTCAAGTTCATGACA 1762Acc715 TAATACGTCCTGTGGAGCATGGCAGCAATGGGAAGGTAAAATCCTTTCAAGTTCATGACA 1762Acc706 TAATACGTCCTGTGGAGCATGGCAGCAATGGGAAGGTAAAATCCTTTCAAGTTCATGACA 1762Acc624 TAATACGTCCTGTGGAGCATGGCAGCAATGGGAAGGTAAAATCCTTTCAAGTTCATGACA 1762Acc1 TAATACGTCCTGTGGAGCATGGCAGCAATGGGAAGGTAAAAGCCTTTCAAGTTCATGACA 1711Acc440 TAATACGTCCTGTGGAGCATGGCAGCAATGGGAAGGTAAAAGCCTTTCAAGTTCATGACA 1711Acc868 TAATACGTCCTGTGGAGCATGGCAGCAATGGGAAGGTAAAAGCCTTTCAAGTTCATGACA 1725Acc718 TAATACGTCCTGTGGAGCATGGCAGCAATGGGAAGGTAAAAGCCTTTCAAGTTCATGACA 1711 ** *** ** ***************************** * **************** Acc414 TGGTTCTTGAATACATCATGTCCAAATCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1738Acc420 TGGTTCTTGAATACATCATGTCCAAATCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1738Acc761 TGGTTCTTGAATACATCATGTCCAAATCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1738Acc504 TGGTTCTTGAATACATCATGTCCAAATCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1738Acc563 TGGTTCTTGAATACATCATGTCCAAATCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1738Acc757 TGGTTCTTGAATACATCATGTCCAAATCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1738Acc848 TGGTTCTTGAATACATCATGTCCAAATCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1738Tsuyuake_Pikm TGGTTCTTGAATACATCATGTCCAAATCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1738Kusabue_Pik TGGTTCTTGAATACATCATGTCCAAATCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1738Kanto51_Pik TGGTTCTTGAATACATCATGTCCAAATCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1738K60_Pikp TGGTTCTTGAATACATCATGTCCAAATCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1738Acc108 TGGTTCTTGAATACATCATGTCCAAATCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1738Acc130 TGGTTCTTGAATACATCATGTCCAAATCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1738Acc719 TGGTTCTTGAATACATCATGTCCAAATCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1738Acc729 TGGTTCTTGAATACATCATGTCCAAATCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1738Acc710 TGGTTCTTGAATACATCATGTCCAAATCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1738Acc709 TGGTTCTTGAATACATCATGTCCAAATCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1738Acc220 TGGTTCTTGAATACATCATGTCGAAGTCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1807Nipponbare TGGTTCTTGAATACATCATGTCGAAGTCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1807Acc224 TGGTTCTTGAATACATCATGTCGAAGTCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1807AccUP3 TGGTTCTTGAATACATCATGTCGAAGTCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1807AccUP1 TGGTTCTTGAATACATCATGTCGAAGTCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1807Acc206 TGGTTCTTGAATACATCATGTCGAAGTCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1807Acc201 TGGTTCTTGAATACATCATGTCGAAGTCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1807Acc724 TGGTTCTTGAATACATCATGTCGAAGTCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1807Acc415 TGGTTCTTGAATACATCATGTCGAAGTCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1807Acc417 TGGTTCTTGAATACATCATGTCGAAGTCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1807Acc435 TGGTTCTTGAATACATCATGTCGAAGTCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1807Acc712 TGGTTCTTGAATACATCATGTCGAAGTCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1807Acc101 TGGTTCTTGAATACATCATGTCCAAGTCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1822Acc715 TGGTTCTTGAATACATCATGTCCAAGTCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1822Acc706 TGGTTCTTGAATACATCATGTCCAAGTCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1822Acc624 TGGTTCTTGAATACATCATGTCCAAGTCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1822Acc1 TGGTTCTTGAATACATCATGTCCAAGTCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1771Acc440 TGGTTCTTGAATACATCATGTCCAAGTCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1771Acc868 TGGTTCTTGAATACATCATGTCCAAGTCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1785Acc718 TGGTTCTTGAATACATCATGTCCAAGTCAATCGAAGAGAATTTTATTACTGTGGTTGGTG 1771 ********************** ** **********************************

Ashikawa et al. Supplementary Fig. S2 (16/28)

Acc414 GACACTGGCAGATGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1798Acc420 GACACTGGCAGATGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1798Acc761 GACACTGGCAGATGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1798Acc504 GACACTGGCAGATGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1798Acc563 GACACTGGCAGATGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1798Acc757 GACACTGGCAGATGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1798Acc848 GACACTGGCAGATGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1798Tsuyuake_Pikm GACACTGGCAGATGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1798Kusabue_Pik GACACTGGCAGATGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1798Kanto51_Pik GACACTGGCAGATGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1798K60_Pikp GACACTGGCAGATGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1798Acc108 GACACTGGCAGATGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1798Acc130 GACACTGGCAGATGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1798Acc719 GACACTGGCAGATGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1798Acc729 GACACTGGCAGATGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1798Acc710 GACACTGGCAGATGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1798Acc709 GACACTGGCAGATGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1798Acc220 GACACTGGCAGATGACTGCGCCAAGCAATAAAGTCCGTCGACTATCGTTGCAAAGCAGTG 1867Nipponbare GACACTGGCAGATGACTGCGCCAAGCAATAAAGTCCGTCGACTATCGTTGCAAAGCAGTG 1867Acc224 GACACTGGCAGATGACTGCGCCAAGCAATAAAGTCCGTCGACTATCGTTGCAAAGCAGTG 1867AccUP3 GACACTGGCAGATGACTGCGCCAAGCAATAAAGTCCGTCGACTATCGTTGCAAAGCAGTG 1867AccUP1 GACACTGGCAGATGACTGCGCCAAGCAATAAAGTCCGTCGACTATCGTTGCAAAGCAGTG 1867Acc206 GACACTGGCAGATGACTGCGCCAAGCAATAAAGTCCGTCGACTATCGTTGCAAAGCAGTG 1867Acc201 GACACTGGCAGATGACTGCGCCAAGCAATAAAGTCCGTCGACTATCGTTGCAAAGCAGTG 1867Acc724 GACACTGGCAGATGACTGCGCCAAGCAATAAAGTCCGTCGACTATCGTTGCAAAGCAGTG 1867Acc415 GACACTGGCAGATGACTGCGCCAAGCAATAAAGTCCGTCGACTATCGTTGCAAAGCAGTG 1867Acc417 GACACTGGCAGATGACTGCGCCAAGCAATAAAGTCCGTCGACTATCGTTGCAAAGCAGTG 1867Acc435 GACACTGGCAGATGACTGCGCCAAGCAATAAAGTCCGTCGACTATCGTTGCAAAGCAGTG 1867Acc712 GACACTGGCAGATGACTGCGCCAAGCAATAAAGTCCGTCGACTATCGTTGCAAAGCAGTG 1867Acc101 GACAGTGGCAGGTGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1882Acc715 GACAGTGGCAGGTGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1882Acc706 GACAGTGGCAGGTGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1882Acc624 GACAGTGGCAGGTGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1882Acc1 GACAGTGGCAGGTGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1831Acc440 GACAGTGGCAGGTGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1831Acc868 GACAGTGGCAGGTGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1845Acc718 GACAGTGGCAGGTGACTGCACCAAGCAATAAAGTCCGTCGACTGTCGATGCAAAGCAGTG 1831 **** ****** ******* *********************** *** ************ Acc414 GATCCAATCGTGGAAGTTCAACAAAAGGCCTGAACTTGGCTCAAGTGAGATCACTGACGG 1858Acc420 GATCCAATCGTGGAAGTTCAACAAAAGGCCTGAACTTGGCTCAAGTGAGATCACTGACGG 1858Acc761 GATCCAATCGTGGAAGTTCAACAAAAGGCCTGAACTTGGCTCAAGTGAGATCACTGACGG 1858Acc504 GATCCAATCGTGGAAGTTCAACAAAAGGCCTGAACTTGGCTCAAGTGAGATCACTGACGG 1858Acc563 GATCCAATCGTGGAAGTTCAACAAAAGGCCTGAACTTGGCTCAAGTGAGATCACTGACGG 1858Acc757 GATCCAATCGTGGAAGTTCAACAAAAGGCCTGAACTTGGCTCAAGTGAGATCACTGACGG 1858Acc848 GATCCAATCGTGGAAGTTCAACAAAAGGCCTGAACTTGGCTCAAGTGAGATCACTGACGG 1858Tsuyuake_Pikm GATCCAATCGTGGAAGTTCAACAAAAGGCCTGAACTTGGCTCAAGTGAGATCACTGACGG 1858Kusabue_Pik GATCCAATCGTGGAAGTTCAACAAAAGGCCTGAACTTGGCTCAAGTGAGATCACTGACGG 1858Kanto51_Pik GATCCAATCGTGGAAGTTCAACAAAAGGCCTGAACTTGGCTCAAGTGAGATCACTGACGG 1858K60_Pikp GATCCAATCGTGGAAGTTCAACAAAAGGCCTGAACTTGGCTCAAGTGAGATCACTGACGG 1858Acc108 GATCCAATCGTGGAAGTTCAACAAAAGGCCTGAACTTGGCTCAAGTGAGATCACTGACGG 1858Acc130 GATCCAATCGTGGAAGTTCAACAAAAGGCCTGAACTTGGCTCAAGTGAGATCACTGACGG 1858Acc719 GATCCAATCGTGGAAGTTCAACAAAAGGCCTGAACTTGGCTCAAGTGAGATCACTGACGG 1858Acc729 GATCCAATCGTGGAAGTTCAACAAAAGGCCTGAACTTGGCTCAAGTGAGATCACTGACGG 1858Acc710 GATCCAATCGTGGAAGTTCAACAAAAGGCCTGAACTTGGCTCAAGTGAGATCACTGACGG 1858Acc709 GATCCAATCGTGGAAGTTCAACAAAAGGCCTGAACTTGGCTCAAGTGAGATCACTGACGG 1858Acc220 GATCCAAGCATGGAAATTCTACAAAAGGCCTGAACTTGGCTCAAGTGCGATCACTGACGG 1927Nipponbare GATCCAAGCATGGAAATTCTACAAAAGGCCTGAACTTGGCTCAAGTGCGATCACTGACGG 1927Acc224 GATCCAAGCATGGAAATTCTACAAAAGGCCTGAACTTGGCTCAAGTGCGATCACTGACGG 1927AccUP3 GATCCAAGCATGGAAATTCTACAAAAGGCCTGAACTTGGCTCAAGTGCGATCACTGACGG 1927AccUP1 GATCCAAGCATGGAAATTCTACAAAAGGCCTGAACTTGGCTCAAGTGCGATCACTGACGG 1927Acc206 GATCCAAGCATGGAAATTCTACAAAAGGCCTGAACTTGGCTCAAGTGCGATCACTGACGG 1927Acc201 GATCCAAGCATGGAAATTCTACAAAAGGCCTGAACTTGGCTCAAGTGCGATCACTGACGG 1927Acc724 GATCCAAGCATGGAAATTCTACAAAAGGCCTGAACTTGGCTCAAGTGCGATCACTGACGG 1927Acc415 GATCCAAGCATGGAAATTCTACAAAAGGCCTGAACTTGGCTCAAGTGCGATCACTGACGG 1927Acc417 GATCCAAGCATGGAAATTCTACAAAAGGCCTGAACTTGGCTCAAGTGCGATCACTGACGG 1927Acc435 GATCCAAGCATGGAAATTCTACAAAAGGCCTGAACTTGGCTCAAGTGCGATCACTGACGG 1927Acc712 GATCCAAGCATGGAAATTCTACAAAAGGCCTGAACTTGGCTCAAGTGCGATCACTGACGG 1927Acc101 GATCCAAGAATGGAAATTCAACAAAAGGCCTGAACTTGGCTCAAGTGCGATCACTGACAG 1942Acc715 GATCCAAGAATGGAAATTCAACAAAAGGCCTGAACTTGGCTCAAGTGCGATCACTGACAG 1942Acc706 GATCCAAGAATGGAAATTCAACAAAAGGCCTGAACTTGGCTCAAGTGCGATCACTGACAG 1942Acc624 GATCCAAGAATGGAAATTCAACAAAAGGCCTGAACTTGGCTCAAGTGCGATCACTGACAG 1942Acc1 GATCCAAGAATGGAAATTCAACAAAAGGCCTGAACTTGGCTCAAGTGCGATCACTGACAG 1891Acc440 GATCCAAGAATGGAAATTCAACAAAAGGCCTGAACTTGGCTCAAGTGCGATCACTGACAG 1891Acc868 GATCCAAGAATGGAAATTCAACAAAAGGCCTGAACTTGGCTCAAGTGCGATCACTGACAG 1905Acc718 GATCCAAGAATGGAAATTCAACAAAAGGCCTGAACTTGGCTCAAGTGCGATCACTGACAG 1891 ******* ***** *** *************************** ********** * 

Ashikawa et al. Supplementary Fig. S2 (17/28)

Acc414 TGTTTGGGAACCTGAACCATGTGCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1918Acc420 TGTTTGGGAACCTGAACCATGTGCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1918Acc761 TGTTTGGGAACCTGAACCATGTGCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1918Acc504 TGTTTGGGAACCTGAACCATGTGCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1918Acc563 TGTTTGGGAACCTGAACCATGTGCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1918Acc757 TGTTTGGGAACCTGAACCATGTGCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1918Acc848 TGTTTGGGAACCTGAACCATGTGCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1918Tsuyuake_Pikm TGTTTGGGAACCTGAACCATGTGCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1918Kusabue_Pik TGTTTGGGAACCTGAACCATGTGCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1918Kanto51_Pik TGTTTGGGAACCTGAACCATGTGCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1918K60_Pikp TGTTTGGGAACCTGAACCATATGCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1918Acc108 TGTTTGGGAACCTGAACCATGTGCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1918Acc130 TGTTTGGGAACCTGAACCATGTGCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1918Acc719 TGTTTGGGAACCTGAACCATGTGCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1918Acc729 TGTTTGGGAACCTGAACCATGTGCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1918Acc710 TGTTTGGGAACCTGAACCATGTGCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1918Acc709 TGTTTGGGAACCTGAACCATGTGCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1918Acc220 TGTTTGGGAACCTGAACCATGTTCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1987Nipponbare TGTTTGGGAACCTGAACCATGTTCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1987Acc224 TGTTTGGGAACCTGAACCATGTTCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1987AccUP3 TGTTTGGGAACCTGAACCATGTTCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1987AccUP1 TGTTTGGGAACCTGAACCATGTTCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1987Acc206 TGTTTGGGAACCTGAACCATGTTCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1987Acc201 TGTTTGGGAACCTGAACCATGTTCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1987Acc724 TGTTTGGGAACCTGAACCATGTTCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1987Acc415 TGTTTGGGAACCTGAACCATGTTCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1987Acc417 TGTTTGGGAACCTGAACCATGTTCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1987Acc435 TGTTTGGGAACCTGAACCATGTTCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1987Acc712 TGTTTGGGAACCTGAACCATGTTCCATTCCATTCATTCAACTATGGGATAATACAGGTGC 1987Acc101 TGTTTGGGAACCTGAACCATGTGCCATTCCGTTCATTCAACTATGGGATAATACATGTGC 2002Acc715 TGTTTGGGAACCTGAACCATGTGCCATTCCGTTCATTCAACTATGGGATAATACATGTGC 2002Acc706 TGTTTGGGAACCTGAACCATGTGCCATTCCGTTCATTCAACTATGGGATAATACATGTGC 2002Acc624 TGTTTGGGAACCTGAACCATGTGCCATTCCGTTCATTCAACTATGGGATAATACATGTGC 2002Acc1 TGTTTGGGAACCTGAACCATGTGCCATTCCGTTCATTCAACTATGGGATAATACATGTGC 1951Acc440 TGTTTGGGAACCTGAACCATGTGCCATTCCGTTCATTCAACTATGGGATAATACATGTGC 1951Acc868 TGTTTGGGAACCTGAACCATGTGCCATTCCGTTCATTCAACTATGGGATAATACATGTGC 1965Acc718 TGTTTGGGAACCTGAACCATGTGCCATTCCGTTCATTCAACTATGGGATAATACATGTGC 1951 ******************** * ******* ************************ **** Acc414 TGGATCTTGAGGACTGGAAGGGTTTGAAAGAGAGACATATGACGGAGATATGTCAAATGC 1978Acc420 TGGATCTTGAGGACTGGAAGGGTTTGAAAGAGAGACATATGACGGAGATATGTCAAATGC 1978Acc761 TGGATCTTGAGGACTGGAAGGGTTTGAAAGAGAGACATATGACGGAGATATGTCAAATGC 1978Acc504 TGGATCTTGAGGACTGGAAGGGTTTGAAAGAGAGACATATGACGGAGATATGTCAAATGC 1978Acc563 TGGATCTTGAGGACTGGAAGGGTTTGAAAGAGAGACATATGACGGAGATATGTCAAATGC 1978Acc757 TGGATCTTGAGGACTGGAAGGGTTTGAAAGAGAGACATATGACGGAGATATGTCAAATGC 1978Acc848 TGGATCTTGAGGACTGGAAGGGTTTGAAAGAGAGACATATGACGGAGATATGTCAAATGC 1978Tsuyuake_Pikm TGGATCTTGAGGACTGGAAGGGTTTGAAAGAGAGACATATGACGGAGATATGTCAAATGC 1978Kusabue_Pik TGGATCTTGAGGACTGGAAGGGTTTGAAAGAGAGACATATGACGGAGATATGTCAAATGC 1978Kanto51_Pik TGGATCTTGAGGACTGGAAGGGTTTGAAAGAGAGACATATGACGGAGATATGTCAAATGC 1978K60_Pikp TGGATCTTGAGGACTGGAAGGGTTTGAAAGAGAGACATATGACGGAGATATGTCAAATGC 1978Acc108 TGGATCTTGAGGACTGGAAGGGTTTGAAAGAGAGACATATGACGGAGATATGTCAAATGC 1978Acc130 TGGATCTTGAGGACTGGAAGGGTTTGAAAGAGAGACATATGACGGAGATATGTCAAATGC 1978Acc719 TGGATCTTGAGGACTGGAAGGGTTTGAAAGAGAGACATATGACGGAGATATGTCAAATGC 1978Acc729 TGGATCTTGAGGACTGGAAGGGTTTGAAAGAGAGACATATGACGGAGATATGTCAAATGC 1978Acc710 TGGATCTTGAGGACTGGAAGGGTTTGAAAGAGAGACATATGACGGAGATATGTCAAATGC 1978Acc709 TGGATCTTGAGGACTGGAAGGGTTTGAAAGAGAGACATATGACGGAGATATGTCAAATGC 1978Acc220 TGGATCTTGAGGGTTGGAAGGGTTTGAAAGAGAGACATGTGACGGAGATATGTCAAATGC 2047Nipponbare TGGATCTTGAGGGTTGGAAGGGTTTGAAAGAGAGACATGTGACGGAGATATGTCAAATGC 2047Acc224 TGGATCTTGAGGGTTGGAAGGGTTTGAAAGAGAGACATGTGACGGAGATATGTCAAATGC 2047AccUP3 TGGATCTTGAGGGTTGGAAGGGTTTGAAAGAGAGACATGTGACGGAGATATGTCAAATGC 2047AccUP1 TGGATCTTGAGGGTTGGAAGGGTTTGAAAGAGAGACATGTGACGGAGATATGTCAAATGC 2047Acc206 TGGATCTTGAGGGTTGGAAGGGTTTGAAAGAGAGACATGTGACGGAGATATGTCAAATGC 2047Acc201 TGGATCTTGAGGGTTGGAAGGGTTTGAAAGAGAGACATGTGACGGAGATATGTCAAATGC 2047Acc724 TGGATCTTGAGGGTTGGAAGGGTTTGAAAGAGAGACATGTGACGGAGATATGTCAAATGC 2047Acc415 TGGATCTTGAGGGTTGGAAGGGTTTGAAAGAGAGACATGTGACGGAGATATGTCAAATGC 2047Acc417 TGGATCTTGAGGGTTGGAAGGGTTTGAAAGAGAGACATGTGACGGAGATATGTCAAATGC 2047Acc435 TGGATCTTGAGGGTTGGAAGGGTTTGAAAGAGAGACATGTGACGGAGATATGTCAAATGC 2047Acc712 TGGATCTTGAGGGTTGGAAGGGTTTGAAAGAGAGACATGTGACGGAGATATGTCAAATGC 2047Acc101 TGGATCTTGAGGGTTGGAAGGGTTTGAAAGGGAGACATATGAAAGAGATATGCCAAATGC 2062Acc715 TGGATCTTGAGGGTTGGAAGGGTTTGAAAGGGAGACATATGAAAGAGATATGCCAAATGC 2062Acc706 TGGATCTTGAGGGTTGGAAGGGTTTGAAAGGGAGACATATGAAAGAGATATGCCAAATGC 2062Acc624 TGGATCTTGAGGGTTGGAAGGGTTTGAAAGGGAGACATATGAAAGAGATATGCCAAATGC 2062Acc1 TGGATCTTGAGGGTTGGAAGGGTTTGAAAGGGAGACATATGAAAGAGATATGCCAAATGC 2011Acc440 TGGATCTTGAGGGTTGGAAGGGTTTGAAAGGGAGACATATGAAAGAGATATGCCAAATGC 2011Acc868 TGGATCTTGAGGGTTGGAAGGGTTTGAAAGGGAGACATATGAAAGAGATATGCCAAATGC 2025Acc718 TGGATCTTGAGGGTTGGAAGGGTTTGAAAGGGAGACATATGAAAGAGATATGCCAAATGC 2011 ************ **************** ******* *** ******** ******* 

Ashikawa et al. Supplementary Fig. S2 (18/28)

Acc414 TTTTACTCAAGTATTTGAGCATCCGACGAACAGAAATTTCCAAAATTCCCTCCAAGATTC 2038Acc420 TTTTACTCAAGTATTTGAGCATCCGACGAACAGAAATTTCCAAAATTCCCTCCAAGATTC 2038Acc761 TTTTACTCAAGTATTTGAGCATCCGACGAACAGAAATTTCCAAAATTCCCTCCAAGATTC 2038Acc504 TTTTACTCAAGTATTTGAGCATCCGACGAACAGAAATTTCCAAAATTCCCTCCAAGATTC 2038Acc563 TTTTACTCAAGTATTTGAGCATCCGACGAACAGAAATTTCCAAAATTCCCTCCAAGATTC 2038Acc757 TTTTACTCAAGTATTTGAGCATCCGACGAACAGAAATTTCCAAAATTCCCTCCAAGATTC 2038Acc848 TTTTACTCAAGTATTTGAGCATCCGACGAACAGAAATTTCCAAAATTCCCTCCAAGATTC 2038Tsuyuake_Pikm TTTTACTCAAGTATTTGAGCATCCGACGAACAGAAATTTCCAAAATTCCCTCCAAGATTC 2038Kusabue_Pik TTTTACTCAAGTATTTGAGCATCCGACGAACAGAAATTTCCAAAATTCCCTCCAAGATTC 2038Kanto51_Pik TTTTACTCAAGTATTTGAGCATCCGACGAACAGAAATTTCCAAAATTCCCTCCAAGATTC 2038K60_Pikp TTTTACTCAAGTATTTGAGCATCCGACGAACAGAAATTTCCAAAATTCCCTCCAAGATTC 2038Acc108 TTTTACTCAAGTATTTGAGCATCCGACGAACAGAAATTTCCAAAATTCCCTCCAAGATTC 2038Acc130 TTTTACTCAAGTATTTGAGCATCCGACGAACAGAAATTTCCAAAATTCCCTCCAAGATTC 2038Acc719 TTTTACTCAAGTATTTGAGCATCCGACGAACAGAAATTTCCAAAATTCCCTCCAAGATTC 2038Acc729 TTTTACTCAAGTATTTGAGCATCCGACGAACAGAAATTTCCAAAATTCCCTCCAAGATTC 2038Acc710 TTTTACTCAAGTATTTGAGCATCCGACGAACAGAAATTTCCAAAATTCCCTCCAAGATTC 2038Acc709 TTTTACTCAAGTATTTGAGCATCCGACGAACAGAAATTTCCAAAATTCCCTCCAAGATTC 2038Acc220 TTGTACTCAAGTATTTGAGCATCCGGCGGACAGAAATTGCCAAAATTCCCTCAAAGATTG 2107Nipponbare TTGTACTCAAGTATTTGAGCATCCGGCGGACAGAAATTGCCAAAATTCCCTCAAAGATTG 2107Acc224 TTGTACTCAAGTATTTGAGCATCCGGCGGACAGAAATTGCCAAAATTCCCTCAAAGATTG 2107AccUP3 TTGTACTCAAGTATTTGAGCATCCGGCGGACAGAAATTGCCAAAATTCCCTCAAAGATTG 2107AccUP1 TTGTACTCAAGTATTTGAGCATCCGGCGGACAGAAATTGCCAAAATTCCCTCAAAGATTG 2107Acc206 TTGTACTCAAGTATTTGAGCATCCGGCGGACAGAAATTGCCAAAATTCCCTCAAAGATTG 2107Acc201 TTGTACTCAAGTATTTGAGCATCCGGCGGACAGAAATTGCCAAAATTCCCTCAAAGATTG 2107Acc724 TTGTACTCAAGTATTTGAGCATCCGGCGGACAGAAATTGCCAAAATTCCCTCAAAGATTG 2107Acc415 TTGTACTCAAGTATTTGAGCATCCGGCGGACAGAAATTGCCAAAATTCCCTCAAAGATTG 2107Acc417 TTGTACTCAAGTATTTGAGCATCCGGCGGACAGAAATTGCCAAAATTCCCTCAAAGATTG 2107Acc435 TTGTACTCAAGTATTTGAGCATCCGGCGGACAGAAATTGCCAAAATTCCCTCAAAGATTG 2107Acc712 TTGTACTCAAGTATTTGAGCATCCGGCGGACAGAAATTGCCAAAATTCCCTCAAAGATTG 2107Acc101 TTGTACTCAAGTATTTGAGCATCCGGCGGACAGAAATTGCCAAAATTCCCTCCAAGATCG 2122Acc715 TTGTACTCAAGTATTTGAGCATCCGGCGGACAGAAATTGCCAAAATTCCCTCCAAGATCG 2122Acc706 TTGTACTCAAGTATTTGAGCATCCGGCGGACAGAAATTGCCAAAATTCCCTCCAAGATCG 2122Acc624 TTGTACTCAAGTATTTGAGCATCCGGCGGACAGAAATTGCCAAAATTCCCTCCAAGATCG 2122Acc1 TTGTACTCAAGTATTTGAGCATCCGGCGGACAGAAATTGCCAAAATTCCCTCCAAGATCG 2071Acc440 TTGTACTCAAGTATTTGAGCATCCGGCGGACAGAAATTGCCAAAATTCCCTCCAAGATCG 2071Acc868 TTGTACTCAAGTATTTGAGCATCCGGCGGACAGAAATTGCCAAAATTCCCTCCAAGATCG 2085Acc718 TTGTACTCAAGTATTTGAGCATCCGGCGGACAGAAATTGCCAAAATTCCCTCCAAGATCG 2071 ** ********************** ** ********* ************* *****  Acc414 AGAAACTTGAGTACTTGGAAACTCTTGACATAAGGGAGACATATGTCAGGGACCTGCCTA 2098Acc420 AGAAACTTGAGTACTTGGAAACTCTTGACATAAGGGAGACATATGTCAGGGACCTGCCTA 2098Acc761 AGAAACTTGAGTACTTGGAAACTCTTGACATAAGGGAGACATATGTCAGGGACCTGCCTA 2098Acc504 AGAAACTTGAGTACTTGGAAACTCTTGACATAAGGGAGACATATGTCAGGGACCTGCCTA 2098Acc563 AGAAACTTGAGTACTTGGAAACTCTTGACATAAGGGAGACATATGTCAGGGACCTGCCTA 2098Acc757 AGAAACTTGAGTACTTGGAAACTCTTGACATAAGGGAGACATATGTCAGGGACCTGCCTA 2098Acc848 AGAAACTTGAGTACTTGGAAACTCTTGACATAAGGGAGACATATGTCAGGGACCTGCCTA 2098Tsuyuake_Pikm AGAAACTTGAGTACTTGGAAACTCTTGACATAAGGGAGACATATGTCAGGGACCTGCCTA 2098Kusabue_Pik AGAAACTTGAGTACTTGGAAACTCTTGACATAAGGGAGACATATGTCAGGGACCTGCCTA 2098Kanto51_Pik AGAAACTTGAGTACTTGGAAACTCTTGACATAAGGGAGACATATGTCAGGGACCTGCCTA 2098K60_Pikp AGAAACTTGAGTACTTGGAAACTCTTGACATAAGGGAGACATATGTCAGGGACCTGCCTA 2098Acc108 AGAAACTTGAGTACTTGGAAACTCTTGACATAAGGGAGACATATGTCAGGGACCTGCCTA 2098Acc130 AGAAACTTGAGTACTTGGAAACTCTTGACATAAGGGAGACATATGTCAGGGACCTGCCTA 2098Acc719 AGAAACTTGAGTACTTGGAAACTCTTGACATAAGGGAGACATATGTCAGGGACCTGCCTA 2098Acc729 AGAAACTTGAGTACTTGGAAACTCTTGACATAAGGGAGACATATGTCAGGGACCTGCCTA 2098Acc710 AGAAACTTGAGTACTTGGAAACTCTTGACATAAGGGAGACATATGTCAGGGACCTGCCTA 2098Acc709 AGAAACTTGAGTACTTGGAAACTCTTGACATAAGGGAGACATATGTCAGGGACCTGCCTA 2098Acc220 AGAAACTTGAGTATTTGGAAACTCTTGACATAAGGGAGACATATGTCGAGGAGCTGCCTA 2167Nipponbare AGAAACTTGAGTATTTGGAAACTCTTGACATAAGGGAGACATATGTCGAGGAGCTGCCTA 2167Acc224 AGAAACTTGAGTATTTGGAAACTCTTGACATAAGGGAGACATATGTCGAGGAGCTGCCTA 2167AccUP3 AGAAACTTGAGTATTTGGAAACTCTTGACATAAGGGAGACATATGTCGAGGAGCTGCCTA 2167AccUP1 AGAAACTTGAGTATTTGGAAACTCTTGACATAAGGGAGACATATGTCGAGGAGCTGCCTA 2167Acc206 AGAAACTTGAGTATTTGGAAACTCTTGACATAAGGGAGACATATGTCGAGGAGCTGCCTA 2167Acc201 AGAAACTTGAGTATTTGGAAACTCTTGACATAAGGGAGACATATGTCGAGGAGCTGCCTA 2167Acc724 AGAAACTTGAGTATTTGGAAACTCTTGACATAAGGGAGACATATGTCGAGGAGCTGCCTA 2167Acc415 AGAAACTTGAGTATTTGGAAACTCTTGACATAAGGGAGACATATGTCGAGGAGCTGCCTA 2167Acc417 AGAAACTTGAGTATTTGGAAACTCTTGACATAAGGGAGACATATGTCGAGGAGCTGCCTA 2167Acc435 AGAAACTTGAGTATTTGGAAACTCTTGACATAAGGGAGACATATGTCGAGGAGCTGCCTA 2167Acc712 AGAAACTTGAGTATTTGGAAACTCTTGACATAAGGGAGACATATGTCGAGGAGCTGCCTA 2167Acc101 AGAAACTCGAGTATTTGGAAACTCTTGACATAAGGGAGACAAACGTCAAGGAGCTGCCTA 2182Acc715 AGAAACTCGAGTATTTGGAAACTCTTGACATAAGGGAGACAAACGTCAAGGAGCTGCCTA 2182Acc706 AGAAACTCGAGTATTTGGAAACTCTTGACATAAGGGAGACAAACGTCAAGGAGCTGCCTA 2182Acc624 AGAAACTCGAGTATTTGGAAACTCTTGACATAAGGGAGACAAACGTCAAGGAGCTGCCTA 2182Acc1 AGAAACTCGAGTATTTGGAAACTCTTGACATAAGGGAGACAAACGTCAAGGAGCTGCCTA 2131Acc440 AGAAACTCGAGTATTTGGAAACTCTTGACATAAGGGAGACAAACGTCAAGGAGCTGCCTA 2131Acc868 AGAAACTCGAGTATTTGGAAACTCTTGACATAAGGGAGACAAACGTCAAGGAGCTGCCTA 2145Acc718 AGAAACTCGTGTATTTGGAAACTCTTGACATAAGGGAGACAAACGTCAAGGAGCTGCCTA 2131 ******* * *** *************************** * *** *** *******

Ashikawa et al. Supplementary Fig. S2 (19/28)

Acc414 AGTCAATAGTCCAGCTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGA 2158Acc420 AGTCAATAGTCCAGCTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGA 2158Acc761 AGTCAATAGTCCAGCTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGA 2158Acc504 AGTCAATAGTCCAGCTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGA 2158Acc563 AGTCAATAGTCCAGCTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGA 2158Acc757 AGTCAATAGTCCAGCTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGA 2158Acc848 AGTCAATAGTCCAGCTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGA 2158Tsuyuake_Pikm AGTCAATAGTCCAGCTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGA 2158Kusabue_Pik AGTCAATAGTCCAGCTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGA 2158Kanto51_Pik AGTCAATAGTCCAGCTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGA 2158K60_Pikp AGTCAATAGTCCAGCTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGA 2158Acc108 AGTCAATAGTCCAGCTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGA 2158Acc130 AGTCAATAGTCCAGCTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGA 2158Acc719 AGTCAATAGTCCAGCTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGA 2158Acc729 AGTCAATAGTCCAGCTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGA 2158Acc710 AGTCAATAGTCCAGCTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGA 2158Acc709 AGTCAATAGTCCAGCTAAAACGGATCATTAGCATACTTGGAGGGAATAAAAACACACGGA 2158Acc220 AGTCTGTAGGCCAGCTAAAACGGATCAGTAGCATACTTGGGGGGAACAAAAATACACGGA 2227Nipponbare AGTCTGTAGGCCAGCTAAAACGGATCAGTAGCATACTTGGGGGGAACAAAAATACACGGA 2227Acc224 AGTCTGTAGGCCAGCTAAAACGGATCAGTAGCATACTTGGGGGGAACAAAAATACACGGA 2227AccUP3 AGTCTGTAGGCCAGCTAAAACGGATCAGTAGCATACTTGGGGGGAACAAAAATACACGGA 2227AccUP1 AGTCTGTAGGCCAGCTAAAACGGATCAGTAGCATACTTGGGGGGAACAAAAATACACGGA 2227Acc206 AGTCTGTAGGCCAGCTAAAACGGATCAGTAGCATACTTGGGGGGAACAAAAATACACGGA 2227Acc201 AGTCTGTAGGCCAGCTAAAACGGATCAGTAGCATACTTGGGGGGAACAAAAATACACGGA 2227Acc724 AGTCTGTAGGCCAGCTAAAACGGATCAGTAGCATACTTGGGGGGAACAAAAATACACGGA 2227Acc415 AGTCTGTAGGCCAGCTAAAACGGATCAGTAGCATACTTGGGGGGAACAAAAATACACGGA 2227Acc417 AGTCTGTAGGCCAGCTAAAACGGATCAGTAGCATACTTGGGGGGAACAAAAATACACGGA 2227Acc435 AGTCTGTAGGCCAGCTAAAACGGATCAGTAGCATACTTGGGGGGAACAAAAATACACGGA 2227Acc712 AGTCTGTAGGCCAGCTAAAACGGATCAGTAGCATACTTGCCGGGAACAAAAATACACGGA 2227Acc101 AGTCTGTAGGCCAGCTAAAACGGATCAATAGCATACTTGGGGGGAACAAAAATACACGGA 2242Acc715 AGTCTGTAGGCCAGCTAAAACGGATCAATAGCATACTTGGGGGGAACAAAAATACACGGA 2242Acc706 AGTCTGTAGGCCAGCTAAAACGGATCAATAGCATACTTGGGGGGAACAAAAATACACGGA 2242Acc624 AGTCTGTAGGCCAGCTAAAACGGATCAGTAGCATACTTGGGGGGAACAAAAATACACGGA 2242Acc1 AGTCTGTAGGCCAGCTAAAACGGATCAATAGCATACTTGGGGGGAACAAAAATACACGGA 2191Acc440 AGTCTGTAGGCCAGCTAAAACGGATCAATAGTATACTTGGAGGGAACAAAAAAACACGGG 2191Acc868 AGTCTGTAGGCCAGCTAAAACGGATCAATAGTATACTTGGAGGGAACAAAAAAACACGGG 2205Acc718 AGTCTGTAGGCCAGCTAAAACGGATCAATAGTATACTTGGAGGGAACAAAAAAACACGGG 2191 **** *** ***************** *** ******* ***** ***** ******  Acc414 AGGGGCTGAGGTTGCCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAG 2218Acc420 AGGGGCTGAGGTTGCCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAG 2218Acc761 AGGGGCTGAGGTTGCCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAG 2218Acc504 AGGGGCTGAGGTTGCCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAG 2218Acc563 AGGGGCTGAGGTTGCCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAG 2218Acc757 AGGGGCTGAGGTTGCCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAG 2218Acc848 AGGGGCTGAGGTTGCCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAG 2218Tsuyuake_Pikm AGGGGCTGAGGTTGCCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAG 2218Kusabue_Pik AGGGGCTGAGGTTGCCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAG 2218Kanto51_Pik AGGGGCTGAGGTTGCCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAG 2218K60_Pikp AGGGGCTGAGGTTGCCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAG 2218Acc108 AGGGGCTGAGGTTGCCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAG 2218Acc130 AGGGGCTGAGGTTGCCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAG 2218Acc719 AGGGGCTGAGGTTGCCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAG 2218Acc729 AGGGGCTGAGGTTGCCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAG 2218Acc710 AGGGGCTGAGGTTGCCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAG 2218Acc709 AGGGGCTGAGGTTGCCTCAAGAAAAAAGTAAGAAGCCAATTAAAAACCCGTCGCCTCAAG 2218Acc220 AGGGGCTGAGGTTGCCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAG 2287Nipponbare AGGGGCTGAGGTTGCCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAG 2287Acc224 AGGGGCTGAGGTTGCCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAG 2287AccUP3 AGGGGCTGAGGTTGCCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAG 2287AccUP1 AGGGGCTGAGGTTGCCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAG 2287Acc206 AGGGGCTGAGGTTGCCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAG 2287Acc201 AGGGGCTGAGGTTGCCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAG 2287Acc724 AGGGGCTGAGGTTGCCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAG 2287Acc415 AGGGGCTGAGGTTGCCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAG 2287Acc417 AGGGGCTGAGGTTGCCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAG 2287Acc435 AGGGGCTGAGGTTGCCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAG 2287Acc712 AGGGGCTGAGGTTGCCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAG 2287Acc101 AGGGGTTGAGGTTGCCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAG 2302Acc715 AGGGGTTGAGGTTGCCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAG 2302Acc706 AGGGGTTGAGGTTGCCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAG 2302Acc624 AGGGGTTGAGGTTGCCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAG 2302Acc1 AGGGGTTGAGGTTGCCTCAAGAAAAAAGAAATAAGGCAATGAAAAACCCGTCACCTCAAG 2251Acc440 AGGGGCTGAGGTTGCCTCAAGAAAAAGGAAATAAGACAATTAAAAACCCGTTGCCTCAAG 2251Acc868 AGGGGCTGAGGTTGCCTCAAGAAAAAGGAAATAAGACAATTAAAAACCCGTTGCCTCAAG 2265Acc718 AGGGGCTGAGGTTGCCTCAAGAAAAAGGAAATAAGAG----------------------- 2228 ***** ******************** * ** ***  

Ashikawa et al. Supplementary Fig. S2 (20/28)

Acc414 GAAAAACAAAGGAGCCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAA 2278Acc420 GAAAAACAAAGGAGCCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAA 2278Acc761 GAAAAACAAAGGAGCCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAA 2278Acc504 GAAAAACAAAGGAGCCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAA 2278Acc563 GAAAAACAAAGGAGCCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAA 2278Acc757 GAAAAACAAAGGAGCCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAA 2278Acc848 GAAAAACAAAGGAGCCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAA 2278Tsuyuake_Pikm GAAAAACAAAGGAGCCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAA 2278Kusabue_Pik GAAAAACAAAGGAGCCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAA 2278Kanto51_Pik GAAAAACAAAGGAGCCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAA 2278K60_Pikp GAAAAACAAAGGAGCCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAA 2278Acc108 GAAAAACAAAGGAGCCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAA 2278Acc130 GAAAAACAAAGGAGCCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAA 2278Acc719 GAAAAACAAAGGAGCCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAA 2278Acc729 GAAAAACAAAGGAGCCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAA 2278Acc710 GAAAAACAAAGGAGCCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAA 2278Acc709 GAAAAACAAAGGAGCCCGCAAAGAAAGGATTCTTATCCCAAGAAAAAGGTAAAGGCGCAA 2278Acc220 GTAAAACAAAGGAGCCTGCAGAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAA 2347Nipponbare GTAAAACAAAGGAGCCTGCAGAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAA 2347Acc224 GTAAAACAAAGGAGCCTGCAGAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAA 2347AccUP3 GTAAAACAAAGGAGCCTGCAGAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAA 2347AccUP1 GTAAAACAAAGGAGCCTGCAGAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAA 2347Acc206 GTAAAACAAAGGAGCCTGCAGAGAAAGGATCCTTGTCCCAAGAAAAAGCTAAAGGCACAA 2347Acc201 GTAAAACAAAGGAGCCTGCAGAGAAAGGATCCTTGTCCCAAGAAAAAGCTAAAGGCACAA 2347Acc724 GTAAAACAAAGGAGCCTGCAGAGAAAGGATCCTTGTCCCAAGAAAAAGCTAAAGGCACAA 2347Acc415 GTAAAACAAAGGAGCCTGCAGAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAA 2347Acc417 GTAAAACAAAGGAGCCTGCAGAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAA 2347Acc435 GTAAAACAAAGGAGCCTGCAGAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAA 2347Acc712 GTAAAACAAAGGAGCCTGCAGAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAA 2347Acc101 GTAAAACAAAGGAGCCTGCAAAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAA 2362Acc715 GTAAAACAAAGGAGCCTGCAAAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAA 2362Acc706 GTAAAACAAAGGAGCCTGCAAAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAA 2362Acc624 GTAAAACAAAGGAGCCTGCAAAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAA 2362Acc1 GTAAAACAAAGGAGCCTGCAAAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAA 2311Acc440 GTAAAACAAAGGAGCCTGCAAAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAA 2311Acc868 GTAAAACAAAGGAGCCTGCAAAGAAAGGATTCTTGTCCCAAGAAAAAGCTAAAGGCACAA 2325Acc718 -------------------------------------------------TAAAGGCATAA 2239 ******* ** Acc414 TGAAAGCACTCCGTGTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTG 2338Acc420 TGAAAGCACTCCGTGTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTG 2338Acc761 TGAAAGCACTCCGTGTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTG 2338Acc504 TGAAAGCACTCCGTGTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTG 2338Acc563 TGAAAGCACTCCGTGTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTG 2338Acc757 TGAAAGCACTCCGTGTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTG 2338Acc848 TGAAAGCACTCCGTGTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTG 2338Tsuyuake_Pikm TGAAAGCACTCCGTGTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTG 2338Kusabue_Pik TGAAAGCACTCCGTGTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTG 2338Kanto51_Pik TGAAAGCACTCCGTGTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTG 2338K60_Pikp TGAAAGCACTCCGTGTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTG 2338Acc108 TGAAAGCACTCCGTGTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTG 2338Acc130 TGAAAGCACTCCGTGTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTG 2338Acc719 TGAAAGCACTCCGTGTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTG 2338Acc729 TGAAAGCACTCCGTGTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTG 2338Acc710 TGAAAGCACTCCGTGTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTG 2338Acc709 TGAAAGCACTCCGTGTACTGTCAGGGATTGAGATTGTTGAGGAATCATCAGAAGTAGCTG 2338Acc220 TGAAGTCACTCCGTGTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTG 2407Nipponbare TGAAGTCACTCCGTGTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTG 2407Acc224 TGAAGTCACTCCGTGTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTG 2407AccUP3 TGAAGTCACTCCGTGTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTG 2407AccUP1 TGAAGTCACTCCGTGTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTG 2407Acc206 TGAAGTCACTCCGTGTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTG 2407Acc201 TGAAGTCACTCCGTGTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTG 2407Acc724 TGAAGTCACTCCGTGTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTG 2407Acc415 TGAAGTCACTCCGTGTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTG 2407Acc417 TGAAGTCACTCCGTGTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTG 2407Acc435 TGAAGTCACTCCGTGTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTG 2407Acc712 TGAAGTCACTCCGTGTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTG 2407Acc101 TGAAGTCACTCCGTGTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTG 2422Acc715 TGAAGTCACTCCGTGTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTG 2422Acc706 TGAAGTCACTCCGTGTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTG 2422Acc624 TGAAGTCACTCCGTGTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTG 2422Acc1 TGAAGTCACTCCGTGTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTG 2371Acc440 TGAAGTCACTCCGTGTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTG 2371Acc868 TGAAGTCACTCCGTGTACTGTCAGGGATTGAGATCGTTGATGAATCAGCAGCAGTAGCTG 2385Acc718 TGAAGTCACTCCATGTGCTGTCAGGGATTGAGATCGATGAGGAATCAGCAGCTGTAGCTG 2299 **** ****** *** ***************** * *** ****** *** *******

Ashikawa et al. Supplementary Fig. S2 (21/28)

Acc414 CAGGCCTTCATCAGTTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAA 2398Acc420 CAGGCCTTCATCAGTTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAA 2398Acc761 CAGGCCTTCATCAGTTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAA 2398Acc504 CAGGCCTTCATCAGTTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAA 2398Acc563 CAGGCCTTCATCAGTTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAA 2398Acc757 CAGGCCTTCATCAGTTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAA 2398Acc848 CAGGCCTTCATCAGTTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAA 2398Tsuyuake_Pikm CAGGCCTTCATCAGTTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAA 2398Kusabue_Pik CAGGCCTTCATCAGTTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAA 2398Kanto51_Pik CAGGCCTTCATCAGTTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAA 2398K60_Pikp CAGGCCTTCATCAGTTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAA 2398Acc108 CAGGCCTTCATCAGTTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAA 2398Acc130 CAGGCCTTCATCAGTTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAA 2398Acc719 CAGGCCTTCATCAGTTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAA 2398Acc729 CAGGCCTTCATCAGTTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAA 2398Acc710 CAGGCCTTCATCAGTTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAA 2398Acc709 CAGGCCTTCATCAGTTGACAGGGCTAAGGAAGCTTGCCATATACAAGCTCAATATAACAA 2398Acc220 CAAGCCTTCATCAGTTGACAGGACTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCG 2467Nipponbare CAAGCCTTCATCAGTTGACAGGACTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCG 2467Acc224 CAAGCCTTCATCAGTTGACAGGACTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCG 2467AccUP3 CAAGCCTTCATCAGTTGACAGGACTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCG 2467AccUP1 CAAGCCTTCATCAGTTGACAGGACTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCG 2467Acc206 CAAGCCTTCATCAGTTGACAGGACTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCG 2467Acc201 CAAGCCTTCATCAGTTGACAGGACTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCG 2467Acc724 CAAGCCTTCATCAGTTGACAGGACTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCG 2467Acc415 CAAGCCTTCATCAGTTGACAGGACTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCG 2467Acc417 CAAGCCTTCATCAGTTGACAGGACTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCG 2467Acc435 CAAGCCTTCATCAGTTGACAGGACTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCG 2467Acc712 CAAGCCTTCATCAGTTGACAGGACTAAGGAAGCTTGCCATTTACAAGCTCAAAATAAGCG 2467Acc101 CAAGCCTTCATCAGTTGACAGGATTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCG 2482Acc715 CAAGCCTTCATCAGTTGACAGGATTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCG 2482Acc706 CAAGCCTTCATCAGTTGACAGGATTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCG 2482Acc624 CAAGCCTTCATCAGTTGACAGGATTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCG 2482Acc1 CAAGCCTTCATCAGTTGACAGGATTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCG 2431Acc440 CAAGCCTTCATCAGTTGACAGGATTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCG 2431Acc868 CAAGCCTTCATCAGTTGACAGGATTAAGGAAGCTTGCCATATACAAGCTCAAAATAAGCG 2445Acc718 CAAGCCTTCATCAGTTGACAGGACTAAGGAAGCTTGCCATATACAAGCTCAACATAGAAT 2359 ** ******************* **************** *********** ***  Acc414 AGGGTGGTGATACCTTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTC 2458Acc420 AGGGTGGTGATACCTTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTC 2458Acc761 AGGGTGGTGATACCTTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTC 2458Acc504 AGGGTGGTGATACCTTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTC 2458Acc563 AGGGTGGTGATACCTTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTC 2458Acc757 AGGGTGGTGATACCTTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTC 2458Acc848 AGGGTGGTGATACCTTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTC 2458Tsuyuake_Pikm AGGGTGGTGATACCTTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTC 2458Kusabue_Pik AGGGTGGTGATACCTTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTC 2458Kanto51_Pik AGGGTGGTGATACCTTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTC 2458K60_Pikp AGGGTGGTGATACCTTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTC 2458Acc108 AGGGTGGTGATACCTTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTC 2458Acc130 AGGGTGGTGATACCTTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTC 2458Acc719 AGGGTGGTGATACCTTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTC 2458Acc729 AGGGTGGTGATACCTTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTC 2458Acc710 AGGGTGGTGATACCTTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTC 2458Acc709 AGGGTGGTGATACCTTCAAACAATTACAGTCCTCCATTGAGTACCTTGGCAGCTGTGGTC 2458Acc220 AGGAAAATGATACATTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCC 2527Nipponbare AGGAAAATGATACATTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCC 2527Acc224 AGGAAAATGATACATTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCC 2527AccUP3 AGGAAAATGATACATTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCC 2527AccUP1 AGGAAAATGATACATTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCC 2527Acc206 AGGAAAATGATACATTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCC 2527Acc201 AGGAAAATGATACATTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCC 2527Acc724 AGGAAAATGATACATTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCC 2527Acc415 AGGAAAATGATACATTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCC 2527Acc417 AGGAAAATGATACATTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCC 2527Acc435 AGGAAAATGATACATTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCC 2527Acc712 AGGAAAATGATACATTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCC 2527Acc101 AGGAAAATGATACATTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCC 2542Acc715 AGGAAAATGATACATTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCC 2542Acc706 AGGAAAATGATACATTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCC 2542Acc624 AGGAAAATGATACATTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCC 2542Acc1 AGGAAAATGATACATTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCAGCTGCGGCC 2491Acc440 AGGAAAATGATACATTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCATCTGCGGCC 2491Acc868 AGGAAAATGATACATTCAAAGAATTACTCTCCTCTATTGAGTACCTTGGCATCTGCGGCC 2505Acc718 GGGGAAGTGAAACATTCCAAGAATTACGCTCCTCTATTGAGTACCTTGGCAGCTGCGGCC 2419 ** *** ** *** ** ****** ***** **************** *** ** *

Ashikawa et al. Supplementary Fig. S2 (22/28)

Acc414 TGCAGACTCTGGCCATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCG 2512Acc420 TGCAGACTCTGGCCATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCG 2512Acc761 TGCAGACTCTGGCCATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCG 2512Acc504 TGCAGACTCTGGCCATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCG 2512Acc563 TGCAGACTCTGGCCATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCG 2512Acc757 TGCAGACTCTGGCCATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCG 2512Acc848 TGCAGACTCTGGCCATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCG 2512Tsuyuake_Pikm TGCAGACTCTGGCCATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCG 2512Kusabue_Pik TGCAGACTCTGGCCATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCG 2512Kanto51_Pik TGCAGACTCTGGCCATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCG 2512K60_Pikp TGCAGACTCTGGCCATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCG 2512Acc108 TGCAGACTCTGGCCATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCG 2512Acc130 TGCAGACTCTGGCCATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCG 2512Acc719 TGCAGACTCTGGCCATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCG 2512Acc729 TGCAGACTCTGGCCATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCG 2512Acc710 TGCAGACTCTGGCCATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCG 2512Acc709 TGCAGACTCTGGCCATCAATGATGAGAATTCTGAATTTATCAACTCACTGG------GCG 2512Acc220 TGCAGACTCTGGCCATCAATGATGAGAATTCTAAATTTATCAACTCACTAT------ACA 2581Nipponbare TGCAGACTCTGGCCATCAATGATGAGAATTCTAAATTTATCAACTCACTAT------ACA 2581Acc224 TGCAGACTCTGGCCATCAATGATGAGAATTCTAAATTTATCAACTCACTAT------ACA 2581AccUP3 TGCAGACTCTGGCCATCAATGATGAGAATTCTAAATTTATCAACTCACTAT------ACA 2581AccUP1 TGCAGACTCTGGCCATCAATGATGAGAATTCTAAATTTATCAACTCACTAT------ACA 2581Acc206 TGCAGACTCTGGCCATCAATGATGAGAATTCTAAATTTATCAACTCACTAT------ACA 2581Acc201 TGCAGACTCTGGCCATCAATGATGAGAATTCTAAATTTATCAACTCACTAT------ACA 2581Acc724 TGCAGACTCTGGCCATCAATGATGAGAATTCTAAATTTATCAACTCACTAT------ACA 2581Acc415 TGCAGACTCTGGCCATCAATGATGAGAATTCTAAATTTATCAACTCACTAT------ACA 2581Acc417 TGCAGACTCTGGCCATCAATGATGAGAATTCTAAATTTATCAACTCACTAT------ACA 2581Acc435 TGCAGACTCTGGCCATCAATGATGAGAATTCTAAATTTATCAACTCACTAT------ACA 2581Acc712 TGCAGACTCTGGCCATCAATGATGAGAATTCTAAATTTATCAACTCACTAT------ACA 2581Acc101 TGCAGACTCTGGCCATCAATGATGAGAATTCTAAATTTATCAACTCACTGCCCCTGCACT 2602Acc715 TGCAGACTCTGGCCATCAATGATGAGAATTCTAAATTTATCAACTCACTGCCCCTGCACT 2602Acc706 TGCAGACTCTGGCCATCAATGATGAGAATTCTAAATTTATCAACTCACTGCCCCTGCACT 2602Acc624 TGCAGACTCTGGCCATCAATGATGAGAATTCTAAATTTATCAACTCACTGCCCCTGCACT 2602Acc1 TGCAGACTCTGGCCATCAATGATGAGAATTCTAAATTTATCAACTCACTGCACCTGCACT 2551Acc440 TGCAGACTCTGGCCATCAATGATGAGAATTCTAAATTTATCAACTCATCGCACCTGCACT 2551Acc868 TGCAGACTCTGGCCATCAATGATGAGAATTCTAAATTTATCAACTCATCGCACCTGCACT 2565Acc718 TGCAGACTCTGGCCATCAATGATGAGAATTCTAACTTTATCAACTCATTGG------ACG 2473 ******************************** * ************ *  Acc414 ACATGCCCGCGCCTCCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGC 2572Acc420 ACATGCCCGCGCCTCCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGC 2572Acc761 ACATGCCCGCGCCTCCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGC 2572Acc504 ACATGCCCGCGCCTCCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGC 2572Acc563 ACATGCCCGCGCCTCCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGC 2572Acc757 ACATGCCCGCGCCTCCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGC 2572Acc848 ACATGCCCGCGCCTCCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGC 2572Tsuyuake_Pikm ACATGCCCGCGCCTCCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGC 2572Kusabue_Pik ACATGCCCGCGCCTCCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGC 2572Kanto51_Pik ACATGCCCGCGCCTCCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGC 2572K60_Pikp ACATGCCCGCGCCTCCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGC 2572Acc108 ACATGCCCGCGCCTCCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGC 2572Acc130 ACATGCCCGCGCCTCCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGC 2572Acc719 ACATGCCCGCGCCTCCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGC 2572Acc729 ACATGCCCGCGCCTCCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGC 2572Acc710 ACATGCCCGCGCCTCCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGC 2572Acc709 ACATGCCCGCGCCTCCAAGATATCTTGTCGCCCTTGAGCTGTCTGGCAAGTTGGAGAAGC 2572Acc220 ACATGTCTGCACCTCCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGAAATGGC 2641Nipponbare ACATGTCTGCACCTCCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGAAATGGC 2641Acc224 ACATGTCTGCACCTCCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGAAATGGC 2641AccUP3 ACATGTCTGCACCTCCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGAAATGGC 2641AccUP1 ACATGTCTGCACCTCCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGAAATGGC 2641Acc206 ACATGTCTGCACCTCCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGAAATGGC 2641Acc201 ACATGTCTGCACCTCCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGAAATGGC 2641Acc724 ACATGTCTGCACCTCCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGAAATGGC 2641Acc415 ACATGTCTGCACCTCCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGAAATGGC 2641Acc417 ACATGTCTGCACCTCCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGAAATGGC 2641Acc435 ACATGTCTGCACCTCCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGAAATGGC 2641Acc712 ACATGTCTGCACCTCCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGAAATGGC 2641Acc101 ACATGTCTGCACCTCCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGGACTGGC 2662Acc715 ACATGTCTGCACCTCCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGGACTGGC 2662Acc706 ACATGTCTGCACCTCCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGGACTGGC 2662Acc624 ACATGTCTGCACCTCCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGGACTGGC 2662Acc1 ACATGTCTGCACCTCCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGGACTGGC 2611Acc440 ACATGTCTGCACCTCCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGGACTGGC 2611Acc868 ACATGTCTGCACCTCCAAGATATCTAGTCTCCCTTGAGCTGTCCGGCAAGTTGGACTGGC 2625Acc718 GCATGTCCGCACCTCCAAGATATCTCATCGCCCTTGAGCTGTCCGGCAAGTTGTACAGGC 2533 **** * ** ************** ** ************* ********* * **

Ashikawa et al. Supplementary Fig. S2 (23/28)

Acc414 TACCCAAGTGGATCACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTC 2632Acc420 TACCCAAGTGGATCACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTC 2632Acc761 TACCCAAGTGGATCACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTC 2632Acc504 TACCCAAGTGGATCACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTC 2632Acc563 TACCCAAGTGGATCACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTC 2632Acc757 TACCCAAGTGGATCACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTC 2632Acc848 TACCCAAGTGGATCACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTC 2632Tsuyuake_Pikm TACCCAAGTGGATCACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTC 2632Kusabue_Pik TACCCAAGTGGATCACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTC 2632Kanto51_Pik TACCCAAGTGGATCACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTC 2632K60_Pikp TACCCAAGTGGATCACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTC 2632Acc108 TACCCAAGTGGATCACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTC 2632Acc130 TACCCAAGTGGATCACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTC 2632Acc719 TACCCAAGTGGATCACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTC 2632Acc729 TACCCAAGTGGATCACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTC 2632Acc710 TACCCAAGTGGATCACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTC 2632Acc709 TACCCAAGTGGATCACCAGCATCACTACTCTCAACAAGCTAACCATATCTGTAACAGTTC 2632Acc220 TACCTGAGTGGATCACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTC 2701Nipponbare TACCTGAGTGGATCACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTC 2701Acc224 TACCTGAGTGGATCACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTC 2701AccUP3 TACCTGAGTGGATCACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTC 2701AccUP1 TACCTGAGTGGATCACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTC 2701Acc206 TACCTGAGTGGATCACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTC 2701Acc201 TACCTGAGTGGATCACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTC 2701Acc724 TACCTGAGTGGATCACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTC 2701Acc415 TACCTGGGTGGATCACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTC 2701Acc417 TACCTGGGTGGATCACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTC 2701Acc435 TACCTGGGTGGATCACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTC 2701Acc712 TACCTGGGTGGATCACCAGCATTACTACTCTCAACAGGTTAACCATATCTATAACAGTTC 2701Acc101 TACCTGTGTGGATCACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTC 2722Acc715 TACCTGTGTGGATCACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTC 2722Acc706 TACCTGTGTGGATCACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTC 2722Acc624 TACCTGTGTGGATCACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTC 2722Acc1 TACCTGTGTGGATCACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTC 2671Acc440 TACCTGTGTGGATCACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTC 2671Acc868 TACCTGTGTGGATCACCAGCATTACTACTCTCAACAAGTTAACCATATCTATAACAGTTC 2685Acc718 TACCCGAGTGGATCACCAGCATTGCTACTCTCAACAAGTTAACCATATCTATAACAGTTC 2593 **** *************** ************ * *********** ********* Acc414 TTAGGACTGAAACTTTGGAGATCCTCCACATTTTACCTTCATTGTTTTCCCTCACCTTCG 2692Acc420 TTAGGACTGAAACTTTGGAGATCCTCCACATTTTACCTTCATTGTTTTCCCTCACCTTCG 2692Acc761 TTAGGACTGAAACTTTGGAGATCCTCCACATTTTACCTTCATTGTTTTCCCTCACCTTCG 2692Acc504 TTAGGACTGAAACTTTGGAGATCCTCCACATTTTACCTTCATTGTTTTCCCTCACCTTCG 2692Acc563 TTAGGACTGAAACTTTGGAGATCCTCCACATTTTACCTTCATTGTTTTCCCTCACCTTCG 2692Acc757 TTAGGACTGAAACTTTGGAGATCCTCCACATTTTACCTTCATTGTTTTCCCTCACCTTCG 2692Acc848 TTAGGACTGAAACTTTGGAGATCCTCCACATTTTACCTTCATTGTTTTCCCTCACCTTCG 2692Tsuyuake_Pikm TTAGGACTGAAACTTTGGAGATCCTCCACATTTTACCTTCATTGTTTTCCCTCACCTTCG 2692Kusabue_Pik TTAGGACTGAAACTTTGGAGATCCTCCACATTTTACCTTCATTGTTTTCCCTCACCTTCG 2692Kanto51_Pik TTAGGACTGAAACTTTGGAGATCCTCCACATTTTACCTTCATTGTTTTCCCTCACCTTCG 2692K60_Pikp TTAGGACTGAAACTTTGGAGATCCTCCACATTTTACCTTCATTGTTTTCCCTCACCTTCG 2692Acc108 TTAGGACTGAAACTTTGGAGATCCTCCACATTTTACCTTCATTGTTTTCCCTCACCTTCG 2692Acc130 TTAGGACTGAAACTTTGGAGATCCTCCACATTTTACCTTCATTGTTTTCCCTCACCTTCG 2692Acc719 TTAGGACTGAAACTTTGGAGATCCTCCACATTTTACCTTCATTGTTTTCCCTCACCTTCG 2692Acc729 TTAGGACTGAAACTTTGGAGATCCTCCACATTTTACCTTCATTGTTTTCCCTCACCTTCG 2692Acc710 TTAGGACTGAAACTTTGGAGATCCTCCACATTTTACCTTCATTGTTTTCCCTCACCTTCG 2692Acc709 TTAGGACTGAAACTTTGGAGATCCTCCACATTTTACCTTCATTGTTTTCCCTCACCTTCG 2692Acc220 TTACGACTGAAACTTTGGAGATCCTCCGCAATTTACCTTCATTGTTTTCCCTCACCTTTG 2761Nipponbare TTACGACTGAAACTTTGGAGATCCTCCGCAATTTACCTTCATTGTTTTCCCTCACCTTTG 2761Acc224 TTACGACTGAAACTTTGGAGATCCTCCGCAATTTACCTTCATTGTTTTCCCTCACCTTTG 2761AccUP3 TTACGACTGAAACTTTGGAGATCCTCCGCAATTTACCTTCATTGTTTTCCCTCACCTTTG 2761AccUP1 TTACGACTGAAACTTTGGAGATCCTCCGCAATTTACCTTCATTGTTTTCCCTCACCTTTG 2761Acc206 TTGCGACTGAAACTTTGGAGATCCTCCGCAATTTACCTTCATTGTTTTCCCTCACCTTTG 2761Acc201 TTGCGACTGAAACTTTGGAGATCCTCCGCAATTTACCTTCATTGTTTTCCCTCACCTTTG 2761Acc724 TTACGACTGAAACTTTGGAGATCCTCCGCAATTTACCTTCATTGTTTTCCCTCACCTTTG 2761Acc415 TTACGACTGAAACTTTGGAGATCCTCCGCAATTTACCTTCATTGTTTTCCCTCACCTTTG 2761Acc417 TTACGACTGAAACTTTGGAGATCCTCCGCAATTTACCTTCATTGTTTTCCCTCACCTTTG 2761Acc435 TTACGACTGAAACTTTGGAGATCCTCCGCAATTTACCTTCATTGTTTTCCCTCACCTTTG 2761Acc712 TTACGACTGAAACTTTGGAGATCCTCCGCAATTTACCTTCATTGTTTTCCCTCACCTTTG 2761Acc101 TTACGACTAAAACTTTGGAGATCCTCTGCAATTTACCTTCATTGTTTTCCCTCACCTTTG 2782Acc715 TTACGACTAAAACTTTGGAGATCCTCTGCAATTTACCTTCATTGTTTTCCCTCACCTTTG 2782Acc706 TTACGACTAAAACTTTGGAGATCCTCTGCAATTTACCTTCATTGTTTTCCCTCACCTTTG 2782Acc624 TTACGACTAAAACTTTGGAGATCCTCTGCAATTTACCTTCATTGTTTTCCCTCACCTTTG 2782Acc1 TTACGACTGAAACTTTGGAGATCCTCTGCAATTTACCTTCATTGTTTTCCCTCACCTTTG 2731Acc440 TTACGACTGAAACTTTGGAGATCCTCTGCAATTTACCTTCATTGTTTTCCCTCACCTTTG 2731Acc868 TTACGACTGAAACTTTGGAGATCCTCTGCAATTTACCTTCATTGTTTTCCCTCACCTTTG 2745Acc718 TTACGACTGAAACTTTGGAGATCCTCCGCAGTTTACCTTCATTGTTTTCCCTCACCTTCG 2653 ** **** ***************** ** *************************** * 

Ashikawa et al. Supplementary Fig. S2 (24/28)

Acc414 CCTTTTCACTTAGTGCAGCGAAGCAGGATCAGGACATAATAAAGGACATCCTTGAGAATA 2752Acc420 CCTTTTCACTTAGTGCAGCGAAGCAGGATCAGGACATAATAAAGGACATCCTTGAGAATA 2752Acc761 CCTTTTCACTTAGTGCAGCGAAGCAGGATCAGGACATAATAAAGGACATCCTTGAGAATA 2752Acc504 CCTTTTCACTTAGTGCAGCGAAGCAGGATCAGGACATAATAAAGGACATCCTTGAGAATA 2752Acc563 CCTTTTCACTTAGTGCAGCGAAGCAGGATCAGGACATAATAAAGGACATCCTTGAGAATA 2752Acc757 CCTTTTCACTTAGTGCAGCGAAGCAGGATCAGGACATAATAAAGGACATCCTTGAGAATA 2752Acc848 CCTTTTCACTTAGTGCAGCGAAGCAGGATCAGGACATAATAAAGGACATCCTTGAGAATA 2752Tsuyuake_Pikm CCTTTTCACTTAGTGCAGCGAAGCAGGATCAGGACATAATAAAGGACATCCTTGAGAATA 2752Kusabue_Pik CCTTTTCACTTAGTGCAGCGAAGCAGGATCAGGACATAATAAAGGACATCCTTGAGAATA 2752Kanto51_Pik CCTTTTCACTTAGTGCAGCGAAGCAGGATCAGGACATAATAAAGGACATCCTTGAGAATA 2752K60_Pikp CCTTTTCACTTAGTGCAGCGAAGCAGGATCAGGACATAATAAAGGACATCCTTGAGAATA 2752Acc108 CCTTTTCACTTAGTGCAGCGAAGCAGGATCAGGACATAATAAAGGACATCCTTGAGAATA 2752Acc130 CCTTTTCACTTAGTGCAGCGAAGCAGGATCAGGACATAATAAAGGACATCCTTGAGAATA 2752Acc719 CCTTTTCACTTAGTGCAGCGAAGCAGGATCAGGACATAATAAAGGACATCCTTGAGAATA 2752Acc729 CCTTTTCACTTAGTGCAGCGAAGCAGGATCAGGACATAATAAAGGACATCCTTGAGAATA 2752Acc710 CCTTTTCACTTAGTGCAGCGAAGCAGGATCAGGACATAATAAAGGACATCCTTGAGAATA 2752Acc709 CCTTTTCACTTAGTGCAGCGAAGCAGGATCAGGACATAATAAAGGACATCCTTGAGAATA 2752Acc220 CCTTTTCACTTAGTGCAGCGAAGCAAGATCAGGACACAGTAAAGGGCATCCTTGAGGACA 2821Nipponbare CCTTTTCACTTAGTGCAGCGAAGCAAGATCAGGACACAGTAAAGGGCATCCTTGAGGACA 2821Acc224 CCTTTTCACTTAGTGCAGCGAAGCAAGATCAGGACACAGTAAAGGGCATCCTTGAGGACA 2821AccUP3 CCTTTTCACTTAGTGCAGCGAAGCAAGATCAGGACACAGTAAAGGGCATCCTTGAGGACA 2821AccUP1 CCTTTTCACTTAGTGCAGCGAAGCAAGATCAGGACACAGTAAAGGGCATCCTTGAGGACA 2821Acc206 CCTTTTCACTTAGTGCAGCGAAGCAAGATCAGGACACAGTAAAGGGCATCCTTGAGGACA 2821Acc201 CCTTTTCACTTAGTGCAGCGAAGCAAGATCAGGACACAGTAAAGGGCATCCTTGAGGACA 2821Acc724 CCTTTTCACTTAGTGCAGCGAAGCAAGATCAGGACACAGTAAAGGGCATCCTTGAGGACA 2821Acc415 CCTTTTCACTTAGTGCAGCGAAGCAAGATCAGGACACAGTAAAGGGCATCCTTGAGGACA 2821Acc417 CCTTTTCACTTAGTGCAGCGAAGCAAGATCAGGACACAGTAAAGGGCATCCTTGAGGACA 2821Acc435 CCTTTTCACTTAGTGCAGCGAAGCAAGATCAGGACACAGTAAAGGGCATCCTTGAGGACA 2821Acc712 CCTTTTCACTTAGTGCAGCGAAGCAAGATCAGGACACAGTAAAGGGCATCCTTGAGGACA 2821Acc101 CCTTTTCACTTAGTGCAGCGAAGCAAGATCAGGACACAGTAAAGGGCATCCTTGAGGACA 2842Acc715 CCTTTTCACTTAGTGCAGCGAAGCAAGATCAGGACACAGTAAAGGGCATCCTTGAGGACA 2842Acc706 CCTTTTCACTTAGTGCAGCGAAGCAAGATCAGGACACAGTAAAGGGCATCCTTGAGGACA 2842Acc624 CCTTTTCACTTAGTGCAGCGAAGCAAGATCAGGACACAGTAAAGGGCATCCTTGAGGACA 2842Acc1 CCTTTTCACTTAGTGCAGCGAAGCAAGATCAGGACACAGTAAAGGGCATCCTTGAGGACA 2791Acc440 CCTTTTCACTTAGTGCAGCGAAGCAAGATCAGGACACAGTAAAGGGCATCCTTGAGGACA 2791Acc868 CCTTTTCACTTAGTGCAGCGAAGCAAGATCAGGACACAGTAAAGGGCATCCTTGAGGACA 2805Acc718 CCTTTTCACTTAGTGCAGCGAAGCAGGATCTGGACGAAATAAAGGACATCCTTGAGAACA 2713 ************************* **** **** * ****** ********** * * Acc414 ATAAATTGGACAGTGATGGGGAAATCGTCATTCCAGCTGAAGGATTCAAGAGTCTTAAGC 2812Acc420 ATAAATTGGACAGTGATGGGGAAATCGTCATTCCAGCTGAAGGATTCAAGAGTCTTAAGC 2812Acc761 ATAAATTGGACAGTGATGGGGAAATCGTCATTCCAGCTGAAGGATTCAAGAGTCTTAAGC 2812Acc504 ATAAATTGGACAGTGATGGGGAAATCGTCATTCCAGCTGAAGGATTCAAGAGTCTTAAGC 2812Acc563 ATAAATTGGACAGTGATGGGGAAATCGTCATTCCAGCTGAAGGATTCAAGAGTCTTAAGC 2812Acc757 ATAAATTGGACAGTGATGGGGAAATCGTCATTCCAGCTGAAGGATTCAAGAGTCTTAAGC 2812Acc848 ATAAATTGGACAGTGATGGGGAAATCGTCATTCCAGCTGAAGGATTCAAGAGTCTTAAGC 2812Tsuyuake_Pikm ATAAATTGGACAGTGATGGGGAAATCGTCATTCCAGCTGAAGGATTCAAGAGTCTTAAGC 2812Kusabue_Pik ATAAATTGGACAGTGATGGGGAAATCGTCATTCCAGCTGAAGGATTCAAGAGTCTTAAGC 2812Kanto51_Pik ATAAATTGGACAGTGATGGGGAAATCGTCATTCCAGCTGAAGGATTCAAGAGTCTTAAGC 2812K60_Pikp ATAAATTGGACAGTGATGGGGAAATCGTCATTCCAGCTGAAGGATTCAAGAGTCTTAAGC 2812Acc108 ATAAATTGGACAGTGATGGGGAAATCGTCATTCCAGCTGAAGGATTCAAGAGTCTTAAGC 2812Acc130 ATAAATTGGACAGTGATGGGGAAATCGTCATTCCAGCTGAAGGATTCAAGAGTCTTAAGC 2812Acc719 ATAAATTGGACAGTGATGGGGAAATCGTCATTCCAGCTGAAGGATTCAAGAGTCTTAAGC 2812Acc729 ATAAATTGGACAGTGATGGGGAAATCGTCATTCCAGCTGAAGGATTCAAGAGTCTTAAGC 2812Acc710 ATAAATTGGACAGTGATGGGGAAATCGTCATTCCAGCTGAAGGATTCAAGAGTCTTAAGC 2812Acc709 ATAAATTGGACAGTGATGGGGAAATCGTCATTCCAGCTGAAGGATTCAAGAGTCTTAAGC 2812Acc220 ATAAATTGGCCACTGACGGGGAAATCGTCATTCCAGCTAAAGAATTCAAGAGTCTTAAGC 2881Nipponbare ATAAATTGGCCACTGACGGGGAAATCGTCATTCCAGCTAAAGAATTCAAGAGTCTTAAGC 2881Acc224 ATAAATTGGCCACTGACGGGGAAATCGTCATTCCAGCTAAAGAATTCAAGAGTCTTAAGC 2881AccUP3 ATAAATTGGCCACTGACGGGGAAATCGTCATTCCAGCTAAAGAATTCAAGAGTCTTAAGC 2881AccUP1 ATAAATTGGCCACTGACGGGGAAATCGTCATTCCAGCTAAAGAATTCAAGAGTCTTAAGC 2881Acc206 ATAAATTGGCCACTGACGGGGAAATCGTCATTCCAGCTAAAGAATTCAAGAGTCTTAAGC 2881Acc201 ATAAATTGGCCACTGACGGGGAAATCGTCATTCCAGCTAAAGAATTCAAGAGTCTTAAGC 2881Acc724 ATAAATTGGCCACTGACGGGGAAATCGTCATTCCAGCTAAAGAATTCAAGAGTCTTAAGC 2881Acc415 ATAAATTGGCCACTGACGGGGAAATCGTCATTCCAGCTAAAGAATTCAAGAGTCTTAAGC 2881Acc417 ATAAATTGGCCACTGACGGGGAAATCGTCATTCCAGCTAAAGAATTCAAGAGTCTTAAGC 2881Acc435 ATAAATTGGCCACTGACGGGGAAATCGTCATTCCAGCTAAAGAATTCAAGAGTCTTAAGC 2881Acc712 ATAAATTGGCCACTGACGGGGAAATCGTCATTCCAGCTAAAGAATTCAAGAGTCTTAAGC 2881Acc101 ATAAATTGGCCACTGACGGGGAAATCGTCATTCCAGCTAAAGAATTCAAGAGTCTTAAGC 2902Acc715 ATAAATTGGCCACTGACGGGGAAATCGTCATTCCAGCTAAAGAATTCAAGAGTCTTAAGC 2902Acc706 ATAAATTGGCCACTGACGGGGAAATCGTCATTCCAGCTAAAGAATTCAAGAGTCTTAAGC 2902Acc624 ATAAATTGGCCACTGACGGGGAAATCGTCATTCCAGCTAAAGAATTCAAGAGTCTTAAGC 2902Acc1 ATAAATTGGCCACTGACGGGGAAATCGTCATTCCAGCTAAAGAATTCAAGAGTCTTAAGC 2851Acc440 ATAAATTGGCCACTGACGGGGAAATCGTCATTCCAGCTAAAGAATTCAAGAGTCTTAAGC 2851Acc868 ATAAATTGGCCACTGACGGGGAAATCGTCATTCCAGCTAAAGAATTCAAGAGTCTTAAGC 2865Acc718 ATAAATTGGCCACTGATGGGGAAATCGTCATTCCAGCTGAAGGATTCAAGAGTCTTAAGC 2773 ********* ** *** ********************* *** ***************** 

Ashikawa et al. Supplementary Fig. S2 (25/28)

Acc414 TGCTTCGCTTCTTTGCACCTTTAGTGCCGAAGCTCAGCTTTTTGGACAAGAATGCAATGC 2872Acc420 TGCTTCGCTTCTTTGCACCTTTAGTGCCGAAGCTCAGCTTTTTGGACAAGAATGCAATGC 2872Acc761 TGCTTCGCTTCTTTGCACCTTTAGTGCCGAAGCTCAGCTTTTTGGACAAGAATGCAATGC 2872Acc504 TGCTTCGCTTCTTTGCACCTTTAGTGCCGAAGCTCAGCTTTTTGGACAAGAATGCAATGC 2872Acc563 TGCTTCGCTTCTTTGCACCTTTAGTGCCGAAGCTCAGCTTTTTGGACAAGAATGCAATGC 2872Acc757 TGCTTCGCTTCTTTGCACCTTTAGTGCCGAAGCTCAGCTTTTTGGACAAGAATGCAATGC 2872Acc848 TGCTTCGCTTCTTTGCACCTTTAGTGCCGAAGCTCAGCTTTTTGGACAAGAATGCAATGC 2872Tsuyuake_Pikm TGCTTCGCTTCTTTGCACCTTTAGTGCCGAAGCTCAGCTTTTTGGACAAGAATGCAATGC 2872Kusabue_Pik TGCTTCGCTTCTTTGCACCTTTAGTGCCGAAGCTCAGCTTTTTGGACAAGAATGCAATGC 2872Kanto51_Pik TGCTTCGCTTCTTTGCACCTTTAGTGCCGAAGCTCAGCTTTTTGGACAAGAATGCAATGC 2872K60_Pikp TGCTTCGCTTCTTTGCACCTTTAGTGCCGAAGCTCAGCTTTTTGGACAAGAATGCAATGC 2872Acc108 TGCTTCGCTTCTTTGCACCTTTAGTGCCGAAGCTCAGCTTTTTGGACAAGAATGCAATGC 2872Acc130 TGCTTCGCTTCTTTGCACCTTTAGTGCCGAAGCTCAGCTTTTTGGACAAGAATGCAATGC 2872Acc719 TGCTTCGCTTCTTTGCACCTTTAGTGCCGAAGCTCAGCTTTTTGGACAAGAATGCAATGC 2872Acc729 TGCTTCGCTTCTTTGCACCTTTAGTGCCGAAGCTCAGCTTTTTGGACAAGAATGCAATGC 2872Acc710 TGCTTCGCTTCTTTGCACCTTTAGTGCCGAAGCTCAGCTTTTTGGACAAGAATGCAATGC 2872Acc709 TGCTTCGCTTCTTTGCACCTTTAGTGCCGAAGCTCAGCTTTTTGGACAAGAATGCAATGC 2872Acc220 TGCTTCGCTTCTTTGCACCTTTCGTGCCAAAGCTCAGCTTTCCGGACAAGAGTGCAATGC 2941Nipponbare TGCTTCGCTTCTTTGCACCTTTCGTGCCAAAGCTCAGCTTTCCGGACAAGAGTGCAATGC 2941Acc224 TGCTTCGCTTCTTTGCACCTTTCGTGCCAAAGCTCAGCTTTCCGGACAAGAGTGCAATGC 2941AccUP3 TGCTTCGCTTCTTTGCACCTTTCGTGCCAAAGCTCAGCTTTCCGGACAAGAGTGCAATGC 2941AccUP1 TGCTTCGCTTCTTTGCACCTTTCGTGCCAAAGCTCAGCTTTCCGGACAAGAGTGCAATGC 2941Acc206 TGCTTCGCTTCTTTGCACCTTTCGTGCCAAAGCTCAGCTTTCCGGACAAGAGTGCAATGC 2941Acc201 TGCTTCGCTTCTTTGCACCTTTCGTGCCAAAGCTCAGCTTTCCGGACAAGAGTGCAATGC 2941Acc724 TGCTTCGCTTCTTTGCACCTTTCGTGCCAAAGCTCAGCTTTCCGGACAAGAGTGCAATGC 2941Acc415 TGCTTCGCTTCTTTGCACCTTTCGTGCCAAAGCTCAGCTTTCCGGACAAGAGTGCAATGC 2941Acc417 TGCTTCGCTTCTTTGCACCTTTCGTGCCAAAGCTCAGCTTTCCGGACAAGAGTGCAATGC 2941Acc435 TGCTTCGCTTCTTTGCACCTTTCGTGCCAAAGCTCAGCTTTCCGGACAAGAGTGCAATGC 2941Acc712 TGCTTCGCTTCTTTGCACCTTTCGTGCCAAAGCTCAGCTTTCCGGACAAGAGTGCAATGC 2941Acc101 TGCTTCGCTTCTTTGCACCTTTCGTGCCAAAGCTCAGCTTTCCGGACAAGAGTGCAATGC 2962Acc715 TGCTTCGCTTCTTTGCACCTTTCGTGCCAAAGCTCAGCTTTCCGGACAAGAGTGCAATGC 2962Acc706 TGCTTCGCTTCTTTGCACCTTTCGTGCCAAAGCTCAGCTTTCCGGACAAGAGTGCAATGC 2962Acc624 TGCTTCGCTTCTTTGCACCTTTCGTGCCAAAGCTCAGCTTTCCGGACAAGAGTGCAATGC 2962Acc1 TGCTTCGCTTCTTTGCACCTTTCGTGCCAAAGCTCAGCTTTCCGGACAAGAGTGCAATGC 2911Acc440 TGCTTCGCTTCTTTGCACCTTTCGTGCCAAAGCTCAGCTTTCCGGACAAGAGTGCAATGC 2911Acc868 TGCTTCGCTTCTTTGCACCTTTCGTGCCAAAGCTCAGCTTTCCGGACAAGAGTGCAATGC 2925Acc718 TGCTTCGTTTCTTTGCACCTTTCGTGCCGAAGCTCAGCTTTTCGGACAAGAATGCAATGC 2833 ******* ************** ***** ************ ******** ******** Acc414 CAGCACTCGAAATCATTGAAATGCGGTTTAAAGACTTCGAAGGTCTATTTGGCATCGAAA 2932Acc420 CAGCACTCGAAATCATTGAAATGCGGTTTAAAGACTTCGAAGGTCTATTTGGCATCGAAA 2932Acc761 CAGCACTCGAAATCATTGAAATGCGGTTTAAAGACTTCGAAGGTCTATTTGGCATCGAAA 2932Acc504 CAGCACTCGAAATCATTGAAATGCGGTTTAAAGACTTCGAAGGTCTATTTGGCATCGAAA 2932Acc563 CAGCACTCGAAATCATTGAAATGCGGTTTAAAGACTTCGAAGGTCTATTTGGCATCGAAA 2932Acc757 CAGCACTCGAAATCATTGAAATGCGGTTTAAAGACTTCGAAGGTCTATTTGGCATCGAAA 2932Acc848 CAGCACTCGAAATCATTGAAATGCGGTTTAAAGACTTCGAAGGTCTATTTGGCATCGAAA 2932Tsuyuake_Pikm CAGCACTCGAAATCATTGAAATGCGGTTTAAAGACTTCGAAGGTCTATTTGGCATCGAAA 2932Kusabue_Pik CAGCACTCGAAATCATTGAAATGCGGTTTAAAGACTTCGAAGGTCTATTTGGCATCGAAA 2932Kanto51_Pik CAGCACTCGAAATCATTGAAATGCGGTTTAAAGACTTCGAAGGTCTATTTGGCATCGAAA 2932K60_Pikp CAGCACTCGAAATCATTGAAATGCGGTTTAAAGACTTCGAAGGTCTATTTGGCATCGAAA 2932Acc108 CAGCACTCGAAATCATTGAAATGCGGTTTAAAGACTTCGAAGGTCTATTTGGCATCGAAA 2932Acc130 CAGCACTCGAAATCATTGAAATGCGGTTTAAAGACTTCGAAGGTCTATTTGGCATCGAAA 2932Acc719 CAGCACTCGAAATCATTGAAATGCGGTTTAAAGACTTCGAAGGTCTATTTGGCATCGAAA 2932Acc729 CAGCACTCGAAATCATTGAAATGCGGTTTAAAGACTTCGAAGGTCTATTTGGCATCGAAA 2932Acc710 CAGCACTCGAAATCATTGAAATGCGGTTTAAAGACTTCGAAGGTCTATTTGGCATCGAAA 2932Acc709 CAGCACTCGAAATCATTGAAATGCGGTTTAAAGACTTCGAAGGTCTATTTGGCATCGAAA 2932Acc220 CAGCACTCGAAATCATTGAAATGCGGTTTCAAGAATTTGAGGGTCTATTCGGCATCGAAA 3001Nipponbare CAGCACTCGAAATCATTGAAATGCGGTTTCAAGAATTTGAGGGTCTATTCGGCATCGAAA 3001Acc224 CAGCACTCGAAATCATTGAAATGCGGTTTCAAGAATTTGAGGGTCTATTCGGCATCGAAA 3001AccUP3 CAGCACTCGAAATCATTGAAATGCGGTTTCAAGAATTTGAGGGTCTATTCGGCATCGAAA 3001AccUP1 CAGCACTCGAAATCATTGAAATGCGGTTTCAAGAATTTGAGGGTCTATTCGGCATCGAAA 3001Acc206 CAGCACTCGAAATCATTGAAATGCGGTTTCAAGAATTTGAGGGTCTATTCGGCATCGAAA 3001Acc201 CAGCACTCGAAATCATTGAAATGCGGTTTCAAGAATTTGAGGGTCTATTCGGCATCGAAA 3001Acc724 CAGCACTCGAAATCATTGAAATGCGGTTTCAAGAATTTGAGGGTCTATTCGGCATCGAAA 3001Acc415 CAGCACTCGAAATCATTGAAATGCGGTTTCAAGAATTTGAGGGTCTATTCGGCATCGAAA 3001Acc417 CAGCACTCGAAATCATTGAAATGCGGTTTCAAGAATTTGAGGGTCTATTCGGCATCGAAA 3001Acc435 CAGCACTCGAAATCATTGAAATGCGGTTTCAAGAATTTGAGGGTCTATTCGGCATCGAAA 3001Acc712 CAGCACTCGAAATCATTGAAATGCGGTTTCAAGAATTTGAGGGTCTATTCGGCATCGAAA 3001Acc101 CAGCACTCGAAATCATTGAAATGCGGTTTCAAGAATTTGAGGGTCTATTCGGCATCGAAA 3022Acc715 CAGCACTCGAAATCATTGAAATGCGGTTTCAAGAATTTGAGGGTCTATTCGGCATCGAAA 3022Acc706 CAGCACTCGAAATCATTGAAATGCGGTTTCAAGAATTTGAGGGTCTATTCGGCATCGAAA 3022Acc624 CAGCACTCGAAATCATTGAAATGCGGTTTCAAGAATTTGAGGGTCTATTCGGCATCGAAA 3022Acc1 CAGCACTCGAAATCATTGAAATGCGGTTTCAAGAATTTGAGGGTCTATTCGGCATCGAAA 2971Acc440 CAGCACTCGAAATCATTGAAATGCGGTTTCAAGAATTTGAGGGTCTATTCGGCATCGAAA 2971Acc868 CAGCACTCGAAATCATTGAAATGCGGTTTCAAGAATTTGAGGGTCTATTCGGCATCGAAA 2985Acc718 CAGCACTTGAAATCATTGAAATGCGGTTTAAAGACTTCGAGGGTCTATTCGGCATCGAAA 2893 ******* ********************* **** ** ** ******** ********** 

Ashikawa et al. Supplementary Fig. S2 (26/28)

Acc414 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGTGATGGGGCAGAAGCAATAACCA 2992Acc420 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGTGATGGGGCAGAAGCAATAACCA 2992Acc761 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGTGATGGGGCAGAAGCAATAACCA 2992Acc504 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGTGATGGGGCAGAAGCAATAACCA 2992Acc563 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGTGATGGGGCAGAAGCAATAACCA 2992Acc757 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGTGATGGGGCAGAAGCAATAACCA 2992Acc848 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGTGATGGGGCAGAAGCAATAACCA 2992Tsuyuake_Pikm TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGTGATGGGGCAGAAGCAATAACCA 2992Kusabue_Pik TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGTGATGGGGCAGAAGCAATAACCA 2992Kanto51_Pik TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGTGATGGGGCAGAAGCAATAACCA 2992K60_Pikp TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGTGATGGGGCAGAAGCAATAACCA 2992Acc108 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGTGATGGGGCAGAAGCAATAACCA 2992Acc130 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGTGATGGGGCAGAAGCAATAACCA 2992Acc719 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGTGATGGGGCAGAAGCAATAACCA 2992Acc729 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGTGATGGGGCAGAAGCAATAACCA 2992Acc710 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGTGATGGGGCAGAAGCAATAACCA 2992Acc709 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGTGATGGGGCAGAAGCAATAACCA 2992Acc220 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGCGATGGGGCAGAAGCAATAACCA 3061Nipponbare TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGCGATGGGGCAGAAGCAATAACCA 3061Acc224 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGCGATGGGGCAGAAGCAATAACCA 3061AccUP3 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGCGATGGGGCAGAAGCAATAACCA 3061AccUP1 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGCGATGGGGCAGAAGCAATAACCA 3061Acc206 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGCGATGGGGCAGAAGCAATAACCA 3061Acc201 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGCGATGGGGCAGAAGCAATAACCA 3061Acc724 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGCGATGGGGCAGAAGCAATAACCA 3061Acc415 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGCGATGGGGCAGAAGCAATAACCA 3061Acc417 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGCGATGGGGCAGAAGCAATAACCA 3061Acc435 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGCGATGGGGCAGAAGCAATAACCA 3061Acc712 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGCGATGGGGCAGAAGCAATAACCA 3061Acc101 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGCGATGGGGCAGAAGCAATAACCA 3082Acc715 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGCGATGGGGCAGAAGCAATAACCA 3082Acc706 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGCGATGGGGCAGAAGCAATAACCA 3082Acc624 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGCGATGGGGCAGAAGCAATAACCA 3082Acc1 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGCGATGGGGCAGAAGCAATAACCA 3031Acc440 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGCGATGGGGCAGAAGCAATAACCA 3031Acc868 TCCTTGAAAATCTCCGTGAGGTGCATCTCAAAGTTAGCGATGGGGCAGAAGCAATAACCA 3045Acc718 TACTTGAAAATCTCCGTGGGGTGCATCTCAAAGTTAGCGATGGGGCAGAAGCAATAACCA 2953 * **************** ****************** ********************** Acc414 AGTTCCTTGTAAATGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3052Acc420 AGTTCCTTGTAAATGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3052Acc761 AGTTCCTTGTAAATGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3052Acc504 AGTTCCTTGTAAATGATTTGAAGGTTAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3052Acc563 AGTTCCTTGTAAATGATTTGAAGGTTAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3052Acc757 AGTTCCTTGTAAATGATTTGAAGGTTAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3052Acc848 AGTTCCTTGTAAATGATTTGAAGGTTAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3052Tsuyuake_Pikm AGTTCCTTGTAAATGATTTGAAGGTTAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3052Kusabue_Pik AGTTCCTTGTAAATGATTTGAAGGTTAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3052Kanto51_Pik AGTTCCTTGTAAATGATTTGAAGGTTAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3052K60_Pikp AGTTCCTTGTAAATGATTTGAAGGTTAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3052Acc108 AGTTCCTTGTAAATGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3052Acc130 AGTTCCTTGTAAATGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3052Acc719 AGTTCCTTGTAAATGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3052Acc729 AGTTCCTTGTAAATGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3052Acc710 AGTTCCTTGTAAATGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3052Acc709 AGTTCCTTGTAAATGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3052Acc220 AGTTCCTAGTAAGTGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3121Nipponbare AGTTCCTAGTAAGTGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3121Acc224 AGTTCCTAGTAAGTGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3121AccUP3 AGTTCCTAGTAAGTGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3121AccUP1 AGTTCCTAGTAAGTGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3121Acc206 AGTTCCTAGTAAGTGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3121Acc201 AGTTCCTAGTAAGTGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3121Acc724 AGTTCCTAGTAAGTGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3121Acc415 AGTTCCTAGTAAGTGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3121Acc417 AGTTCCTAGTAAGTGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3121Acc435 AGTTCCTAGTAAGTGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3121Acc712 AGTTCCTAGTAAGTGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3121Acc101 AGTTCCTAGTAAGTGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3142Acc715 AGTTCCTAGTAAGTGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3142Acc706 AGTTCCTAGTAAGTGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3142Acc624 AGTTCCTAGTAAGTGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3142Acc1 AGTTCCTAGTAAGTGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3091Acc440 AGTTCCTAGTAAGTGATTTGAAGGATCATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3091Acc868 AGTTCCTAGTAAGTGATTTGAAGGATCATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3105Acc718 ATTTCCTAGCAAATGATTTGAAGGATAATACTGAGAAACCAAAAGTATTTGTTGATGGCA 3013 * ***** * ** *********** * ********************************* 

Ashikawa et al. Supplementary Fig. S2 (27/28)

Acc414 TCGTCACTGCATGA 3066Acc420 TCGTCACTGCATGA 3066Acc761 TCGTCACTGCATGA 3066Acc504 TCGTCACTGCATGA 3066Acc563 TCGTCACTGCATGA 3066Acc757 TCGTCACTGCATGA 3066Acc848 TCGTCACTGCATGA 3066Tsuyuake_Pikm TCGTCACTGCATGA 3066Kusabue_Pik TCGTCACTGCATGA 3066Kanto51_Pik TCGTCACTGCATGA 3066K60_Pikp TCGTCACTGCATGA 3066Acc108 TCGTCACTGCATGA 3066Acc130 TCGTCACTGCATGA 3066Acc719 TCGTCACTGCATGA 3066Acc729 TCGTCACTGCATGA 3066Acc710 TCGTCACTGCATGA 3066Acc709 TCGTCACTGCATGA 3066Acc220 TCGTCACTGCATGA 3135Nipponbare TCGTCACTGCATGA 3135Acc224 TCGTCACTGCATGA 3135AccUP3 TCGTCACTGCATGA 3135AccUP1 TCGTCACTGCATGA 3135Acc206 TCGTCACTGCATGA 3135Acc201 TCGTCACTGCATGA 3135Acc724 TCGTCACTGCATGA 3135Acc415 TCGTCACTGCATGA 3135Acc417 TCGTCACTGCATGA 3135Acc435 TCGTCACTGCATGA 3135Acc712 TCGTCACTGCATGA 3135Acc101 TCGTCACTGCATGA 3156Acc715 TCGTCACTGCATGA 3156Acc706 TCGTCACTGCATGA 3156Acc624 TCGTCACTGCATGA 3156Acc1 TCGTCACTGCATGA 3105Acc440 TCGTCACTGCATGA 3105Acc868 TCGTCACTGCATGA 3119Acc718 TCGTCACTGCATGA 3027 **************

Ashikawa et al. Supplementary Fig. S2 (28/28)