Acc414 ATGGAGGCGGCTGCCATGGCCGTA---ACCGCAGCCACGGGGGCCTTGGCGCCCGTGCTA 57Acc420 ATGGAGGCGGCTGCCATGGCCGTA---ACCGCAGCCACGGGGGCCTTGGCGCCCGTGCTA 57Acc761 ATGGAGGCGGCTGCCATGGCCGTA---ACCGCAGCCACGGGGGCCTTGGCGCCCGTGCTA 57K60_Pik-p ATGGAGGCGGCTGCCATGGCCGTA---ACCGCAGCCACGGGGGCCTTGGCGCCCGTGCTA 57Acc130 ATGGAGGCGGCTGCCATGGCCGTA---ACCGCAGCCACGGGGGCCTTGGCGCCCGTGCTA 57Acc108 ATGGAGGCGGCTGCCATGGCCGTA---ACCGCAGCCACGGGGGCCTTGGCGCCCGTGCTA 57Acc719 ATGGAGGCGGCTGCCATGGCCGTA---ACCGCAGCCACGGGGGCCTTGGCGCCCGTGCTA 57Acc729 ATGGAGGCGGCTGCCATGGCCGTA---ACCGCAGCCACGGGGGCCTTGGCGCCCGTGCTA 57Acc709 ATGGAGGCGGCTGCCATGGCCGTA---ACCGCAGCCACGGGGGCCTTGGCGCCCGTGCTA 57Acc710 ATGGAGGCGGCTGCCATGGCCGTA---ACCGCAGCCACGGGGGCCTTGGCGCCCGTGCTA 57Acc504 ATGGAGGCGGCTGCCATGGCCGTA---ACCGCAGCCACGGGGGCCTTGGCGCCCGTGCTA 57Acc848 ATGGAGGCGGCTGCCATGGCCGTA---ACCGCAGCCACGGGGGCCTTGGCGCCCGTGCTA 57Acc563 ATGGAGGCGGCTGCCATGGCCGTA---ACCGCAGCCACGGGGGCCTTGGCGCCCGTGCTA 57Acc757 ATGGAGGCGGCTGCCATGGCCGTA---ACCGCAGCCACGGGGGCCTTGGCGCCCGTGCTA 57Tsuyuake_Pik-m ATGGAGGCGGCTGCCATGGCCGTA---ACCGCAGCCACGGGGGCCTTGGCGCCCGTGCTA 57Kanto51_Pik ATGGAGGCGGCTGCCATGGCCGTA---ACCGCAGCCACGGGGGCCTTGGCGCCCGTGCTA 57Kusabue_Pik ATGGAGGCGGCTGCCATGGCCGTA---ACCGCAGCCACGGGGGCCTTGGCGCCCGTGCTA 57Acc201 ---------------ATGGCCGTATACAGCGTCGCCACGGGGGCCTTGGCTCCCGTCCTA 45Acc206 ---------------ATGGCCGTATACAGCGTCGCCACGGGGGCCTTGGCTCCCGTCCTA 45Acc1 ---------------ATGGCCGTATACAGCGTCGCCACGGGGGCCTTGGCTCCCGTCCTA 45Acc101 ---------------ATGGCCGTATACAGCGTCGCCACGGGGGCCTTGGCTCCCGTCCTA 45Acc718 ---------------ATGGCCGTATACAGCGTCGCCACGGGGGCCTTGGCTCCCGTCCTA 45Acc724 ---------------ATGGCCGTATACAGCGTCGCCACGGGGGCCTTGGCTCCCGTCCTA 45Acc715 ---------------ATGGCCGTATACAGCGTCGCCACGGGGGCCTTGGCTCCCGTCCTA 45Acc706 ---------------ATGGCCGTATACAGCGTCGCCACGGGGGCCTTGGCTCCCGTCCTA 45Acc624 ---------------ATGGCCGTATACAGCGTCGCCACGGGGGCCTTGGCTCCCGTCCTA 45Acc440 ---------------ATGGCCGTATACAGCGTCGCCACGGGGGCCTTGGCTCCCGTCCTA 45Acc868 ---------------ATGGCCGTATACAGCGTCGCCACGGGGGCCTTGGCTCCCGTCCTA 45Acc220 ---------------ATGGCCGTATACAGCGTCGCCACGGGGGCCTTGGCTCCCGTCCTA 45Nipponbare ---------------ATGGCCGTATACAGCGTCGCCACGGGGGCCTTGGCTCCCGTCCTA 45AccUP3 ---------------ATGGCCGTATACAGCGTCGCCACGGGGGCCTTGGCTCCCGTCCTA 45AccUP1 ---------------ATGGCCGTATACAGCGTCGCCACGGGGGCCTTGGCTCCCGTCCTA 45Acc224 ---------------ATGGCCGTATACAGCGTCGCCACGGGGGCCTTGGCTCCCGTCCTA 45 ********* * ** .***************** ***** *** Acc414 GTGAAGCTGGCCGCTTTGCTGGACGACGGGGAGTGCAATCTTCTGGAGGGGAGCCGGAGC 117Acc420 GTGAAGCTGGCCGCTTTGCTGGACGACGGGGAGTGCAATCTTCTGGAGGGGAGCCGGAGC 117Acc761 GTGAAGCTGGCCGCTTTGCTGGACGACGGGGAGTGCAATCTTCTGGAGGGGAGCCGGAGC 117K60_Pik-p GTGAAGCTGGCCGCTTTGCTGGACGACGGGGAGTGCAATCTTCTGGAGGGGAGCCGGAGC 117Acc130 GTGAAGCTGGCCGCTTTGCTGGACGACGGGGAGTGCAATCTTCTGGAGGGGAGCCGGAGC 117Acc108 GTGAAGCTGGCCGCTTTGCTGGACGACGGGGAGTGCAATCTTCTGGAGGGGAGCCGGAGC 117Acc719 GTGAAGCTGGCCGCTTTGCTGGACGACGGGGAGTGCAATCTTCTGGAGGGGAGCCGGAGC 117Acc729 GTGAAGCTGGCCGCTTTGCTGGACGACGGGGAGTGCAATCTTCTGGAGGGGAGCCGGAGC 117Acc709 GTGAAGCTGGCCGCTTTGCTGGACGACGGGGAGTGCAATCTTCTGGAGGGGAGCCGGAGC 117Acc710 GTGAAGCTGGCCGCTTTGCTGGACGACGGGGAGTGCAATCTTCTGGAGGGGAGCCGGAGC 117Acc504 GTGAAGCTGGCCGCTTTGCTGGACGACGGGGAGTGCAATCTTCTGGAGGGGAGCCGGAGC 117Acc848 GTGAAGCTGGCCGCTTTGCTGGACGACGGGGAGTGCAATCTTCTGGAGGGGAGCCGGAGC 117Acc563 GTGAAGCTGGCCGCTTTGCTGGACGACGGGGAGTGCAATCTTCTGGAGGGGAGCCGGAGC 117Acc757 GTGAAGCTGGCCGCTTTGCTGGACGACGGGGAGTGCAATCTTCTGGAGGGGAGCCGGAGC 117Tsuyuake_Pik-m GTGAAGCTGGCCGCTTTGCTGGACGACGGGGAGTGCAATCTTCTGGAGGGGAGCCGGAGC 117Kanto51_Pik GTGAAGCTGGCCGCTTTGCTGGACGACGGGGAGTGCAATCTTCTGGAGGGGAGCCGGAGC 117Kusabue_Pik GTGAAGCTGGCCGCTTTGCTGGACGACGGGGAGTGCAATCTTCTGGAGGGGAGCCGGAGC 117Acc201 TCGAAGCTCTCCGCTTTGCTGGGCGACGAGCACTTGGATCTTGCGGAGAGGACCCGGAGC 105Acc206 TCGAAGCTCTCCGCTTTGCTGGGCGACGAGCACTTGGATCTTGCGGAGAGGACCCGGAGC 105Acc1 TCGAAGCTCTCCGCTTTGCTGGGCGACGAGCACTTGGATCTTGCGGAGAGGACCCGGAGC 105Acc101 TCGAAGCTCTCCGCTTTGCTGGGCGACGAGCACTTGGATCTTGCGGAGAGGACCCGGAGC 105Acc718 TCGAAGCTCTCCGCTTTGCTGGGCGACGAGCACTTGGATCTTGCGGAGAGGACCCGGAGC 105Acc724 TCGAAGCTCTCCGCTTTGCTGGGCGACGAGCACTTGGATCTTGCGGAGAGGACCCGGAGC 105Acc715 TCGAAGCTCTCCGCTTTGCTGGGCGACGAGCACTTGGATCTTGCGGAGAGGACCCGGAGC 105Acc706 TCGAAGCTCTCCGCTTTGCTGGGCGACGAGCACTTGGATCTTGCGGAGAGGACCCGGAGC 105Acc624 TCGAAGCTCTCCGCTTTGCTGGGCGACGAGCACTTGGATCTTGCGGAGAGGACCCGGAGC 105Acc440 TCGAAGCTCTCCGCTTTGCTGGGCGACGAGCACTTGGATCTTGCGGAGAGGACCCGGAGC 105Acc868 TCGAAGCTCTCCGCTTTGCTGGGCGACGAGCACTTGGATCTTGCGGAGAGGACCCGGAGC 105Acc220 TCGAAGCTCTCCGCTTTGCTGGGCGACGAGCACTTGGATCTTGCGGAGAGGACCCGGAGC 105Nipponbare TCGAAGCTCTCCGCTTTGCTGGGCGACGAGCACTTGGATCTTGCGGAGAGGACCCGGAGC 105AccUP3 TCGAAGCTCTCCGCTTTGCTGGGCGACGAGCACTTGGATCTTGCGGAGAGGACCCGGAGC 105AccUP1 TCGAAGCTCTCCGCTTTGCTGGGCGACGAGCACTTGGATCTTGCGGAGAGGACCCGGAGC 105Acc224 TCGAAGCTCTCCGCTTTGCTGGGCGACGAGCACTTGGATCTTGCGGAGAGGACCCGGAGC 105 ****** ************.*****.* * * .***** ****.*** *******

Fig. S1. Multiple alignment of the first-gene sequences of the 28 rice lines, cultivars showing Pik-family-specific blast resistance (Kusabue, Kanto 51, Tsuyuake, and K60) and the susceptible Nipponbare. Sequences grouped in clade 1 are black, and those in clade 2 are red.

Ashikawa et al. Supplementary Fig. S1 (1/30)

Acc414 GACGCAGAGTTCATCAGATCCGAGCTGGAGGCCGTTCATTCTCTCCTCACCCCAAATATC 177Acc420 GACGCAGAGTTCATCAGATCCGAGCTGGAGGCCGTTCATTCTCTCCTCACCCCAAATATC 177Acc761 GACGCAGAGTTCATCAGATCCGAGCTGGAGGCCGTTCATTCTCTCCTCACCCCAAATATC 177K60_Pik-p GACGCAGAGTTCATCAGATCCGAGCTGGAGGCCGTTCATTCTCTCCTCACCCCAAATATC 177Acc130 GACGCAGAGTTCATCAGATCCGAGCTGAAGGCCGTTCATTCTCTCCTCACCCCAAATATC 177Acc108 GACGCAGAGTTCATCAGATCCGAGCTGAAGGCCGTTCATTCTCTCCTCACCCCAAATATC 177Acc719 GACGCAGAGTTCATCAGATCCGAGCTGAAGGCCGTTCATTCTCTCCTCACCCCAAATATC 177Acc729 GACGCAGAGTTCATCAGATCCGAGCTGAAGGCCGTTCATTCTCTCCTCACCCCAAATATC 177Acc709 GACGCAGAGTTCATCAGATCCGAGCTGAAGGCCGTTCATTCTCTCCTCACCCCAAATATC 177Acc710 GACGCAGAGTTCATCAGATCCGAGCTGAAGGCCGTTCATTCTCTCCTCACCCCAAATATC 177Acc504 GACGCAGAGTTCATCAGATCCGAGCTGGAGGCCGTGCACTCTCTCCTCACCCCAAATATC 177Acc848 GACGCAGAGTTCATCAGATCCGAGCTGGAGGCCGTGCACTCTCTCCTCACCCCAAATATC 177Acc563 GACGCAGAGTTCATCAGATCCGAGCTGGAGGCCGTGCACTCTCTCCTCACCCCAAATATC 177Acc757 GACGCAGAGTTCATCAGATCCGAGCTGGAGGCCGTGCACTCTCTCCTCACCCCAAATATC 177Tsuyuake_Pik-m GACGCAGAGTTCATCAGATCCGAGCTGGAGGCCGTGCACTCTCTCCTCACCCCAAATATC 177Kanto51_Pik GACGCAGAGTTCATCAGATCCGAGCTGGAGGCCGTGCACTCTCTCCTCACCCCAAATATC 177Kusabue_Pik GACGCAGAGTTCATCAGATCCGAGCTGGAGGCCGTGCACTCTCTCCTCACCCCAAATATC 177Acc201 GACGCCATGTTCATCAGGTCCCAGCTGGAGGCCGTGCACTCTCTCCTCCTCCCGAGGATT 165Acc206 GACGCCATGTTCATCAGGTCCCAGCTGGAGGCCGTGCACTCTCTCCTCCTCCCGAGGATT 165Acc1 GACGCCATGTTCATCAGGTCCCAGCTGGAGGCCGTGCACTCTCTCCTCCTCCCGAGGATT 165Acc101 GACGCCATGTTCATCAGGTCCCAGCTGGAGGCCGTGCACTCTCTCCTCCTCCCGAGGATT 165Acc718 GACGCCATGTTCATCAGGTCCCAGCTGGAGGCCGTGCACTCTCTCCTCCTCCCGAGGATT 165Acc724 GACGCCATGTTCATCAGGTCCCAGCTGGAGGCCGTGCACTCTCTCCTCCTCCCGAGGATT 165Acc715 GACGCCATGTTCATCAGGTCCCAGCTGGAGGCCGTGCACTCTCTCCTCCTCCCGAGGATT 165Acc706 GACGCCATGTTCATCAGGTCCCAGCTGGAGGCCGTGCACTCTCTCCTCCTCCCGAGGATT 165Acc624 GACGCCATGTTCATCAGGTCCCAGCTGGAGGCCGTGCACTCTCTCCTCCTCCCGAGGATT 165Acc440 GACGCCATGTTCATCAGGTTCCAGCTGGAGGCCGTGCACTCTCTCCTCCTCCCGAGGATT 165Acc868 GACGCCATGTTCATCAGGTTCCAGCTGGAGGCCGTGCACTCTCTCCTCCTCCCGAGGATT 165Acc220 GACGCCATGTTCATCAGGTCCCAGCTGGAGGCCGTGCACTCTCTCCTCCTCCCGAGGATT 165Nipponbare GACGCCATGTTCATCAGGTCCCAGCTGGAGGCCGTGCACTCTCTCCTCCTCCCGAGGATT 165AccUP3 GACGCCATGTTCATCAGGTCCCAGCTGGAGGCCGTGCACTCTCTCCTCCTCCCGAGGATT 165AccUP1 GACGCCATGTTCATCAGGTCCCAGCTGGAGGCCGTGCACTCTCTCCTCCTCCCGAGGATT 165Acc224 GACGCCATGTTCATCAGGTCCCAGCTGGAGGCCGTGCACTCTCTCCTCCTCCCGAGGATT 165 *****..:*********.* * *****.******* ** *********. ***.*. **  Acc414 --TTGGGGAG-GATGGGGGATGA---CGATGCGGCGTGCAAGGATGGCTTGATTGCGGAG 231Acc420 --TTGGGGAG-GATGGGGGATGA---CGATGCGGCGTGCAAGGATGGCTTGATTGCGGAG 231Acc761 --TTGGGGAG-GATGGGGGATGA---CGATGCGGCGTGCAAGGATGGCTTGATTGCGGAG 231K60_Pik-p --TTGGGGAG-GATGGGGGATGA---CGATGCGGCGTGCAAGGATGGCTTGATTGCGGAG 231Acc130 --TTGGGGAG-GATGGGGGATGA---CGATGCGGCGTGCAAGGATGGCTTGATTGCGGAG 231Acc108 --TTGGGGAG-GATGGGGGATGA---CGATGCGGCGTGCAAGGATGGCTTGATTGCGGAG 231Acc719 --TTGGGGAG-GATGGGGGATGA---CGATGCGGCGTGCAAGGATGGCTTGATTGCGGAG 231Acc729 --TTGGGGAG-GATGGGGGATGA---CGATGCGGCGTGCAAGGATGGCTTGATTGCGGAG 231Acc709 --TTGGGGAG-GATGGGGGATGA---CGATGCGGCGTGCAAGGATGGCTTGATTGCGGAG 231Acc710 --TTGGGGAG-GATGGGGGATGA---CGATGCGGCGTGCAAGGATGGCTTGATTGCGGAG 231Acc504 --TTGGGGAG-GATGGGGGATGA---CGATGCGGCGTGCAAGGATGGCTTGATTGCGGAG 231Acc848 --TTGGGGAG-GATGGGGGATGA---CGATGCGGCGTGCAAGGATGGCTTGATTGCGGAG 231Acc563 --TTGGGGAG-GATGGGGGATGA---CGATGCGGCGTGCAAGGATGGCTTGATTGCGGAG 231Acc757 --TTGGGGAG-GATGGGGGATGA---CGATGCGGCGTGCAAGGATGGCTTGATTGCGGAG 231Tsuyuake_Pik-m --TTGGGGAG-GATGGGGGATGA---CGATGCGGCGTGCAAGGATGGCTTGATTGCGGAG 231Kanto51_Pik --TTGGGGAG-GATGGGGGATGA---CGATGCGGCGTGCAAGGATGGCTTGATTGCGGAG 231Kusabue_Pik --TTGGGGAG-GATGGGGGATGA---CGATGCGGCGTGCAAGGATGGCTTGATTGCGGAG 231Acc201 AGTTGGGGAATGACGGGGGAGGAAGTCGATGCTTTGTGCAAGGATGAGTTGATGGCGGAG 225Acc206 AGTTGGGGAATGACGGGGGAGGAAGTCGATGCTTTGTGCAAGGATGAGTTGATGGCGGAG 225Acc1 AGTTGGGGAATGACGGGGGAGGAAGTCGATGCTTTGTGCAAGGATGAGTTGATGGCGGAG 225Acc101 AGTTGGGGAATGACGGGGGAGGAAGTCGATGCTTTGTGCAAGGATGAGTTGATGGCGGAG 225Acc718 AGTTGGGGAATGACGGGGGAGGAAGTCGATGCTTTGTGCAAGGATGAGTTGATGGCGGAG 225Acc724 AGTTGGGGAATGACGGGGGAGGAAGTCGATGCTTTGTGCAAGGATGAGTTGATGGCGGAG 225Acc715 AGTTGGGGAATGACGGGGGAGGAAGTCGATGCTTTGTGCAAGGATGAGTTGATGGCGGAG 225Acc706 AGTTGGGGAATGACGGGGGAGGAAGTCGATGCTTTGTGCAAGGATGAGTTGATGGCGGAG 225Acc624 AGTTGGGGAATGACGGGGGAGGAAGTCGATGCTTTGTGCAAGGATGAGTTGATGGCGGAG 225Acc440 AGTTGGGGAATGACGGGGGAGGAAGTCGATGCTTTGTGCAAGGATGAGTTGATGGCGGAG 225Acc868 AGTTGGGGAATGACGGGGGAGGAAGTCGATGCTTTGTGCAAGGATGAGTTGATGGCGGAG 225Acc220 AGTTGGGGAATGACGGGGGAGGAAGTCGATGCTTTGTGCAAGGATGAGTTGATGGCGGAG 225Nipponbare AGTTGGGGAATGACGGGGGAGGAAGTCGATGCTTTGTGCAAGGATGAGTTGATGGCGGAG 225AccUP3 AGTTGGGGAATGACGGGGGAGGAAGTCGATGCTTTGTGCAAGGATGAGTTGATGGCGGAG 225AccUP1 AGTTGGGGAATGACGGGGGAGGAAGTCGATGCTTTGTGCAAGGATGAGTTGATGGCGGAG 225Acc224 AGTTGGGGAATGACGGGGGAGGAAGTCGATGCTTTGTGCAAGGATGAGTTGATGGCGGAG 225 *******. ** ****** ** ****** ***********. ***** ****** 

Ashikawa et al. Supplementary Fig. S1 (2/30)

Acc414 GTCCGGGAGCTGTCCTACGACCTGGATGATGCCGTCGACGACTTCTT------GGAGCTC 285Acc420 GTCCGGGAGCTGTCCTACGACCTGGATGATGCCGTCGACGACTTCTT------GGAGCTC 285Acc761 GTCCGGGAGCTGTCCTACGACCTGGATGATGCCGTCGACGACTTCTT------GGAGCTC 285K60_Pik-p GTCCGGGAGCTGTCCTACGACCTGGATGATGCCGTCGACGACTTCTT------GGAGCTC 285Acc130 GTCCGGGAGCTGTCCTACGACCTGGATGATGCCGTCGACGACTTCTT------GGAGCTC 285Acc108 GTCCGGGAGCTGTCCTACGACCTGGATGATGCCGTCGACGACTTCTT------GGAGCTC 285Acc719 GTCCGGGAGCTGTCCTACGACCTGGATGATGCCGTCGACGACTTCTT------GGAGCTC 285Acc729 GTCCGGGAGCTGTCCTACGACCTGGATGATGCCGTCGACGACTTCTT------GGAGCTC 285Acc709 GTCCGGGAGCTGTCCTACGACCTGGATGATGCCGTCGACGACTTCTT------GGAGCTC 285Acc710 GTCCGGGAGCTGTCCTACGACCTGGATGATGCCGTCGACGACTTCTT------GGAGCTC 285Acc504 GTCCGGGAGCTGTCCTACGACCTGGATGATGCCGTCGACGACTTCTT------GGAGCTC 285Acc848 GTCCGGGAGCTGTCCTACGACCTGGATGATGCCGTCGACGACTTCTT------GGAGCTC 285Acc563 GTCCGGGAGCTGTCCTACGACCTGGATGATGCCGTCGACGACTTCTT------GGAGCTC 285Acc757 GTCCGGGAGCTGTCCTACGACCTGGATGATGCCGTCGACGACTTCTT------GGAGCTC 285Tsuyuake_Pik-m GTCCGGGAGCTGTCCTACGACCTGGATGATGCCGTCGACGACTTCTT------GGAGCTC 285Kanto51_Pik GTCCGGGAGCTGTCCTACGACCTGGATGATGCCGTCGACGACTTCTT------GGAGCTC 285Kusabue_Pik GTCCGGGAGCTGTCCTACGACCTGGATGATGCCGTCGACGACTTCTT------GGAGCTC 285Acc201 GTGCGTGAGCTGTCCTACGACATGGACGACGCCATCGACGAATTCTTCTTAGAGGAGCCC 285Acc206 GTGCGTGAGCTGTCCTACGACATGGACGACGCCATCGACGAATTCTTCTTAGAGGAGCCC 285Acc1 GTGCGTGAGCTGTCCTACGACATGGACGACGCCATCGACGAATTCTTCTTAGAGGAGCCC 285Acc101 GTGCGTGAGCTGTCCTACGACATGGACGACGCCATCGACGAATTCTTCTTAGAGGAGCCC 285Acc718 GTGCGTGAGCTGTCCTACGACATGGACGACGCCATCGACGAATTCTTCTTAGAGGAGCCC 285Acc724 GTGCGTGAGCTGTCCTACGACATGGACGACGCCATCGACGAATTCTTCTTAGAGGAGCCC 285Acc715 GTGCGTGAGCTGTCCTACGACATGGACGACGCCATCGACGAATTCTTCTTAGAGGAGCCC 285Acc706 GTGCGTGAGCTGTCCTACGACATGGACGACGCCATCGACGAATTCTTCTTAGAGGAGCCC 285Acc624 GTGCGTGAGCTGTCCTACGACATGGACGACGCCATCGACGAATTCTTCTTAGAGGAGCCC 285Acc440 GTGCGTGAGCTGTCCTACGACATGGACGACGCCATCGACGAATTCTTCTTAGAGGAGCCC 285Acc868 GTGCGTGAGCTGTCCTACGACATGGACGACGCCATCGACGAATTCTTCTTAGAGGAGCCC 285Acc220 GTGCGTGAGCTGTCCTACGACATGGACGACGCCATCGACGAATTCTTCTTAGAGGAGCCC 285Nipponbare GTGCGTGAGCTGTCCTACGACATGGACGACGCCATCGACGAATTCTTCTTAGAGGAGCCC 285AccUP3 GTGCGTGAGCTGTCCTACGACATGGACGACGCCATCGACGAATTCTTCTTAGAGGAGCCC 285AccUP1 GTGCGTGAGCTGTCCTACGACATGGACGACGCCATCGACGAATTCTTCTTAGAGGAGCCC 285Acc224 GTGCGTGAGCTGTCCTACGACATGGACGACGCCATCGACGAATTCTTCTTAGAGGAGCCC 285 ** ** ***************.**** ** ***.*******.***** ***** * Acc414 AATTTCGAGCAGCGAAGAAGCGCAAGCCCTTTCGGTGAGCTCAAGGCAAGAGTTGAGGAG 345Acc420 AATTTCGAGCAGCGAAGAAGCGCAAGCCCTTTCGGTGAGCTCAAGGCAAGAGTTGAGGAG 345Acc761 AATTTCGAGCAGCGAAGAAGCGCAAGCCCTTTCGGTGAGCTCAAGGCAAGAGTTGAGGAG 345K60_Pik-p AATTTCGAGCAGCGAAGAAGCGCAAGCCCTTTCGGTGAGCTCAAGGCAAGAGTTGAGGAG 345Acc130 AATTTCGAGCAGCGAAGAAGCGCAAGCCCTTTCGGTGAGCTCAAGGCAAGAGTTGAGGAG 345Acc108 AATTTCGAGCAGCGAAGAAGCGCAAGCCCTTTCGGTGAGCTCAAGGCAAGAGTTGAGGAG 345Acc719 AATTTCGAGCAGCGAAGAAGCGCAAGCCCTTTCGGTGAGCTCAAGGCAAGAGTTGAGGAG 345Acc729 AATTTCGAGCAGCGAAGAAGCGCAAGCCCTTTCGGTGAGCTCAAGGCAAGAGTTGAGGAG 345Acc709 AATTTCGAGCAGCGAAGAAGCGCAAGCCCTTTCGGTGAGCTCAAGGCAAGAGTTGAGGAG 345Acc710 AATTTCGAGCAGCGAAGAAGCGCAAGCCCTTTCGGTGAGCTCAAGGCAAGAGTTGAGGAG 345Acc504 AATTTCGAGCAGCGAAGAAGCGCAAGCCCTTTCGGTGAGCTCAAGGCAAGAGTTGAGGAG 345Acc848 AATTTCGAGCAGCGAAGAAGCGCAAGCCCTTTCGGTGAGCTCAAGGCAAGAGTTGAGGAG 345Acc563 AATTTCGAGCAGCGAAGAAGCGCAAGCCCTTTCGGTGAGCTCAAGGCAAGAGTTGAGGAG 345Acc757 AATTTCGAGCAGCGAAGAAGCGCAAGCCCTTTCGGTGAGCTCAAGGCAAGAGTTGAGGAG 345Tsuyuake_Pik-m AATTTCGAGCAGCGAAGAAGCGCAAGCCCTTTCGGTGAGCTCAAGGCAAGAGTTGAGGAG 345Kanto51_Pik AATTTCGAGCAGCGAAGAAGCGCAAGCCCTTTCGGTGAGCTCAAGGCAAGAGTTGAGGAG 345Kusabue_Pik AATTTCGAGCAGCGAAGAAGCGCAAGCCCTTTCGGTGAGCTCAAGGCAAGAGTTGAGGAG 345Acc201 A-TGGCGGGCGGCGA-----CGGTGGCCCTTTCGATGAGCTCAAGACAAGAGTTGAGGA- 338Acc206 A-TGGCGGGCGGCGA-----CGGTGGCCCTTTCGATGAGCTCAAGACAAGAGTTGAGGA- 338Acc1 A-TGGCGGGCGGCGA-----CGGTGGCCCTTTCGATGAGCTCAAGACAAGAGTTGAGGA- 338Acc101 A-TGGCGGGCGGCGA-----CGGTGGCCCTTTCGATGAGCTCAAGACAAGAGTTGAGGA- 338Acc718 A-TGGCGGGCGGCGA-----CGGTGGCCCTTTCGATGAGCTCAAGACAAGAGTTGAGGA- 338Acc724 A-TGGCGGGCGGCGA-----CGGTGGCCCTTTCGATGAGCTCAAGACAAGAGTTGAGGA- 338Acc715 A-TGGCGGGCGGCGA-----CGGTGGCCCTTTCGATGAGCTCAAGACAAGAGTTGAGGA- 338Acc706 A-TGGCGGGCGGCGA-----CGGTGGCCCTTTCGATGAGCTCAAGACAAGAGTTGAGGA- 338Acc624 A-TGGCGGGCGGCGA-----CGGTGGCCCTTTCGATGAGCTCAAGACAAGAGTTGAGGA- 338Acc440 A-TGGCGGGCGGCGA-----CGGTGGCCCTTTCGATGAGCTCAAGACAAGAGTTGAGGA- 338Acc868 A-TGGCGGGCGGCGA-----CGGTGGCCCTTTCGATGAGCTCAAGACAAGAGTTGAGGA- 338Acc220 A-TGGCGGGCGGCGA-----CGGTGGCCCTTTCGATGAGCTCAAGACAAGAGTTGAGGA- 338Nipponbare A-TGGCGGGCGGCGA-----CGGTGGCCCTTTCGATGAGCTCAAGACAAGAGTTGAGGA- 338AccUP3 A-TGGCGGGCGGCGA-----CGGTGGCCCTTTCGATGAGCTCAAGACAAGAGTTGAGGA- 338AccUP1 A-TGGCGGGCGGCGA-----CGGTGGCCCTTTCGATGAGCTCAAGACAAGAGTTGAGGA- 338Acc224 A-TGGCGGGCGGCGA-----CGGTGGCCCTTTCGATGAGCTCAAGACAAGAGTTGAGGA- 338 * * **.**.**** ** :.*********.**********.*************  

Ashikawa et al. Supplementary Fig. S1 (3/30)

Acc414 CGTGTCTCCAATCGCTTCTCTGAC---------TGGAAGCTACCGGCGGCG-------AG 389Acc420 CGTGTCTCCAATCGCTTCTCTGAC---------TGGAAGCTACCGGCGGCG-------AG 389Acc761 CGTGTCTCCAATCGCTTCTCTGAC---------TGGAAGCTACCGGCGGCG-------AG 389K60_Pik-p CATGTCTCCAATCGCTTCTCTGAC---------TGGAAGCTACCGGCGGCG-------AG 389Acc130 CGTGTCTCCAATCGCTTCTCTGAC---------TGGAAGCTACCGGCGGCG-------AG 389Acc108 CGTGTCTCCAATCGCTTCTCTGAC---------TGGAAGCTACCGGCGGCG-------AG 389Acc719 CGTGTCTCCAATCGCTTCTCTGAC---------TGGAAGCTACCGGCGGCG-------AG 389Acc729 CGTGTCTCCAATCGCTTCTCTGAC---------TGGAAGCTACCGGCGGCG-------AG 389Acc709 CGTGTCTCCAATCGCTTCTCTGAC---------TGGAAGCTACCGGCGGCG-------AG 389Acc710 CGTGTCTCCAATCGCTTCTCTGAC---------TGGAAGCTACCGGCGGCG-------AG 389Acc504 CGTGTCTCCAATCGCTTCTCTGAC---------TGGAAGCTACCGGCGGCG-------AG 389Acc848 CGTGTCTCCAATCGCTTCTCTGAC---------TGGAAGCTACCGGCGGCG-------AG 389Acc563 CGTGTCTCCAATCGCTTCTCTGAC---------TGGAAGCTACCGGCGGCG-------AG 389Acc757 CGTGTCTCCAATCGCTTCTCTGAC---------TGGAAGCTACCGGCGGCG-------AG 389Tsuyuake_Pik-m CGTGTCTCCAATCGCTTCTCTGAC---------TGGAAGCTACCGGCGGCG-------AG 389Kanto51_Pik CGTGTCTCCAATCGCTTCTCTGAC---------TGGAAGCTACCGGCGGCG-------AG 389Kusabue_Pik CGTGTCTCCAATCGCTTCTCTGAC---------TGGAAGCTACCGGCGGCG-------AG 389Acc201 --TGTCTCCAAGCGGTTCTCCGACAGCCGGCGGTGGAGGCCACCGGTGGAGCAACATCAA 396Acc206 --TGTCTCCAAGCGGTTCTCCGACAGCCGGCGGTGGAGGCCACCGGTGGAGCAACATCAA 396Acc1 --TGTCTCCAAGCGGTTCTCCGACAGCCGGCGGTGGAGGCCACCGGTGGAGCAACATCAA 396Acc101 --TGTCTCCAAGCGGTTCTCCGACAGCCGGCGGTGGAGGCCACCGGTGGAGCAACATCAA 396Acc718 --TGTCTCCAAGCGGTTCTCCGACAGCCGGCGGTGGAGGCCACCGGTGGAGCAACATCAA 396Acc724 --TGTCTCCAAGCGGTTCTCCGACAGCCGGCGGTGGAGGCCACCGGTGGAGCAACATCAA 396Acc715 --TGTCTCCAAGCGGTTCTCCGACAGCCGGCGGTGGAGGCCACCGGTGGAGCAACATCAA 396Acc706 --TGTCTCCAAGCGGTTCTCCGACAGCCGGCGGTGGAGGCCACCGGTGGAGCAACATCAA 396Acc624 --TGTCTCCAAGCGGTTCTCCGACAGCCGGCGGTGGAGGCCACCGGTGGAGCAACATCAA 396Acc440 --TGTCTCCAAGCGGTTCTCCGACAGCCGGCGGTGGAGGCCACCGGTGGAGCAACATCAA 396Acc868 --TGTCTCCAAGCGGTTCTCCGACAGCCGGCGGTGGAGGCCACCGGTGGAGCAACATCAA 396Acc220 --TGTCTCCAAGCGGTTCTCCGACAGCCGGCGGTGGAGGCCACCGGTGGAGCAACATCAA 396Nipponbare --TGTCTCCAAGCGGTTCTCCGACAGCCGGCGGTGGAGGCCACCGGTGGAGCAACATCAA 396AccUP3 --TGTCTCCAAGCGGTTCTCCGACAGCCGGCGGTGGAGGCCACCGGTGGAGCAACATCAA 396AccUP1 --TGTCTCCAAGCGGTTCTCCGACAGCCGGCGGTGGAGGCCACCGGTGGAGCAACATCAA 396Acc224 --TGTCTCCAAGCGGTTCTCCGACAGCCGGCGGTGGAGGCCACCGGTGGAGCAACATCAA 396 ********* ** ***** *** ****.** ***** **.* *. Acc414 CCTTCC---GCCGTCGT--CGGTACACCGCCGA---------GCTGGCTTG--CCGCCAC 433Acc420 CCTTCC---GCCGTCGT--CGGTACACCGCCGA---------GCTGGCTTG--CCGCCAC 433Acc761 CCTTCC---GCCGTCGT--CGGTACACCGCCGA---------GCTGGCTTG--CCGCCAC 433K60_Pik-p CCTTCC---GCCGTCGT--CGGTACACCGCCGA---------GCTGGCTTG--CCGCCAC 433Acc130 CCTTCC---GCCGTCGT--CGGTACACCGTCGA---------GCTGGCTTG--CCGCCAC 433Acc108 CCTTCC---GCCGTCGT--CGGTACACCGTCGA---------GCTGGCTTG--CCGCCAC 433Acc719 CCTTCC---GCCGTCGT--CGGTACACCGTCGA---------GCTGGCTTG--CCGCCAC 433Acc729 CCTTCC---GCCGTCGT--CGGTACACCGTCGA---------GCTGGCTTG--CCGCCAC 433Acc709 CCTTCC---GCCGTCGT--CGGTACACCGTCGA---------GCTGGCTTG--CCGCCAC 433Acc710 CCTTCC---GCCGTCGT--CGGTACACCGTCGA---------GCTGGCTTG--CCGCCAC 433Acc504 CCTTCC---GCCGTCGT--CGGTACACCGTCGA---------GCTGGCTTG--CCGCCAC 433Acc848 CCTTCC---GCCGTCGT--CGGTACACCGTCGA---------GCTGGCTTG--CCGCCAC 433Acc563 CCTTCC---GCCGTCGT--CGGTACACCGTCGA---------GCTGGCTTG--CCGCCAC 433Acc757 CCTTCC---GCCGTCGT--CGGTACACCGTCGA---------GCTGGCTTG--CCGCCAC 433Tsuyuake_Pik-m CCTTCC---GCCGTCGT--CGGTACACCGTCGA---------GCTGGCTTG--CCGCCAC 433Kanto51_Pik CCTTCC---GCCGTCGT--CGGTACACCGTCGA---------GCTGGCTTG--CCGCCAC 433Kusabue_Pik CCTTCC---GCCGTCGT--CGGTACACCGTCGA---------GCTGGCTTG--CCGCCAC 433Acc201 CCATCCCTAACTGCCGCAACCGTAGACTGTCCACCTCCTCACGCTCGCTTCGTCCACAAC 456Acc206 CCATCCCTAACTGCCGCAACCGTAGACTGTCCACCTCCTCACGCTCGCTTCGTCCACAAC 456Acc1 CCATCCCTAACCGCCGCAACCGTAGACTCTCCACCTCCTCACGCTCGCTTCGTCCACAAC 456Acc101 CCATCCCTAACCGCCGCAACCGTAGACTGTCCACCTCCTCACGCTCGCTTCGTCCACAAC 456Acc718 CCATCCCTAACCGCCGCAACCGTAGACTGTCCACCTCCTCACGCTCGCTTCGTCCACAAC 456Acc724 CCATCCCTAACCGCCGCAACCGTAGACTGTCCACCTCCTCACGCTCGCTTCGTCCACAAC 456Acc715 CCATCCCTAACCGCCGCAACCGTAGACTGTCCACCTCCTCACGCTCGCTTCGTCCACAAC 456Acc706 CCATCCCTAACCGCCGCAACCGTAGACTGTCCACCTCCTCACGCTCGCTTCGTCCACAAC 456Acc624 CCATCCCTAACCGCCGCAACCGTAGACTGTCCACCTCCTCACGCTCGCTTCGTCCACAAC 456Acc440 CCATCCCTAACCGCCGCAACCGTAGACTGTCCACCTCCTCACGCTCGCTTCGTCCACAAC 456Acc868 CCATCCCTAACCGCCGCAACCGTAGACTGTCCACCTCCTCACGCTCGCTTCGTCCACAAC 456Acc220 CCATCCCTAACCGCCGCAACCGTAGACTGTCCACCTCCTCACGCTCGCTTCGTCCACAAC 456Nipponbare CCATCCCTAACCGCCGCAACCGTAGACTGTCCACCTCCTCACGCTCGCTTCGTCCACAAC 456AccUP3 CCATCCCTAACCGCCGCAACCGTAGACTGTCCACCTCCTCACGCTCGCTTCGTCCACAAC 456AccUP1 CCATCCCTAACCGCCGCAACCGTAGACTGTCCACCTCCTCACGCTCGCTTCGTCCACAAC 456Acc224 CCATCCCTAACCGCCGCAACCGTAGACTGTCCACCTCCTCACGCTCGCTTCGTCCACAAC 456 **:*** .* * ** * *** ** * * *** **** **.*.**

Ashikawa et al. Supplementary Fig. S1 (4/30)

Acc414 CAGATG-------CAGAGCTGGTGGGGATGGACAAAC---GTATGGAAGAGCTCACCAAA 483Acc420 CAGATG-------CAGAGCTGGTGGGGATGGACAAAC---GTATGGAAGAGCTCACCAAA 483Acc761 CAGATG-------CAGAGCTGGTGGGGATGGACAAAC---GTATGGAAGAGCTCACCAAA 483K60_Pik-p CAGATG-------CAGAGCTGGTGGGGATGGACAAAC---GTATGGAAGAGCTCACCAAA 483Acc130 CAGATG-------CAGGGCTGGTGGGGATGGACAAAC---GTAAGGAAGAGCTCATCGAG 483Acc108 CAGATG-------CAGGGCTGGTGGGGATGGACAAAC---GTAAGGAAGAGCTCATCGAG 483Acc719 CAGATG-------CAGGGCTGGTGGGGATGGACAAAC---GTAAGGAAGAGCTCATCGAG 483Acc729 CAGATG-------CAGGGCTGGTGGGGATGGACAAAC---GTAAGGAAGAGCTCATCGAG 483Acc709 CAGATG-------CAGGGCTGGTGGGGATGGACAAAC---GTAAGGAAGAGCTCATCGAG 483Acc710 CAGATG-------CAGGGCTGGTGGGGATGGACAAAC---GTAAGGAAGAGCTCATCGAG 483Acc504 CAGATG-------CAGGGCTGGTGGGGATGCACAAAC---GTAAGGAAGAGCTCATCGAG 483Acc848 CAGATG-------CAGGGCTGGTGGGGATGCACAAAC---GTAAGGAAGAGCTCATCGAG 483Acc563 CAGATG-------CAGGGCTGGTGGGGATGCACAAAC---GTAAGGAAGAGCTCATCGAG 483Acc757 CAGATG-------CAGGGCTGGTGGGGATGCACAAAC---GTAAGGAAGAGCTCATCGAG 483Tsuyuake_Pik-m CAGATG-------CAGGGCTGGTGGGGATGCACAAAC---GTAAGGAAGAGCTCATCGAG 483Kanto51_Pik CAGATG-------CAGGGCTGGTGGGGATGCACAAAC---GTAAGGAAGAGCTCATCGAG 483Kusabue_Pik CAGATG-------CAGGGCTGGTGGGGATGCACAAAC---GTAAGGAAGAGCTCATCGAG 483Acc201 ATGATGGATGTGTCAGAGCTCGTGGAGATGGACAAACTACATGAGAAAGAGCTCATCAAA 516Acc206 ATGATGGATGTGTCAGAGCTCGTGGAGATGGACAAACTACATGAGAAAGAGCTCATCAAA 516Acc1 ATGATGGATGTGTCAGAGCTCGTGGAGATGGACAAACAACATGAGAAAGAGCTCATCAAA 516Acc101 ATGATGGATGTGTCAGAGCTCGTGGAGATGGACAAACTACATGAGAAAGAGCTCATCAAA 516Acc718 ATGATGGATGTGTCAGAGCTCGTGGAGATGGACAAACTACATGAGAAAGAGCTCATCAAA 516Acc724 ATGATGGATGTGTCAGAGCTCGTGGAGATGGACAAACTACATGAGAAAGAGCTCATCAAA 516Acc715 ATGATGGATGTGTCAGAGCTCGTGGAGATGGACAAACTACATGAGAAAGAGCTCATCAAA 516Acc706 ATGATGGATGTGTCAGAGCTCGTGGAGATGGACAAACTACATGAGAAAGAGCTCATCAAA 516Acc624 ATGATGGATGTGTCAGAGCTCGTGGAGATGGACAAACTACATGAGAAAGAGCTCATCAAA 516Acc440 ATGATGGATGTGTCAGAGCTCGTGGAGATGGACAAACAACATGAGAAAGAGCTCATCAAA 516Acc868 ATGATGGATGTGTCAGAGCTCGTGGAGATGGACAAACAACATGAGAAAGAGCTCATCAAA 516Acc220 ATGATGGATGTGTCAGAGCTCGTGGAGATGGACAAACAACATGAGAAAGAGCTCATCAAA 516Nipponbare ATGATGGATGTGTCAGAGCTCGTGGAGATGGACAAACAACATGAGAAAGAGCTCATCAAA 516AccUP3 ATGATGGATGTGTCAGAGCTCGTGGAGATGGACAAACAACATGAGAAAGAGCTCATCAAA 516AccUP1 ATGATGGATGTGTCAGAGCTCGTGGAGATGGACAAACAACATGAGAAAGAGCTCATCAAA 516Acc224 ATGATGGATGTGTCAGAGCTCGTGGAGATGGACAAACAACATGAGAAAGAGCTCATCAAA 516 .:**** ***.*** ****.**** ****** .*.:*.********* *.*. Acc414 TTGCTGGAACAAGG---------GAGCAATGATGCTTCACGATGGCGCAAGCGAAAACCG 534Acc420 TTGCTGGAACAAGG---------GAGCAATGATGCTTCACGATGGCGCAAGCGAAAACCG 534Acc761 TTGCTGGAACAAGG---------GAGCAATGATGCTTCACGATGGCGCAAGCGAAAACCG 534K60_Pik-p TTGCTGGAACAAGG---------GAGCAATGATGCTTCACGATGGCGCAAGCGAAAACCG 534Acc130 TTGCTGGAACAAGG---------GAGCAGTGATGCTTCACGATGGCGCAAGCGAAAACCT 534Acc108 TTGCTGGAACAAGG---------GAGCAGTGATGCTTCACGATGGCGCAAGCGAAAACCT 534Acc719 TTGCTGGAACAAGG---------GAGCAGTGATGCTTCACGATGGCGCAAGCGAAAACCT 534Acc729 TTGCTGGAACAAGG---------GAGCAGTGATGCTTCACGATGGCGCAAGCGAAAACCT 534Acc709 TTGCTGGAACAAGG---------GAGCAGTGATGCTTCACGATGGCGCAAGCGAAAACCT 534Acc710 TTGCTGGAACAAGG---------GAGCAGTGATGCTTCACGATGGCGCAAGCGAAAACCT 534Acc504 TTGCTGGAACAAGG---------GAGCAGTGATGCTTCACGATGGCGCAAGCGAAAACCT 534Acc848 TTGCTGGAACAAGG---------GAGCAGTGATGCTTCACGATGGCGCAAGCGAAAACCT 534Acc563 TTGCTGGAACAAGG---------GAGCAGTGATGCTTCACGATGGCGCAAGCGAAAACCT 534Acc757 TTGCTGGAACAAGG---------GAGCAGTGATGCTTCACGATGGCGCAAGCGAAAACCT 534Tsuyuake_Pik-m TTGCTGGAACAAGG---------GAGCAGTGATGCTTCACGATGGCGCAAGCGAAAACCT 534Kanto51_Pik TTGCTGGAACAAGG---------GAGCAGTGATGCTTCACGATGGCGCAAGCGAAAACCT 534Kusabue_Pik TTGCTGGAACAAGG---------GAGCAGTGATGCTTCACGATGGCGCAAGCGAAAACCT 534Acc201 TTGCTGGAACAAGGTGCGGACACAAGCATATATGCTTCCCGGTGGCGCA--------TCG 568Acc206 TTGCTGGAACAAGGTGCGGACACAAGCATATATGCTTCCCGGTGGCGCA--------TCG 568Acc1 TTGCTGGAACAAGGTGCGGACACAAGCATATATGCTTCCCGGTGGCGCA--------TCG 568Acc101 TTGCTGGAACAAGGTGCGGACACAAGCATATATGCTTCCCGGTGGCGCA--------TCG 568Acc718 TTGCTGGAACAAGGTGCGGACACAAGCATATATGCTTCCCGGTGGCGCA--------TCG 568Acc724 TTGCTGGAACAAGGTGCGGACACAAGCATATATGCTTCCCGGTGGCGCA--------TCG 568Acc715 TTGCTGGAACAAGGTGCGGACACAAGCATATATGCTTCCCGGTGGCGCA--------TCG 568Acc706 TTGCTGGAACAAGGTGCGGACACAAGCATATATGCTTCCCGGTGGCGCA--------TCG 568Acc624 TTGCTGGAACAAGGTGCGGACACAAGCATATATGCTTCCCGGTGGCGCA--------TCG 568Acc440 TTGCTGGAACAAGGTGCGGACACAAGCATATATGCTTCCCGGTGGCGCA--------TCG 568Acc868 TTGCTGGAACAAGGTGCGGACACAAGCATATATGCTTCCCGGTGGCGCA--------TCG 568Acc220 TTGCTGGAACAAGGTGCGGACACAAGCATATATGCTTCCCGGTGGCGCA--------TCG 568Nipponbare TTGCTGGAACAAGGTGCGGACACAAGCATATATGCTTCCCGGTGGCGCA--------TCG 568AccUP3 TTGCTGGAACAAGGTGCGGACACAAGCATATATGCTTCCCGGTGGCGCA--------TCG 568AccUP1 TTGCTGGAACAAGGTGCGGACACAAGCATATATGCTTCCCGGTGGCGCA--------TCG 568Acc224 TTGCTGGAACAAGGTGCGGACACAAGCATATATGCTTCCCGGTGGCGCA--------TCG 568 ************** .**** : *******.**.******* *

Ashikawa et al. Supplementary Fig. S1 (5/30)

Acc414 CATTTCCCGCTCAGAAAAAC---AGGGCTAAAG---CAAAAAATCGTGATCAAGGTTGCC 588Acc420 CATTTCCCGCTCAGAAAAAC---AGGGCTAAAG---CAAAAAATCGTGATCAAGGTTGCC 588Acc761 CATTTCCCGCTCAGAAAAAC---AGGGCTAAAG---CAAAAAATCGTGATCAAGGTTGCC 588K60_Pik-p CATTTCCCGCTCAGAAAAAC---AGGGCTAAAGGTACGAAAAATCGTGATCAAGGTTGCC 591Acc130 CATGTCCCCCTCAGGATAATGGGAGGGGAAATG---CAAAAAATCGTGTTCAAGATTCCC 591Acc108 CATGTCCCCCTCAGGATAATGGGAGGGGAAATG---CAAAAAATCGTGTTCAAGATTCCC 591Acc719 CATGTCCCCCTCAGGATAATGGGAGGGGAAATG---CAAAAAATCGTGTTCAAGATTCCC 591Acc729 CATGTCCCCCTCAGGATAATGGGAGGGGAAATG---CAAAAAATCGTGTTCAAGATTCCC 591Acc709 CATGTCCCCCTCAGGATAATGGGAGGGGAAATG---CAAAAAATCGTGTTCAAGATTCCC 591Acc710 CATGTCCCCCTCAGGATAATGGGAGGGGAAATG---CAAAAAATCGTGTTCAAGATTCCC 591Acc504 CATGTCCCCCTCAGGATAATGGGAGGGGAAATG---CAAAAAATCGTGTTCAAGATTCCC 591Acc848 CATGTCCCCCTCAGGATAATGGGAGGGGAAATG---CAAAAAATCGTGTTCAAGATTCCC 591Acc563 CATGTCCCCCTCAGGATAATGGGAGGGGAAATG---CAAAAAATCGTGTTCAAGATTCCC 591Acc757 CATGTCCCCCTCAGGATAATGGGAGGGGAAATG---CAAAAAATCGTGTTCAAGATTCCC 591Tsuyuake_Pik-m CATGTCCCCCTCAGGATAATGGGAGGGGAAATG---CAAAAAATCGTGTTCAAGATTCCC 591Kanto51_Pik CATGTCCCCCTCAGGATAATGGGAGGGGAAATG---CAAAAAATCGTGTTCAAGATTCCC 591Kusabue_Pik CATGTCCCCCTCAGGATAATGGGAGGGGAAATG---CAAAAAATCGTGTTCAAGATTCCC 591Acc201 CAACACCATGGCATGATAA----------GGAG---CAAAGTATTGTGGTCAAGGT-GCC 614Acc206 CAACACCATGGCATGATAA----------GGAG---CAAAGTATTGTGGTCAAGGT-GCC 614Acc1 CAACACCATGGCATGATAA----------GGAG---CAAAGTATTGTGGTCAAGGT-GCC 614Acc101 CAACACCATGGCATGATAA----------GGAG---CAAAGTATTGTGGTCAAGGT-GCC 614Acc718 CAACACCATGGCATGATAA----------GGAG---CAAAGTATTGTGGTCAAGGT-GCC 614Acc724 CAACACCATGGCATGATAA----------GGAG---CAAAGTATTGTGGTCAAGGT-GCC 614Acc715 CAACACCATGGCATGATAA----------GGAG---CAAAGTATTGTGGTCAAGGT-GCC 614Acc706 CAACACCATGGCATGATAA----------GGAG---CAAAGTATTGTGGTCAAGGT-GCC 614Acc624 CAACACCATGGCATGATAA----------GGAG---CAAAGTATTGTGGTCAAGGT-GCC 614Acc440 CAACACCATGGCATGATAA----------GGAG---CAAAGTATTGTGGTCAAGGT-GCC 614Acc868 CAACACCATGGCATGATAA----------GGAG---CAAAGTATTGTGGTCAAGGT-GCC 614Acc220 CAACACCATGGCATGATAA----------GGAG---CAAAGTACTGTGGTCAAGGT-GCC 614Nipponbare CAACACCATGGCATGATAA----------GGAG---CAAAGTACTGTGGTCAAGGT-GCC 614AccUP3 CAACACCATGGCATGATAA----------GGAG---CAAAGTACTGTGGTCAAGGT-GCC 614AccUP1 CAACACCATGGCATGATAA----------GGAG---CAAAGTACTGTGGTCAAGGT-GCC 614Acc224 CAACACCATGGCATGATAA----------GGAG---CAAAGTACTGTGGTCAAGGT-GCC 614 **: :**. ** .*:** ..:* *.**.:* *** *****.* ** Acc414 ATGGAGGGCAATAATTGCCGTTCAAAAGCAATGGC-----TTTAGTTAAGA-GCACTGGA 642Acc420 ATGGAGGGCAATAATTGCCGTTCAAAAGCAATGGC-----TTTAGTTAAGA-GCACTGGA 642Acc761 ATGGAGGGCAATAATTGCCGTTCAAAAGCAATGGC-----TTTAGTTAAGA-GCACTGGA 642K60_Pik-p ATGGAGGGCAATAATTGCCGTTCAAAAGCAATGGC-----TTTAGTTGCGA-GCACTGGA 645Acc130 ATGGTGGACGATAAGAGCCGTACAAAAGCAATGTC-----ATTGGTTGCAA-GCACGGTT 645Acc108 ATGGTGGACGATAAGAGCCGTACAAAAGCAATGTC-----ATTGGTTGCAA-GCACGGTT 645Acc719 ATGGTGGACGATAAGAGCCGTACAAAAGCAATGTC-----ATTGGTTGCAA-GCACGGTT 645Acc729 ATGGTGGACGATAAGAGCCGTACAAAAGCAATGTC-----ATTGGTTGCAA-GCACGGTT 645Acc709 ATGGTGGACGATAAGAGCCGTACAAAAGCAATGTC-----ATTGGTTGCAA-GCACGGTT 645Acc710 ATGGTGGACGATAAGAGCCGTACAAAAGCAATGTC-----ATTGGTTGCAA-GCACGGTT 645Acc504 ATGGTGGACGATAAGAGCCGTACAAAAGCAATGTC-----ATTGGTTGCAA-GTACGGTT 645Acc848 ATGGTGGACGATAAGAGCCGTACAAAAGCAATGTC-----ATTGGTTGCAA-GTACGGTT 645Acc563 ATGGTGGACGATAAGAGCCGTACAAAAGCAATGTC-----ATTGGTTGCAA-GTACGGTT 645Acc757 ATGGTGGACGATAAGAGCCGTACAAAAGCAATGTC-----ATTGGTTGCAA-GTACGGTT 645Tsuyuake_Pik-m ATGGTGGACGATAAGAGCCGTACAAAAGCAATGTC-----ATTGGTTGCAA-GTACGGTT 645Kanto51_Pik ATGGTGGACGATAAGAGCCGTACAAAAGCAATGTC-----ATTGGTTGCAA-GTACGGTT 645Kusabue_Pik ATGGTGGACGATAAGAGCCGTACAAAAGCAATGTC-----ATTGGTTGCAA-GTACGGTT 645Acc201 --GGAAAA-AAGAAGGGACG-ACATGAACGAT------------GATGCATTGCACTGGG 658Acc206 --GGAAAA-AAGAAGGGACG-ACATGAACGAT------------GATGCATTGCACTGGG 658Acc1 --GGAAAA-AAGAAGGGACG-ACATGAACGAT------------GATGCATTGCACTGGG 658Acc101 --GGAAAA-AAGAAGTGACG-ACATGAACGAT------------GATGCATTGCACTGGG 658Acc718 --GGAAAA-AAGAAGGGACG-ACATGAACGAT------------GATGCATTGCACTGGG 658Acc724 --GGAAAA-AAGAAGTGACG-ACATGAACGAT------------GATGCATTGCACTGGG 658Acc715 --GGAAAA-AAGAAGTGACG-ACATGAACGAT------------GATGCATTGCACTGGG 658Acc706 --GGAAAA-AAGAAGTGACG-ACATGAACGAT------------GATGCATTGCACTGGG 658Acc624 --GGAAAA-AAGAAGTGACG-ACATGAACGAT------------GATGCATTGCACTGGG 658Acc440 --GGGAAA-AAGAAGGGACG-ACATGAACGATGACGACCAACCCAGTGCATTGCACTGGG 670Acc868 --GGGAAA-AAGAAGGGACG-ACATGAACGATGACGACCAACCCAGTGCATTGCACTGGG 670Acc220 --GGAAAG-AGAGTGGGGCT-TCCCGGACAAT------CGGAACAGTCCATTTATATGGG 664Nipponbare --GGAAAG-AGAGTGGGGCT-TCCCGGACAAT------CGGAACAGTCCATTTATATGGG 664AccUP3 --GGAAAG-AGAGTGGGGCT-TCCCGGACAAT------CGGAACAGTCCATTTATATGGG 664AccUP1 --GGAAAG-AGAGTGGGGCT-TCCCGGACAAT------CGGAACAGTCCATTTATATGGG 664Acc224 --GGAAAG-AGAGTGGGGCT-TCCCGGACAAT------CGGAACAGTCCATTTATATGGG 664 ** ... .. .: * * :*. ...*.** . * ..: :. *

Ashikawa et al. Supplementary Fig. S1 (6/30)

Acc414 GGAGTGTACTC--GGTTGC-------GCTCGCAGGTGATCTA---AGAGAC--------- 681Acc420 GGAGTGTACTC--GGTTGC-------GCTCGCAGGTGATCTA---AGAGAC--------- 681Acc761 GGAGTGTACTC--GGTTGC-------GCTCGCAGGTGATCTA---AGAGAC--------- 681K60_Pik-p GGAGTGGACTC--GGTTGC-------GCTCGTAGGTGATCTA---AGAGAC--------- 684Acc130 GGAGTGCACTC--GGTTGC-------AATCGCCGGTGACCTA---AGAGAC--------- 684Acc108 GGAGTGCACTC--GGTTGC-------AATCGCCGGTGACCTA---AGAGAC--------- 684Acc719 GGAGTGCACTC--GGTTGC-------AATCGCCGGTGACCTA---AGAGAC--------- 684Acc729 GGAGTGCACTC--GGTTGC-------AATCGCCGGTGACCTA---AGAGAC--------- 684Acc709 GGAGTGCACTC--GGTTGC-------AATCGCCGGTGACCTA---AGAGAC--------- 684Acc710 GGAGTGCACTC--GGTTGC-------AATCGCCGGTGACCTA---AGAGAC--------- 684Acc504 GGAGTGCACTC--GGTTGC-------AATCGCCGGTGACCTA---AGAGAC--------- 684Acc848 GGAGTGCACTC--GGTTGC-------AATCGCCGGTGACCTA---AGAGAC--------- 684Acc563 GGAGTGCACTC--GGTTGC-------AATCGCCGGTGACCTA---AGAGAC--------- 684Acc757 GGAGTGCACTC--GGTTGC-------AATCGCCGGTGACCTA---AGAGAC--------- 684Tsuyuake_Pik-m GGAGTGCACTC--GGTTGC-------AATCGCCGGTGACCTA---AGAGAC--------- 684Kanto51_Pik GGAGTGCACTC--GGTTGC-------AATCGCCGGTGACCTA---AGAGAC--------- 684Kusabue_Pik GGAGTGCACTC--GGTTGC-------AATCGCCGGTGACCTA---AGAGAC--------- 684Acc201 CG-GTGAGTTT---GTTGCATGGAGTGCCCTCGGGTGGTACGTTTGGAGATTGT----AG 710Acc206 CG-GTGAGTTT---GTTGCATGGAGTGCCCTCGGGTGGTACGTTTGGAGATTGT----AG 710Acc1 CG-GTGAGTTT---GTTGCATGGAGTGCCCTCGGGTGGTACGTCTGGAGATTGT----AG 710Acc101 CG-GTGAGTTT---GTCGCATGGAGTGCCCTCGGGTGGTACGTCTGGAGATTGT----AG 710Acc718 CG-GTGAGTTT---GTTGCATGGAGTGCCCTCGGGTGGTACGTCTGGAGATTGT----AG 710Acc724 CG-GTGAGTTT---GTCGCATGGAGTGCCCTCGGGTGGTACGTCTGGAGATTGT----AG 710Acc715 CG-GTGAGTTT---GTCGCATGGAGTGCCCTCGGGTGGTACGTCTGGAGATTGT----AG 710Acc706 CG-GTGAGTTT---GTCGCATGGAGTGCCCTCGGGTGGTACGTCTGGAGATTGT----AG 710Acc624 CG-GTGAGTTT---GTCGCATGGAGTGCCCTCGGGTGGTACGTCTGGAGATTGT----AG 710Acc440 CG-GTGAGTAGTAGGTTGCATGGAGTGCCCTCGGGTGGTGCGTCTGGAGATTGT----AG 725Acc868 CG-GTGAGTAGTAGGTTGCATGGAGTGCCCTCGGGTGGTGCGTCTGGAGATTGT----AG 725Acc220 CGAGTGATTCGT---TTGAACG-ATTGCGTTCGGGAAGTTTGTGTGGAGAT--------- 711Nipponbare CGAGTGATTCGT---TTGAACG-ATTGCGTTCGGGAAGTTTGTGTGGAGAT--------- 711AccUP3 CGAGTGATTCGT---TTGAACG-ATTGCGTTCGGGAAGTTTGTGTGGAGAT--------- 711AccUP1 CGAGTGATTCGT---TTGAACG-ATTGCGTTCGGGAAGTTTGTGTGGAGAT--------- 711Acc224 CGAGTGATTCGT---TTGAACG-ATTGCGTTCGGGAAGTTTGTGTGGAGAT--------- 711 * *** * *. .. **:.. . .****  Acc414 AAGATAGTGGAGATAGTGGTGGTCGGTTATGGCATTGACCCCATCAAGCTGATCTCCGCG 741Acc420 AAGATAGTGGAGATAGTGGTGGTCGGTTATGGCATTGACCCCATCAAGCTGATCTCCGCG 741Acc761 AAGATAGTGGAGATAGTGGTGGTCGGTTATGGCATTGACCCCATCAAGCTGATCTCCGCG 741K60_Pik-p AAGAT---------AGAGGTGGTCGGTTATGGCATTGACCCCATCAAGCTGATCTCCGCG 735Acc130 GAGGT---------TGTGGTGGTCGGTGATGGCATTGACTCCATCAATCTGGTCTCTGCG 735Acc108 GAGGT---------TGTGGTGGTCGGTGATGGCATTGACTCCATCAATCTGGTCTCTGCG 735Acc719 GAGGT---------TGTGGTGGTCGGTGATGGCATTGACTCCATCAATCTGGTCTCTGCG 735Acc729 GAGGT---------TGTGGTGGTCGGTGATGGCATTGACTCCATCAATCTGGTCTCTGCG 735Acc709 GAGGT---------TGTGGTGGTCGGTGATGGCATTGACTCCATCAATCTGGTCTCTGCG 735Acc710 GAGGT---------TGTGGTGGTCGGTGATGGCATTGACTCCATCAATCTGGTCTCTGCG 735Acc504 GAGGT---------TGTGGTGGTCGGTGATGGCATTGACTCCATCAATCTGGTCTCTGCG 735Acc848 GAGGT---------TGTGGTGGTCGGTGATGGCATTGACTCCATCAATCTGGTCTCTGCG 735Acc563 GAGGT---------TGTGGTGGTCGGTGATGGCATTGACTCCATCAATCTGGTCTCTGCG 735Acc757 GAGGT---------TGTGGTGGTCGGTGATGGCATTGACTCCATCAATCTGGTCTCTGCG 735Tsuyuake_Pik-m CAGGT---------TGTGGTGGTCGGTGATGGCATTGACTCCATCAATCTGGTCTCTGCG 735Kanto51_Pik GAGGT---------TGTGGTGGTCGGTGATGGCATTGACTCCATCAATCTGGTCTCTGCG 735Kusabue_Pik GAGGT---------TGTGGTGGTCGGTGATGGCATTGACTCCATCAATCTGGTCTCTGCG 735Acc201 TAGGT--------TGCAGTTGAATGGTGAAGGCGCGAACATCCGCAAGCTCTTGTCCACC 762Acc206 TAGGT--------TGCAGTTGAATGGTGAAGGCGCGAACATCCGCAAGCTCTTGTCCACC 762Acc1 TAGGT--------TGCAGTTGAATGGTGAAGGCGCGAACATCCGCAAGCTCTTGTCCACC 762Acc101 TAGGT--------TGCAGTTGGATGGTGAAGGCGCGAACATCCGCAAGCTCTTGTCCACC 762Acc718 TAGGT--------TGCAGTTGCATGGTGAAGGCGCGAACATCCGCAAGCTCTTGTCCACC 762Acc724 TAGGT--------TGCAGTTGGATGGTGAAGGCGCGAACATCCGCAAGCTCTTGTCCACC 762Acc715 TAGGT--------TGCAGTTGGATGGTGAAGGCGCGAACATCCGCAAGCTCTTGTCCACC 762Acc706 TAGGT--------TGCAGTTGGATGGTGAAGGCGCGAACATCCGCAAGCTCTTGTCCACC 762Acc624 TAGGT--------TGCAGTTGGATGGTGAAGGCGCGAACATCCGCAAGCTCTTGTCCACC 762Acc440 TAGGT--------TGCAGTTGGATGGTGAAGGCGCGAACATCCGCAAGCTCTTGTCCACC 777Acc868 TAGGT--------TGCAGTTGGATGGTGAAGGCGCGAACATCCGCAAGCTCTTGTCCACC 777Acc220 -ACGT--------TGCGGTTGGATGGTGAAGGCGCGAACATCCGCAAGCTCTTGTCCACC 762Nipponbare -ACGT--------TGCGGTTGGATGGTGAAGGCGCGAACATCCGCAAGCTCTTGTCCACC 762AccUP3 -ACGT--------TGCGGTTGGATGGTGAAGGCGCGAACATCCGCAAGCTCTTGTCCACC 762AccUP1 -ACGT--------TGCGGTTGGATGGTGAAGGCGCGAACATCCGCAAGCTCTTGTCCACC 762Acc224 -ACGT--------TGCGGTTGGATGGTGAAGGCGCGAACATCCGCAAGCTCTTGTCCACC 762 * .* * ** : *** *:***. .** *. *** ** * ** .*

Ashikawa et al. Supplementary Fig. S1 (7/30)

Acc414 CTCCGGAAGAAGGTGGGCCATGCGGAGTTGCTGCAGGTCA--GCCAAGCAAATAAAGATG 799Acc420 CTCCGGAAGAAGGTGGGCCATGCGGAGTTGCTGCAGGTCA--GCCAAGCAAATAAAGATG 799Acc761 CTCCGGAAGAAGGTGGGCCATGCGGAGTTGCTGCAGGTCA--GCCAAGCAAATAAAGATG 799K60_Pik-p CTCCGGAAGAAGGTGGGCGATGCGGAGTTGCTGCAGGTCA--GCCAAGCAAATAAAGATG 793Acc130 CTCCGGAAGAAGGTGGACCCTGCGATGTTTCTGGAGGTCA--GCCAAGCAAAGGAAGATG 793Acc108 CTCCGGAAGAAGGTGGACCCTGCGATGTTTCTGGAGGTCA--GCCAAGCAAAGGAAGATG 793Acc719 CTCCGGAAGAAGGTGGACCCTGCGATGTTTCTGGAGGTCA--GCCAAGCAAAGGAAGATG 793Acc729 CTCCGGAAGAAGGTGGACCCTGCGATGTTTCTGGAGGTCA--GCCAAGCAAAGGAAGATG 793Acc709 CTCCGGAAGAAGGTGGACCCTGCGATGTTTCTGGAGGTCA--GCCAAGCAAAGGAAGATG 793Acc710 CTCCGGAAGAAGGTGGACCCTGCGATGTTTCTGGAGGTCA--GCCAAGCAAAGGAAGATG 793Acc504 CTCCGGAAGAAGGTGGGCCCTGCGATGTTTCTGGAGGTCA--GCCAAGCAAAGGAAGATG 793Acc848 CTCCGGAAGAAGGTGGGCCCTGCGATGTTTCTGGAGGTCA--GCCAAGCAAAGGAAGATG 793Acc563 CTCCGGAAGAAGGTGGGCCCTGCGATGTTTCTGGAGGTCA--GCCAAGCAAAGGAAGATG 793Acc757 CTCCGGAAGAAGGTGGGCCCTGCGATGTTTCTGGAGGTCA--GCCAAGCAAAGGAAGATG 793Tsuyuake_Pik-m CTCCGGAAGAAGGTGGGCCCTGCGATGTTTCTGGAGGTCA--GCCAAGTAAAGGAAGATG 793Kanto51_Pik CTCCGGAAGAAGGTGGGCCATGCGGAGTTGCTGCAGGTCA--GCCAAGTAAAGGAAGATG 793Kusabue_Pik CTCCGGAAGAAGGTGGGCCATGCGGAGTTGCTGCAGGTCA--GCCAAGTAAAGGAAGATG 793Acc201 CTCCGGAATAAGGTGGGCCGCGCCCAGTTGGTGCAGGTCGAGGATAAGAGAAAAAGG--G 820Acc206 CTCCGGAATAAGGTGGGCCGCGCCCAGTTGGTGCAGGTCGAGGATAAGAGAAAAAGG--G 820Acc1 CTCCGGAATAAGGTGGGCCGCGCCCAGTTGGTGCAGGTCGAGGATAAGAGAAAAAGG--G 820Acc101 CTCCGGAATAAGGTGGGCCACGCCCAGTTGGTGCAGGTCGAGGATAAGAGAAAAAGG--G 820Acc718 CTCCGGAATAAGGTGGGCCGCGCCCAGTTGGTGCAGGTCGAGGATAAGAGAAAAAGG--G 820Acc724 CTCCGGAATAAGGTGGGCCACGCCCAGTTGGTGCAGGTCGAGGATAAGAGAAAAAGG--G 820Acc715 CTCCGGAATAAGGTGGGCCACGCCCAGTTGGTGCAGGTCGAGGATAAGAGAAAAAGG--G 820Acc706 CTCCGGAATAAGGTGGGCCACGCCCAGTTGGTGCAGGTCGAGGATAAGAGAAAAAGG--G 820Acc624 CTCCGGAATAAGGTGGGCCACGCCCAGTTGGTGCAGGTCGAGGATAAGAGAAAAAGG--G 820Acc440 CTCCGGAATAAGGTGGGCCGCGCCCAGTTGGTGCAGGTCGAGGATAAGAGAAAAAGG--G 835Acc868 CTCCGGAATAAGGTGGGCCGCGCCCAGTTGGTGCAGGTCGAGGATAAGAGAAAAAGG--G 835Acc220 CTCCGGAATAAGGTGGGCCGCGCCCAGTTGGTGCAGGTCGAGGATAAGAGAAAAAGG--G 820Nipponbare CTCCGGAATAAGGTGGGCCGCGCCCAGTTGGTGCAGGTCGAGGATAAGAGAAAAAGG--G 820AccUP3 CTCCGGAATAAGGTGGGCCGCGCCCAGTTGGTGCAGGTCGAGGATAAGAGAAAAAGG--G 820AccUP1 CTCCGGAATAAGGTGGGCCGCGCCCAGTTGGTGCAGGTCGAGGATAAGAGAAAAAGG--G 820Acc224 CTCCGGAATAAGGTGGGCCGCGCCCAGTTGGTGCAGGTCGAGGATAAGAGAAAAAGG--G 820 ******** *******.* ** :*** ** *****. *. *** .** .*.* * Acc414 TGAAGGAGACGACGCCGATGCTTGCGCCGGTGAAATCCATATGTGAATTTCACAAGGTCA 859Acc420 TGAAGGAGACGACGCCGATGCTTGCGCCGGTGAAATCCATATGTGAATTTCACAAGGTCA 859Acc761 TGAAGGAGACGACGCCGATGCTTGCGCCGGTGAAATCCATATGTGAATTTCACAAGGTCA 859K60_Pik-p TGAAGGAGACGACGCCGATGCTTGCGCCGGTGAAATCCATATGTGAATTTCACAAGGTCA 853Acc130 TGAAGGAGATAACGGCGATGCTTGCGCCGGTGAAATCCATATGTGAATTTCACGAGGTCA 853Acc108 TGAAGGAGATAACGGCGATGCTTGCGCCGGTGAAATCCATATGTGAATTTCACGAGGTCA 853Acc719 TGAAGGAGATAACGGCGATGCTTGCGCCGGTGAAATCCATATGTGAATTTCACGAGGTCA 853Acc729 TGAAGGAGATAACGGCGATGCTTGCGCCGGTGAAATCCATATGTGAATTTCACGAGGTCA 853Acc709 TGAAGGAGATAACGGCGATGCTTGCGCCGGTGAAATCCATATGTGAATTTCACGAGGTCA 853Acc710 TGAAGGAGATAACGGCGATGCTTGCGCCGGTGAAATCCATATGTGAATTTCACGAGGTCA 853Acc504 TGAAGGAGATAACGGCGATGCTTGCGCCGGTGAAATCCATATGTGAATTTCACGAGGTCA 853Acc848 TGAAGGAGATAACGGCGATGCTTGCGCCGGTGAAATCCATATGTGAATTTCACGAGGTCA 853Acc563 TGAAGGAGATAACGGCGATGCTTGCGCCGGTGAAATCCATATGTGAATTTCACGAGGTCA 853Acc757 TGAAGGAGATAACGGCGATGCTTGCGCCGGTGAAATCCATATGTGAATTTCACGAGGTCA 853Tsuyuake_Pik-m TGAAGGAGATAACGGCGATGCTTGCGCCGGTGAAATCCATATGTGAATTTCACGAGGTCA 853Kanto51_Pik TGAAGGAGATAACGGCGATGCTTGCGCCGGTGAAATCCATATGTGAATTTCACGAGGTCA 853Kusabue_Pik TGAAGGAGATAACGGCGATGCTTGCGCCGGTGAAATCCATATGTGAATTTCACGAGGTCA 853Acc201 TAGAGGAGGCGA---CGAAGCCT------------------TGTGAATTTCACGAGGTCA 859Acc206 TAGAGGAGGCGA---CGAAGCCT------------------TGTGAATTTCACGAGGTCA 859Acc1 TAGAGGAGGCGA---CGAAGCCT------------------TGTGAATTTCACGAGGTCA 859Acc101 TAGAGGAGGCGA---CGAAGCCT------------------TGTGAATTTCACGAGGTCA 859Acc718 TAGAGGAGGCGA---CGAAGCCT------------------TGTGAATTTCACGAGGTCA 859Acc724 TAGAGGAGGCGA---CGAAGCCT------------------TGTGAATTTCACGAGGTCA 859Acc715 TAGAGGAGGCGA---CGAAGCCT------------------TGTGAATTTCACGAGGTCA 859Acc706 TAGAGGAGGCGA---CGAAGCCT------------------TGTGAATTTCACGAGGTCA 859Acc624 TAGAGGAGGCGA---CGAAGCCT------------------TGTGAATTTCACGAGGTCA 859Acc440 TAGAGGAGGCGA---CGAAGCCT------------------TGTGAATTTCACGAGGTCA 874Acc868 TAGAGGAGGCGA---CGAAGCCT------------------TGTGAATTTCACGAGGTCA 874Acc220 TAGAGGAGGCGA---CGAAGCCT------------------TGTGAATTTCACGAGGTCA 859Nipponbare TAGAGGAGGCGA---CGAAGCCT------------------TGTGAATTTCACGAGGTCA 859AccUP3 TAGAGGAGGCGA---CGAAGCCT------------------TGTGAATTTCACGAGGTCA 859AccUP1 TAGAGGAGGCGA---CGAAGCCT------------------TGTGAATTTCACGAGGTCA 859Acc224 TAGAGGAGGCGA---CGAAGCCT------------------TGTGAATTTCACGAGGTCA 859 *..*****. .* ***:** * ************.******

Ashikawa et al. Supplementary Fig. S1 (8/30)

Acc414 AAACAGTTTGCATCCTTGGATTGCCAGGTGGAGGCAAAACAACGGTTGCCAGAGAATTAT 919Acc420 AAACAGTTTGCATCCTTGGATTGCCAGGTGGAGGCAAAACAACGGTTGCCAGAGAATTAT 919Acc761 AAACAGTTTGCATCCTTGGATTGCCAGGTGGAGGCAAAACAACGGTTGCCAGAGAATTAT 919K60_Pik-p AAACAGTTTGCATCCTTGGATTGCCAGGTGGAGGCAAAACAACGGTTGCCAGAGAATTAT 913Acc130 AAACAATTTGCATCCTTGGATTGCCAGGGGGAGGCAAAACAACGATTGCCCGAGTACTAT 913Acc108 AAACAATTTGCATCCTTGGATTGCCAGGGGGAGGCAAAACAACGATTGCCCGAGTACTAT 913Acc719 AAACAATTTGCATCCTTGGATTGCCAGGGGGAGGCAAAACAACGATTGCCCGAGTACTAT 913Acc729 AAACAATTTGCATCCTTGGATTGCCAGGGGGAGGCAAAACAACGATTGCCCGAGTACTAT 913Acc709 AAACAATTTGCATCCTTGGATTGCCAGGGGGAGGCAAAACAACGATTGCCCGAGTACTAT 913Acc710 AAACAATTTGCATCCTTGGATTGCCAGGGGGAGGCAAAACAACGATTGCCCGAGTACTAT 913Acc504 AAACAATTTGCATCCTTGGATTGCCAGGGGGAGGCAAAACAACGATTGCCCGAGTACTAT 913Acc848 AAACAATTTGCATCCTTGGATTGCCAGGGGGAGGCAAAACAACGATTGCCCGAGTACTAT 913Acc563 AAACAATTTGCATCCTTGGATTGCCAGGGGGAGGCAAAACAACGATTGCCCGAGTACTAT 913Acc757 AAACAATTTGCATCCTTGGATTGCCAGGGGGAGGCAAAACAACGATTGCCCGAGTACTAT 913Tsuyuake_Pik-m AAACAATTTGCATCCTTGGATTGCCAGGGGGAGGCAAAACAACGATTGCCCGAGTACTAT 913Kanto51_Pik AAACAATTTGCATCCTTGGATTGCCAGGGGGAGGCAAAACAACGATTGCCCGAGTACTAT 913Kusabue_Pik AAACAATTTGCATCCTTGGATTGCCAGGGGGAGGCAAAACAACGATTGCCCGAGTACTAT 913Acc201 AAACAATATGCATCCTTGGATTGCCTGGCGCAGGCAAAACAACTCTTGCAAAACTGTTGT 919Acc206 AAACAATATGCATCCTTGGATTGCCTGGCGCAGGCAAAACAACTCTTGCAAAACTGTTGT 919Acc1 AAACAATATGCATCCTTGGATTGCCTGGCGCAGGCAAAACAACTCTTGCAAAACTGTTGT 919Acc101 AAACAATATGCATCCTTGGATTGCCTGGCGCAGGCAAAACAACTCTTGCAAAACTGTTGT 919Acc718 AAACAATATGCATCCTTGGATTGCCTGGCGCAGGCAAAACAACTCTTGCAAAACTGTTGT 919Acc724 AAACAATATGCATCCTTGGATTGCCTGGCGCAGGCAAAACAACTCTTGCAAAACTGTTGT 919Acc715 AAACAATATGCATCCTTGGATTGCCTGGCGCAGGCAAAACAACTCTTGCAAAACTGTTGT 919Acc706 AAACAATATGCATCCTTGGATTGCCTGGCGCAGGCAAAACAACTCTTGCAAAACTGTTGT 919Acc624 AAACAATATGCATCCTTGGATTGCCTGGCGCAGGCAAAACAACTCTTGCAAAACTGTTGT 919Acc440 AAACAATATGCATCCTTGGATTGCCTGGCGCAGGCAAAACAACTCTTGCAAAACTGTTGT 934Acc868 AAACAATATGCATCCTTGGATTGCCTGGCGCAGGCAAAACAACTCTTGCAAAACTGTTGT 934Acc220 AAACAATATGCATCCTTGGATTGCCTGGCGCAGGCAAAACAACTCTTGCAAAACTGTTGT 919Nipponbare AAACAATATGCATCCTTGGATTGCCTGGCGCAGGCAAAACAACTCTTGCAAAACTGTTGT 919AccUP3 AAACAATATGCATCCTTGGATTGCCTGGCGCAGGCAAAACAACTCTTGCAAAACTGTTGT 919AccUP1 AAACAATATGCATCCTTGGATTGCCTGGCGCAGGCAAAACAACTCTTGCAAAACTGTTGT 919Acc224 AAACAATATGCATCCTTGGATTGCCTGGCGCAGGCAAAACAACTCTTGCAAAACTGTTGT 919 *****.*:*****************:** * ************ ****...* :. *.* Acc414 A------TGACGCCTTGG--GAAC-GCACTTCCCATGCCGGGTTTTCGTGTCAGTCTCTC 970Acc420 A------TGACGCCTTGG--GAAC-GCACTTCCCATGCCGGGTTTTCGTGTCAGTCTCTC 970Acc761 A------TGACGCCTTGG--GAAC-GCACTTCCCATGCCGGGTTTTCGTGTCAGTCTCTC 970K60_Pik-p A------TGACGCCTTGG--GAAC-GCACTTCCCATGCCGGGTTTTCGTGTCAGTCTCTC 964Acc130 A------TCATGCATTGG--GAAC-GCAGTTCCAATGCCGGGTTTTCGCATCAATCTCTC 964Acc108 A------TCATGCATTGG--GAAC-GCAGTTCCAATGCCGGGTTTTCGCATCAATCTCTC 964Acc719 A------TCATGCATTGG--GAAC-GCAGTTCCAATGCCGGGTTTTCGCATCAATCTCTC 964Acc729 A------TCATGCATTGG--GAAC-GCAGTTCCAATGCCGGGTTTTCGCATCAATCTCTC 964Acc709 A------TCATGCATTGG--GAAC-GCAGTTCCAATGCCGGGTTTTCGCATCAATCTCTC 964Acc710 A------TCATGCATTGG--GAAC-GCAGTTCCAATGCCGGGTTTTCGCATCAATCTCTC 964Acc504 A------TCATGCATTGG--GAAC-GCAGTTCCAATGCCGGGTTTTCGCATCAATCTCTC 964Acc848 A------TCATGCATTGG--GAAC-GCAGTTCCAATGCCGGGTTTTCGCATCAATCTCTC 964Acc563 A------TCATGCATTGG--GAAC-GCAGTTCCAATGCCGGGTTTTCGCATCAATCTCTC 964Acc757 A------TCATGCATTGG--GAAC-GCAGTTCCAATGCCGGGTTTTCGCATCAATCTCTC 964Tsuyuake_Pik-m A------TCATGCATTGG--GAAC-GCAGTTCCAATGCCGGGTTTTCGCATCAATCTCTC 964Kanto51_Pik A------TCATGCATTGG--GAAC-GCAGTTCCAATGCCGGGTTTTCGCATCAATCTCTC 964Kusabue_Pik A------TCATGCATTGG--GAAC-GCAGTTCCAATGCCGGGTTTTCGCATCAATCTCTC 964Acc201 ACTCCCATCACTCAACGACAGAGCAGCAATTCCAACACCGGGCTTTCGTGTCACTCTCTC 979Acc206 ACTCCCATCACTCAACGACAGAGCAGCAATTCCAACACCGGGCTTTCGTGTCACTCTCTC 979Acc1 ACTCCCATCACTCAACGACAGAGCAGCAATTCCAACACCGGGCTTTCGTGTCACTCTCTC 979Acc101 ACTCCCATCACTCAACGACAGAGCAGCAATTCCAACACCGGGCTTTCGTGTCACTCTCTC 979Acc718 ACTCCCATCACTCAACGACAGAGCAGCAATTCCAACACCGGGCTTTCGTGTCACTCTCTC 979Acc724 ACTCCCATCACTCAACGACAGAGCAGCAATTCCAACACCGGGCTTTCGTGTCACTCTCTC 979Acc715 ACTCCCATCACTCAACGACAGAGCAGCAATTCCAACACCGGGCTTTCGTGTCACTCTCTC 979Acc706 ACTCCCATCACTCAACGACAGAGCAGCAATTCCAACACCGGGCTTTCGTGTCACTCTCTC 979Acc624 ACTCCCATCACTCAACGACAGAGCAGCAATTCCAACACCGGGCTTTCGTGTCACTCTCTC 979Acc440 ACTCCCATCACTCAACGACAGAGCAGCAATTCCAACACCGGGCTTTCGTGTCACTCTCTC 994Acc868 ACTCCCATCACTCAACGACAGAGCAGCAATTCCAACACCGGGCTTTCGTGTCACTCTCTC 994Acc220 ACTCCCATCACTCAACGACAGAGCAGCAATTCCAACACCGGGCTTTCGTGTCACTCTCTC 979Nipponbare ACTCCCATCACTCAACGACAGAGCAGCAATTCCAACACCGGGCTTTCGTGTCACTCTCTC 979AccUP3 ACTCCCATCACTCAACGACAGAGCAGCAATTCCAACACCGGGCTTTCGTGTCACTCTCTC 979AccUP1 ACTCCCATCACTCAACGACAGAGCAGCAATTCCAACACCGGGCTTTCGTGTCACTCTCTC 979Acc224 ACTCCCATCACTCAACGACAGAGCAGCAATTCCAACACCGGGCTTTCGTGTCACTCTCTC 979 * * * *.: *. **.* *** ****.* .***** ***** .*** ****** 

Ashikawa et al. Supplementary Fig. S1 (9/30)

Acc414 CAAGTTCTAGTCCCAGTCCCAATCTCACAAAGACTCTTGCAGACATTTTCGCTCAAGCAC 1030Acc420 CAAGTTCTAGTCCCAGTCCCAATCTCACAAAGACTCTTGCAGACATTTTCGCTCAAGCAC 1030Acc761 CAAGTTCTAGTCCCAGTCCCAATCTCACAAAGACTCTTGCAGACATTTTCGCTCAAGCAC 1030K60_Pik-p CAAGTTCTAGTCCCAGTCCCAATCTCACAAAGACTCTTGCAGACATTTTCGCTCAAGCAC 1024Acc130 CAAGTTCCAGCCCCAGTCCCAATCTAACAGAGACTCTTGCAGACATTTTCGCTCAAGCAC 1024Acc108 CAAGTTCCAGCCCCAGTCCCAATCTAACAGAGACTCTTGCAGACATTTTCGCTCAAGCAC 1024Acc719 CAAGTTCCAGCCCCAGTCCCAATCTAACAGAGACTCTTGCAGACATTTTCGCTCAAGCAC 1024Acc729 CAAGTTCCAGCCCCAGTCCCAATCTAACAGAGACTCTTGCAGACATTTTCGCTCAAGCAC 1024Acc709 CAAGTTCCAGCCCCAGTCCCAATCTAACAGAGACTCTTGCAGACATTTTCGCTCAAGCAC 1024Acc710 CAAGTTCCAGCCCCAGTCCCAATCTAACAGAGACTCTTGCAGACATTTTCGCTCAAGCAC 1024Acc504 CAAGTTCCAGCCCCAGTCCCAATCTAACAGAGACTCTTGCAGACATTTTCGCTCAAGCAC 1024Acc848 CAAGTTCCAGCCCCAGTCCCAATCTAACAGAGACTCTTGCAGACATTTTCGCTCAAGCAC 1024Acc563 CAAGTTCCAGCCCCAGTCCCAATCTAACAGAGACTCTTGCAGACATTTTCGCTCAAGCAC 1024Acc757 CAAGTTCCAGCCCCAGTCCCAATCTAACAGAGACTCTTGCAGACATTTTCGCTCAAGCAC 1024Tsuyuake_Pik-m CAAGTTCCAGCCCCAGTCCCAATCTAACAGAGACTCTTGCAGACATTTTCGCTCAAGCAC 1024Kanto51_Pik CAAGTTCCAGCCCCAGTCCCAATCTAACAGAGACTCTTGCAGACATTTTCGCTCAAGCAC 1024Kusabue_Pik CAAGTTCCAGCCCCAGTCCCAATCTAACAGAGACTCTTGCAGACATTTTCGCTCAAGCAC 1024Acc201 CGGGTGC------------CAATCTCACCGACACTCTTACTGATATTTT------ATTGC 1021Acc206 CGGGTGC------------CAATCTCACCGACACTCTTACTGATATTTT------ATTGC 1021Acc1 CGGGTGC------------CAATCTCACCGACACTCTTACTGATATTTT------ATTGC 1021Acc101 CGGGTGC------------CAATCTCACCGACACTCTTACTGATATTTT------ATTGC 1021Acc718 CGGGTGC------------CAATCTCACCGACACTCTTACTGATATTTT------ATTGC 1021Acc724 CGGGTGC------------CAATCTCACCGACACTCTTACTGATATTTT------ATTGC 1021Acc715 CGGGTGC------------CAATCTCACCGACACTCTTACTGATATTTT------ATTGC 1021Acc706 CGGGTGC------------CAATCTCACCGACACTCTTACTGATATTTT------ATTGC 1021Acc624 CGGGTGC------------CAATCTCACCGACACTCTTACTGATATTTT------ATTGC 1021Acc440 CGGGTGC------------CAATCTCACCGACACTCTTACTGATATTTT------ATTGC 1036Acc868 CGGGTGC------------CAATCTCACCGACACTCTTACTGATATTTT------ATTGC 1036Acc220 CGGGTGC------------CAATCTCACCGACACTCTTACTGATATTTT------ATTGC 1021Nipponbare CGGGTGC------------CAATCTCACCGACACTCTTACTGATATTTT------ATTGC 1021AccUP3 CGGGTGC------------CAATCTCACCGACACTCTTACTGATATTTT------ATTGC 1021AccUP1 CGGGTGC------------CAATCTCACCGACACTCTTACTGATATTTT------ATTGC 1021Acc224 CGGGTGC------------CAATCTCACCGACACTCTTACTGATATTTT------ATTGC 1021 *..** * ******.**..* ******.*:** ***** * .* Acc414 AACTAGGAGTAACCGATACACTTAGCACACCATATGGTGGGAGTGGGACCGGGAGAGCTC 1090Acc420 AACTAGGAGTAACCGATACACTTAGCACACCATATGGTGGGAGTGGGACCGGGAGAGCTC 1090Acc761 AACTAGGAGTAACCGATACACTTAGCACACCATATGGTGGGAGTGGGACCGGGAGAGCTC 1090K60_Pik-p AACTAGGAGTAACCGATACACTTAGCACACCATATGGTGGGAGTGGGACCGGGAGAGCTC 1084Acc130 AACTAGGAGTAACTGATACACTTAGCACACCATATGGTGGGAGTGGGACCGGGAGAGCTC 1084Acc108 AACTAGGAGTAACTGATACACTTAGCACACCATATGGTGGGAGTGGGACCGGGAGAGCTC 1084Acc719 AACTAGGAGTAACTGATACACTTAGCACACCATATGGTGGGAGTGGGACCGGGAGAGCTC 1084Acc729 AACTAGGAGTAACTGATACACTTAGCACACCATATGGTGGGAGTGGGACCGGGAGAGCTC 1084Acc709 AACTAGGAGTAACTGATACACTTAGCACACCATATGGTGGGAGTGGGACCGGGAGAGCTC 1084Acc710 AACTAGGAGTAACTGATACACTTAGCACACCATATGGTGGGAGTGGGACCGGGAGAGCTC 1084Acc504 AACTAGGAGTAACTGATACACTTAGCACACCATATGGTGGGAGTGGGACCGGGAGAGCTC 1084Acc848 AACTAGGAGTAACTGATACACTTAGCACACCATATGGTGGGAGTGGGACCGGGAGAGCTC 1084Acc563 AACTAGGAGTAACTGATACACTTAGCACACCATATGGTGGGAGTGGGACCGGGAGAGCTC 1084Acc757 AACTAGGAGTAACTGATACACTTAGCACACCATATGGTGGGAGTGGGACCGGGAGAGCTC 1084Tsuyuake_Pik-m AACTAGGAGTAACTGATACACTTAGCACACCATATGGTGGGAGTGGGACCGGGAGAGCTC 1084Kanto51_Pik AACTAGGAGTAACTGATACACTTAGCACACCATATGGTGGGAGTGGGACCGGGAGAGCTC 1084Kusabue_Pik AACTAGGAGTAACTGATACACTTAGCACACCATATGGTGGGAGTGGGACCGGGAGAGCTC 1084Acc201 AAGTAGGAGCATATAATGATGATGCAACACCATATTGTGG------GACCGGAACACCGC 1075Acc206 AAGTAGGAGCATATAATGATGATGCAACCCCATATTGTGG------GACCGGAACACCGC 1075Acc1 AAGTAGGAGCATATAATGATGATGCAACACCATATTGTGG------GACCGGAACACCGC 1075Acc101 AAGTAGGAGCATATAATGATGATGCAACACCATATTGTGG------GACCGGAACACCGC 1075Acc718 AAGTAGGAGCATATAATGATGATGCAACACCATATTGTGG------GACCGGAACACCGC 1075Acc724 AAGTAGGAGCATATAATGATGATGCAACACCATATTGTGG------GACCGGAACACCGC 1075Acc715 AAGTAGGAGCATATAATGATGATGCAACACCATATTGTGG------GACCGGAACACCGC 1075Acc706 AAGTAGGAGCATATAATGATGATGCAACACCATATTGTGG------GACCGGAACACCGC 1075Acc624 AAGTAGGAGCATATAATGATGATGCAACACCATATTGTGG------GACCGGAACACCGC 1075Acc440 AAGTAGGAGCATATAATGATGATGCAACACCATATTGTGG------GACCGGAACACCGC 1090Acc868 AAGTAGGAGCATATAATGATGATGCAACACCATATTGTGG------GACCGGAACACCGC 1090Acc220 AAGTAGGAGCATATAATGATGATGCAACACCATATTGTGG------GACCGGAACACCGC 1075Nipponbare AAGTAGGAGCATATAATGATGATGCAACACCATATTGTGG------GACCGGAACACCGC 1075AccUP3 AAGTAGGAGCATATAATGATGATGCAACACCATATTGTGG------GACCGGAACACCGC 1075AccUP1 AAGTAGGAGCATATAATGATGATGCAACACCATATTGTGG------GACCGGAACACCGC 1075Acc224 AAGTAGGAGCATATAATGATGATGCAACACCATATTGTGG------GACCGGAACACCGC 1075 ** ****** *:. .**..: :*. .**.****** **** ******.* * * * 

Ashikawa et al. Supplementary Fig. S1 (10/30)

Acc414 TTCAACAACATCTCATCGACAACATATCAGCTTTCCTCCTCAACAAAAAGTATCTCATTG 1150Acc420 TTCAACAACATCTCATCGACAACATATCAGCTTTCCTCCTCAACAAAAAGTATCTCATTG 1150Acc761 TTCAACAACATCTCATCGACAACATATCAGCTTTCCTCCTCAACAAAAAGTATCTCATTG 1150K60_Pik-p TTCAACAACATCTCATCGACAACATATCAGCTTTCCTCCTCAACAAAAAGTATCTCATTG 1144Acc130 TTCAACAACATCTCATCGACAACATATCAGCTTTCCTCCTCAACAAAAAGTATCTCATTG 1144Acc108 TTCAACAACATCTCATCGACAACATATCAGCTTTCCTCCTCAACAAAAAGTATCTCATTG 1144Acc719 TTCAACAACATCTCATCGACAACATATCAGCTTTCCTCCTCAACAAAAAGTATCTCATTG 1144Acc729 TTCAACAACATCTCATCGACAACATATCAGCTTTCCTCCTCAACAAAAAGTATCTCATTG 1144Acc709 TTCAACAACATCTCATCGACAACATATCAGCTTTCCTCCTCAACAAAAAGTATCTCATTG 1144Acc710 TTCAACAACATCTCATCGACAACATATCAGCTTTCCTCCTCAACAAAAAGTATCTCATTG 1144Acc504 TTCAACAACATCTCATCGACAACATATCAGCTTTCCTCCTCAACAAAAAGTATCTCATTG 1144Acc848 TTCAACAACATCTCATCGACAACATATCAGCTTTCCTCCTCAACAAAAAGTATCTCATTG 1144Acc563 TTCAACAACATCTCATCGACAACATATCAGCTTTCCTCCTCAACAAAAAGTATCTCATTG 1144Acc757 TTCAACAACATCTCATCGACAACATATCAGCTTTCCTCCTCAACAAAAAGTATCTCATTG 1144Tsuyuake_Pik-m TTCAACAACATCTCATCGACAACATATCAGCTTTCCTCCTCAACAAAAAGTATCTCATTG 1144Kanto51_Pik TTCAACAACATCTCATCGACAACATATCAGCTTTCCTCCTCAACAAAAAGTATCTCATTG 1144Kusabue_Pik TTCAACAACATCTCATCGACAACATATCAGCTTTCCTCCTCAACAAAAAGTATCTCATTG 1144Acc201 ACCAACAGTATCTCATTGACAATATATCAGCTTATCTCATTGGCAAAAAGTATCTTATTA 1135Acc206 ACCAACAGTATCTCATTGACAATATATCAGCTTATCTCATTGGCAAAAAGTATCTTATTA 1135Acc1 ACCAACAGTATCTCATTGACAACATGTCAGCTTATCTCATTGGCAAAAAGTATCTTATTA 1135Acc101 ACCAACAGTATCTCATTGACAACATATCAGCTTATCTCATTGGCAAAAAGTATCTTATTA 1135Acc718 ACCAACAGTATCTCATTGACAACATATCAGCTTATCTCATTGGCAAAAAGTATCTTATTA 1135Acc724 ACCAACAGTATCTCATTGACAACATATCAGCTTATCTCATTGGCAAAAAGTATCTTATTA 1135Acc715 ACCAACAGTATCTCATTGACAACATATCAGCTTATCTCATTGGCAAAAAGTATCTTATTA 1135Acc706 ACCAACAGTATCTCATTGACAACATATCAGCTTATCTCATTGGCAAAAAGTATCTTATTA 1135Acc624 ACCAACAGTATCTCATTGACAACATATCAGCTTATCTCATTGGCAAAAAGTATCTTATTA 1135Acc440 ACCAACAGTATCTCATTGACAACATATCAGCTTATCTCATTGGCAAAAAGTATCTTATTA 1150Acc868 ACCAACAGTATCTCATTGACAACATATCAGCTTATCTCATTGGCAAAAAGTATCTTATTA 1150Acc220 ACCAACAGTATCTCATTGACAATATATCAGCTTATCTCATTGGCAAAAAGTATCTTATTA 1135Nipponbare ACCAACAGTATCTCATTGACAATATATCAGCTTATCTCATTGGCAAAAAGTATCTTATTA 1135AccUP3 ACCAACAGTATCTCATTGACAATATATCAGCTTATCTCATTGGCAAAAAGTATCTTATTA 1135AccUP1 ACCAACAGTATCTCATTGACAATATATCAGCTTATCTCATTGGCAAAAAGTATCTTATTA 1135Acc224 ACCAACAGTATCTCATTGACAATATATCAGCTTATCTCATTGGCAAAAAGTATCTTATTA 1135 : *****. ******* ***** **.*******: ***.* ..************ ***. Acc414 TAATCGATGACATTTGGCATTGGGAAGAATGGGAAGTCATCAGAAAGTCCATTCCCAAGA 1210Acc420 TAATCGATGACATTTGGCATTGGGAAGAATGGGAAGTCATCAGAAAGTCCATTCCCAAGA 1210Acc761 TAATCGATGACATTTGGCATTGGGAAGAATGGGAAGTCATCAGAAAGTCCATTCCCAAGA 1210K60_Pik-p TAATCGATGACATTTGGCATTGGGAAGAATGGGAAGTCATCAGAAAGTCCATTCCCAAGA 1204Acc130 TAATCGATGACATTTGGCATTGGGAAGAATGGGAAGTCATCAGAAAGTCCATTCCCAAGA 1204Acc108 TAATCGATGACATTTGGCATTGGGAAGAATGGGAAGTCATCAGAAAGTCCATTCCCAAGA 1204Acc719 TAATCGATGACATTTGGCATTGGGAAGAATGGGAAGTCATCAGAAAGTCCATTCCCAAGA 1204Acc729 TAATCGATGACATTTGGCATTGGGAAGAATGGGAAGTCATCAGAAAGTCCATTCCCAAGA 1204Acc709 TAATCGATGACATTTGGCATTGGGAAGAATGGGAAGTCATCAGAAAGTCCATTCCCAAGA 1204Acc710 TAATCGATGACATTTGGCATTGGGAAGAATGGGAAGTCATCAGAAAGTCCATTCCCAAGA 1204Acc504 TAATCGATGACATTTGGCATTGGGAAGAATGGGAAGTCATCAGAAAGTCCATTCCCAAGA 1204Acc848 TAATCGATGACATTTGGCATTGGGAAGAATGGGAAGTCATCAGAAAGTCCATTCCCAAGA 1204Acc563 TAATCGATGACATTTGGCATTGGGAAGAATGGGAAGTCATCAGAAAGTCCATTCCCAAGA 1204Acc757 TAATCGATGACATTTGGCATTGGGAAGAATGGGAAGTCATCAGAAAGTCCATTCCCAAGA 1204Tsuyuake_Pik-m TAATCGATGACATTTGGCATTGGGAAGAATGGGAAGTCATCAGAAAGTCCATTCCCAAGA 1204Kanto51_Pik TAATCGATGACATTTGGCATTGGGAAGAATGGGAAGTCATCAGAAAGTCCATTCCCAAGA 1204Kusabue_Pik TAATCGATGACATTTGGCATTGGGAAGAATGGGAAGTCATCAGAAAGTCCATTCCCAAGA 1204Acc201 TAATTGATGACGTTTGGCACTGGGAAGAGTGGGAAGTCATCAGAAAGTCCATTCCAAAGA 1195Acc206 TAATTGATGACGTTTGGCACTGGGAAGAGTGGGAAGTCATCAGAAAGTCCATTCCAAAGA 1195Acc1 TAATTGATGACGTTTGGCGCTGGGAAGAGTGGGAAGTCATCAGAAAGTCCATTCCAAAGA 1195Acc101 TAATTGATGACGTTTGGCGCTGGGAAGAGTGGGAAGTCATCAGAAAGTCCATTCCAAAGA 1195Acc718 TAATTGATGACGTTTGGCGCTGGGAAGAGTGGGAAGTCATCAGAAAGTCCATTCCAAAGA 1195Acc724 TAATTGATGACGTTTGGCGCTGGGAAGAGTGGGAAGTCATCAGAAAGTCCATTCCAAAGA 1195Acc715 TAATTGATGACGTTTGGCGCTGGGAAGAGTGGGAAGTCATCAGAAAGTCCATTCCAAAGA 1195Acc706 TAATTGATGACGTTTGGCGCTGGGAAGAGTGGGAAGTCATCAGAAAGTCCATTCCAAAGA 1195Acc624 TAATTGATGACGTTTGGCGCTGGGAAGAGTGGGAAGTCATCAGAAAGTCCATTCCAAAGA 1195Acc440 TAATTGATGACGTTTGGCGCTGGGAAGAGTGGGAAGTCATCAGAAAGTCCATTCCAAAGA 1210Acc868 TAATTGATGACGTTTGGCGCTGGGAAGAGTGGGAAGTCATCAGAAAGTCCATTCCAAAGA 1210Acc220 TAATTGATGACGTTTGGCACTGGGAAGAGTGGGAAGTCATCAGAAAGTCCATTCCAAAGA 1195Nipponbare TAATTGATGACGTTTGGCACTGGGAAGAGTGGGAAGTCATCAGAAAGTCCATTCCAAAGA 1195AccUP3 TAATTGATGACGTTTGGCACTGGGAAGAGTGGGAAGTCATCAGAAAGTCCATTCCAAAGA 1195AccUP1 TAATTGATGACGTTTGGCACTGGGAAGAGTGGGAAGTCATCAGAAAGTCCATTCCAAAGA 1195Acc224 TAATTGATGACGTTTGGCACTGGGAAGAGTGGGAAGTCATCAGAAAGTCCATTCCAAAGA 1195 **** ******.******. ********.**************************.****

Ashikawa et al. Supplementary Fig. S1 (11/30)

Acc414 ATGATCTGGGTGGTAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGCC 1270Acc420 ATGATCTGGGTGGTAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGCC 1270Acc761 ATGATCTGGGTGGTAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGCC 1270K60_Pik-p ATGATCTGGGTGGTAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGCC 1264Acc130 ATGATCTGGGTGGTAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGCC 1264Acc108 ATGATCTGGGTGGTAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGCC 1264Acc719 ATGATCTGGGTGGTAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGCC 1264Acc729 ATGATCTGGGTGGTAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGCC 1264Acc709 ATGATCTGGGTGGTAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGCC 1264Acc710 ATGATCTGGGTGGTAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGCC 1264Acc504 ATGATCTGGGTGGTAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGCC 1264Acc848 ATGATCTGGGTGGTAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGCC 1264Acc563 ATGATCTGGGTGGTAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGCC 1264Acc757 ATGATCTGGGTGGTAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGCC 1264Tsuyuake_Pik-m ATGATCTGGGTGGTAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGCC 1264Kanto51_Pik ATGATCTGGGTGGTAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGCC 1264Kusabue_Pik ATGATCTGGGTGGTAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGCC 1264Acc201 ATGATCTGGGTAGCAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGTC 1255Acc206 ATGATCTGGGTAGCAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGTC 1255Acc1 ATGATCTGGGTAGCAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGTC 1255Acc101 ATGATCTGGGTAGCAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGTC 1255Acc718 ATGATCTGGGTAGCAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGTC 1255Acc724 ATGATCTGGGTAGCAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGTC 1255Acc715 ATGATCTGGGTAGCAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGTC 1255Acc706 ATGATCTGGGTAGCAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGTC 1255Acc624 ATGATCTGGGTAGCAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGTC 1255Acc440 ATGATCTGGGTAGCAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGTC 1270Acc868 ATGATCTGGGTAGCAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGTC 1270Acc220 ATGATCTGGGTAGCAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGTC 1255Nipponbare ATGATCTGGGTAGCAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGTC 1255AccUP3 ATGATCTGGGTAGCAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGTC 1255AccUP1 ATGATCTGGGTAGCAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGTC 1255Acc224 ATGATCTGGGTAGCAGAATAATCATGACTACTCGTCTTAATTCAATAGCTGAGAAGTGTC 1255 ***********.* ******************************************** * Acc414 ACACTGATGACAATGATGTTTTTGTCTACGAAGTTGGGGATCTAGATAATAATGATGCTT 1330Acc420 ACACTGATGACAATGATGTTTTTGTCTACGAAGTTGGGGATCTAGATAATAATGATGCTT 1330Acc761 ACACTGATGACAATGATGTTTTTGTCTACGAAGTTGGGGATCTAGATAATAATGATGCTT 1330K60_Pik-p ACACTGATGACAATGATGTTTTTGTCTACGAAGTTGGGGATCTAGATAATAATGATGCTT 1324Acc130 ACACTGATGACAATGATGTTTTTGTCTACGAAGTTGGGGATCTAGATAATAATGATGCTT 1324Acc108 ACACTGATGACAATGATGTTTTTGTCTACGAAGTTGGGGATCTAGATAATAATGATGCTT 1324Acc719 ACACTGATGACAATGATGTTTTTGTCTACGAAGTTGGGGATCTAGATAATAATGATGCTT 1324Acc729 ACACTGATGACAATGATGTTTTTGTCTACGAAGTTGGGGATCTAGATAATAATGATGCTT 1324Acc709 ACACTGATGACAATGATGTTTTTGTCTACGAAGTTGGGGATCTAGATAATAATGATGCTT 1324Acc710 ACACTGATGACAATGATGTTTTTGTCTACGAAGTTGGGGATCTAGATAATAATGATGCTT 1324Acc504 ACACTGATGACAATGATGTTTTTGTCTACGAAGTTGGGGATCTAGATAATAATGATGCTT 1324Acc848 ACACTGATGACAATGATGTTTTTGTCTACGAAGTTGGGGATCTAGATAATAATGATGCTT 1324Acc563 ACACTGATGACAATGATGTTTTTGTCTACGAAGTTGGGGATCTAGATAATAATGATGCTT 1324Acc757 ACACTGATGACAATGATGTTTTTGTCTACGAAGTTGGGGATCTAGATAATAATGATGCTT 1324Tsuyuake_Pik-m ACACTGATGACAATGATGTTTTTGTCTACGAAGTTGGGGATCTAGATAATAATGATGCTT 1324Kanto51_Pik ACACTGATGACAATGATGTTTTTGTCTACGAAGTTGGGGATCTAGATAATAATGATGCTT 1324Kusabue_Pik ACACTGATGACAATGATGTTTTTGTCTACGAAGTTGGGGATCTAGATAATAATGATGCTT 1324Acc201 GCAATGATGACATGGATGCGTTTGTTTATGAAACTGAGGCTCTGGATTATGTGGATGCTT 1315Acc206 GCAATGATGACATGGATGCGTTTGTTTATGAAACTGAGGCTCTGGATTATGTGGATGCTT 1315Acc1 GCAATGATGACATGGATGCGTTTGTTTATGAAACTGAGGCTCTGGATTATGTGGATGCTT 1315Acc101 GCAATGATGACATGGATGCGTTTGTTTATGAAACTGAGGCTCTGGATTATGTGGATGCTT 1315Acc718 GCAATGATGACATGGATGCGTTTGTTTATGAAACTGAGGCTCTGGATTATGTGGATGCTT 1315Acc724 GCAATGATGACATGGATGCGTTTGTTTATGAAACTGAGGCTCTGGATTATGTGGATGCTT 1315Acc715 GCAATGATGACATGGATGCGTTTGTTTATGAAACTGAGGCTCTGGATTATGTGGATGCTT 1315Acc706 GCAATGATGACATGGATGCGTTTGTTTATGAAACTGAGGCTCTGGATTATGTGGATGCTT 1315Acc624 GCAATGATGACATGGATGCGTTTGTTTATGAAACTGAGGCTCTGGATTATGTGGATGCTT 1315Acc440 GCAATGATGACATGGATGCGTTTGTTTATGAAACTGAGGCTCTGGATTATGTGGATGCTT 1330Acc868 GCAATGATGACATGGATGCGTTTGTTTATGAAACTGAGGCTCTGGATTATGTGGATGCTT 1330Acc220 GCAATGATGACATGGATGCGTTTGTTTATGAAACTGAGGCTCTGGATTATGTGGATGCTT 1315Nipponbare GCAATGATGACATGGATGCGTTTGTTTATGAAACTGAGGCTCTGGATTATGTGGATGCTT 1315AccUP3 GCAATGATGACATGGATGCGTTTGTTTATGAAACTGAGGCTCTGGATTATGTGGATGCTT 1315AccUP1 GCAATGATGACATGGATGCGTTTGTTTATGAAACTGAGGCTCTGGATTATGTGGATGCTT 1315Acc224 GCAATGATGACATGGATGCGTTTGTTTATGAAACTGAGGCTCTGGATTATGTGGATGCTT 1315 .**.********: **** ***** ** ***. **.**.***.***:**.: ******* 

Ashikawa et al. Supplementary Fig. S1 (12/30)

Acc414 TGTCGTTGTCTTGGGGGATAGCAACAAAGTCTGGGGCAGGCAACAGGATCGGAACTGGAG 1390Acc420 TGTCGTTGTCTTGGGGGATAGCAACAAAGTCTGGGGCAGGCAACAGGATCGGAACTGGAG 1390Acc761 TGTCGTTGTCTTGGGGGATAGCAACAAAGTCTGGGGCAGGCAACAGGATCGGAACTGGAG 1390K60_Pik-p TGTCGTTGTCTTGGGGGATAGCAACAAAGTCTGGGGCAGGCAACAGGATCGGAACTGGAG 1384Acc130 TGTCGTTGTCTTGGGGGATAGCAACAAAGTCTGGGGCAGGCAACAGGATCGGAACTGGAG 1384Acc108 TGTCGTTGTCTTGGGGGATAGCAACAAAGTCTGGGGCAGGCAACAGGATCGGAACTGGAG 1384Acc719 TGTCGTTGTCTTGGGGGATAGCAACAAAGTCTGGGGCAGGCAACAGGATCGGAACTGGAG 1384Acc729 TGTCGTTGTCTTGGGGGATAGCAACAAAGTCTGGGGCAGGCAACAGGATCGGAACTGGAG 1384Acc709 TGTCGTTGTCTTGGGGGATAGCAACAAAGTCTGGGGCAGGCAACAGGATCGGAACTGGAG 1384Acc710 TGTCGTTGTCTTGGGGGATAGCAACAAAGTCTGGGGCAGGCAACAGGATCGGAACTGGAG 1384Acc504 GGTCGTTGTCTTGGGGGATAGCAACAAAGTCTGGGGCAGGCAACAGGATCGGAACTGGAG 1384Acc848 GGTCGTTGTCTTGGGGGATAGCAACAAAGTCTGGGGCAGGCAACAGGATCGGAACTGGAG 1384Acc563 GGTCGTTGTCTTGGGGGATAGCAACAAAGTCTGGGGCAGGCAACAGGATCGGAACTGGAG 1384Acc757 GGTCGTTGTCTTGGGGGATAGCAACAAAGTCTGGGGCAGGCAACAGGATCGGAACTGGAG 1384Tsuyuake_Pik-m GGTCGTTGTCTTGGGGGATAGCAACAAAGTCTGGGGCAGGCAACAGGATCGGAACTGGAG 1384Kanto51_Pik TGTCGTTGTCTTGGGGGATAGCAACAAAGTCTGGGGCAGGCAACAGGATCGGAACTGGAG 1384Kusabue_Pik TGTCGTTGTCTTGGGGGATAGCAACAAAGTCTGGGGCAGGCAACAGGATCGGAACTGGAG 1384Acc201 GGTTGTTGTGTGACAAGGTAGCAAGAAAGTCTGTCACATGTATGAACAT----------- 1364Acc206 GGTTGTTGTGTGACAAGGTAGCAAGAAAGTCTGTCACATGTATGAACAT----------- 1364Acc1 GGTTGTTGTGTGACAAGGTAGCAAGAAAGTCTGTCACATGTATGAACAT----------- 1364Acc101 GGCTGTTGTGTGACAAGGTAGCAAGAAAGTCTGTCACATGTATGAACAT----------- 1364Acc718 GGCTGTTGTGTGACAAGGTAGCAAGAAAGTCTGTCACATGTATGAACAT----------- 1364Acc724 GGTTGTTGTGTGACAAGGTAGCAAGAAAGTCTGTCACATGTATGAACAT----------- 1364Acc715 GGTTGTTGTGTGACAAGGTAGCAAGAAAGTCTGTCACATGTATGAACAT----------- 1364Acc706 GGTTGTTGTGTGACAAGGTAGCAAGAAAGTCTGTCACATGTATGAACAT----------- 1364Acc624 GGTTGTTGTGTGACAAGGTAGCAAGAAAGTCTGTCACATGTATGAACAT----------- 1364Acc440 GGTTGTTGTGTGACAAGGTAGCAAGAAAGTCTGTCACATGTATGAACAT----------- 1379Acc868 GGTTGTTGTGTGACAAGGTAGCAAGAAAGTCTGTCACATGTATGAACAT----------- 1379Acc220 GGTTGTTGTGTGACAAGGTAGCAAGAAAGTCTGTCACATGTATGAACAT----------- 1364Nipponbare GGTTGTTGTGTGACAAGGTAGCAAGAAAGTCTGTCACATGTATGAACAT----------- 1364AccUP3 GGTTGTTGTGTGACAAGGTAGCAAGAAAGTCTGTCACATGTATGAACAT----------- 1364AccUP1 GGTTGTTGTGTGACAAGGTAGCAAGAAAGTCTGTCACATGTATGAACAT----------- 1364Acc224 GGTTGTTGTGTGACAAGGTAGCAAGAAAGTCTGTCACATGTATGAACAT----------- 1364 * ***** * . ..*.****** ******** .** * *: *. **  Acc414 AGGATAATCCATGCTATGATATTGTGAACATGTGTTATGGTATGCCTTTAGCACTTATTT 1450Acc420 AGGATAATCCATGCTATGATATTGTGAACATGTGTTATGGTATGCCTTTAGCACTTATTT 1450Acc761 AGGATAATCCATGCTATGATATTGTGAACATGTGTTATGGTATGCCTTTAGCACTTATTT 1450K60_Pik-p AGGATAATCCATGCTATGATATTGTGAACATGTGTTATGGTATGCCTTTAGCACTTATTT 1444Acc130 AGGATAATCCATGCTATGATATTGTGAACATGTGTTATGGTATGCCTTTAGCACTTATTT 1444Acc108 AGGATAATCCATGCTATGATATTGTGAACATGTGTTATGGTATGCCTTTAGCACTTATTT 1444Acc719 AGGATAATCCATGCTATGATATTGTGAACATGTGTTATGGTATGCCTTTAGCACTTATTT 1444Acc729 AGGATAATCCATGCTATGATATTGTGAACATGTGTTATGGTATGCCTTTAGCACTTATTT 1444Acc709 AGGATAATCCATGCTATGATATTGTGAACATGTGTTATGGTATGCCTTTAGCACTTATTT 1444Acc710 AGGATAATCCATGCTATGATATTGTGAACATGTGTTATGGTATGCCTTTAGCACTTATTT 1444Acc504 AGGATAATTCATGCTATGATATTGTGAACATGTGTTATGGTATGCCTTTAGCACTTATTT 1444Acc848 AGGATAATTCATGCTATGATATTGTGAACATGTGTTATGGTATGCCTTTAGCACTTATTT 1444Acc563 AGGATAATTCATGCTATGATATTGTGAACATGTGTTATGGTATGCCTTTAGCACTTATTT 1444Acc757 AGGATAATTCATGCTATGATATTGTGAACATGTGTTATGGTATGCCTTTAGCACTTATTT 1444Tsuyuake_Pik-m AGGATAATTCATGCTATGATATTGTGAACATGTGTTATGGTATGCCTTTAGCACTTATTT 1444Kanto51_Pik AGGATAATCCATGCTATGATATTGTGAACATGTGTTATGGTATGCCTTTAGCACTTATTT 1444Kusabue_Pik AGGATAATTCATGCTATGATATTGTGAACATGTGTTATGGTATGCCTTTAGCACTTATTT 1444Acc201 ----TAATCCATGCTATGATATCGTGGACATGTGCTATGGTATGCCGTTAGCACTAATTC 1420Acc206 ----TAATCCATGCTATGATATCGTGGACATGTGCTATGGTATGCCGTTAGCACTAATTC 1420Acc1 ----TAATCCATGCTATGATATCGTGGACATGTGCTATGGTATGCCGTTAGCACTAATTC 1420Acc101 ----TAATCCATGCTATGATATCGTGGACGTGTGCTATGGTATGCCGTTAGCACTAATTC 1420Acc718 ----TAATCCATGCTATGATATCGTGGACGTGTGCTATGGTATGCCGTTAGCACTAATTC 1420Acc724 ----TAATCCATGCTATGATATCGTGGACATGTGCTATGGTATGCCGTTAGCACTAATTC 1420Acc715 ----TAATCCATGCTATGATATCGTGGACATGTGCTATGGTATGCCGTTAGCACTAATTC 1420Acc706 ----TAATCCATGCTATGATATCGTGGACATGTGCTATGGTATGCCGTTAGCACTAATTC 1420Acc624 ----TAATCCATGCTATGATATCGTGGACATGTGCTATGGTATGCCGTTAGCACTAATTC 1420Acc440 ----TAATCCATGCTATGATATCGTGGACATGTGCTATGGTATGCCGTTAGCACTAATTC 1435Acc868 ----TAATCCATGCTATGATATCGTGGACATGTGCTATGGTATGCCGTTAGCACTAATTC 1435Acc220 ----TAATCCATGCTATGATATCGTGGACATGTGCTATGGTATGCCGTTAGCACTAATTC 1420Nipponbare ----TAATCCATGCTATGATATCGTGGACATGTGCTATGGTATGCCGTTAGCACTAATTC 1420AccUP3 ----TAATCCATGCTATGATATCGTGGACATGTGCTATGGTATGCCGTTAGCACTAATTC 1420AccUP1 ----TAATCCATGCTATGATATCGTGGACATGTGCTATGGTATGCCGTTAGCACTAATTC 1420Acc224 ----TAATCCATGCTATGATATCGTGGACATGTGCTATGGTATGCCGTTAGCACTAATTC 1420 **** ************* ***.**.**** *********** ********:***  

Ashikawa et al. Supplementary Fig. S1 (13/30)

Acc414 GGCTGTCGTCAGCATTGGTTGGAGAGATAGAAGAATTAGGTGGTGCTGAAGTGAAAAAAT 1510Acc420 GGCTGTCGTCAGCATTGGTTGGAGAGATAGAAGAATTAGGTGGTGCTGAAGTGAAAAAAT 1510Acc761 GGCTGTCGTCAGCATTGGTTGGAGAGATAGAAGAATTAGGTGGTGCTGAAGTGAAAAAAT 1510K60_Pik-p GGCTGTCGTCAGCATTGGTTGGAGAGATAGAAGAATTAGGTGGTGCTGAAGTGAAAAAAT 1504Acc130 GGCTGTCGTCAGCATTGGTTGGAGAGATAGAAGAATTAGGTGGTGCTGAAGTGAAAAAAT 1504Acc108 GGCTGTCGTCAGCATTGGTTGGAGAGATAGAAGAATTAGGTGGTGCTGAAGTGAAAAAAT 1504Acc719 GGCTGTCGTCAGCATTGGTTGGAGAGATAGAAGAATTAGGTGGTGCTGAAGTGAAAAAAT 1504Acc729 GGCTGTCGTCAGCATTGGTTGGAGAGATAGAAGAATTAGGTGGTGCTGAAGTGAAAAAAT 1504Acc709 GGCTGTCGTCAGCATTGGTTGGAGAGATAGAAGAATTAGGTGGTGCTGAAGTGAAAAAAT 1504Acc710 GGCTGTCGTCAGCATTGGTTGGAGAGATAGAAGAATTAGGTGGTGCTGAAGTGAAAAAAT 1504Acc504 GGCTGTCGTCAGCATTGGTTGGAGAGATAGAAGAATTAGGTGGTGCTGAAGTGAAAAAAT 1504Acc848 GGCTGTCGTCAGCACTGGTTGGAGAGATAGAAGAATTAGGTGGTGCTGAAGTGAAAAAAT 1504Acc563 GGCTGTCGTCAGCATTGGTTGGAGAGATAGAAGAATTAGGTGGTGCTGAAGTGAAAAAAT 1504Acc757 GGCTGTCGTCAGCATTGGTTGGAGAGATAGAAGAATTAGGTGGTGCTGAAGTGAAAAAAT 1504Tsuyuake_Pik-m GGCTGTCGTCAGCATTGGTTGGAGAGATAGAAGAATTAGGTGGTGCTGAAGTGAAAAAAT 1504Kanto51_Pik GGCTGTCGTCAGCATTGGTTGGAGAGATAGAAGAATTACGTGGTGCTGAAGTGAAAAAAT 1504Kusabue_Pik GGCTGTCGTCAGCATTGGTTGGAGAGATAGAAGAATTAGGTGGTGCTGAAGTGAAAAAAT 1504Acc201 GTGTGTCGTCAGCATTGGCAGAAGAGATACAAGCTTTAGACAGTGATGAACGGCAAATAT 1480Acc206 GTGTGTCGTCAGCATTGGCAGAAGAGATACAAGCTTTAGACAGTGATGAACGGCAAATAT 1480Acc1 GTGTGTCGTCAGCATTGGCAGAAGAGATACAAGCTTTAGACAGTGATGAACGGCAAATAT 1480Acc101 GTGTGTCGTCAGCATTGGCAGAAGAGATACAAGCTTTAGACAGTGATGAACGGCAAATAT 1480Acc718 GTGTGTCGTCAGCATTGGCAGAAGAGATACAAGCTTTAGACAGTGATGAACGGCAAATAT 1480Acc724 GTGTGTCGTCAGCATTGGCAGAAGAGATACAAGCTTTAGACAGTGATGAACGGCAAATAT 1480Acc715 GTGTGTCGTCAGCATTGGCAGAAGAGATACAAGCTTTAGACAGTGATGAACGGCAAATAT 1480Acc706 GTGTGTCGTCAGCATTGGCAGAAGAGATACAAGCTTTAGACAGTGATGAACGGCAAATAT 1480Acc624 GTGTGTCGTCAGCATTGGCAGAAGAGATACAAGCTTTAGACAGTGATGAACGGCAAATAT 1480Acc440 GTGTGTCGTCAGCATTGGCAGAAGAGATACAAGCTTTAGACAGTGATGAACGGCAAATAT 1495Acc868 GTGTGTCGTCAGCATTGGCAGAAGAGATACAAGCTTTAGACAGTGATGAACGGCAAATAT 1495Acc220 GTGTGTCGTCAGCATTGGCAGAAGAGATACAAGCTTTAGACAGTGATGAACGGCAAATAT 1480Nipponbare GTGTGTCGTCAGCATTGGCAGAAGAGATACAAGCTTTAGACAGTGATGAACGGCAAATAT 1480AccUP3 GTGTGTCGTCAGCATTGGCAGAAGAGATACAAGCTTTAGACAGTGATGAACGGCAAATAT 1480AccUP1 GTGTGTCGTCAGCATTGGCAGAAGAGATACAAGCTTTAGACAGTGATGAACGGCAAATAT 1480Acc224 GTGTGTCGTCAGCATTGGCAGAAGAGATACAAGCTTTAGACAGTGATGAACGGCAAATAT 1480 * *********** *** :*.******* ***.:*** . .***.**** *.***:** Acc414 GTAGGGATTTGAGACACATAGAGGATGGTATTTTGGACATCCCATCCTTACAACCATTGG 1570Acc420 GTAGGGATTTGAGACACATAGAGGATGGTATTTTGGACATCCCATCCTTACAACCATTGG 1570Acc761 GTAGGGATTTGAGACACATAGAGGATGGTATTTTGGACATCCCATCCTTACAACCATTGG 1570K60_Pik-p GTAGGGATTTGAGACACATAGAGGATGGTATTTTGGACATCCCATCCTTACAACCATTGG 1564Acc130 GTAGGGATTTGAGACACATAGAGGATGGTATTTTGGACATCCCATCCTTACAACCATTGG 1564Acc108 GTAGGGATTTGAGACACATAGAGGATGGTATTTTGGACATCCCATCCTTACAACCATTGG 1564Acc719 GTAGGGATTTGAGACACATAGAGGATGGTATTTTGGACATCCCATCCTTACAACCATTGG 1564Acc729 GTAGGGATTTGAGACACATAGAGGATGGTATTTTGGACATCCCATCCTTACAACCATTGG 1564Acc709 GTAGGGATTTGAGACACATAGAGGATGGTATTTTGGACATCCCATCCTTACAACCATTGG 1564Acc710 GTAGGGATTTGAGACACATAGAGGATGGTATTTTGGACATCCCATCCTTACAACCATTGG 1564Acc504 GTAGGGATTTGAGACACATAGAGGATGGTATTTTGGACATCCCATCCTTACAACCATTGG 1564Acc848 GTAGGGATTTGAGACACATAGAGGATGGTATTTTGGACATCCCATCCTTACAACCATTGG 1564Acc563 GTAGGGATTTGAGACACATAGAGGATGGTATTTTGGACATCCCATCCTTACAACCATTGG 1564Acc757 GTAGGGATTTGAGACACATAGAGGATGGTATTTTGGACATCCCATCCTTACAACCATTGG 1564Tsuyuake_Pik-m GTAGGGATTTGAGACACATAGAGGATGGTATTTTGGACATCCCATCCTTACAACCATTGG 1564Kanto51_Pik GTAGGGATTTGAGACACATAGAGGATGGTATTTTGGACATCCCATCCTTACAACCATTGG 1564Kusabue_Pik GTAGGGATTTGAGACACATAGAGGATGGTATTTTGGACATCCCATCCTTACAACCATTGG 1564Acc201 GGAGGGCTCTGAGACGGGTAGAGGATGGTATTTTGGACATCCCATCCTTGAAGCCATTGG 1540Acc206 GGAGGGCTCTGAGACGGGTAGAGGATGGTATTTTGGACATCCCATCCTTGAAGCCATTGG 1540Acc1 GGAGGGCTCTGAGACGGGTAGAGGATGGTATTTTGGACATCCCATCCTTGAAGCCATTGG 1540Acc101 GGAGGGCTCTGAGACGGGTAGAGGATGGTATTTTGGACATCCCATCCTTGAAGCCATTGG 1540Acc718 GGAGGGCTCTGAGACGGGTAGAGGATGGTATTTTGGACATCCCATCCTTGAAGCCATTGG 1540Acc724 GGAGGGCTCTGAGACGGGTAGAGGATGGTATTTTGGACATCCCATCCTTGAAGCCATTGG 1540Acc715 GGAGGGCTCTGAGACGGGTAGAGGATGGTATTTTGGACATCCCATCCTTGAAGCCATTGG 1540Acc706 GGAGGGCTCTGAGACGGGTAGAGGATGGTATTTTGGACATCCCATCCTTGAAGCCATTGG 1540Acc624 GGAGGGCTCTGAGACGGGTAGAGGATGGTATTTTGGACATCCCATCCTTGAAGCCATTGG 1540Acc440 GGAGGGCTCTGAGACGGGTAGAGGATGGTATTTTGGACATCCCATCCTTGCAGCCATTGG 1555Acc868 GGAGGGCTCTGAGACGGGTAGAGGATGGTATTTTGGACATCCCATCCTTGAAGCCATTGG 1555Acc220 GGAGGGCTCTGAGACGGGTAGAGGATGGTATTTTGGACATCCCATCCTTGAAGCCATTGG 1540Nipponbare GGAGGGCTCTGAGACGGGTAGAGGATGGTATTTTGGACATCCCATCCTTGAAGCCATTGG 1540AccUP3 GGAGGGCTCTGAGACGGGTAGAGGATGGTATTTTGGACATCCCATCCTTGAAGCCATTGG 1540AccUP1 GGAGGGCTCTGAGACGGGTAGAGGATGGTATTTTGGACATCCCATCCTTGAAGCCATTGG 1540Acc224 GGAGGGCTCTGAGACGGGTAGAGGATGGTATTTTGGACATCCCATCCTTGAAGCCATTGG 1540 * ****.* ******. .*******************************..*.*******

Ashikawa et al. Supplementary Fig. S1 (14/30)

Acc414 CGGAGAGTTTATGCCTTGGTTATAACCATCTTCCTCTTTATCTGAGGACTTTGTTGTTGT 1630Acc420 CGGAGAGTTTATGCCTTGGTTATAACCATCTTCCTCTTTATCTGAGGACTTTGTTGTTGT 1630Acc761 CGGAGAGTTTATGCCTTGGTTATAACCATCTTCCTCTTTATCTGAGGACTTTGTTGTTGT 1630K60_Pik-p CGGAGAGTTTATGCCTTGGTTATAACCATCTTCCTCTTTATCTGAGGACTTTGTTGTTGT 1624Acc130 CGGAGAGTTTATGCCTTGGTTATAACCATCTTCCTCTTTATCTGAGGACTTTGTTGTTGT 1624Acc108 CGGAGAGTTTATGCCTTGGTTATAACCATCTTCCTCTTTATCTGAGGACTTTGTTGTTGT 1624Acc719 CGGAGAGTTTATGCCTTGGTTATAACCATCTTCCTCTTTATCTGAGGACTTTGTTGTTGT 1624Acc729 CGGAGAGTTTATGCCTTGGTTATAACCATCTTCCTCTTTATCTGAGGACTTTGTTGTTGT 1624Acc709 CGGAGAGTTTATGCCTTGGTTATAACCATCTTCCTCTTTATCTGAGGACTTTGTTGTTGT 1624Acc710 CGGAGAGTTTATGCCTTGGTTATAACCATCTTCCTCTTTATCTGAGGACTTTGTTGTTGT 1624Acc504 CGGAGAGTTTATGCCTTGGTTATAACCATCTTCCTCTTTATCTGAGGACTTTGTTGTTGT 1624Acc848 CGGAGAGTTTATGCCTTGGTTATAACCATCTTCCTCTTTATCTGAGGACTTTGTTGTTGT 1624Acc563 CGGAGAGTTTATGCCTTGGTTATAACCATCTTCCTCTTTATCTGAGGACTTTGTTGTTGT 1624Acc757 CGGAGAGTTTATGCCTTGGTTATAACCATCTTCCTCTTTATCTGAGGACTTTGTTGTTGT 1624Tsuyuake_Pik-m CGGAGAGTTTATGCCTTGGTTATAACCATCTTCCTCTTTATCTGAGGACTTTGTTGTTGT 1624Kanto51_Pik CGGAGAGTTTATGCCTTGGTTATAACCATCTTCCTCTTTATCTGAGGACTTTGTTGTTGT 1624Kusabue_Pik CGGAGAGTTTATGCCTTGGTTATAACCATCTTCCTCTTTATCTGAGGACTTTGTTGTTGT 1624Acc201 CAGAGAGTTTATGCCTTGGTTACGACCATCTTCCTCTCTATCTGAGGACTTTGTTGTTAT 1600Acc206 CAGAGAGTTTATGCCTTGGTTACGACCATCTTCCTCTCTATCTGAGGACTTTGTTGTTAT 1600Acc1 CAGAGAGTTTATGCCTTGGTTACGACCATCTTCCTCTCTATCTGAGGACTTTGTTGTTAT 1600Acc101 CAGAGAGTTTATGCCTTGGTTACGACCATCTTCCTCTCTATCTGAGGACTTTGTTGTTAT 1600Acc718 CAGAGAGTTTATGCCTTGGTTACGACCATCTTCCTCTCTATCTGAGGACTTTGTTGTTAT 1600Acc724 CAGAGAGTTTATGCCTTGGTTACGACCATCTTCCTCTCTATCTGAGGACTTTGTTGTTAT 1600Acc715 CAGAGAGTTTATGCCTTGGTTACGACCATCTTCCTCTCTATCTGAGGACTTTGTTGTTAT 1600Acc706 CAGAGAGTTTATGCCTTGGTTACGACCATCTTCCTCTCTATCTGAGGACTTTGTTGTTAT 1600Acc624 CAGAGAGTTTATGCCTTGGTTACGACCATCTTCCTCTCTATCTGAGGACTTTGTTGTTAT 1600Acc440 CAGAGAGTTTATGCCTTGGTTACGACCATCTTCCTCTCTATCTGAGGACTTTGTTGTTAT 1615Acc868 CAGAGAGTTTATGCCTTGGTTACGACCATCTTCCTCTCTATCTGAGGACTTTGTTGTTAT 1615Acc220 CAGAGAGTTTATGCCTTGGTTACGACCATCTTCCTCTCTATCTGAGGACTTTGTTGTTAT 1600Nipponbare CAGAGAGTTTATGCCTTGGTTACGACCATCTTCCTCTCTATCTGAGGACTTTGTTGTTAT 1600AccUP3 CAGAGAGTTTATGCCTTGGTTACGACCATCTTCCTCTCTATCTGAGGACTTTGTTGTTAT 1600AccUP1 CAGAGAGTTTATGCCTTGGTTACGACCATCTTCCTCTCTATCTGAGGACTTTGTTGTTAT 1600Acc224 CAGAGAGTTTATGCCTTGGTTACGACCATCTTCCTCTCTATCTGAGGACTTTGTTGTTAT 1600 *.******************** .************* ********************.* Acc414 ACTGTAGTGCATACCATTGGTCTAACAG---AATCG---AAAGGGGTCGTCTGGTCAGGA 1684Acc420 ACTGTAGTGCATACCATTGGTCTAACAG---AATCG---AAAGGGGTCGTCTGGTCAGGA 1684Acc761 ACTGTAGTGCATACCATTGGTCTAACAG---AATCG---AAAGGGGTCGTCTGGTCAGGA 1684K60_Pik-p ACTGTAGTGCATACCATTGGTCTAACAG---AATCG---AAAGGGGTCGTCTGGTCAGGA 1678Acc130 ACTGTAGTGCATACCATTGGTCTAACAG---AATCG---AAAGGGGTCGTCTGGTCAGGA 1678Acc108 ACTGTAGTGCATACCATTGGTCTAACAG---AATCG---AAAGGGGTCGTCTGGTCAGGA 1678Acc719 ACTGTAGTGCATACCATTGGTCTAACAG---AATCG---AAAGGGGTCGTCTGGTCAGGA 1678Acc729 ACTGTAGTGCATACCATTGGTCTAACAG---AATCG---AAAGGGGTCGTCTGGTCAGGA 1678Acc709 ACTGTAGTGCATACCATTGGTCTAACAG---AATCG---AAAGGGGTCGTCTGGTCAGGA 1678Acc710 ACTGTAGTGCATACCATTGGTCTAACAG---AATCG---AAAGGGGTCGTCTGGTCAGGA 1678Acc504 ACTGTAGTGCATACCATTGGTCTAACAG---AATCG---AAAGGGGTCGTCTGGTCAGGA 1678Acc848 ACTGTAGTGCATACCATTGGTCTAACAG---AATCG---AAAGGGGTCGTCTGGTCAGGA 1678Acc563 ACTGTAGTGCATACCATTGGTCTAACAG---AATCG---AAAGGGGTCGTCTGGTCAGGA 1678Acc757 ACTGTAGTGCATACCATTGGTCTAACAG---AATCG---AAAGGGGTCGTCTGGTCAGGA 1678Tsuyuake_Pik-m ACTGTAGTGCATACCATTGGTCTAACAG---AATCG---AAAGGGGTCGTCTGGTCAGGA 1678Kanto51_Pik ACTGTAGTGCATACCATTGGTCTAACAG---AATCG---AAAGGGGTCGTCTGGTCAGGA 1678Kusabue_Pik ACTGTAGTGCATACCATTGGTCTAACAG---AATCG---AAAGGGGTCGTCTGGTCAGGA 1678Acc201 GTTGTAGTGTGTACCATTGGCTTGATGGTGGGATTGTTCAAAGGGGCCGTTTGGTCACAA 1660Acc206 GTTGTAGTGTGTACCATTGGCTTGATGGTGGGATTGTTCAAAGGGGCCGTTTGGTCACAA 1660Acc1 GTTGTAGTGTGTACCATTGGCTTGATGGTGGGATTGTTCAAAGGGGCCGTTTGGTCACAA 1660Acc101 GTTGTAGTGTGTACCATTGGCTTGATGGTGGGATTGTTCAAAGGGGCCGTTTGGTCACAA 1660Acc718 GTTGTAGTGTGTACCATTGGCTTGATGGTGGGATTGTTCAAAGGGGCCGTTTGGTCACAA 1660Acc724 GTTGTAGTGTGTACCATTGGCTTGATGGTGGGATTGTTCAAAGGGGCCGTTTGGTCACAA 1660Acc715 GTTGTAGTGTGTACCATTGGCTTGATGGTGGGATTGTTCAAAGGGGCCGTTTGGTCACAA 1660Acc706 GTTGTAGTGTGTACCATTGGCTTGATGGTGGGATTGTTCAAAGGGGCCGTTTGGTCACAA 1660Acc624 GTTGTAGTGTGTACCATTGGCTTGATGGTGGGATTGTTCAAAGGGGCCGTTTGGTCACAA 1660Acc440 GTTGTAGTGTGTACCATTGGCTTGATGGTGGGATTGTTCAAAGGGGCCGTTTGGTCACAA 1675Acc868 GTTGTAGTGTGTACCATTGGCTTGATGGTGGGATTGTTCAAAGGGGCCGTTTGGTCACAA 1675Acc220 GTTGTAGTGTGTACCATTGGCTTGATGGTGGGATTGTTCAAAGGGGCCGTTTGGTCACAA 1660Nipponbare GTTGTAGTGTGTACCATTGGCTTGATGGTGGGATTGTTCAAAGGGGCCGTTTGGTCACAA 1660AccUP3 GTTGTAGTGTGTACCATTGGCTTGATGGTGGGATTGTTCAAAGGGGCCGTTTGGTCACAA 1660AccUP1 GTTGTAGTGTGTACCATTGGCTTGATGGTGGGATTGTTCAAAGGGGCCGTTTGGTCACAA 1660Acc224 GTTGTAGTGTGTACCATTGGCTTGATGGTGGGATTGTTCAAAGGGGCCGTTTGGTCACAA 1660 . ******* .********* *.* .* .** * ******* *** ****** .* 

Ashikawa et al. Supplementary Fig. S1 (15/30)

Acc414 GGTGGATTGCGGAAGGATTTGTGTCGGAAGAGAAAGAAGCAGAAGGTTACTTTGGCGAGC 1744Acc420 GGTGGATTGCGGAAGGATTTGTGTCGGAAGAGAAAGAAGCAGAAGGTTACTTTGGCGAGC 1744Acc761 GGTGGATTGCGGAAGGATTTGTGTCGGAAGAGAAAGAAGCAGAAGGTTACTTTGGCGAGC 1744K60_Pik-p GGTGGATTGCGGAAGGATTTGTGTCGGAAGAGAAAGAAGCAGAAGGTTACTTTGGCGAGC 1738Acc130 GGTGGATTGCGGAAGGATTTGTGTCGGAAGAGAAAGAAGCAGAAGGTTACTTTGGCGAGC 1738Acc108 GGTGGATTGCGGAAGGATTTGTGTCGGAAGAGAAAGAAGCAGAAGGTTACTTTGGCGAGC 1738Acc719 GGTGGATTGCGGAAGGATTTGTGTCGGAAGAGAAAGAAGCAGAAGGTTACTTTGGCGAGC 1738Acc729 GGTGGATTGCGGAAGGATTTGTGTCGGAAGAGAAAGAAGCAGAAGGTTACTTTGGCGAGC 1738Acc709 GGTGGATTGCGGAAGGATTTGTGTCGGAAGAGAAAGAAGCAGAAGGTTACTTTGGCGAGC 1738Acc710 GGTGGATTGCGGAAGGATTTGTGTCGGAAGAGAAAGAAGCAGAAGGTTACTTTGGCGAGC 1738Acc504 GGTGGATTGCGGAAGGATTTGTGTCGGAAGAGAAAGAAGCAGAAGGTTACTTTGGCGAGC 1738Acc848 GGTGGATTGCGGAAGGATTTGTGTCGGAAGAGAAAGAAGCAGAAGGTTACTTTGGCGAGC 1738Acc563 GGTGGATTGCGGAAGGATTTGTGTCGGAAGAGAAAGAAGCAGAAGGTTACTTTGGCGAGC 1738Acc757 GGTGGATTGCGGAAGGATTTGTGTCGGAAGAGAAAGAAGCAGAAGGTTACTTTGGCGAGC 1738Tsuyuake_Pik-m GGTGGATTGCGGAAGGATTTGTGTCGGAAGAGAAAGAAGCAGAAGGTTACTTTGGCGAGC 1738Kanto51_Pik GGTGGATTGCGGAAGGATTTGTGTCGGAAGAGAAAGAAGCAGAAGGTTACTTTGGCGAGC 1738Kusabue_Pik GGTGGATTGCGGAAGGATTTGTGTCGGAAGAGAAAGAAGCAGAAGGTTACTTTGGCGAGC 1738Acc201 GGTGGATTGCTGAAGGATTTGTTTCAGAAGAGAAAGCAGCAGAAGGTTACTTTGATGAGC 1720Acc206 GGTGGATTGCTGAAGGATTTGTTTCAGAAGAGAAAGCAGCAGAAGGTTACTTTGATGAGC 1720Acc1 GGTGGATTGCTGAAGGATTTGTTTCAGAAGAGAAAGCAGCAGAAGGTTACTTTGATGAGC 1720Acc101 GGTGGATTGCTGAAGGATTTGTTTCAGAAGAGAAAGCAGCAGAAGGTTACTTTGATGAGC 1720Acc718 GGTGGATTGCTGAAGGATTTGTTTCAGAAGAGAAAGCAGCAGAAGGTTACTTTGATGAGC 1720Acc724 GGTGGATTGCTGAAGGATTTGTTTCAGAAGAGAAAGCAGCAGAAGGTTACTTTGATGAGC 1720Acc715 GGTGGATTGCTGAAGGATTTGTTTCAGAAGAGAAAGCAGCAGAAGGTTACTTTGATGAGC 1720Acc706 GGTGGATTGCTGAAGGATTTGTTTCAGAAGAGAAAGCAGCAGAAGGTTACTTTGATGAGC 1720Acc624 GGTGGATTGCTGAAGGATTTGTTTCAGAAGAGAAAGCAGCAGAAGGTTACTTTGATGAGC 1720Acc440 GGTGGATTGCTGAAGGATTTGTTTCAGAAGAGAAAGCAGCAGAAGGTTACTTTGATGAGC 1735Acc868 GGTGGATTGCTGAAGGATTTGTTTCAGAAGAGAAAGCAGCAGAAGGTTACTTTGATGAGC 1735Acc220 GGTGGATTGCTGAAGGATTTGTTTCAGAAGAGAAAGCAGCAGAAGGTTACTTTGATGAGC 1720Nipponbare GGTGGATTGCTGAAGGATTTGTTTCAGAAGAGAAAGCAGCAGAAGGTTACTTTGATGAGC 1720AccUP3 GGTGGATTGCTGAAGGATTTGTTTCAGAAGAGAAAGCAGCAGAAGGTTACTTTGATGAGC 1720AccUP1 GGTGGATTGCTGAAGGATTTGTTTCAGAAGAGAAAGCAGCAGAAGGTTACTTTGATGAGC 1720Acc224 GGTGGATTGCTGAAGGATTTGTTTCAGAAGAGAAAGCAGCAGAAGGTTACTTTGATGAGC 1720 ********** *********** **.**********.*****************. **** Acc414 TTATTGACAGAGGATGGATTACGCAGCACGGAGACAACAACAGTTATAATTACTATGAGA 1804Acc420 TTATTGACAGAGGATGGATTACGCAGCACGGAGACAACAACAGTTATAATTACTATGAGA 1804Acc761 TTATTGACAGAGGATGGATTACGCAGCACGGAGACAACAACAGTTATAATTACTATGAGA 1804K60_Pik-p TTATTAACAGAGGATGGATTACGCAGCACGGAGACAACAACAGTTATAATTACTATGAGA 1798Acc130 TTATTAACAGAGGATGGATTACGCAGCACGGAGACAACAACAGTTATAATTACTATGAGA 1798Acc108 TTATTAACAGAGGATGGATTACGCAGCACGGAGACAACAACAGTTATAATTACTATGAGA 1798Acc719 TTATTAACAGAGGATGGATTACGCAGCACGGAGACAACAACAGTTATAATTACTATGAGA 1798Acc729 TTATTAACAGAGGATGGATTACGCAGCACGGAGACAACAACAGTTATAATTACTATGAGA 1798Acc709 TTATTAACAGAGGATGGATTACGCAGCACGGAGACAACAACAGTTATAATTACTATGAGA 1798Acc710 TTATTAACAGAGGATGGATTACGCAGCACGGAGACAACAACAGTTATAATTACTATGAGA 1798Acc504 TTATTAACAGAGGATGGATTACGCAGCACGGAGACAACAACAGTTATAATTACTATGAGA 1798Acc848 TTATTAACAGAGGATGGATTACGCAGCACGGAGACAACAACAGTTATAATTACTATGAGA 1798Acc563 TTATTAACAGAGGATGGATTACGCAGCACGGAGACAACAACAGTTATAATTACTATGAGA 1798Acc757 TTATTAACAGAGGATGGATTACGCAGCACGGAGACAACAACAGTTATAATTACTATGAGA 1798Tsuyuake_Pik-m TTATTAACAGAGGATGGATTACGCAGCACGGAGACAACAACAGTTATAATTACTATGAGA 1798Kanto51_Pik TTATTAACAGAGGATGGATTACGCAGCACGGAGACAACAACAGTTATAATTACTATGAGA 1798Kusabue_Pik TTATTAACAGAGGATGGATTACGCAGCACGGAGACAACAACAGTTATAATTACTATGAGA 1798Acc201 TTGTCGGCAGAGGATGGATGA---AGCATAGAGG--------GTTG-AACGAGTATGAGA 1768Acc206 TTGTCGGCAGAGGATGGATGA---AGCATAGAGG--------GTTG-AACGAGTATGAGA 1768Acc1 TTGTCGGCAGAGGATGGATGA---AGCATAGAGA--------GTTG-AACGAGTATGAGA 1768Acc101 TTGTCGGCAGAGGATGGATTA---AGCATAGAGA--------GTGG-AACGAGTATGAGA 1768Acc718 TTGTCGGCAGAGGATGGATTA---AGCATAGAGA--------GTGG-AACGAGTATGAGA 1768Acc724 TTGTCGGCAGAGGATGGATGA---AGCATAGAGA--------GTTG-AACGAGTATGAGA 1768Acc715 TTGTCGGCAGAGGATGGATGA---AGCATAGAGA--------GTTG-AACGAGTATGAGA 1768Acc706 TTGTCGGCAGAGGATGGATGA---AGCATAGAGA--------GTTG-AACGAGTATGAGA 1768Acc624 TTGTCGGCAGAGGATGGATGA---AGCATAGAGA--------GTTG-AACGAGTATGAGA 1768Acc440 TTGTCGGCAGAGGATGGATGA---AGCATAGAGA--------GTTG-AACGAGTATGAGA 1783Acc868 TTGTCGGCAGAGGATGGATGA---AGCATAGAGA--------GTTG-AACGAGTATGAGA 1783Acc220 TTGTCGGCAGAGGATGGATGA---AGCATAGAGG--------GTTG-AACGAGTATGAGA 1768Nipponbare TTGTCGGCAGAGGATGGATGA---AGCATAGAGG--------GTTG-AACGAGTATGAGA 1768AccUP3 TTGTCGGCAGAGGATGGATGA---AGCATAGAGG--------GTTG-AACGAGTATGAGA 1768AccUP1 TTGTCGGCAGAGGATGGATGA---AGCATAGAGG--------GTTG-AACGAGTATGAGA 1768Acc224 TTGTCGGCAGAGGATGGATGA---AGCATAGAGG--------GTTG-AACGAGTATGAGA 1768 **.* ..************ * **** .***. ** . ** * *******

Ashikawa et al. Supplementary Fig. S1 (16/30)

Acc414 TCCACCCCGTGATGCTGGCCTTCCTGAGATGCAAGTCCAAGGAGTACAATTTTTTAACAT 1864Acc420 TCCACCCCGTGATGCTGGCCTTCCTGAGATGCAAGTCCAAGGAGTACAATTTTTTAACAT 1864Acc761 TCCACCCCGTGATGCTGGCCTTCCTGAGATGCAAGTCCAAGGAGTACAATTTTTTAACAT 1864K60_Pik-p TCCACCCCGTGATGCTGGCCTTCCTGAGATGCAAGTCCAAGGAGTACAATTTTTTAACAT 1858Acc130 TCCACCCCGTGATGCTGGCCTTCCTGAGATGCAAGTCCAAGGAGTACAATTTTTTAACAT 1858Acc108 TCCACCCCGTGATGCTGGCCTTCCTGAGATGCAAGTCCAAGGAGTACAATTTTTTAACAT 1858Acc719 TCCACCCCGTGATGCTGGCCTTCCTGAGATGCAAGTCCAAGGAGTACAATTTTTTAACAT 1858Acc729 TCCACCCCGTGATGCTGGCCTTCCTGAGATGCAAGTCCAAGGAGTACAATTTTTTAACAT 1858Acc709 TCCACCCCGTGATGCTGGCCTTCCTGAGATGCAAGTCCAAGGAGTACAATTTTTTAACAT 1858Acc710 TCCACCCCGTGATGCTGGCCTTCCTGAGATGCAAGTCCAAGGAGTACAATTTTTTAACAT 1858Acc504 TCCACCCCGTGATGCTGGCCTTCCTGAGATGCAAGTCCAAGGAGTACAATTTTTTAACAT 1858Acc848 TCCACCCCGTGATGCTGGCCTTCCTGAGATGCAAGTCCAAGGAGTACAATTTTTTAACAT 1858Acc563 TCCACCCCGTGATGCTGGCCTTCCTGAGATGCAAGTCCAAGGAGTACAATTTTTTAACAT 1858Acc757 TCCACCCCGTGATGCTGGCCTTCCTGAGATGCAAGTCCAAGGAGTACAATTTTTTAACAT 1858Tsuyuake_Pik-m TCCACCCCGTGATGCTGGCCTTCCTGAGATGCAAGTCCAAGGAGTACAATTTTTTAACAT 1858Kanto51_Pik TCCACCCCGTGATGCTGGCCTTCCTGAGATGCAAGTCCAAGGAGTACAATTTTTTAACAT 1858Kusabue_Pik TCCACCCCGTGATGCTGGCCTTCCTGAGATGCAAGTCCAAGGAGTACAATTTTTTAACAT 1858Acc201 TCCACCCTATGATGCTGGCCATCCTTAGATACAAATCGAAGGAGTACAATTTTGTAACTT 1828Acc206 TCCACCCTATGATGCTGGCCATCCTTAGATACAAATCGAAGGAGTACAATTTTGTAACTT 1828Acc1 TCCACCCTATGATGCTGGCCATCCTTAGATACAAGTCGAAGGAGTACAATTTTGTAACTT 1828Acc101 TCCACCCTATGATGCTGGCCATCCTTAGATACAAGTCGAAGGAGTACAATTTTGTAACTT 1828Acc718 TCCACCCTATGATGCTGGCCATCCTTAGATACAAGTCGAAGGAGTACAATTTTGTAACTT 1828Acc724 TCCACCCTATGATGCTGGCCATCCTTAGATACAAGTCGAAGGAGTACAATTTCGTAACTT 1828Acc715 TCCACCCTATGATGCTGGCCATCCTTAGATACAAGTCGAAGGAGTACAATTTCGTAACTT 1828Acc706 TCCACCCTATGATGCTGGCCATCCTTAGATACAAGTCGAAGGAGTACAATTTCGTAACTT 1828Acc624 TCCACCCTATGATGCTGGCCATCCTTAGATACAAGTCGAAGGAGTACAATTTCGTAACTT 1828Acc440 TCCACCCTATGATGCTGGCCATCCTTAGATACAAGTCGAAGGAGTACAATTTTGTAACTT 1843Acc868 TCCACCCTATGATGCTGGCCATCCTTAGATACAAGTCGAAGGAGTACAATTTTGTAACTT 1843Acc220 TCCACCCTATGATGCTGGCCATCCTTAGATACAAATCGAAGGAGTACAATTTTGTAACTT 1828Nipponbare TCCACCCTATGATGCTGGCCATCCTTAGATACAAATCGAAGGAGTACAATTTTGTAACTT 1828AccUP3 TCCACCCTATGATGCTGGCCATCCTTAGATACAAATCGAAGGAGTACAATTTTGTAACTT 1828AccUP1 TCCACCCTATGATGCTGGCCATCCTTAGATACAAATCGAAGGAGTACAATTTTGTAACTT 1828Acc224 TCCACCCTATGATGCTGGCCATCCTTAGATACAAATCGAAGGAGTACAATTTTGTAACTT 1828 ******* .***********:**** ****.***.** ************** ****:* Acc414 GCTTGGGTCTGGGATCTGATACTAGTACTAGTGCATC------------CTCCCCAAGGT 1912Acc420 GCTTGGGTCTGGGATCTGATACTAGTACTAGTGCATC------------CTCCCCAAGGT 1912Acc761 GCTTGGGTCTGGGATCTGATACTAGTACTAGTGCATC------------CTCCCCAAGGT 1912K60_Pik-p GCTTGGGTCTGGGATCTGATACTAGTACTAGTGCATC------------CTCCCCAAGGT 1906Acc130 GCTTGGGTCTGGGATCTGATACTAGTACTAGTGCATC------------CTCCCCAAGGT 1906Acc108 GCTTGGGTCTGGGATCTGATACTAGTACTAGTGCATC------------CTCCCCAAGGT 1906Acc719 GCTTGGGTCTGGGATCTGATACTAGTACTAGTGCATC------------CTCCCCAAGGT 1906Acc729 GCTTGGGTCTGGGATCTGATACTAGTACTAGTGCATC------------CTCCCCAAGGT 1906Acc709 GCTTGGGTCTGGGATCTGATACTAGTACTAGTGCATC------------CTCCCCAAGGT 1906Acc710 GCTTGGGTCTGGGATCTGATACTAGTACTAGTGCATC------------CTCCCCAAGGT 1906Acc504 GCTTGGGTCTGGGATCTGATACTAGTACTAGTGCATC------------CTCCCCAAGGT 1906Acc848 GCTTGGGTCTGGGATCTGATACTAGTACTAGTGCATC------------CTCCCCAAGGT 1906Acc563 GCTTGGGTCTGGGATCTGATACTAGTACTAGTGCATC------------CTCCCCAAGGT 1906Acc757 GCTTGGGTCTGGGATCTGATACTAGTACTAGTGCATC------------CTCCCCAAGGT 1906Tsuyuake_Pik-m GCTTGGGTCTGGGATCTGATACTAGTACTAGTGCATC------------CTCCCCAAGGT 1906Kanto51_Pik GCTTGGGTCTGGGATCTGATACTAGTACTAGTGCATC------------CTCCCCAAGGT 1906Kusabue_Pik GCTTGGGTCTGGGATCTGATACTAGTACTAGTGCATC------------CTCCCCAAGGT 1906Acc201 GTTTGGGTACGGGATCTGATACTTGTACTAGTGCATCTCTATCCTACTCCTCTCCAACAA 1888Acc206 GTTTGGGTACGGGATCTGATACTTGTACTAGTGCATCTCTATCCTACTCCTCTCCAACAA 1888Acc1 GTTTGGGTACGGGATCTGATACTTGTACTAGTGCATCTCTATCCTACTCCTCTCCAACAA 1888Acc101 GTTTGGGTACGGGATCTGATACTTGTACTAGTGCATCTCTATCCTACTCCTCTCCAACAA 1888Acc718 GTTTGGGTACGGGATCTGATACTTGTACTAGTGCATCTCTATCCTACTCCTCTCCAACAA 1888Acc724 GTTTGGGTACGGGATCTGATACTTGTACTAGTGCATCTCTATCCTACTCCTCTCCAACAA 1888Acc715 GTTTGGGTACGGGATCTGATACTTGTACTAGTGCATCTCTATCCTACTCCTCTCCAACAA 1888Acc706 GTTTGGGTACGGGATCTGATACTTGTACTAGTGCATCTCTATCCTACTCCTCTCCAACAA 1888Acc624 GTTTGGGTACGGGATCTGATACTTGTACTAGTGCATCTCTATCCTACTCCTCTCCAACAA 1888Acc440 GTTTGGGTACGGGATCTGATACTTGTACTAGTGCATCTCTATCCTACTCCTCTCCAACAA 1903Acc868 GTTTGGGTACGGGATCTGATACTTGTACTAGTGCATCTCTATCCTACTCCTCTCCAACAA 1903Acc220 GTTTGGGTACGGGATCTGATACTTGTACTAGTGCATCTCTATCCTACTCCTCTCCAACAA 1888Nipponbare GTTTGGGTACGGGATCTGATACTTGTACTAGTGCATCTCTATCCTACTCCTCTCCAACAA 1888AccUP3 GTTTGGGTACGGGATCTGATACTTGTACTAGTGCATCTCTATCCTACTCCTCTCCAACAA 1888AccUP1 GTTTGGGTACGGGATCTGATACTTGTACTAGTGCATCTCTATCCTACTCCTCTCCAACAA 1888Acc224 GTTTGGGTACGGGATCTGATACTTGTACTAGTGCATCTCTATCCTACTCCTCTCCAACAA 1888 * ******. *************:************* *** **** .:

Ashikawa et al. Supplementary Fig. S1 (17/30)

Acc414 TG---ATTCGCCGGCTGTCTCTTCAGGGGGGGTATCCAGTGGACTGCTTGTCAAGCATGA 1969Acc420 TG---ATTCGCCGGCTGTCTCTTCAGGGGGGGTATCCAGTGGACTGCTTGTCAAGCATGA 1969Acc761 TG---ATTCGCCGGCTGTCTCTTCAGGGGGGGTATCCAGTGGACTGCTTGTCAAGCATGA 1969K60_Pik-p TG---ATTCGCCGGCTGTCTCTTCAGGGGGGGTATCCAGTGGACTGCTTGTCAAGCATGA 1963Acc130 TG---ATTCGCCGGCTGTCTCTTCAGGGGGGGTATCCAGTGGACTGCTTGTCAAGCATGA 1963Acc108 TG---ATTCGCCGGCTGTCTCTTCAGGGGGGGTATCCAGTGGACTGCTTGTCAAGCATGA 1963Acc719 TG---ATTCGCCGGCTGTCTCTTCAGGGGGGGTATCCAGTGGACTGCTTGTCAAGCATGA 1963Acc729 TG---ATTCGCCGGCTGTCTCTTCAGGGGGGGTATCCAGTGGACTGCTTGTCAAGCATGA 1963Acc709 TG---ATTCGCCGGCTGTCTCTTCAGGGGGGGTATCCAGTGGACTGCTTGTCAAGCATGA 1963Acc710 TG---ATTCGCCGGCTGTCTCTTCAGGGGGGGTATCCAGTGGACTGCTTGTCAAGCATGA 1963Acc504 TG---ATTCGCCGGCTGTCTCTTCAGGGGGGGTATCCAGTGGACTGCTTGTCAAGCATGA 1963Acc848 TG---ATTCGCCGGCTGTCTCTTCAGGGGGGGTATCCAGTGGACTGCTTGTCAAGCATGA 1963Acc563 TG---ATTCGCCGGCTGTCTCTTCAGGGGGGGTATCCAGTGGACTGCTTGTCAAGCATGA 1963Acc757 TG---ATTCGCCGGCTGTCTCTTCAGGGGGGGTATCCAGTGGACTGCTTGTCAAGCATGA 1963Tsuyuake_Pik-m TG---ATTCGCCGGCTGTCTCTTCAGGGGGGGTATCCAGTGGACTGCTTGTCAAGCATGA 1963Kanto51_Pik TG---ATTCGCCGGCTGTCTCTTCAGGGGGGGTATCCAGTGGACTGCTTGTCAAGCATGA 1963Kusabue_Pik TG---ATTCGCCGGCTGTCTCTTCAGGGGGGGTATCCAGTGGACTGCTTGTCAAGCATGA 1963Acc201 TGGCGATTCGCCGGCTTTGTCTTCAAAGGGGGTACCCAATGAAATGCTTCTCAAG----- 1943Acc206 TGGCGATTCGCCGGCTTTGTCTTCAAAGGGGGTACCCAATGAAATGCTTCTCAAG----- 1943Acc1 TGGCGATTCGCCGGCTTTGTCTTCAAAGGGGGTACCCAATGAAATGCTTCTCAAG----- 1943Acc101 TGGCGATTCGCCGGCTTTGTCTTCAAAGGGGGTACCCAATGAAATGCTTCTCAAG----- 1943Acc718 TGGCGATTCGCCGGCTTTGTCTTCAAAGGGGGTACCCAATGAAATGCTTCTCAAG----- 1943Acc724 TGGCGATTCGCCGGCTTTGTCTTCAAAGGGGGTACCCAATGAAATGCTTCTCAAG----- 1943Acc715 TGGCGATTCGCCGGCTTTGTCTTCAAAGGGGGTACCCAATGAAATGCTTCTCAAG----- 1943Acc706 TGGCGATTCGCCGGCTTTGTCTTCAAAGGGGGTACCCAATGAAATGCTTCTCAAG----- 1943Acc624 TGGCGATTCGCCGGCTTTGTCTTCAAAGGGGGTACCCAATGAAATGCTTCTCAAG----- 1943Acc440 TGGCGATTCGCCGGCTTTGTCTTCAAAGGGGGTACCCAATGAAATGCTTCTCAAG----- 1958Acc868 TGGCGATTCGCCGGCTTTGTCTTCAAAGGGGGTACCCAATGAAATGCTTCTCAAG----- 1958Acc220 TGGCGATTCGCCGGCTTTGTCTTCAAAGGGGGTACCCAATGAAATGCTTCTCAAG----- 1943Nipponbare TGGCGATTCGCCGGCTTTGTCTTCAAAGGGGGTACCCAATGAAATGCTTCTCAAG----- 1943AccUP3 TGGCGATTCGCCGGCTTTGTCTTCAAAGGGGGTACCCAATGAAATGCTTCTCAAG----- 1943AccUP1 TGGCGATTCGCCGGCTTTGTCTTCAAAGGGGGTACCCAATGAAATGCTTCTCAAG----- 1943Acc224 TGGCGATTCGCCGGCTTTGTCTTCAAAGGGGGTACCCAATGAAATGCTTCTCAAG----- 1943 ** *********** * ******..******* ***.**.*.***** *****  Acc414 GTATGGATGTGTCACACACTTGCAGCCTTGTCGTCCTTGGTGACGTGGCGCGATCCAAGG 2029Acc420 GTATGGATGTGTCACACACTTGCAGCCTTGTCGTCCTTGGTGACGTGGCGCGATCCAAGG 2029Acc761 GTATGGATGTGTCACACACTTGCAGCCTTGTCGTCCTTGGTGACGTGGCGCGATCCAAGG 2029K60_Pik-p GTATGGATGTGTCACACACTTGCAGCCTTGTCGTCCTTGGTGACGTGGCGCGACCCAAGG 2023Acc130 GTATGGATGTGTCACACACTTGCAGCCTTGTCGTCCTTGGTGACGTGGCGCGACCCAAGG 2023Acc108 GTATGGATGTGTCACACACTTGCAGCCTTGTCGTCCTTGGTGACGTGGCGCGACCCAAGG 2023Acc719 GTATGGATGTGTCACACACTTGCAGCCTTGTCGTCCTTGGTGACGTGGCGCGACCCAAGG 2023Acc729 GTATGGATGTGTCACACACTTGCAGCCTTGTCGTCCTTGGTGACGTGGCGCGACCCAAGG 2023Acc709 GTATGGATGTGTCACACACTTGCAGCCTTGTCGTCCTTGGTGACGTGGCGCGACCCAAGG 2023Acc710 GTATGGATGTGTCACACACTTGCAGCCTTGTCGTCCTTGGTGACGTGGCGCGACCCAAGG 2023Acc504 GTATGGATGTGTCACACACTTGCAGCCTTGTCGTCCTTGGTGACGTGGCGCGACCCAAGG 2023Acc848 GTATGGATGTGTCACACACTTGCAGCCTTGTCGTCCTTGGTGACGTGGCGCGACCCAAGG 2023Acc563 GTATGGATGTGTCACACACTTGCAGCCTTGTCGTCCTTGGTGACGTGGCGCGACCCAAGG 2023Acc757 GTATGGATGTGTCACACACTTGCAGCCTTGTCGTCCTTGGTGACGTGGCGCGACCCAAGG 2023Tsuyuake_Pik-m GTATGGATGTGTCACACACTTGCAGCCTTGTCGTCCTTGGTGACGTGGCGCGACCCAAGG 2023Kanto51_Pik GTATGGATGTGTCACACACTTGCAGCCTTGTCGTCCTTGGTGACGTGGCGCGACCCAAGG 2023Kusabue_Pik GTATGGATGTGTCACACACTTGCAGCCTTGTCGTCCTTGGTGACGTGGCGCGACCCAAGG 2023Acc201 -TATGGATGTGTCACACACTCGCAGCCTTGTCATCCTTGGCGACGTGATA---------G 1993Acc206 -TATGGATGTGTCACACACTCGCAGCCTTGTCATCCTTGGCGACGTGATA---------G 1993Acc1 -TATGGATGTGTCACACACTCGCAGCCTTGTCATCCTTGGCGACGTGATA---------G 1993Acc101 -TATGGATGTGTCACACACTCGCAGCCTTGTCATCCTTGGCGACGTGATA---------G 1993Acc718 -TATGGATGTGTCACACACTCGCAGCCTTGTCATCCTTGGCGACGTGATA---------G 1993Acc724 -TATGGATGTGTCACACACTCGCAGCCTTGTCATCCTTGGCGACGTGATA---------G 1993Acc715 -TATGGATGTGTCACACACTCGCAGCCTTGTCATCCTTGGCGACGTGATA---------G 1993Acc706 -TATGGATGTGTCACACACTCGCAGCCTTGTCATCCTTGGCGACGTGATA---------G 1993Acc624 -TATGGATGTGTCACACACTCGCAGCCTTGTCATCCTTGGCGACGTGATA---------G 1993Acc440 -TATGGATGTGTCACACACTCGCAGCCTTGTCATCCTTGGCGACGTGATA---------G 2008Acc868 -TATGGATGTGTCACACACTCGCAGCCTTGTCATCCTTGGCGACGTGATA---------G 2008Acc220 -TATGGATGTGTCACACACTCGCAGCCTTGTCATCCTTGGCGACGTGATA---------G 1993Nipponbare -TATGGATGTGTCACACACTCGCAGCCTTGTCATCCTTGGCGACGTGATA---------G 1993AccUP3 -TATGGATGTGTCACACACTCGCAGCCTTGTCATCCTTGGCGACGTGATA---------G 1993AccUP1 -TATGGATGTGTCACACACTCGCAGCCTTGTCATCCTTGGCGACGTGATA---------G 1993Acc224 -TATGGATGTGTCACACACTCGCAGCCTTGTCATCCTTGGCGACGTGATA---------G 1993 ******************* ***********.******* ******. . *

Ashikawa et al. Supplementary Fig. S1 (18/30)

Acc414 GAATCCCCTTCTATATGTTTAAGCGCTTGCGAGTGTTGGACCTTGAAGATAATAAGGATA 2089Acc420 GAATCCCCTTCTATATGTTTAAGCGCTTGCGAGTGTTGGACCTTGAAGATAATAAGGATA 2089Acc761 GAATCCCCTTCTATATGTTTAAGCGCTTGCGAGTGTTGGACCTTGAAGATAATAAGGATA 2089K60_Pik-p GAATCCCCTTCTATATGTTTAAGCGCTTGCGAGTGTTGGACCTTGAAGATAATAAGGATA 2083Acc130 GAATCCCCTTCTATATGTTTAAGCGCTTGCGAGTGTTGGACCTTGAAGATAATAAGGATA 2083Acc108 GAATCCCCTTCTATATGTTTAAGCGCTTGCGAGTGTTGGACCTTGAAGATAATAAGGATA 2083Acc719 GAATCCCCTTCTATATGTTTAAGCGCTTGCGAGTGTTGGACCTTGAAGATAATAAGGATA 2083Acc729 GAATCCCCTTCTATATGTTTAAGCGCTTGCGAGTGTTGGACCTTGAAGATAATAAGGATA 2083Acc709 GAATCCCCTTCTATATGTTTAAGCGCTTGCGAGTGTTGGACCTTGAAGATAATAAGGATA 2083Acc710 GAATCCCCTTCTATATGTTTAAGCGCTTGCGAGTGTTGGACCTTGAAGATAATAAGGATA 2083Acc504 GAATCCCCTTCTATATGTTTAAGCGCTTGCGAGTGTTGGACCTTGAAGATAATAAGGATA 2083Acc848 GAATCCCCTTCTATATGTTTAAGCGCTTGCGAGTGTTGGACCTTGAAGATAATAAGGATA 2083Acc563 GAATCCCCTTCTATATGTTTAAGCGCTTGCGAGTGTTGGACCTTGAAGATAATAAGGATA 2083Acc757 GAATCCCCTTCTATATGTTTAAGCGCTTGCGAGTGTTGGACCTTGAAGATAATAAGGATA 2083Tsuyuake_Pik-m GAATCCCCTTCTATATGTTTAAGCGCTTGCGAGTGTTGGACCTTGAAGATAATAAGGATA 2083Kanto51_Pik GAATCCCCTTCTATATGTTTAAGCGCTTGCGAGTGTTGGACCTTGAAGATAATAAGGATA 2083Kusabue_Pik GAATCCCCTTCTATATGTTTAAGCGCTTGCGAGTGTTGGACCTTGAAGATAATAAGGATA 2083Acc201 GAGTCCCCTTGGATATGTTTAAAAGATTGCGAGTGTTGGACCTTGAAGATAATATCGGTA 2053Acc206 GAGTCCCCTTGGATATGTTTAAAAGATTGCGAGTGTTGGACCTTGAAGATAATATCGGTA 2053Acc1 GAGTCCCCTTGAATATGTTTAAAAGATTGCGAGTGTTGGACCTTGAAGATAATATCGGTA 2053Acc101 GAGTCCCCTTGGATATGTTTAAAAGATTGCGAGTGTTGGACCTTGAAGATAATATCGGTA 2053Acc718 GAGTCCCCTTGGATATGTTTAAAAGATTGCGAGTGTTGGACCTTGAAGATAATATCGGTA 2053Acc724 GAGTCCCCTTGGATATGTTTAAAAGATTGCGAGTGTTGGACCTTGAAGACAATCTCGATA 2053Acc715 GAGTCCCCTTGGATATGTTTAAAAGATTGCGAGTGTTGGACCTTGAAGACAATCTCGATA 2053Acc706 GAGTCCCCTAGGATATGTTTAAAAGATGGCGAGTGTTGGACCTTGAAGACAATCTCGATA 2053Acc624 GAGTCCCCTTGGATATGTTTAAAAGATTGCGAGTGTTGGACCTTGAAGACAATCTCGATA 2053Acc440 GAGTCCCCTTGAATATGTTTAAAAGATTGCGAGTGTTGGACCTTGAAGATAATATCGGTA 2068Acc868 GAGTCCCCTTGAATATGTTTAAAAGATTGCGAGTGTTGGACCTTGAAGATAATATCGGTA 2068Acc220 GAGTCCCCTTGGATATGTTTAAAAGATTGCGAGTGTTGGACCTTGAAGATAATATCGGTA 2053Nipponbare GAGTCCCCTTGGATATGTTTAAAAGATTGCGAGTGTTGGACCTTGAAGATAATATCGGTA 2053AccUP3 GAGTCCCCTTGGATATGTTTAAAAGATTGCGAGTGTTGGACCTTGAAGATAATATCGGTA 2053AccUP1 GAGTCCCCTTGGATATGTTTAAAAGATTGCGAGTGTTGGACCTTGAAGATAATATCGGTA 2053Acc224 GAGTCCCCTTGGATATGTTTAAAAGATTGCGAGTGTTGGACCTTGAAGATAATATCGGTA 2053 **.******: **********..*.* ********************* ***.: *.** Acc414 TACAGGATTCTCATCTGCAGGGCATATGTGAACAGTTA---AGCCTCAGAGTG---AGGT 2143Acc420 TACAGGATTCTCATCTGCAGGGCATATGTGAACAGTTA---AGCCTCAGAGTG---AGGT 2143Acc761 TACAGGATTCTCATCTGCAGGGCATATGTGAACAGTTA---AGCCTCAGAGTG---AGGT 2143K60_Pik-p TACAGGATTCTCATCTGCAGGGCATATGTGAACAGTTA---AGCCTCAGAGTG---AGGT 2137Acc130 TACAGGATTCTCATCTGCAGGGCATATGTGAACAGTTA---AGCCTCAGAGTG---AGGT 2137Acc108 TACAGGATTCTCATCTGCAGGGCATATGTGAACAGTTA---AGCCTCAGAGTG---AGGT 2137Acc719 TACAGGATTCTCATCTGCAGGGCATATGTGAACAGTTA---AGCCTCAGAGTG---AGGT 2137Acc729 TACAGGATTCTCATCTGCAGGGCATATGTGAACAGTTA---AGCCTCAGAGTG---AGGT 2137Acc709 TACAGGATTCTCATCTGCAGGGCATATGTGAACAGTTA---AGCCTCAGAGTG---AGGT 2137Acc710 TACAGGATTCTCATCTGCAGGGCATATGTGAACAGTTA---AGCCTCAGAGTG---AGGT 2137Acc504 TACAGGATTCTCATCTGCAGGGCATATGTGAACAGTTA---AGCCTCAGAGTG---AGGT 2137Acc848 TACAGGATTCTCATCTGCAGGGCATATGTGAACAGTTA---AGCCTCAGAGTG---AGGT 2137Acc563 TACAGGATTCTCATCTGCAGGGCATATGTGAACAGTTA---AGCCTCAGAGTG---AGGT 2137Acc757 TACAGGATTCTCATCTGCAGGGCATATGTGAACAGTTA---AGCCTCAGAGTG---AGGT 2137Tsuyuake_Pik-m TACAGGATTCTCATCTGCAGGGCATATGTGAACAGTTA---AGCCTCAGAGTG---AGGT 2137Kanto51_Pik TACAGGATTCTCATCTGCAGGGCATATGTGAACAGTTA---AGCCTCAGAGTG---AGGT 2137Kusabue_Pik TACAGGATTCTCATCTGCAGGGCATATGTGAACAGTTA---AGCCTCAGAGTG---AGGT 2137Acc201 TAGAGGACTCCCACCTGAAGAAGATATGTGAGCAGCTAGAGAGCCTCAGGCTGCTCAAGT 2113Acc206 TAGAGGACTCCCACCTGAAGAAGATATGTGAGCAGCTAGAGAGCCTCAGGCTGCTCAAGT 2113Acc1 TAGAGGACTCCCACCTGAAGAAGATATGTGAGCAGCTAGAGAGCCTCAGGCTGCTCAAGT 2113Acc101 TAGAGGACTCCCACCTGAAGAAGATATGTGAGCAGCTAGAGAGCCTCAGGCTGCTCAAGT 2113Acc718 TAGAGGACTCCCACCTGAAGAAGATATGTGAGCAGCTAGAGAGCCTCAGGCTGCTCAAGT 2113Acc724 TAGATGACTCTCACCTGAAGAAGATATGTGAGCAGCTAGAGAGCCTCAGGCTGCTCAAGT 2113Acc715 TAGATGACTCTCACCTGAAGAAGATATGTGAGCAGCTAGAGAGCCTCAGGCTGCTCAAGT 2113Acc706 TAGATGACTCTCACCTGAAGAAGATATGTGAGCAGCTAGAGAGCCTCAGGCTGCTCAAGT 2113Acc624 TAGATGACTCTCACCTGAAGAAGATATGTGAGCAGCTAGAGAGCCTCAGGCTGCTCAAGT 2113Acc440 TAGAGGACTCCCACCTGAAGAAGATATGTGAGCAGCTAGAGAGCCTCAGGCTGCTCAAGT 2128Acc868 TAGAGGACTCCCACCTGAAGAAGATATGTGAGCAGCTAGAGAGCCTCAGGCTGCTCAAGT 2128Acc220 TAGAGGACTCCCACCTGAAGAAGATATGTGAGCAGCTAGAGAGCCTCAGGCTGCTCAAGT 2113Nipponbare TAGAGGACTCCCACCTGAAGAAGATATGTGAGCAGCTAGAGAGCCTCAGGCTGCTCAAGT 2113AccUP3 TAGAGGACTCCCACCTGAAGAAGATATGTGAGCAGCTAGAGAGCCTCAGGCTGCTCAAGT 2113AccUP1 TAGAGGACTCCCACCTGAAGAAGATATGTGAGCAGCTAGAGAGCCTCAGGCTGCTCAAGT 2113Acc224 TAGAGGACTCCCACCTGAAGAAGATATGTGAGCAGCTAGAGAGCCTCAGGCTGCTCAAGT 2113 ** * ** ** ** ***.**.. ********.*** ** ********. ** *.**

Ashikawa et al. Supplementary Fig. S1 (19/30)

Acc414 ACCTTGGTCTCAAGGGAACGCGGATCCGAAAGCTCCCTCAGGAGATGAGGAAGCTGAAGC 2203Acc420 ACCTTGGTCTCAAGGGAACGCGGATCCGAAAGCTCCCTCAGGAGATGAGGAAGCTGAAGC 2203Acc761 ACCTTGGTCTCAAGGGAACGCGGATCCGAAAGCTCCCTCAGGAGATGAGGAAGCTGAAGC 2203K60_Pik-p ACCTTGGTCTCAAGGGAACGCGGATCCGAAAGCTCCCTCAGGAGATGAGGAAGCTGAAGC 2197Acc130 ACCTTGGTCTCAAGGGAACGCGGATCCGAAAGCTCCCTCAGGAGATGAGGAAGCTGAAGC 2197Acc108 ACCTTGGTCTCAAGGGAACGCGGATCCGAAAGCTCCCTCAGGAGATGAGGAAGCTGAAGC 2197Acc719 ACCTTGGTCTCAAGGGAACGCGGATCCGAAAGCTCCCTCAGGAGATGAGGAAGCTGAAGC 2197Acc729 ACCTTGGTCTCAAGGGAACGCGGATCCGAAAGCTCCCTCAGGAGATGAGGAAGCTGAAGC 2197Acc709 ACCTTGGTCTCAAGGGAACGCGGATCCGAAAGCTCCCTCAGGAGATGAGGAAGCTGAAGC 2197Acc710 ACCTTGGTCTCAAGGGAACGCGGATCCGAAAGCTCCCTCAGGAGATGAGGAAGCTGAAGC 2197Acc504 ACCTTGGTCTCAAGGGAACGCGGATCCGAAAGCTCCCTCAGGAGATGAGGAAGCTGAAGC 2197Acc848 ACCTTGGTCTCAAGGGAACGCGGATCCGAAAGCTCCCTCAGGAGATGAGGAAGCTGAAGC 2197Acc563 ACCTTGGTCTCAAGGGAACGCGGATCCGAAAGCTCCCTCAGGAGATGAGGAAGCTGAAGC 2197Acc757 ACCTTGGTCTCAAGGGAACGCGGATCCGAAAGCTCCCTCAGGAGATGAGGAAGCTGAAGC 2197Tsuyuake_Pik-m ACCTTGGTCTCAAGGGAACGCGGATCCGAAAGCTCCCTCAGGAGATGAGGAAGCTGAAGC 2197Kanto51_Pik ACCTTGGTCTCAAGGGAACGCGGATCCGAAAGCTCCCTCAGGAGATGAGGAAGCTGAAGC 2197Kusabue_Pik ACCTTGGTCTCAAGGGAACGCGGATCCGAAAGCTCCCTCAGGAGATGAGGAAGCTGAAGC 2197Acc201 ACCTAGGTCTCAAGGGTACGCGAATCACTAAGCTCCCACAGGAGATACAGAAGCTGAAGC 2173Acc206 ACCTAGGTCTCAAGGGTACGCGAATCACTAAGCTCCCACAGGAGATACAGAAGCTGAAGC 2173Acc1 ACCTAGGTCTCAAGGGTACGCGAATCACTAAGCTCCCACAGGAGATACAGAAGCTGAAGC 2173Acc101 ACCTAGGTCTCAAGGGTACGCGAATCACTAAGCTCCCACAGGAGATACAGAAGCTGAAGC 2173Acc718 ACCTAGGTCTCAAGGGTACGCGAATCACTAAGCTCCCACAGGAGATACAGAAGCTGAAGC 2173Acc724 ACCTGGGTATCAAGGGTACACGGATCACTAAGCTCCCACAGGAGATACAGAAGCTGAAGC 2173Acc715 ACCTGGGTATCAAGGGTACACGGATCACTAAGCTCCCACAGGAGATACAGAAGCTGAAGC 2173Acc706 ACCTGGGTATCAAGGGTACACGGATCACTAAGCTCCCACAGGAGATACAGAAGCTGAAGC 2173Acc624 ACCTGGGTATCAAGGGTACACGGATCACTAAGCTCCCACAGGAGATACAGAAGCTGAAGC 2173Acc440 ACCTAGGTCTCAAGGGTACGCGAATCACTAAGCTCCCACAGGAGATACAGAAGCTGAAGC 2188Acc868 ACCTAGGTCTCAAGGGTACGCGAATCACTAAGCTCCCACAGGAGATACAGAAGCTGAAGC 2188Acc220 ACCTAGGTCTCAAGGGTACGCGAATCACTAAGCTCCCACAGGAGATACAGAAGCTGAAGC 2173Nipponbare ACCTAGGTCTCAAGGGTACGCGAATCACTAAGCTCCCACAGGAGATACAGAAGCTGAAGC 2173AccUP3 ACCTAGGTCTCAAGGGTACGCGAATCACTAAGCTCCCACAGGAGATACAGAAGCTGAAGC 2173AccUP1 ACCTAGGTCTCAAGGGTACGCGAATCACTAAGCTCCCACAGGAGATACAGAAGCTGAAGC 2173Acc224 ACCTAGGTCTCAAGGGTACGCGAATCACTAAGCTCCCACAGGAGATACAGAAGCTGAAGC 2173 **** ***.*******:**.**.***. :********:********...*********** Acc414 ATTTGGAGATTTTGTATGTGGGGAGCACTCGGATCAGTGAACTTCCGCAAGAGATTGGAG 2263Acc420 ATTTGGAGATTTTGTATGTGGGGAGCACTCGGATCAGTGAACTTCCGCAAGAGATTGGAG 2263Acc761 ATTTGGAGATTTTGTATGTGGGGAGCACTCGGATCAGTGAACTTCCGCAAGAGATTGGAG 2263K60_Pik-p ATTTGGAGATTTTGTATGTGGGGAGCACTCGGATCAGTGAACTTCCGCAAGAGATTGGAG 2257Acc130 ATTTGGAGATTTTGTATGTGGGGAGCACTCGGATCAGTGAACTTCCGCAAGAGATTGGAG 2257Acc108 ATTTGGAGATTTTGTATGTGGGGAGCACTCGGATCAGTGAACTTCCGCAAGAGATTGGAG 2257Acc719 ATTTGGAGATTTTGTATGTGGGGAGCACTCGGATCAGTGAACTTCCGCAAGAGATTGGAG 2257Acc729 ATTTGGAGATTTTGTATGTGGGGAGCACTCGGATCAGTGAACTTCCGCAAGAGATTGGAG 2257Acc709 ATTTGGAGATTTTGTATGTGGGGAGCACTCGGATCAGTGAACTTCCGCAAGAGATTGGAG 2257Acc710 ATTTGGAGATTTTGTATGTGGGGAGCACTCGGATCAGTGAACTTCCGCAAGAGATTGGAG 2257Acc504 ATTTGGAGATTTTGTATGTGGGGAGCACTCGGATCAGTGAACTTCCGCAAGAGATTGGAG 2257Acc848 ATTTGGAGATTTTGTATGTGGGGAGCACTCGGATCAGTGAACTTCCGCAAGAGATTGGAG 2257Acc563 ATTTGGAGATTTTGTATGTGGGGAGCACTCGGATCAGTGAACTTCCGCAAGAGATTGGAG 2257Acc757 ATTTGGAGATTTTGTATGTGGGGAGCACTCGGATCAGTGAACTTCCGCAAGAGATTGGAG 2257Tsuyuake_Pik-m ATTTGGAGATTTTGTATGTGGGGAGCACTCGGATCAGTGAACTTCCGCAAGAGATTGGAG 2257Kanto51_Pik ATTTGGAGATTTTGTATGTGGGGAGCACTCGGATCAGTGAACTTCCGCAAGAGATTGGAG 2257Kusabue_Pik ATTTGGAGATTTTGTATGTGGGGAGCACTCGGATCAGTGAACTTCCGCAAGAGATTGGAG 2257Acc201 AACTGGAGATTTTGTACGTGAGGAGCACAGGCATCGAAGAGCTCCCATGGGAGATCGGGG 2233Acc206 AACTGGAGATTTTGTACGTGAGGAGCACAGGCATCGAAGAGCTCCCATGGGAGATCGGGG 2233Acc1 AACTGGAGATTTTGTACGTGAGGAGCACAGGCATCAAAGAGCTCCCACGGGAGATCGGGG 2233Acc101 AACTGGAGATTTTGTACGTGAGGAGCACAGGCATCGAAGAGCTCCCACAGGAGATCGGGG 2233Acc718 AACTGGAGATTTTGTACGTGAGGAGCACAGGCATCGAAGAGCTCCCACAGGAGATCGGGG 2233Acc724 ATCTGGAGATTTTGTACGTGAGGAGCACAGGCATCAAAGAGCTCCCACGGGAGATCGGGG 2233Acc715 ATCTGGAGATTTTGTACGTGAGGAGCACAGGCATCAAAGAGCTCCCACGGGAGATCGGGG 2233Acc706 ATCTGGAGATTTTGTACGTGAGGAGCACAGGCATCAAAGAGCTCCCACGGGAGATCGGGG 2233Acc624 ATCTGGAGATTTTGTACGTGAGGAGCACAGGCATCAAAGAGCTCCCACGGGAGATCGGGG 2233Acc440 AACTAGAGATTTTGTACGTGAGGAGCACAGGCATCAAAGAGCTCCCACGGGAGATCGGGG 2248Acc868 AACTAGAGATTTTGTACGTGAGGAGCACAGGCATCAAAGAGCTCCCACGGGAGATCGGGG 2248Acc220 AACTGGAGATTTTGTACGTGAGGAGCACAGGCATCGAAGAGCTCCCATGGGAGATCGGGG 2233Nipponbare AACTGGAGATTTTGTACGTGAGGAGCACAGGCATCGAAGAGCTCCCATGGGAGATCGGGG 2233AccUP3 AACTGGAGATTTTGTACGTGAGGAGCACAGGCATCGAAGAGCTCCCATGGGAGATCGGGG 2233AccUP1 AACTGGAGATTTTGTACGTGAGGAGCACAGGCATCGAAGAGCTCCCATGGGAGATCGGGG 2233Acc224 AACTGGAGATTTTGTACGTGAGGAGCACAGGCATCGAAGAGCTCCCATGGGAGATCGGGG 2233 *: *.*********** ***.*******: * ***..:**.** **. ..***** **.* 

Ashikawa et al. Supplementary Fig. S1 (20/30)Ashikawa et al. Supplementary Fig.

Acc414 AGCTGAAGCATCTGCGGATTCTGGACGTGAGAAACACGGACATCACTGAGCTCCCACTGC 2323Acc420 AGCTGAAGCATCTGCGGATTCTGGACGTGAGAAACACGGACATCACTGAGCTCCCACTGC 2323Acc761 AGCTGAAGCATCTGCGGATTCTGGACGTGAGAAACACGGACATCACTGAGCTCCCACTGC 2323K60_Pik-p AGCTGAAGCATCTGCGGATTCTGGACGTGAGAAACACGGACATCACTGAGCTCCCACTGC 2317Acc130 AGCTGAAGCATCTGCGGATTCTGGACGTGAGAAACACGGACATCACTGAGCTCCCACTGC 2317Acc108 AGCTGAAGCATCTGCGGATTCTGGACGTGAGAAACACGGACATCACTGAGCTCCCACTGC 2317Acc719 AGCTGAAGCATCTGCGGATTCTGGACGTGAGAAACACGGACATCACTGAGCTCCCACTGC 2317Acc729 AGCTGAAGCATCTGCGGATTCTGGACGTGAGAAACACGGACATCACTGAGCTCCCACTGC 2317Acc709 AGCTGAAGCATCTGCGGATTCTGGACGTGAGAAACACGGACATCACTGAGCTCCCACTGC 2317Acc710 AGCTGAAGCATCTGCGGATTCTGGACGTGAGAAACACGGACATCACTGAGCTCCCACTGC 2317Acc504 AGCTGAAGCATCTGCGGATTCTGGACGTGAGAAACACGGACATCACTGAGCTCCCACTGC 2317Acc848 AGCTGAAGCATCTGCGGATTCTGGACGTGAGAAACACGGACATCACTGAGCTCCCACTGC 2317Acc563 AGCTGAAGCATCTGCGGATTCTGGACGTGAGAAACACGGACATCACTGAGCTCCCACTGC 2317Acc757 AGCTGAAGCATCTGCGGATTCTGGACGTGAGAAACACGGACATCACTGAGCTCCCACTGC 2317Tsuyuake_Pik-m AGCTGAAGCATCTGCGGATTCTGGACGTGAGAAACACGGACATCACTGAGCTCCCACTGC 2317Kanto51_Pik AGCTGAAGCATCTGCGGATTCTGGACGTGAGAAACACGGACATCACTGAGCTCCCACTGC 2317Kusabue_Pik AGCTGAAGCATCTGCGGATTCTGGACGTGAGAAACACGGACATCACTGAGCTCCCACTGC 2317Acc201 AATTGAAACAACTGCGGACTCTGGACGTGAGGAACACGCGGATCAGCGAGCTCCCGTCGC 2293Acc206 AATTGAAACAACTGCGGACTCTGGACGTGAGGAACACGCGGATCAGCGAGCTCCCGTCGC 2293Acc1 AATTGAAACAACTGCGGACTCTGGACGTGAGGAACACGCGGATCAGCGAGCTCCCGTCGC 2293Acc101 AATTGAAACAACTGCGGACTCTGGACGTGAGGAACACGCAGATCAGCGAGCTCCCGTCGC 2293Acc718 AATTGAAACAACTGCGGACTCTGGACGTGAGGAACACGCAGATCAGCGAGCTCCCGTCGC 2293Acc724 AATTGAAACAACTGCGGACTCTGGACATGAGGAACACGCGGATCAGCGAGCTCCCGTCGC 2293Acc715 AATTGAAACAACTGCGGACTCTGGACATGAGGAACACGCGGATCAGCGAGCTCCCGTCGC 2293Acc706 AATTGAAACAACTGCGGACTCTGGACATGAGGAACACGCGGATCAGCGAGCTCCCGTCGC 2293Acc624 AATTGAAACAACTGCGGACTCTGGACATGAGGAACACGCGGATCAGCGAGCTCCCGTCGC 2293Acc440 AATTGAAACAACTGCGGACTCTGGACGTGAGGAACACGCGGATCAGTGAGCTCCCGTCGC 2308Acc868 AATTGAAACAACTGCGGACTCTGGACGTGAGGAACACGCGGATCAGTGAGCTCCCGTCGC 2308Acc220 AATTGAAACAACTGCGGACTCTGGACGTGAGGAACACGCGGATCAGCGAGCTCCCGTCGC 2293Nipponbare AATTGAAACAACTGCGGACTCTGGACGTGAGGAACACGCGGATCAGCGAGCTCCCGTCGC 2293AccUP3 AATTGAAACAACTGCGGACTCTGGACGTGAGGAACACGCGGATCAGCGAGCTCCCGTCGC 2293AccUP1 AATTGAAACAACTGCGGACTCTGGACGTGAGGAACACGCGGATCAGCGAGCTCCCGTCGC 2293Acc224 AATTGAAACAACTGCGGACTCTGGACGTGAGGAACACGCGGATCAGCGAGCTCCCGTCGC 2293 *. ****.**:******* *******.****.****** . **** ********. ** Acc414 AGATACGGGAGCTGCAGCATCTGCACACTCTGGACGTGAGGAA---CACGCCAA---TCA 2377Acc420 AGATACGGGAGCTGCAGCATCTGCACACTCTGGACGTGAGGAA---CACGCCAA---TCA 2377Acc761 AGATACGGGAGCTGCAGCATCTGCACACTCTGGACGTGAGGAA---CACGCCAA---TCA 2377K60_Pik-p AGATACGGGAGCTGCAGCATCTGCACACTCTGGACGTGAGGAA---CACTCCAA---TCA 2371Acc130 AGATACGGGAGCTGCAGCATCTGCACACTCTGGACGTGAGGAA---CACTCCAA---TCA 2371Acc108 AGATACGGGAGCTGCAGCATCTGCACACTCTGGACGTGAGGAA---CACTCCAA---TCA 2371Acc719 AGATACGGGAGCTGCAGCATCTGCACACTCTGGACGTGAGGAA---CACTCCAA---TCA 2371Acc729 AGATACGGGAGCTGCAGCATCTGCACACTCTGGACGTGAGGAA---CACTCCAA---TCA 2371Acc709 AGATACGGGAGCTGCAGCATCTGCACACTCTGGACGTGAGGAA---CACTCCAA---TCA 2371Acc710 AGATACGGGAGCTGCAGCATCTGCACACTCTGGACGTGAGGAA---CACTCCAA---TCA 2371Acc504 AGATACGGGAGCTGCAGCATCTGCACACTCTGGACGTGAGGAA---CACTCCAA---TCA 2371Acc848 AGATACGGGAGCTGCAGCATCTGCACACTCTGGACGTGAGGAA---CACTCCAA---TCA 2371Acc563 AGATACGGGAGCTGCAGCATCTGCACACTCTGGACGTGAGGAA---CACTCCAA---TCA 2371Acc757 AGATACGGGAGCTGCAGCATCTGCACACTCTGGACGTGAGGAA---CACTCCAA---TCA 2371Tsuyuake_Pik-m AGATACGGGAGCTGCAGCATCTGCACACTCTGGACGTGAGGAA---CACTCCAA---TCA 2371Kanto51_Pik AGATACGGGAGCTGCAGCATCTGCACACTCTGGACGTGAGGAA---CACGCCAA---TCA 2371Kusabue_Pik AGATACGGGAGCTGCAGCATCTGCACACTCTGGACGTGAGGAA---CACTCCAA---TCA 2371Acc201 AGATCGGGGAGCTCAAACATCTGCGGACTCTGGACGTGAGTAA---CATGTGGAATATCA 2350Acc206 AGATCGGGGAGCTCAAACATCTGCGGACTCTGGACGTGAGTAA---CATGTGGAATATCA 2350Acc1 AGATCGGGGAGCTCAAACATCTGCGGACTCTGGACGTGAGTAA---CATGTGGAATATCA 2350Acc101 AGATCGGGGAGCTCAAACATCTGCGGACTCTGGACGTGAGTAA---CATGTGGAATATCA 2350Acc718 AGATCGGGGAGCTCAAACATCTGCGGACTCTGGACGTGAGTAA---CATGTGGAATATCA 2350Acc724 AGATCGGGGAGCTCAAACATCTGCGGACTCTGGACGTGAGTAACAACATGTGGAATATCA 2353Acc715 AGATCGGGGAGCTCAAACATCTGCGGACTCTGGACGTGAGTAACAACATGTGGAATATCA 2353Acc706 AGATCGGGGAGCTCAAACATCTGCGGACTCTGGACGTGAGTAACAACATGTGGAATATCA 2353Acc624 AGATCGGGGAGCTCAAACATCTGCGGACTCTGGACGTGAGTAACAACATGTGGAATATCA 2353Acc440 AGATCGGGGAGCTCAAACATCTGCGGACTCTGGACGTGAGTAA---CATGTGGAATATCA 2365Acc868 AGATCGGGGAGCTCAAACATCTGCGGACTCTGGACGTGAGTAA---CATGTGGAATATCA 2365Acc220 AGATCGGGGAGCTCAAACATCTGCGGACTCTGGACGTGAGTAA---CATGTGGAATATCA 2350Nipponbare AGATCGGGGAGCTCAAACATCTGCGGACTCTGGACGTGAGTAA---CATGTGGAATATCA 2350AccUP3 AGATCGGGGAGCTCAAACATCTGCGGACTCTGGACGTGAGTAA---CATGTGGAATATCA 2350AccUP1 AGATCGGGGAGCTCAAACATCTGCGGACTCTGGACGTGAGTAA---CATGTGGAATATCA 2350Acc224 AGATCGGGGAGCTCAAACATCTGCGGACTCTGGACGTGAGTAA---CATGTGGAATATCA 2350 ****. ******* .*.*******. ************** ** ** .* ***

Ashikawa et al. Supplementary Fig. S1 (21/30)

Acc414 GTGAGCTCCCGCCGCAGGTTGGCAAGCTGCAGAATCTCAAGATTATGTGCGTGAGGAGCA 2437Acc420 GTGAGCTCCCGCCGCAGGTTGGCAAGCTGCAGAATCTCAAGATTATGTGCGTGAGGAGCA 2437Acc761 GTGAGCTCCCGCCGCAGGTTGGCAAGCTGCAGAATCTCAAGATTATGTGCGTGAGGAGCA 2437K60_Pik-p GTGAGCTCCCGCCGCAGGTTGGCAAGCTGCAGAATCTCAAGATTATGTGCGTGAGGAGCA 2431Acc130 GTGAGCTCCCGCCGCAGGTTGGCAAGCTGCAGAATCTCAAGATTATGTGCGTGAGGAGCA 2431Acc108 GTGAGCTCCCGCCGCAGGTTGGCAAGCTGCAGAATCTCAAGATTATGTGCGTGAGGAGCA 2431Acc719 GTGAGCTCCCGCCGCAGGTTGGCAAGCTGCAGAATCTCAAGATTATGTGCGTGAGGAGCA 2431Acc729 GTGAGCTCCCGCCGCAGGTTGGCAAGCTGCAGAATCTCAAGATTATGTGCGTGAGGAGCA 2431Acc709 GTGAGCTCCCGCCGCAGGTTGGCAAGCTGCAGAATCTCAAGATTATGTGCGTGAGGAGCA 2431Acc710 GTGAGCTCCCGCCGCAGGTTGGCAAGCTGCAGAATCTCAAGATTATGTGCGTGAGGAGCA 2431Acc504 GTGAGCTCCCGCCGCAGGTTGGCAAGCTGCAGAATCTCAAGATTATGTGCGTGAGGAGCA 2431Acc848 GTGAGCTCCCGCCGCAGGTTGGCAAGCTGCAGAATCTCAAGATTATGTGCGTGAGGAGCA 2431Acc563 GTGAGCTCCCGCCGCAGGTTGGCAAGCTGCAGAATCTCAAGATTATGTGCGTGAGGAGCA 2431Acc757 GTGAGCTCCCGCCGCAGGTTGGCAAGCTGCAGAATCTCAAGATTATGTGCGTGAGGAGCA 2431Tsuyuake_Pik-m GTGAGCTCCCGCCGCAGGTTGGCAAGCTGCAGAATCTCAAGATTATGTGCGTGAGGAGCA 2431Kanto51_Pik GTGAGCTCCCGCCGCAGGTTGGCAAGCTGCAGAATCTCAAGATTATGTGCGTGAGGAGCA 2431Kusabue_Pik GTGAGCTCCCGCCGCAGGTTGGCAAGCTGCAGAATCTCAAGATTATGTGCGTGAGGAGCA 2431Acc201 GCGAGCTGCCGTCGCAAATCGGGGAGCTGAAGCATCT----------------------- 2387Acc206 GCGAGCTGCCGTCGCAAATCGGGGAGCTGAAGCATCT----------------------- 2387Acc1 GCGAGCTGCCGTTGCAAATCGGGGAGCTGAAGCATCTACAAACTCTGGATGTGAGGAACA 2410Acc101 GCGAGCTGCCGTCGCAAATCGGGGAGCTGAAGCATCT----------------------- 2387Acc718 GCGAGCTGCCGTCGCAAATCGGGGAGCTGAAGCATCTACAAACTCTGGATGTGAGGAACA 2410Acc724 GCGAGCTGCCGTCGCAAATCGGGGAGCTGAAGCATCTACAAACTCTGGATGTGAGGAATA 2413Acc715 GCGAGCTGCCGTCGCAAATCGGGGAGCTGAAGCATCTACAAACTCTGGATGTGAGGAATA 2413Acc706 GCGAGCTGCCGTCGCAAATCGGGGAGCTGAAGCATCT----------------------- 2390Acc624 GCGAGCTGCCGTCGCAAATCGGGGAGCTGAAGCATCT----------------------- 2390Acc440 GCAAGCTGCCGTCGCAAATCGGGGAGCTAAAGCATCT----------------------- 2402Acc868 GCAAGCTGCCGTCGCAAATCGGGGAGCTAAAGCATCT----------------------- 2402Acc220 GCGAGCTGCCGTCGCAAATCGGGGAGCTGAAGCATCTACAAACTCTGGATGTGAGGAACA 2410Nipponbare GCGAGCTGCCGTCGCAAATCGGGGAGCTGAAGCATCTACAAACTCTGGATGTGAGGAACA 2410AccUP3 GCGAGCTGCCGTCGCAAATCGGGGAGCTGAAGCATCTACAAACTCTGGATGTGAGGAACA 2410AccUP1 GCGAGCTGCCGTCGCAAATCGGGGAGCTGAAGCATCTACAAACTCTGGATGTGAGGAACA 2410Acc224 GCGAGCTGCCGTCGCAAATCGGGGAGCTGAAGCATCT----------------------- 2387 * .**** *** ***..* ** .****..**.****  Acc414 CTGGGGTTAGGGAGCTCCCAAAGGAGATTGGGGAGCTGAATCATCTACAGATTCTGGACG 2497Acc420 CTGGGGTTAGGGAGCTCCCAAAGGAGATTGGGGAGCTGAATCATCTACAGATTCTGGACG 2497Acc761 CTGGGGTTAGGGAGCTCCCAAAGGAGATTGGGGAGCTGAATCATCTACAGATTCTGGACG 2497K60_Pik-p CTGGGGTTAGGGAGCTCCCAAAGGAGATTGGGGAGCTGAATCATCTACAGACTCTGGACG 2491Acc130 CTGGGGTTAGGGAGCTCCCAAAGGAGATTGGGGAGCTGAATCATCTACAGACTCTGGACG 2491Acc108 CTGGGGTTAGGGAGCTCCCAAAGGAGATTGGGGAGCTGAATCATCTACAGACTCTGGACG 2491Acc719 CTGGGGTTAGGGAGCTCCCAAAGGAGATTGGGGAGCTGAATCATCTACAGACTCTGGACG 2491Acc729 CTGGGGTTAGGGAGCTCCCAAAGGAGATTGGGGAGCTGAATCATCTACAGACTCTGGACG 2491Acc709 CTGGGGTTAGGGAGCTCCCAAAGGAGATTGGGGAGCTGAATCATCTACAGACTCTGGACG 2491Acc710 CTGGGGTTAGGGAGCTCCCAAAGGAGATTGGGGAGCTGAATCATCTACAGACTCTGGACG 2491Acc504 CTGGGGTTAGGGAGCTCCCAAAGGAGATTGGGGAGCTGAATCATCTACAGACTCTGGACG 2491Acc848 CTGGGGTTAGGGAGCTCCCAAAGGAGATTGGGGAGCTGAATCATCTACAGACTCTGGACG 2491Acc563 CTGGGGTTAGGGAGCTCCCAAAGGAGATTGGGGAGCTGAATCATCTACAGACTCTGGACG 2491Acc757 CTGGGGTTAGGGAGCTCCCAAAGGAGATTGGGGAGCTGAATCATCTACAGACTCTGGACG 2491Tsuyuake_Pik-m CTGGGGTTAGGGAGCTCCCAAAGGAGATTGGGGAGCTGAATCATCTACAGACTCTGGACG 2491Kanto51_Pik CTGGGGTTAGGGAGCTCCCAAAGGAGATTGGGGAGCTGAATCATCTACAGACTCTGGACG 2491Kusabue_Pik CTGGGGTTAGGGAGCTCCCAAAGGAGATTGGGGAGCTGAATCATCTACAGACTCTGGACG 2491Acc201 ----------------------------------------------GCGGACTCTGGATG 2401Acc206 ----------------------------------------------GCGGACTCTGGATG 2401Acc1 CGTCAGTGAGAGAGCTGCCATCGCAAATCGGGGAGCTGAAGCATCTGCGGACTCTGGATG 2470Acc101 ----------------------------------------------GCGGACTCTGGATG 2401Acc718 CGTCAGTGAGAGAGCTGCCATCGCAAATCGGGGAGCTGAAGCATCTGCGGACTCTGGATG 2470Acc724 CGTCGGTGAGAGAGCTGCCATCGCAAATCGGGGAGCTGAAGCATCTGCGGACTCTGGATG 2473Acc715 CGTCGGTGAGAGAGCTGCCATCGCAAATCGGGGAGCTGAAGCATCTGCGGACTCTGGATG 2473Acc706 ----------------------------------------------GCGGACTCTGGATG 2404Acc624 ----------------------------------------------GCGGACTCTGGATG 2404Acc440 ----------------------------------------------GCGGACTCTGGATG 2416Acc868 ----------------------------------------------GCGGACTCTGGATG 2416Acc220 CGTCAGTGAGAGAGCTGCCATCGCAAATCGGGGAGCTGAAGCATCTGCGGACTCTGGATG 2470Nipponbare CGTCAGTGAGAGAGCTGCCATCGCAAATCGGGGAGCTGAAGCATCTGCGGACTCTGGATG 2470AccUP3 CGTCAGTGAGAGAGCTGCCATCGCAAATCGGGGAGCTGAAGCATCTGCGGTCTCTGGATG 2470AccUP1 CGTCAGTGAGAGAGCTGCCATCGCAAATCGGGGAGCTGAAGCATCTGCGGTCTCTGGATG 2470Acc224 ----------------------------------------------GCGGACTCTGGATG 2401 .*.*: ****** * 

Ashikawa et al. Supplementary Fig. S1 (22/30)

Acc414 TGAGAAACACGAGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCCCAATCGTTGC 2557Acc420 TGAGAAACACGAGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCCCAATCGTTGC 2557Acc761 TGAGAAACACGAGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCCCAATCGTTGC 2557K60_Pik-p TGAGAAACACGAGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCCCAATCGTTGC 2551Acc130 TGAGAAACACGAGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCCCAATCGTTGC 2551Acc108 TGAGAAACACGAGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCCCAATCGTTGC 2551Acc719 TGAGAAACACGAGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCCCAATCGTTGC 2551Acc729 TGAGAAACACGAGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCCCAATCGTTGC 2551Acc709 TGAGAAACACGAGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCCCAATCGTTGC 2551Acc710 TGAGAAACACGAGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCCCAATCGTTGC 2551Acc504 TGAGAAACACGAGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCCCAATCGTTGC 2551Acc848 TGAGAAACACGAGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCCCAATCGTTGC 2551Acc563 TGAGAAACACGAGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCCCAATCGTTGC 2551Acc757 TGAGAAACACGAGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCCCAATCGTTGC 2551Tsuyuake_Pik-m TGAGAAACACGAGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCCCAATCGTTGC 2551Kanto51_Pik TGAGAAACACGAGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCCCAATCGTTGC 2551Kusabue_Pik TGAGAAACACGAGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCCCAATCGTTGC 2551Acc201 TGAGGAACACGGGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCGGGATCGCTGC 2461Acc206 TGAGGAACACGGGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCGGGATCGCTGC 2461Acc1 TGAGGAACACGGGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCGGGATCGCTGC 2530Acc101 TGAGGAACACGGGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCGGGATCGCTGC 2461Acc718 TGAGGAACACGGGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCGGGATCGCTGC 2530Acc724 TGAGGAACACGGGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCGGGATCGCTGC 2533Acc715 TGAGGAACACGGGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCGGGATCGCTGC 2533Acc706 TGAGGAACACGGGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCGGGATCGCTGC 2464Acc624 TGAGGAACACGGGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCGGGATCGCTGC 2464Acc440 TGAGGAACACGAGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCGGGATCGCTGC 2476Acc868 TGAGGAACACGAGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCGGGATCGCTGC 2476Acc220 TGAGGAACACGGGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCGGGATCGCTGC 2530Nipponbare TGAGGAACACGGGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCGGGATCGCTGC 2530AccUP3 TGAGGAACACGGGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCGGGATCGCTGC 2530AccUP1 TGAGGAACACGGGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCGGGATCGCTGC 2530Acc224 TGAGGAACACGGGGGTGAGAGAGCTGCCATGGCAAGCTGGCCAGATCTCGGGATCGCTGC 2461 ****.******.************************************* .**** *** Acc414 GCGTGCTTGCCGGTGACAGTGGCGATGGCGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTC 2617Acc420 GCGTGCTTGCCGGTGACAGTGGCGATGGCGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTC 2617Acc761 GCGTGCTTGCCGGTGACAGTGGCGATGGCGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTC 2617K60_Pik-p GCGTGCTTGCCGGTGACAGTGGCGATGGCGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTC 2611Acc130 GCGTGCTTGCCGGTGACAGTGGCGATGGCGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTC 2611Acc108 GCGTGCTTGCCGGTGACAGTGGCGATGGCGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTC 2611Acc719 GCGTGCTTGCCGGTGACAGTGGCGATGGCGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTC 2611Acc729 GCGTGCTTGCCGGTGACAGTGGCGATGGCGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTC 2611Acc709 GCGTGCTTGCCGGTGACAGTGGCGATGGCGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTC 2611Acc710 GCGTGCTTGCCGGTGACAGTGGCGATGGCGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTC 2611Acc504 GCGTGCTTGCCGGTGACAGTGGCGATGGCGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTC 2611Acc848 GCGTGCTTGCCGGTGACAGTGGCGATGGCGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTC 2611Acc563 GCGTGCTTGCCGGTGACAGTGGCGATGGCGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTC 2611Acc757 GCGTGCTTGCCGGTGACAGTGGCGATGGCGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTC 2611Tsuyuake_Pik-m GCGTGCTTGCCGGTGACAGTGGCGATGGCGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTC 2611Kanto51_Pik GCGTGCTTGCCGGTGACAGTGGCGATGGCGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTC 2611Kusabue_Pik GCGTGCTTGCCGGTGACAGTGGCGATGGCGTGCGGTTGCCCGAAGGCGTCTGCGAAGCTC 2611Acc201 ACGTGCATACAGATGACAGTGACGAGGGCATGCGGCTGCCAGAAGGCGTATGCGAAGATC 2521Acc206 ACGTGCATACAGATGACAGTGACGAGGGCATGCGGCTGCCAGAAGGCGTATGCGAAGATC 2521Acc1 ACGTGCATACAGATGACAGTGACGAGGGCATGCGGCTGCCAGAAGGCGTATGCGAAGATC 2590Acc101 ACGTGCATACAGATGACAGTGACGAGGGCATGCGGCTGCCAGAAGGCGTATGCGAAGATC 2521Acc718 ACGTGCATACAGATGACAGTGACGAGGGCATGCGGCTGCCAGAAGGCGTATGCGAAGATC 2590Acc724 ACGTGCATACAGATGACAGTGACGAGGGCATGCGGCTGCCAGAAGGCGTATGCGAAGATC 2593Acc715 ACGTGCATACAGATGACAGTGACGAGGGCATGCGGCTGCCAGAAGGCGTATGCGAAGATC 2593Acc706 ACGTGCATACAGATGACAGTGACGAGGGCATGCGGCTGCCAGAAGGCGTATGCGAAGATC 2524Acc624 ACGTGCATACAGATGACAGTGACGAGGGCATGCGGCTGCCAGAAGGCGTATGCGAAGATC 2524Acc440 ACGTGCATACAGATGACAGTGACGAGGGCATGCGGCTGCCAGAAGGCGTATGCGAAGATC 2536Acc868 ACGTGCATACAGATGACAGTGACGAGGGCATGCGGCTGCCAGAAGGCGTATGCGAAGATC 2536Acc220 ACGTGCATACAGATGACAGTGACGAGGGCATGCGGCTGCCAGAAGGCGTATGCGAAGATC 2590Nipponbare ACGTGCATACAGATGACAGTGACGAGGGCATGCGGCTGCCAGAAGGCGTATGCGAAGATC 2590AccUP3 ACGTGCATACAGATGACAGTGACGAGGGCATGCGGCTGCCAGAAGGCGTATGCGAAGATC 2590AccUP1 ACGTGCATACAGATGACAGTGACGAGGGCATGCGGCTGCCAGAAGGCGTATGCGAAGATC 2590Acc224 ACGTGCATACAGATGACAGTGACGAGGGCATGCGGCTGCCAGAAGGCGTATGCGAAGATC 2521 .*****:*.*.*.********.*** ***.***** ****.********.*******.** 

Ashikawa et al. Supplementary Fig. S1 (23/30)

Acc414 TGATCAACGGTATTCCAGGGGCTACGCGTGCAAAATGCAGGGAGGTTCTGTCCATCGCGA 2677Acc420 TGATCAACGGTATTCCAGGGGCTACGCGTGCAAAATGCAGGGAGGTTCTGTCCATCGCGA 2677Acc761 TGATCAACGGTATTCCAGGGGCTACGCGTGCAAAATGCAGGGAGGTTCTGTCCATCGCGA 2677K60_Pik-p TGATCAACGGTATTCCAGGGGCTACGCGTGCAAAATGCAGGGAGGTTCTGTCCATCGCGA 2671Acc130 TGATCAACGGTATTCCAGGGGCTACGCGTGCAAAATGCAGGGAGGTTCTGTCCATCGCGA 2671Acc108 TGATCAACGGTATTCCAGGGGCTACGCGTGCAAAATGCAGGGAGGTTCTGTCCATCGCGA 2671Acc719 TGATCAACGGTATTCCAGGGGCTACGCGTGCAAAATGCAGGGAGGTTCTGTCCATCGCGA 2671Acc729 TGATCAACGGTATTCCAGGGGCTACGCGTGCAAAATGCAGGGAGGTTCTGTCCATCGCGA 2671Acc709 TGATCAACGGTATTCCAGGGGCTACGCGTGCAAAATGCAGGGAGGTTCTGTCCATCGCGA 2671Acc710 TGATCAACGGTATTCCAGGGGCTACGCGTGCAAAATGCAGGGAGGTTCTGTCCATCGCGA 2671Acc504 TGATCAACGGTATTCCAGGGGCTACGCGTGCAAAATGCAGGGAGGTTCTGTCCATCGCGA 2671Acc848 TGATCAACGGTATTCCAGGGGCTACGCGTGCAAAATGCAGGGAGGTTCTGTCCATCGCGA 2671Acc563 TGATCAACGGTATTCCAGGGGCTACGCGTGCAAAATGCAGGGAGGTTCTGTCCATCGCGA 2671Acc757 TGATCAACGGTATTCCAGGGGCTACGCGTGCAAAATGCAGGGAGGTTCTGTCCATCGCGA 2671Tsuyuake_Pik-m TGATCAACGGTATTCCAGGGGCTACGCGTGCAAAATGCAGGGAGGTTCTGTCCATCGCGA 2671Kanto51_Pik TGATCAACGGTATTCCAGGGGCTACGCGTGCAAAATGCAGGGAGGTTCTGTCCATCGCGA 2671Kusabue_Pik TGATCAACGGTATTCCAGGGGCTACGCGTGCAAAATGCAGGGAGGTTCTGTCCATCGCGA 2671Acc201 TGATCAAGGGTATTCCCAAGGCTGAGCTCGCAAAGTGCAGTGAGGTCCTATCCATCAATA 2581Acc206 TGATCAAGGGTATTCCCAAGGCTGAGCTCGCAAAGTGCAGTGAGGTCCTATCCATCAATA 2581Acc1 TGATCAAGGGTATTCCCAAGGCTGAGCTCGCAAAGTGCAGTGAGGTCCTATCCATCAATA 2650Acc101 TGATCAAGGGTATTCCCAAGGCTGAGCTCGCAAAGTGCAGTGAGGTCCTATCCATCAATA 2581Acc718 TGATCAAGGGTATTCCCAAGGCTGAGCTCGCAAAGTGCAGTGAGGTCCTATCCATCAATA 2650Acc724 TGATCAAGGGTATTCCCAAGGCTGAGCTCGCAAAGTGCAGTGAGGTCCTATCCATCAATA 2653Acc715 TGATCAAGGGTATTCCCAAGGCTGAGCTCGCAAAGTGCAGTGAGGTCCTATCCATCAATA 2653Acc706 TGATCAAGGGTATTCCCAAGGCTGAGCTCGCAAAGTGCAGTGAGGTCCTATCCATCAATA 2584Acc624 TGATCAAGGGTATTCCCAAGGCTGAGCTCGCAAAGTGCAGTGAGGTCCTATCCATCAATA 2584Acc440 TGATCAAGGGTATTCCCAAGGCTGAGCTCGCAAAGTGCAGTGAGGTCCTATCCATCAATA 2596Acc868 TGATCAAGGGTATTCCCAAGGCTGAGCTCGCAAAGTGCAGTGAGGTCCTATCCATCAATA 2596Acc220 TGATCAAGGGTATTCCCAAGGCTGAGCTCGCAAAGTGCAGTGAGGTCCTATCCATCAATA 2650Nipponbare TGATCAAGGGTATTCCCAAGGCTGAGCTCGCAAAGTGCAGTGAGGTCCTATCCATCAATA 2650AccUP3 TGATCAAGGGTATTCCCAAGGCTGAGCTGGCAAAGTGCAGTGAGGTCCTATCCATCAATA 2650AccUP1 TGATCAAGGGTATTCCCAAGGCTGAGCTGGCAAAGTGCAGTGAGGTCCTATCCATCAATA 2650Acc224 TGATCAAGGGTATTCCCAAGGCTGAGCTCGCAAAGTGCAGTGAGGTCCTATCCATCAATA 2581 ******* ********...****..** *****.***** ***** **.******.. * Acc414 TCATCGATCGTTTCGGACCTCCCCTTGTTGGGATATTCAAAGTTCCCGGCAGTCATATGC 2737Acc420 TCATCGATCGTTTCGGACCTCCCCTTGTTGGGATATTCAAAGTTCCCGGCAGTCATATGC 2737Acc761 TCATCGATCGTTTCGGACCTCCCCTTGTTGGGATATTCAAAGTTCCCGGCAGTCATATGC 2737K60_Pik-p TCATCGATCGTTTCGGACCTCCCCTTGTTGGGATATTCAAAGTTCCCGGCAGTCATATGC 2731Acc130 TCATCGATCGTTTCGGACCTCCCCTTGTTGGGATATTCAAAGTTCCCGGCAGTCATATGC 2731Acc108 TCATCGATCGTTTCGGACCTCCCCTTGTTGGGATATTCAAAGTTCCCGGCAGTCATATGC 2731Acc719 TCATCGATCGTTTCGGACCTCCCCTTGTTGGGATATTCAAAGTTCCCGGCAGTCATATGC 2731Acc729 TCATCGATCGTTTCGGACCTCCCCTTGTTGGGATATTCAAAGTTCCCGGCAGTCATATGC 2731Acc709 TCATCGATCGTTTCGGACCTCCCCTTGTTGGGATATTCAAAGTTCCCGGCAGTCATATGC 2731Acc710 TCATCGATCGTTTCGGACCTCCCCTTGTTGGGATATTCAAAGTTCCCGGCAGTCATATGC 2731Acc504 TCATCGATCGTTTCGGACCTCCCCTTGTTGGGATATTCAAAGTTCCCGGCAGTCATATGC 2731Acc848 TCATCGATCGTTTCGGACCTCCCCTTGTTGGGATATTCAAAGTTCCCGGCAGTCATATGC 2731Acc563 TCATCGATCGTTTCGGACCTCCCCTTGTTGGGATATTCAAAGTTCCCGGCAGTCATATGC 2731Acc757 TCATCGATCGTTTCGGACCTCCCCTTGTTGGGATATTCAAAGTTCCCGGCAGTCATATGC 2731Tsuyuake_Pik-m TCATCGATCGTTTCGGACCTCCCCTTGTTGGGATATTCAAAGTTCCCGGCAGTCATATGC 2731Kanto51_Pik TCATCGATCGTTTCGGACCTCCCCTTGTTGGGATATTCAAAGTTCCCGGCAGTCATATGC 2731Kusabue_Pik TCATCGATCGTTTCGGACCTCCCCTTGTTGGGATATTCAAAGTTCCCGGCAGTCATATGC 2731Acc201 TTGTCGATCGTTTAGGATCTCCCCCTATTGGCATATTCAAGGTTATTGGCTTGCACAAGA 2641Acc206 TTGTCGATCGTTTAGGATCTCCCCCTATTGGCATATTCAAGGTTATTGGCTTGCACAAGA 2641Acc1 TTGTCGATCGTTTAGGATCTCCCCCTATTGGCATATTCAAGGTTATTGGCTTGCACAAGA 2710Acc101 TTGTCGATCGTTTAGGATCTCCCCCTATTGGCATATTCAAGGTTATTGGCTTGCACAAGA 2641Acc718 TTGTCGATCGTTTAGGATCTCCCCCTATTGGCATATTCAAGGTTATTGGCTTGCACAAGA 2710Acc724 TTGTCGATCGTTTAGGATCTCCCCCTATTGGCATATTCAAGGTTATTGGCTTGCACAAGA 2713Acc715 TTGTCGATCGTTTAGGATCTCCCCCTATTGGCATATTCAAGGTTATTGGCTTGCACAAGA 2713Acc706 TTGTCGATCGTTTAGGATCTCCCCCTATTGGCATATTCAAGGTTATTGGCTTGCACAAGA 2644Acc624 TTGTCGATCGTTTAGGATCTCCCCCTATTGGCATATTCAAGGTTATTGGCTTGCACAAGA 2644Acc440 TTGTCGATCGTTTAGGATCTCCCCCTATTGGCATATTCAAGGTTATTGGCTTGCACAAGA 2656Acc868 TTGTCGATCGTTTAGGATCTCCCCCTATTGGCATATTCAAGGTTATTGGCTTGCACAAGA 2656Acc220 TTGTCGATCGTTTAGGATCTCCCCCTATTGGCATATTCAAGGTTATTGGCTTGCACAAGA 2710Nipponbare TTGTCGATCGTTTAGGATCTCCCCCTATTGGCATATTCAAGGTTATTGGCTTGCACAAGA 2710AccUP3 TTGTCGATCGTTTAGGATCTCCCCCTATTGGCATATTCAAGGTTATTGGCTTGCACAAGA 2710AccUP1 TTGTCGATCGTTTAGGATCTCCCCCTATTGGCATATTCAAGGTTATTGGCTTGCACAAGA 2710Acc224 TTGTCGATCGTTTAGGATCTCCCCCTATTGGCATATTCAAGGTTATTGGCTTGCACAAGA 2641 * .**********.*** ****** *.**** ********.***. ***: ** *:*. 

Ashikawa et al. Supplementary Fig. S1 (24/30)

Acc414 GTATCCCGAAGATGATCAAAGACCACTTCCGCGTTCTTTCTTGCCTAGACATCAGGCTCT 2797Acc420 GTATCCCGAAGATGATCAAAGACCACTTCCGCGTTCTTTCTTGCCTAGACATCAGGCTCT 2797Acc761 GTATCCCGAAGATGATCAAAGACCACTTCCGCGTTCTTTCTTGCCTAGACATCAGGCTCT 2797K60_Pik-p GTATCCCGAAGATGATCAAAGACCACTTCCGCGTTCTTTCTTGCCTAGACATCAGGCTCT 2791Acc130 GTATCCCGAAGATGATCAAAGACCACTTCCGCGTTCTTTCTTGCCTAGACATCAGGCTCT 2791Acc108 GTATCCCGAAGATGATCAAAGACCACTTCCGCGTTCTTTCTTGCCTAGACATCAGGCTCT 2791Acc719 GTATCCCGAAGATGATCAAAGACCACTTCCGCGTTCTTTCTTGCCTAGACATCAGGCTCT 2791Acc729 GTATCCCGAAGATGATCAAAGACCACTTCCGCGTTCTTTCTTGCCTAGACATCAGGCTCT 2791Acc709 GTATCCCGAAGATGATCAAAGACCACTTCCGCGTTCTTTCTTGCCTAGACATCAGGCTCT 2791Acc710 GTATCCCGAAGATGATCAAAGACCACTTCCGCGTTCTTTCTTGCCTAGACATCAGGCTCT 2791Acc504 GTATCCCGAAGATGATCAAAGACCACTTCCGCGTTCTTTCTTGCCTAGACATCAGGCTCT 2791Acc848 GTATCCCGAAGATGATCAAAGACCACTTCCGCGTTCTTTCTTGCCTAGACATCAGGCTCT 2791Acc563 GTATCCCGAAGATGATCAAAGACCACTTCCGCGTTCTTTCTTGCCTAGACATCAGGCTCT 2791Acc757 GTATCCCGAAGATGATCAAAGACCACTTCCGCGTTCTTTCTTGCCTAGACATCAGGCTCT 2791Tsuyuake_Pik-m GTATCCCGAAGATGATCAAAGACCACTTCCGCGTTCTTTCTTGCCTAGACATCAGGCTCT 2791Kanto51_Pik GTATCCCGAAGATGATCAAAGACCACTTCCGCGTTCTTTCTTGCCTAGACATCAGGCTCT 2791Kusabue_Pik GTATCCCGAAGATGATCAAAGACCACTTCCGCGTTCTTTCTTGCCTAGACATCAGGCTCT 2791Acc201 GTATCCCGAAGCTGATCAAAGATCATTTCAATGTTCTTTCTTCCCTAGACATCAGGCGGT 2701Acc206 GTATCCCGAAGCTGATCAAAGATCATTTCAATGTTCTTTCTTCCCTAGACATCAGGCGGT 2701Acc1 GTATCCCGAAGCTGATCAAAGATCATTTCAATGTTCTTTCTTCCCTAGACATCAGGCGGT 2770Acc101 GTATCCCGAAGCTGATCAAAGATCATTTCAATGTTCTTTCTTCCCTAGACATCAGGCGGT 2701Acc718 GTATCCCGAAGCTGATCAAAGATCATTTCAATGTTCTTTCTTCCCTAGACATCAGGCGGT 2770Acc724 GTATCCCGAAGCTGATCAAAGATCATTTCAATGTTCTTTCTTCCCTAGACATCAGGCGGT 2773Acc715 GTATCCCGAAGCTGATCAAAGATCATTTCAATGTTCTTTCTTCCCTAGACATCAGGCGGT 2773Acc706 GTATCCCGAAGCTGATCAAAGATCATTTCAATGTTCTTTCTTCCCTAGACATCAGGCGGT 2704Acc624 GTATCCCGAAGCTGATCAAAGATCATTTCAATGTTCTTTCTTCCCTAGACATCAGGCGGT 2704Acc440 GTATCCCGAAGCTGATCAAAGATCATTTCAATGTTCTTTCTTCCCTAGACATCAGGCGGT 2716Acc868 GTATCCCGAAGCTGATCAAAGATCATTTCAATGTTCTTTCTTCCCTAGACATCAGGCGGT 2716Acc220 GTATCCCGAAGCTGATCAAAGATCATTTCAATGTTCTTTCTTCCCTAGACATCAGGCGGT 2770Nipponbare GTATCCCGAAGCTGATCAAAGATCATTTCAATGTTCTTTCTTCCCTAGACATCAGGCGGT 2770AccUP3 GTATCCCGAAGCTGATCAAAGATCATTTCAATGTTCTTTCTTCCCTAGACATCAGGCGGT 2770AccUP1 GTATCCCGAAGCTGATCAAAGATCATTTCAATGTTCTTTCTTCCCTAGACATCAGGCGGT 2770Acc224 GTATCCCGAAGCTGATCAAAGATCATTTCAATGTTCTTTCTTCCCTAGACATCAGGCGGT 2701 ***********.********** ** ***.. ********** ************** * Acc414 GCCACAAGCTTGAGGATGATGACCAAAAGTTCCTCGCCGAGA---TGCCCAACCTGCAGA 2854Acc420 GCCACAAGCTTGAGGATGATGACCAAAAGTTCCTCGCCGAGA---TGCCCAACCTGCAGA 2854Acc761 GCCACAAGCTTGAGGATGATGACCAAAAGTTCCTCGCCGAGA---TGCCCAACCTGCAGA 2854K60_Pik-p GCCACAAGCTTGAGGATGATGACCAAAAGTTCCTCGCCGAGA---TGCCCAACCTGCAGA 2848Acc130 GCCACAAGCTTGAGGATGATGACCAAAAGTTCCTCGCCGAGA---TGCCCAACCTGCAGA 2848Acc108 GCCACAAGCTTGAGGATGATGACCAAAAGTTCCTCGCCGAGA---TGCCCAACCTGCAGA 2848Acc719 GCCACAAGCTTGAGGATGATGACCAAAAGTTCCTCGCCGAGA---TGCCCAACCTGCAGA 2848Acc729 GCCACAAGCTTGAGGATGATGACCAAAAGTTCCTCGCCGAGA---TGCCCAACCTGCAGA 2848Acc709 GCCACAAGCTTGAGGATGATGACCAAAAGTTCCTCGCCGAGA---TGCCCAACCTGCAGA 2848Acc710 GCCACAAGCTTGAGGATGATGACCAAAAGTTCCTCGCCGAGA---TGCCCAACCTGCAGA 2848Acc504 GCCACAAGCTTGAGGATGATGACCAAAAGTTCCTCGCCGAGA---TGCCCAACCTGCAGA 2848Acc848 GCCACAAGCTTGAGGATGATGACCAAAAGTTCCTCGCCGAGA---TGCCCAACCTGCAGA 2848Acc563 GCCACAAGCTTGAGGATGATGACCAAAAGTTCCTCGCCGAGA---TGCCCAACCTGCAGA 2848Acc757 GCCACAAGCTTGAGGATGATGACCAAAAGTTCCTCGCCGAGA---TGCCCAACCTGCAGA 2848Tsuyuake_Pik-m GCCACAAGCTTGAGGATGATGACCAAAAGTTCCTCGCCGAGA---TGCCCAACCTGCAGA 2848Kanto51_Pik GCCACAAGCTTGAGGATGATGACCAAAAGTTCCTCGCCGAGA---TGCCCAACCTGCAGA 2848Kusabue_Pik GCCACAAGCTTGAGGATGATGACCAAAAGTTCCTCGCCGAGA---TGCCCAACCTGCAGA 2848Acc201 ACAACAAGCTAGAGGAGGATGACCATGAGTTTCTAGCCAACAATATGCCTAACCTCCAGA 2761Acc206 ACAACAAGCTAGAGGAGGATGACCATGAGTTTCTAGCCAACAATATGCCTAACCTCCAGA 2761Acc1 ACAACAAGCTAGAGGAGGATGACCATGAGTTTCTAGCCAACAATATGCCTAACCTCCAGA 2830Acc101 ACAACAAGCTAGAGGAGGATGACCATGAGTTTCTAGCCAACAATATGCCTAACCTCCAGA 2761Acc718 ACAACAAGCTAGAGGAGGATGACCATGAGTTTCTAGCCAACAATATGCCTAACCTCCAGA 2830Acc724 ACAACAAGCTAGAGGAGGATGACCATGAGTTTCTAGCCAACAATATGCCTAACCTCCAGA 2833Acc715 ACAACAAGCTAGAGGAGGATGACCATGAGTTTCTAGCCAACAATATGCCTAACCTCCAGA 2833Acc706 ACAACAAGCTAGAGGAGGATGACCATGAGTTTCTAGCCAACAATATGCCTAACCTCCAGA 2764Acc624 ACAACAAGCTAGAGGAGGATGACCATGAGTTTCTAGCCAACAATATGCCTAACCTCCAGA 2764Acc440 ACAACAAGCTAGAGGAGGATGACCATGAGTTTCTAGCCAACAATATGCCTAACCTCCAGA 2776Acc868 ACAACAAGCTAGAGGAGGATGACCATGAGTTTCTAGCCAACAATATGCCTAACCTCCAGA 2776Acc220 ACAACAAGCTAGAGGAGGATGACCATGAGTTTCTAGCCAACAATATGCCTAACCTCCAGA 2830Nipponbare ACAACAAGCTAGAGGAGGATGACCATGAGTTTCTAGCCAACAATATGCCTAACCTCCAGA 2830AccUP3 ACAACAAGCTAGAGGAGGATGACCATGAGTTTCTAGCCAACAATATGCCTAACCTCCAGA 2830AccUP1 ACAACAAGCTAGAGGAGGATGACCATGAGTTTCTAGCCAACAATATGCCTAACCTCCAGA 2830Acc224 ACAACAAGCTAGAGGAGGATGACCATGAGTTTCTAGCCAACAATATGCCTAACCTCCAGA 2761 .*.*******:***** ********:.**** **.***.* * **** ***** **** 

Ashikawa et al. Supplementary Fig. S1 (25/30)

Acc414 CGCTCGTGCTGAGGTTCGAGGCCCTACCAAGACAACCCATAACCATCAACGGCACAGGCT 2914Acc420 CGCTCGTGCTGAGGTTCGAGGCCCTACCAAGACAACCCATAACCATCAACGGCACAGGCT 2914Acc761 CGCTCGTGCTGAGGTTCGAGGCCCTACCAAGACAACCCATAACCATCAACGGCACAGGCT 2914K60_Pik-p CGCTCGTGCTGAGGTTCGAGGCCCTACCAAGACAACCCATAACCATCAACGGCACAGGCT 2908Acc130 CGCTCGTGCTGAGGTTCGAGGCCCTACCAAGACAACCCATAACCATCAACGGCACAGGCT 2908Acc108 CGCTCGTGCTGAGGTTCGAGGCCCTACCAAGACAACCCATAACCATCAACGGCACAGGCT 2908Acc719 CGCTCGTGCTGAGGTTCGAGGCCCTACCAAGACAACCCATAACCATCAACGGCACAGGCT 2908Acc729 CGCTCGTGCTGAGGTTCGAGGCCCTACCAAGACAACCCATAACCATCAACGGCACAGGCT 2908Acc709 CGCTCGTGCTGAGGTTCGAGGCCCTACCAAGACAACCCATAACCATCAACGGCACAGGCT 2908Acc710 CGCTCGTGCTGAGGTTCGAGGCCCTACCAAGACAACCCATAACCATCAACGGCACAGGCT 2908Acc504 CGCTCGTGCTGAGGTTCGAGGCCCTACCAAGACAACCCATAACCATCAACGGCACAGGCT 2908Acc848 CGCTCGTGCTGAGGTTCGAGGCCCTACCAAGACAACCCATAACCATCAACGGCACAGGCT 2908Acc563 CGCTCGTGCTGAGGTTCGAGGCCCTACCAAGACAACCCATAACCATCAACGGCACAGGCT 2908Acc757 CGCTCGTGCTGAGGTTCGAGGCCCTACCAAGACAACCCATAACCATCAACGGCACAGGCT 2908Tsuyuake_Pik-m CGCTCGTGCTGAGGTTCGAGGCCCTACCAAGACAACCCATAACCATCAACGGCACAGGCT 2908Kanto51_Pik CGCTCGTGCTGAGGTTCGAGGCCCTACCAAGACAACCCATAACCATCAACGGCACAGGCT 2908Kusabue_Pik CGCTCGTGCTGAGGTTCGAGGCCCTACCAAGACAACCCATAACCATCAACGGCACAGGCT 2908Acc201 TGCTTGTACTGAGGTTCGAGGCCCCACAAAGAGAGCCCATCATCATTAACCGCACAGGCT 2821Acc206 TGCTTGTACTGAGGTTCGAGGCCCCACAAAGAGAGCCCATCATCATTAACCGCACAGGCT 2821Acc1 TGCTTGTACTGAGGTTCGAGGCCCCACAAAGAGAGCCCATCATCATTAACCGCACAGGCT 2890Acc101 TGCTTGTACTGAGGTTCGAGGCCCCACAAAGAGAGCCCATCATCATTAACCGCACAGGCT 2821Acc718 TGCTTGTACTGAGGTTCGAGGCCCCACAAAGAGAGCCCATCATCATTAACCGCACAGGCT 2890Acc724 TGCTTGTACTGAGGTTCGAGGCCCCACAAAGAGAGCCCATCATCATTAACCGCACAGGCT 2893Acc715 TGCTTGTACTGAGGTTCGAGGCCCCACAAAGAGAGCCCATCATCATTAACCGCACAGGCT 2893Acc706 TGCTTGTACTGAGGTTCGAGGCCCCACAAAGAGAGCCCATCATCATTAACCGCACAGGCT 2824Acc624 TGCTTGTACTGAGGTTCGAGGCCCCACAAAGAGAGCCCATCATCATTAACCGCACAGGCT 2824Acc440 TGCTTGTACTGAGGTTCGAGGCCCCACAAAGAGAGCCCATCATCATTAACCGCACAGGCT 2836Acc868 TGCTTGTACTGAGGTTCGAGGCCCCACAAAGAGAGCCCATCATCATTAACCGCACAGGCT 2836Acc220 TGCTTGTACTGAGGTTCGAGGCCCCACAAAGAGAGCCCATCATCATTAACCGCACAGGCT 2890Nipponbare TGCTTGTACTGAGGTTCGAGGCCCCACAAAGAGAGCCCATCATCATTAACCGCACAGGCT 2890AccUP3 TGCTTGTACTGAGGTTCGAGGCCCCACAAAGAGAGCCCATCATCATTAACCGCACAGGCT 2890AccUP1 TGCTTGTACTGAGGTTCGAGGCCCCACAAAGAGAGCCCATCATCATTAACCGCACAGGCT 2890Acc224 TGCTTGTACTGAGGTTCGAGGCCCCACAAAGAGAGCCCATCATCATTAACCGCACAGGCT 2821 *** **.**************** **.**** *.*****.* *** *** ********* Acc414 TCCAGATGCTGGAGAGCTTCCGTGTCGACAGCCGGGTGCCAAGGATAGCCTTCCATGAAG 2974Acc420 TCCAGATGCTGGAGAGCTTCCGTGTCGACAGCCGGGTGCCAAGGATAGCCTTCCATGAAG 2974Acc761 TCCAGATGCTGGAGAGCTTCCGTGTCGACAGCCGGGTGCCAAGGATAGCCTTCCATGAAG 2974K60_Pik-p TCCAGATGCTGGAGAGCTTCCGTGTCGACAGCCGGGTGCCAAGGATAGCCTTCCATGAAG 2968Acc130 TCCAGATGCTGGAGAGCTTCCGTGTCGACAGCCGGGTGCCAAGGATAGCCTTCCATGAAG 2968Acc108 TCCAGATGCTGGAGAGCTTCCGTGTCGACAGCCGGGTGCCAAGGATAGCCTTCCATGAAG 2968Acc719 TCCAGATGCTGGAGAGCTTCCGTGTCGACAGCCGGGTGCCAAGGATAGCCTTCCATGAAG 2968Acc729 TCCAGATGCTGGAGAGCTTCCGTGTCGACAGCCGGGTGCCAAGGATAGCCTTCCATGAAG 2968Acc709 TCCAGATGCTGGAGAGCTTCCGTGTCGACAGCCGGGTGCCAAGGATAGCCTTCCATGAAG 2968Acc710 TCCAGATGCTGGAGAGCTTCCGTGTCGACAGCCGGGTGCCAAGGATAGCCTTCCATGAAG 2968Acc504 TCCAGATGCTGGAGAGCTTCCGTGTCGACAGCCGGGTGCCAAGGATAGCCTTCCATGAAG 2968Acc848 TCCAGATGCTGGAGAGCTTCCGTGTCGACAGCCGGGTGCCAAGGATAGCCTTCCATGAAG 2968Acc563 TCCAGATGCTGGAGAGCTTCCGTGTCGACAGCCGGGTGCCAAGGATAGCCTTCCATGAAG 2968Acc757 TCCAGATGCTGGAGAGCTTCCGTGTCGACAGCCGGGTGCCAAGGATAGCCTTCCATGAAG 2968Tsuyuake_Pik-m TCCAGATGCTGGAGAGCTTCCGTGTCGACAGCCGGGTGCCAAGGATAGCCTTCCATGAAG 2968Kanto51_Pik TCCAGATGCTGGAGAGCTTCCGTGTCGACAGCCGGTTGCCAAGGATAGCCTTCCATGAAG 2968Kusabue_Pik TCCAGATGCTGGAGAGCTTCCGTGTCGACAGCCGGTTGCCAAGGATAGCCTTCCATGAAG 2968Acc201 TCCAGATGCTGGAGAGATTCCTTGTGGAGAGCCGGGTGCCACGGATAACCTTCCAGGAAG 2881Acc206 TCCAGATGCTGGAGAGATTCCTTGTGGAGAGCCGGGTGCCACGGATAACCTTCCAGGAAG 2881Acc1 TCCAGATGCTGGAGAGATTCCTTGTGGAGAGCCGGGTGCCACGGATAACCTTCCAGGAAG 2950Acc101 TCCAGATGCTGGAGAGATTCCTTGTGGAGAGCCGGGTGCCACGGATAACCTTCCAGGAAG 2881Acc718 TCCAGATGCTGGAGAGATTCCTTGTGGAGAGCCGGGTGCCACGGATAACCTTCCAGGAAG 2950Acc724 TCCAGATGATGGAGAGATTCCTTGTGGAGAGCCGGGTGCCACGGCTAACCTTCCAGGAAG 2953Acc715 TCCAGATGATGGAGAGATTCCTTGTGGAGAGCCGGGTGCCACGGCTAACCTTCCAGGAAG 2953Acc706 TCCAGATGATGGAGAGATTCCTTGTGGAGAGCCGGGTGCCACGGCTAACCTTCCAGGAAG 2884Acc624 TCCAGATGATGGAGAGATTCCTTGTGGAGAGCCGGGTGCCACGGCTAACCTTCCAGGAAG 2884Acc440 TCCAGATGCTGGAGAGATTCCTTGTGGAGAGCCGGGTGCCACGGATAACCTTCCAGGAAG 2896Acc868 TCCAGATGCTGGAGAGATTCCTTGTGGAGAGCCGGGTGCCACGGATAACCTTCCAGGAAG 2896Acc220 TCCAGATGCTGGAGAGATTCCTTGTGGAGAGCCGGGTGCCACGGATAACCTTCCAGGAAG 2950Nipponbare TCCAGATGCTGGAGAGATTCCTTGTGGAGAGCCGGGTGCCACGGATAACCTTCCAGGAAG 2950AccUP3 TCCAGATGCTGGAGAGATTCCTTGTGGAGAGCCGGGTGCCACGGATAACCTTCCAGGAAG 2950AccUP1 TCCAGATGCTGGAGAGATTCCTTGTGGAGAGCCGGGTGCCACGGATAACCTTCCAGGAAG 2950Acc224 TCCAGATGCTGGAGAGATTCCTTGTGGAGAGCCGGGTGCCACGGATAACCTTCCAGGAAG 2881 ********.*******.**** *** ** ****** *****.**.**.******* ****

Ashikawa et al. Supplementary Fig. S1 (26/30)

Acc414 ACGCCATGCCCAACCTCAAGCTTCTCGAGTTCAAGTTCTACGCCGGCCCAGCAAGCAACG 3034Acc420 ACGCCATGCCCAACCTCAAGCTTCTCGAGTTCAAGTTCTACGCCGGCCCAGCAAGCAACG 3034Acc761 ACGCCATGCCCAACCTCAAGCTTCTCGAGTTCAAGTTCTACGCCGGCCCAGCAAGCAACG 3034K60_Pik-p ACGCCATGCCCAACCTCAAGCTTCTCGAGTTCAAGTTCTACGCCGGCCCAGCAAGCAACG 3028Acc130 ACGCCATGCCCAACCTCAAGCTTCTCGAGTTCAAGTTCTACGCCGGCCCAGCAAGCAACG 3028Acc108 ACGCCATGCCCAACCTCAAGCTTCTCGAGTTCAAGTTCTACGCCGGCCCAGCAAGCAACG 3028Acc719 ACGCCATGCCCAACCTCAAGCTTCTCGAGTTCAAGTTCTACGCCGGCCCAGCAAGCAACG 3028Acc729 ACGCCATGCCCAACCTCAAGCTTCTCGAGTTCAAGTTCTACGCCGGCCCAGCAAGCAACG 3028Acc709 ACGCCATGCCCAACCTCAAGCTTCTCGAGTTCAAGTTCTACGCCGGCCCAGCAAGCAACG 3028Acc710 ACGCCATGCCCAACCTCAAGCTTCTCGAGTTCAAGTTCTACGCCGGCCCAGCAAGCAACG 3028Acc504 ACGCCATGCCCAACCTCAAGCTTCTCGAGTTCAAGTTCTACGCCGGCCCAGCAAGCAACG 3028Acc848 ACGCCATGCCCAACCTCAAGCTTCTCGAGTTCAAGTTCTACGCCGGCCCAGCAAGCAACG 3028Acc563 ACGCCATGCCCAACCTCAAGCTTCTCGAGTTCAAGTTCTACGCCGGCCCAGCAAGCAACG 3028Acc757 ACGCCATGCCCAACCTCAAGCTTCTCGAGTTCAAGTTCTACGCCGGCCCAGCAAGCAACG 3028Tsuyuake_Pik-m ACGCCATGCCCAACCTCAAGCTTCTCGAGTTCAAGTTCTACGCCGGCCCAGCAAGCAACG 3028Kanto51_Pik ACGCCATGCCCAACCTCAAGCTTCTCGAGTTCAAGTTCTACGCCGGCCCAGCAAGCAACG 3028Kusabue_Pik ACGCCATGCCCAACCTCAAGCTTCTCGAGTTCAAGTTCTACGCCGGCCCAGCAAGCAACG 3028Acc201 GAGCCATGCCCAAGCTCAAGCATCTCGAGTTTAAGTTCTACGCTGGCCCACCAAGCAAAG 2941Acc206 GAGCCATGCCCAAGCTCAAGCATCTCGAGTTTAAGTTCTACGCTGGCCCACCAAGCAAAG 2941Acc1 GAGCCATGCCCAAGCTCAAGCATCTCGAGTTCAAGTTCTACGCTGGCCCACCAAGCAAAG 3010Acc101 GAGCCATGCCCAAGCTCAAGCATCTCGAGTTTAAGTTCTACGCTGGCCCACCAAACAAAG 2941Acc718 GAGCCATGCCCAAGCTCAAGCATCTCGAGTTTAAGTTCTACGCTGGCCCACCAAACAAAG 3010Acc724 GAGCCATGCCCAAGCTCAAGCATCTCGAGTTCAAGTTCTACGCTGGCCCACCAAGCAAAG 3013Acc715 GAGCCATGCCCAAGCTCAAGCATCTCGAGTTCAAGTTCTACGCTGGCCCACCAAGCAAAG 3013Acc706 GAGCCATGCCCAAGCTCAAGCATCTCGAGTTCAAGTTCTACGCTGGCCCACCAAGCAAAG 2944Acc624 GAGCCATGCCCAAGCTCAAGCATCTCGAGTTCAAGTTCTACGCTGGCCCACCAAGCAAAG 2944Acc440 GAGCCATGCCCAAGCTCAAGCATCTCGAGTTCAAGTTCTACGCTGGCCCACCAAGCAAAG 2956Acc868 GAGCCATGCCCAAGCTCAAGCATCTCGAGTTCAAGTTCTACGCTGGCCCACCAAGCAAAG 2956Acc220 GAGCCATGCCCAAGCTCAAGCATCTCGAGTTTAAGTTCTACGCTGGCCCACCAAGCAAAG 3010Nipponbare GAGCCATGCCCAAGCTCAAGCATCTCGAGTTTAAGTTCTACGCTGGCCCACCAAGCAAAG 3010AccUP3 GAGCCATGCCCAAGCTCAAGCATCTCGAGTTTAAGTTCTACGCTGGCCCACCAAGCAAAG 3010AccUP1 GAGCCATGCCCAAGCTCAAGCATCTCGAGTTCAAGTTCTACGCTGGCCCACCAAGCAAAG 3010Acc224 GAGCCATGCCCAAGCTCAAGCATCTCGAGTTTAAGTTCTACGCTGGCCCACCAAGCAAAG 2941 ..*********** *******:********* *********** ****** ***.***.* Acc414 ATGCCATCGGCATCACCAACCTGAAGAGCCTCCAAAAGGTGGTCTTTCGGTGCTCGCCAT 3094Acc420 ATGCCATCGGCATCACCAACCTGAAGAGCCTCCAAAAGGTGGTCTTTCGGTGCTCGCCAT 3094Acc761 ATGCCATCGGCATCACCAACCTGAAGAGCCTCCAAAAGGTGGTCTTTCGGTGCTCGCCAT 3094K60_Pik-p ATGCCATCGGCATCACCAACCTGAAGAGCCTCCAAAAGGTGGTCTTTCGGTGCTCGCCAT 3088Acc130 ATGCCATCGGCATCACCAACCTGAAGAGCCTCCAAAAGGTGGTCTTTCGGTGCTCGCCAT 3088Acc108 ATGCCATCGGCATCACCAACCTGAAGAGCCTCCAAAAGGTGGTCTTTCGGTGCTCGCCAT 3088Acc719 ATGCCATCGGCATCACCAACCTGAAGAGCCTCCAAAAGGTGGTCTTTCGGTGCTCGCCAT 3088Acc729 ATGCCATCGGCATCACCAACCTGAAGAGCCTCCAAAAGGTGGTCTTTCGGTGCTCGCCAT 3088Acc709 ATGCCATCGGCATCACCAACCTGAAGAGCCTCCAAAAGGTGGTCTTTCGGTGCTCGCCAT 3088Acc710 ATGCCATCGGCATCACCAACCTGAAGAGCCTCCAAAAGGTGGTCTTTCGGTGCTCGCCAT 3088Acc504 ATGCCATCGGCATCACCAACCTGAAGAGCCTCCAAAAGGTGGTCTTTCGGTGCTCGCCAT 3088Acc848 ATGCCATCGGCATCACCAACCTGAAGAGCCTCCAAAAGGTGGTCTTTCGGTGCTCGCCAT 3088Acc563 ATGCCATCGGCATCACCAACCTGAAGAGCCTCCAAAAGGTGGTCTTTCGGTGCTCGCCAT 3088Acc757 ATGCCATCGGCATCACCAACCTGAAGAGCCTCCAAAAGGTGGTCTTTCGGTGCTCGCCAT 3088Tsuyuake_Pik-m ATGCCATCGGCATCACCAACCTGAAGAGCCTCCAAAAGGTGGTCTTTCGGTGCTCGCCAT 3088Kanto51_Pik ATGCCATCGGCATCACCAACCTGAAGAGCCTCCAAAAGGTGGTCTTTCGGTGCTCGCCAT 3088Kusabue_Pik ATGCCATCGGCATCACCAACCTGAAGAGCCTCCAAAAGGTGGTCTTTCGGTGCTCGCCAT 3088Acc201 ATCCCATAGGAATCACCCACCTCAAGAGCCTCCAAAAGGTGGTCTTTCGCTGCTCCAAAT 3001Acc206 ATCCCATAGGAATCACCCACCTCAAGAGCCTCCAAAAGGTGGTCTTTCGCTGCTCCAAAT 3001Acc1 ATCCCATAGGAATCACCCACCTCAAGAGCCTCCAAAAGGTGGTCTTTCGCTGCTCCAAAT 3070Acc101 ATCCCATAGGAATCACCCACCTCAAGAGCCTCCAAAAGGTGGTCTTTCGCTGCTCCAAAT 3001Acc718 ATCCCATAGGAATCACCCACCTCAAGAGCCTCCAAAAGGTGGTCTTTCGCTGCTCCAAAT 3070Acc724 ATCCCATAGGAATCACCCACCTCAAGAGCCTCCAAAAGGTGGTCTTTCGCTGCTCCAAAT 3073Acc715 ATCCCATAGGAATCACCCACCTCAAGAGCCTCCAAAAGGTGGTCTTTCGCTGCTCCAAAT 3073Acc706 ATCCCATAGGAATCACCCACCTCAAGAGCCTCCAAAAGGTGGTCTTTCGCTGCTCCAAAT 3004Acc624 ATCCCATAGGAATCACCCACCTCAAGAGCCTCCAAAAGGTGGTCTTTCGCTGCTCCAAAT 3004Acc440 ATCCCATAGGAATCACCCACCTCAAGAGCCTCCAAAAGGTGGTCTTTCGCTGCTCCAAAT 3016Acc868 ATCCCATAGGAATCACCCACCTCAAGAGCCTCCAAAAGGTGGTCTTTCGCTGCTCCAAAT 3016Acc220 ATCCCATAGGAATCACCCACCTCAAGAGCCTCCAAAAGGTGGTCTTTCGCTGCTCCAAAT 3070Nipponbare ATCCCATAGGAATCACCCACCTCAAGAGCCTCCAAAAGGTGGTCTTTCGCTGCTCCAAAT 3070AccUP3 ATCCCATAGGAATCACCCACCTCAAGAGCCTCCAAAAGGTGGTCTTTCGCTGCTCCAAAT 3070AccUP1 ATCCCATAGGAATCACCCACCTCAAGAGCCTCCAAAAGGTGGTCTTTCGCTGCTCCAAAT 3070Acc224 ATCCCATAGGAATCACCCACCTCAAGAGCCTCCAAAAGGTGGTCTTTCGCTGCTCCAAAT 3001 ** ****.**.******.**** ************************** ***** ..** 

Ashikawa et al. Supplementary Fig. S1 (27/30)

Acc414 GGTACAAGAGCGACGCCCCTGGCATCAGCGCCACCATTGACGTCGTGAAGAAAGAAGCCG 3154Acc420 GGTACAAGAGCGACGCCCCTGGCATCAGCGCCACCATTGACGTCGTGAAGAAAGAAGCCG 3154Acc761 GGTACAAGAGCGACGCCCCTGGCATCAGCGCCACCATTGACGTCGTGAAGAAAGAAGCCG 3154K60_Pik-p GGTACAAGAGCGACGCCCCTGGCATCAGCGCCACCATTGACGTCGTGAAGAAAGAAGCCG 3148Acc130 GGTACAAGAGCGACGCCCCTGGCATCAGCGCCACCATTGACGTCGTGAAGAAAGAAGCCG 3148Acc108 GGTACAAGAGCGACGCCCCTGGCATCAGCGCCACCATTGACGTCGTGAAGAAAGAAGCCG 3148Acc719 GGTACAAGAGCGACGCCCCTGGCATCAGCGCCACCATTGACGTCGTGAAGAAAGAAGCCG 3148Acc729 GGTACAAGAGCGACGCCCCTGGCATCAGCGCCACCATTGACGTCGTGAAGAAAGAAGCCG 3148Acc709 GGTACAAGAGCGACGCCCCTGGCATCAGCGCCACCATTGACGTCGTGAAGAAAGAAGCCG 3148Acc710 GGTACAAGAGCGACGCCCCTGGCATCAGCGCCACCATTGACGTCGTGAAGAAAGAAGCCG 3148Acc504 GGTACAAGAGCGACGCCCCTGGCATCAGCGCCACCATTGACGTCGTGAAGAAAGAAGCCG 3148Acc848 GGTACAAGAGCGACGCCCCTGGCATCAGCGCCACCATTGACGTCGTGAAGAAAGAAGCCG 3148Acc563 GGTACAAGAGCGACGCCCCTGGCATCAGCGCCACCATTGACGTCGTGAAGAAAGAAGCCG 3148Acc757 GGTACAAGAGCGACGCCCCTGGCATCAGCGCCACCATTGACGTCGTGAAGAAAGAAGCCG 3148Tsuyuake_Pik-m GGTACAAGAGCGACGCCCCTGGCATCAGCGCCACCATTGACGTCGTGAAGAAAGAAGCCG 3148Kanto51_Pik GGTACAAGAGCGACGCCCCTGGCATCAGCGCCACCATTGACGTCGTGAAGAAAGAAGCCG 3148Kusabue_Pik GGTACAAGAGCGACGCCCCTGGCATCAGCGCCACCATTGACGTCGTGAAGAAAGAAGCCG 3148Acc201 GGTACAAGAGCGACAACCCTGGCATCAAGGCTGCCATTGACGTCGTGAAGAAAGAAGCAA 3061Acc206 GGTACAAGAGCGACAACCCTGGCATCAAGGCTGCCATTGACGTCGTGAAGAAAGAAGCAA 3061Acc1 GGTACAAGAGCGACAACCCTGGCATCAAGGCTGCCATTGACGTCGTGAAGAAAGAAGCAA 3130Acc101 GGTACAAGAGCGACAACCCTGGCATCAAGGCTGCCATTGACGTCGTGAAGAAAGAAGCAA 3061Acc718 GGTACAAGAGCGACAACCCTGGCATCAAGGCTGCCATTGACGTCGTGAAGAAAGAAGCAA 3130Acc724 GGTACAAGAGCGACAACCCTGGCATCAAGGCTGCCATTGACGTCGTGAAGAAAGAAGCAA 3133Acc715 GGTACAAGAGCGACAACCCTGGCATCAAGGCTGCCATTGACGTCGTGAAGAAAGAAGCAA 3133Acc706 GGTACAAGAGCGACAACCCTGGCATCAAGGCTGCCATTGACGTCGTGAAGAAAGAAGCAA 3064Acc624 GGTACAAGAGCGACAACCCTGGCATCAAGGCTGCCATTGACGTCGTGAAGAAAGAAGCAA 3064Acc440 GGTACAAGAGCGACAACCCTGGCATCAAGGCTGCCATTGACGTCGTGAAGAAAGAAGCAA 3076Acc868 GGTACAAGAGCGACAACCCTGGCATCAAGGCTGCCATTGACGTCGTGAAGAAAGAAGCAA 3076Acc220 GGTACAAGAGCGACAACCCTGGCATCAAGGCTGCCATTGACGTCGTGAAGAAAGAAGCAA 3130Nipponbare GGTACAAGAGCGACAACCCTGGCATCAAGGCTGCCATTGACGTCGTGAAGAAAGAAGCAA 3130AccUP3 GGTACAAGAGCGACAACCCTGGCATCAAGGCTGCCATTGACGTCGTGAAGAAAGAAGCAA 3130AccUP1 GGTACAAGAGCGACAACCCTGGCATCAAGGCTGCCATTGACGTCGTGAAGAAAGAAGCAA 3130Acc224 GGTACAAGAGCGACAACCCTGGCATCAAGGCTGCCATTGACGTCGTGAAGAAAGAAGCAA 3061 **************..***********. ** .*************************.. Acc414 AGGAGCATCCCAACCGGCCGATCACCCTCCTCATCAATGCTGGGTATAAGGAGATATCAA 3214Acc420 AGGAGCATCCCAACCGGCCGATCACCCTCCTCATCAATGCTGGGTATAAGGAGATATCAA 3214Acc761 AGGAGCATCCCAACCGGCCGATCACCCTCCTCATCAATGCTGGGTATAAGGAGATATCAA 3214K60_Pik-p AGGAGCATCCCAACCGGCCGATCACCCTCCTCATCAATGCTGGGTATAAGGAGATATCAA 3208Acc130 AGGAGCATCCCAACCGGCCGATCACCCTCCTCATCAATGCTGGGTATAAGGAGATATCAA 3208Acc108 AGGAGCATCCCAACCGGCCGATCACCCTCCTCATCAATGCTGGGTATAAGGAGATATCAA 3208Acc719 AGGAGCATCCCAACCGGCCGATCACCCTCCTCATCAATGCTGGGTATAAGGAGATATCAA 3208Acc729 AGGAGCATCCCAACCGGCCGATCACCCTCCTCATCAATGCTGGGTATAAGGAGATATCAA 3208Acc709 AGGAGCATCCCAACCGGCCGATCACCCTCCTCATCAATGCTGGGTATAAGGAGATATCAA 3208Acc710 AGGAGCATCCCAACCGGCCGATCACCCTCCTCATCAATGCTGGGTATAAGGAGATATCAA 3208Acc504 AGGAGCATCCCAACCGGCCGATCACCCTCCTCATCAATGCTGGGTATAAGGAGATATCAA 3208Acc848 AGGAGCATCCCAACCGGCCGATCACCCTCCTCATCAATGCTGGGTATAAGGAGATATCAA 3208Acc563 AGGAGCATCCCAACCGGCCGATCACCCTCCTCATCAATGCTGGGTATAAGGAGATATCAA 3208Acc757 AGGAGCATCCCAACCGGCCGATCACCCTCCTCATCAATGCTGGGTATAAGGAGATATCAA 3208Tsuyuake_Pik-m AGGAGCATCCCAACCGGCCGATCACCCTCCTCATCAATGCTGGGTATAAGGAGATATCAA 3208Kanto51_Pik AGGAGCATCCCAACCGGCCGATCACCCTCCTCATCAATGCTGGGTATAAGGAGATATCAA 3208Kusabue_Pik AGGAGCATCCCAACCGGCCGATCACCCTCCTCATCAATGCTGGGTATAAGGAGATATCAA 3208Acc201 GGCAGCATCCCAACCGGCCGATCAGCCTTCTCATCACTGAGGGCGATAAGGAGGTACCGA 3121Acc206 GGCAGCATCCCAACCGGCCGATCAGCCTTCTCATCACTGAGGGCGATAAGGAGGTACCGA 3121Acc1 GGCAGCATCCCAACCGGCCGATCAGCCTTCTCATCACTGAGGGCGATAAGGAGGTACCGA 3190Acc101 GGCAGCATCCCAACCGGCCGATCAGCCTTCTCATCACTGAGGGCGATAAGGAGGTACCGA 3121Acc718 GGCAGCATCCCAACCGGCCGATCAGCCTTCTCATCACTGAGGGCGATAAGGAGGTACCGA 3190Acc724 GGCAGCATCCCAACCGGCCGATCAGCCTTCTCATCACTGAGGGCGATAAGGAGGTACCAA 3193Acc715 GGCAGCATCCCAACCGGCCGATCAGCCTTCTCATCACTGAGGGCGATAAGGAGGTACCAA 3193Acc706 GGCAGCATCCCAACCGGCCGATCAGCCTTCTCATCACTGAGGGCGATAAGGAGGTACCAA 3124Acc624 GGCAGCATCCCAACCGGCCGATCAGCCTTCTCATCACTGAGGGCGATAAGGAGGTACCAA 3124Acc440 GGCAGCATCCCAACCGGCCGATCAGCCTTCTCATCACTGAGGGCGATAAGGAGGTACCGA 3136Acc868 GGCAGCATCCCAACCGGCCGATCAGCCTTCTCATCACTGAGGGCGATAAGGAGGTACCGA 3136Acc220 GGCAGCATCCCAACCGGCCGATCAGCCTTCTCATCACTGAGGGCGATAAGGAGGTACCGA 3190Nipponbare GGCAGCATCCCAACCGGCCGATCAGCCTTCTCATCACTGAGGGCGATAAGGAGGTACCGA 3190AccUP3 GGCAGCATCCCAACCGGCCGATCAGCCTTCTCATCACTGAGGGCGATAAGGAGGTACCGA 3190AccUP1 GGCAGCATCCCAACCGGCCGATCAGCCTTCTCATCACTGAGGGCGATAAGGAGGTACCGA 3190Acc224 GGCAGCATCCCAACCGGCCGATCAGCCTTCTCATCACTGAGGGCGATAAGGAGGTACCGA 3121 .* ********************* *** *******.**. ** ********.** *.*

Ashikawa et al. Supplementary Fig. S1 (28/30)

Acc414 ---CTGAGTCACACGGGAGCAGTGAAAACATTGCGGGCAGCAGTGGGATCGATACTGAGC 3271Acc420 ---CTGAGTCACACGGGAGCAGTGAAAACATTGCGGGCAGCAGTGGGATCGATACTGAGC 3271Acc761 ---CTGAGTCACACGGGAGCAGTGAAAACATTGCGGGCAGCAGTGGGATCGATACTGAGC 3271K60_Pik-p ---CTGAGTCACACGGGAGCAGTGAAAACATTGCGGGCAGCAGTGGGATCGATACTGAGC 3265Acc130 ---CTGAGTCACACGGGAGCAGTGAAAACATTGCGGGCAGCAGTGGGATCGATACTGAGC 3265Acc108 ---CTGAGTCACACGGGAGCAGTGAAAACATTGCGGGCAGCAGTGGGATCGATACTGAGC 3265Acc719 ---CTGAGTCACACGGGAGCAGTGAAAACATTGCGGGCAGCAGTGGGATCGATACTGAGC 3265Acc729 ---CTGAGTCACACGGGAGCAGTGAAAACATTGCGGGCAGCAGTGGGATCGATACTGAGC 3265Acc709 ---CTGAGTCACACGGGAGCAGTGAAAACATTGCGGGCAGCAGTGGGATCGATACTGAGC 3265Acc710 ---CTGAGTCACACGGGAGCAGTGAAAACATTGCGGGCAGCAGTGGGATCGATACTGAGC 3265Acc504 ---CTGAGTCACACGGGAGCAGTGAAAACATTGCGGGCAGCAGTGGGATCGATACTGAGC 3265Acc848 ---CTGAGTCACACGGGAGCAGTGAAAACATTGCGGGCAGCAGTGGGATCGATACTGAGC 3265Acc563 ---CTGAGTCACACGGGAGCAGTGAAAACATTGCGGGCAGCAGTGGGATCGATACTGAGC 3265Acc757 ---CTGAGTCACACGGGAGCAGTGAAAACATTGCGGGCAGCAGTGGGATCGATACTGAGC 3265Tsuyuake_Pik-m ---CTGAGTCACACGGGAGCAGTGAAAACATTGCGGGCAGCAGTGGGATCGATACTGAGC 3265Kanto51_Pik ---CTGAGTCACACGGGAGCAGTGAAAACATTGCGGGCAGCAGTGGGATCGATACTGAGC 3265Kusabue_Pik ---CTGAGTCACACGGGAGCAGTGAAAACATTGCGGGCAGCAGTGGGATCGATACTGAGC 3265Acc201 ATATTGAGGCACACGGGAGCAGTGAAAACATTGT------CGTTG---TCCACGCTGCTC 3172Acc206 ATATTGAGGCACACGGGAGCAGTGAAAACATTGT------CGTTG---TCCACGCTGCTC 3172Acc1 ATATTGAGGCACACGGGAGCAGTGAAAACATTGT------CGTTG---TCCACACTGCTC 3241Acc101 ATATTGAGGCACACGGGAGCAGTGAAAATATTGT------CGTTG---TCCACGCTGCTC 3172Acc718 ATATTGAGGCACACGGGAGCAGTGAAAATATTGT------CGTTG---TCCACGCTGCTC 3241Acc724 ATATTGAGGCACACGGGAGCAGTGAAAACATTGT------CGTTG---TCCACGCTGCTC 3244Acc715 ATATTGAGGCACACGGGAGCAGTGAAAACATTGT------CGTTG---TCCACGCTGCTC 3244Acc706 ATATTGAGGCACACGGGAGCAGTGAAAACATTGT------CGTTG---TCCACGCTGCTC 3175Acc624 ATATTGAGGCACACGGGAGCAGTGAAAACATTGT------CGTTG---TCCACGCTGCTC 3175Acc440 ATATTGAGGCACACGGGAGCAGTGTAAACATTGT------CGTTG---TCCACGCTGCTC 3187Acc868 ATATTGAGGCACACGGGAGCAGTGTAAACATTGT------CGTTG---TCCACGCTGCTC 3187Acc220 ATATTGAGGCACACGGGAGCAGTGAAAACATTGT------CGTTG---TCCACGCTGCTC 3241Nipponbare ATATTGAGGCACACGGGAGCAGTGAAAACATTGT------CGTTG---TCCACGCTGCTC 3241AccUP3 ATATTGAGGCACACGGGAGCAGTGAAAACATTGT------CGTTG---TCCACGCTGCTC 3241AccUP1 ATATTGAGGCACACGGGAGCAGTGAAAACATTGT------CGTTG---TCCACACTGCTC 3241Acc224 ATATTGAGGCACACGGGAGCAGTGAAAACATTGT------CGTTG---TCCACGCTGCTC 3172 **** ***************:*** **** *. ** ** * .***. * Acc414 CTGCACAGGCACAGCATGATAATCTCCCTGCTGTTCGAGATG--ACTACAAGGGAAAAGG 3329Acc420 CTGCACAGGCACAGCATGATAATCTCCCTGCTGTTCGAGATG--ACTACAAGGGAAAAGG 3329Acc761 CTGCACAGGCACAGCATGATAATCTCCCTGCTGTTCGAGATG--ACTACAAGGGAAAAGG 3329K60_Pik-p CTGCACAGGCACAGCATGATAATCTCCCTGCTGTTCGAGATG--ACTACAAGGGAAAAGG 3323Acc130 CTGCACAGGCACAGCATGATAATCTCCCTGCTGTTCGAGATG--ACTACAAGGGAAAAGG 3323Acc108 CTGCACAGGCACAGCATGATAATCTCCCTGCTGTTCGAGATG--ACTACAAGGGAAAAGG 3323Acc719 CTGCACAGGCACAGCATGATAATCTCCCTGCTGTTCGAGATG--ACTACAAGGGAAAAGG 3323Acc729 CTGCACAGGCACAGCATGATAATCTCCCTGCTGTTCGAGATG--ACTACAAGGGAAAAGG 3323Acc709 CTGCACAGGCACAGCATGATAATCTCCCTGCTGTTCGAGATG--ACTACAAGGGAAAAGG 3323Acc710 CTGCACAGGCACAGCATGATAATCTCCCTGCTGTTCGAGATG--ACTACAAGGGAAAAGG 3323Acc504 CTGCACAGGCACAGCATGATAATCTCCCTGCTGTTCGAGATG--ACTACAAGGGAAAAGG 3323Acc848 CTGCACAGGCACAGCATGATAATCTCCCTGCTGTTCGAGATG--ACTACAAGGGAAAAGG 3323Acc563 CTGCACAGGCACAGCATGATAATCTCCCTGCTGTTCGAGATG--ACTACAAGGGAAAAGG 3323Acc757 CTGCACAGGCACAGCATGATAATCTCCCTGCTGTTCGAGATG--ACTACAAGGGAAAAGG 3323Tsuyuake_Pik-m CTGCACAGGCACAGCATGATAATCTCCCTGCTGTTCGAGATG--ACTACAAGGGAAAAGG 3323Kanto51_Pik CTGCACAGGCACAGCATGATAATCTCCCTGCTGTTCGAGATG--ACTACAAGGGAAAAGG 3323Kusabue_Pik CTGCACAGGCACAGCATGATAATCTCCCTGCTGTTCGAGATG--ACTACAAGGGAAAAGG 3323Acc201 CTG-AC-GACGCCATCAGTTGCTCTAGCTGC-GGCCGAACCAGCACTAGTATCCAAGAGG 3229Acc206 CTG-AC-GACGCCATCAGTTGCTCTAGCTGC-GGCCGAACCAGCACTAGTATCCAAGAGG 3229Acc1 CTG-AC-GACGCCATCAGTTGCTCTAGCTGC-GGCCGAACCAGCACTAGTATCCAAGAGG 3298Acc101 CTG-AC-GACGCCATCAGTTGCTCTAGCTGC-GGCCGAACCAGCACTAGTATCCAACAGG 3229Acc718 CTG-AC-GACGCCATCAGTTGCTCTAGCTGC-GGCCGAACCAGCACTAGTATCCAACAGG 3298Acc724 CTG-AC-GACGCCATCAGTTGCTCTAGCTGC-GGCCGAACCAGCACTAGTATCCAAGAGG 3301Acc715 CTG-AC-GACGCCATCAGTTGCTCTAGCTGC-GGCCGAACCAGCACTAGTATCCAAGAGG 3301Acc706 CTG-AC-GACGCCATCAGTTGCTCTAGCTGC-GGCCGAACCAGCACTAGTATCCAAGAGG 3232Acc624 CTG-AC-GACGCCATCAGTTGCTCTAGCTGC-GGCCGAACCAGCACTAGTATCCAAGAGG 3232Acc440 CTG-AC-GACGCCATCAGTTGCTCTAGCTGC-GGCCGAACCAGCACTAGTATCCAAGAGG 3244Acc868 CTG-AC-GACGCCATCAGTTGCTCTAGCTGC-GGCCGAACCAGCACTAGTATCCAAGAGG 3244Acc220 CTG-AC-GACGCCATCAGTTGCTCTAGCTGC-GGCCGAACCAGCACTAGTATCCAAGAGG 3298Nipponbare CTG-AC-GACGCCATCAGTTGCTCTAGCTGC-GGCCGAACCAGCACTAGTATCCAAGAGG 3298AccUP3 CTG-AC-GACGCCATCAGTTGCTCTAGCTGC-GGCCGAACCAGCACTAGTATCCAAGAGG 3298AccUP1 CTG-AC-GACGCCATCAGTTGCTCTAGCTGC-GGCCGAACCAGCACTAGTATCCAAGAGG 3298Acc224 CTG-AC-GACGCCATCAGTTGCTCTAGCTGC-GGCCGAACCAGCACTAGTATCCAAGAGG 3229 *** ** *.*.*.. .:*:*..***. **** * ***.. . **** :* ** *** 

Ashikawa et al. Supplementary Fig. S1 (29/30)

Acc414 GATTCTTCTTGATGGCAGGTGTCCTACCTGCGGCCGAGCGACTAAAATTGAAGAGGAAAC 3389Acc420 GATTCTTCTTGATGGCAGGTGTCCTACCTGCGGCCGAGCGACTAAAATTGAAGAGGAAAC 3389Acc761 GATTCTTCTTGATGGCAGGTGTCCTACCTGCGGCCGAGCGACTAAAATTGAAGAGGAAAC 3389K60_Pik-p GATTCTTCTTGATGGCAGGTGTCCTACCTGCGGCCGAGCGACTAAAATTGAAGAGGAAAC 3383Acc130 GATTCTTCTTGATGGCAGGTGTCCTACCTGCGGCCGAGCGACTAAAATTGAAGAGGAAAC 3383Acc108 GATTCTTCTTGATGGCAGGTGTCCTACCTGCGGCCGAGCGACTAAAATTGAAGAGGAAAC 3383Acc719 GATTCTTCTTGATGGCAGGTGTCCTACCTGCGGCCGAGCGACTAAAATTGAAGAGGAAAC 3383Acc729 GATTCTTCTTGATGGCAGGTGTCCTACCTGCGGCCGAGCGACTAAAATTGAAGAGGAAAC 3383Acc709 GATTCTTCTTGATGGCAGGTGTCCTACCTGCGGCCGAGCGACTAAAATTGAAGAGGAAAC 3383Acc710 GATTCTTCTTGATGGCAGGTGTCCTACCTGCGGCCGAGCGACTAAAATTGAAGAGGAAAC 3383Acc504 GATTCTTCTTGATGGCAGGTGTCCTACCTGCGGCCGAGCGACTAAAATTGAAGAGGAAAC 3383Acc848 GATTCTTCTTGATGGCAGGTGTCCTACCTGCGGCCGAGCGACTAAAATTGAAGAGGAAAC 3383Acc563 GATTCTTCTTGATGGCAGGTGTCCTACCTGCGGCCGAGCGACTAAAATTGAAGAGGAAAC 3383Acc757 GATTCTTCTTGATGGCAGGTGTCCTACCTGCGGCCGAGCGACTAAAATTGAAGAGGAAAC 3383Tsuyuake_Pik-m GATTCTTCTTGATGGCAGGTGTCCTACCTGCGGCCGAGCGACTAAAATTGAAGAGGAAAC 3383Kanto51_Pik GATTCTTCTTGATGGCAGGTGTCCTACCTGCGGCCGAGCGACTAAAATTGAAGAGGAAAC 3383Kusabue_Pik GATTCTTCTTGATGGCAGGTGTCCTACCTGCGGCCGAGCGACTAAAATTGAAGAGGAAAC 3383Acc201 GAACAGTCC-GAGATCGAATA--CCAGCTATGG------------ATTTGTTCTGG---- 3270Acc206 GAACAGTCC-GAGATCGAATA--CCAGCTATGG------------ATTTGTTCTGG---- 3270Acc1 GAACAGTCC-GAGATCGAATA--CCAGCTATGG------------ATTTGTTCTGG---- 3339Acc101 GAACAGTCC-GAGATCGAATA--CCAGCTATGG------------ATTTGTTCTGG---- 3270Acc718 GAACAGTCC-GAGATCGAATA--CCAGCTATGG------------ATTTGTTCTGG---- 3339Acc724 GAACAGTCC-GAGATCGAATA--CCAGCTATGG------------ATTTGTTCTGG---- 3342Acc715 GAACAGTCC-GAGATCGAATA--CCAGCTATGG------------ATTTGTTCTGG---- 3342Acc706 GAACAGTCC-GAGATCGAATA--CCAGCTATGG------------ATTTGTTCTGG---- 3273Acc624 GAACAGTCC-GAGATCGAATA--CCAGCTATGG------------ATTTGTTCTGG---- 3273Acc440 GAACAGTCC-GAGATCGAATA--CCAGCTATGG------------ATTTGTTCTGG---- 3285Acc868 GAACAGTCC-GAGATCGAATA--CCAGCTATGG------------ATTTGTTCTGG---- 3285Acc220 GAACAGTCC-GAGATCGAATA--CCAGCTATGG------------ATTTGTTCTGG---- 3339Nipponbare GAACAGTCC-GAGATCGAATA--CCAGCTATGG------------ATTTGTTCTGG---- 3339AccUP3 GAACAGTCC-GAGATCGAATA--CCAGCTATGG------------ATTTGTTCTGG---- 3339AccUP1 GAACAGTCC-GAGATCGAATA--CCAGCTATGG------------ATTTGTTCTGG---- 3339Acc224 GAACAGTCC-GAGATCGAATA--CCAGCTATGG------------ATTTGTTCTGG---- 3270 **: . ** ** . *...*. * * **. ** *:***:: :**  Acc414 CCAAGATCGAGTAGCAGATATTGAAATTCAAACAGAAACTACTAGCTAG 3438Acc420 CCAAGATCGAGTAGCAGATATTGAAATTCAAACAGAAACTACTAGCTAG 3438Acc761 CCAAGATCGAGTAGCAGATATTGAAATTCAAACAGAAACTACTAGCTAG 3438K60_Pik-p CCAAGATCGAGTAGCAGATATTGAAATTCAAACAGAAACTACTAGCTAG 3432Acc130 CCAAGATCGAGTAGCAGATATTGAAATTCAAACAGAAACTACTAGCTAG 3432Acc108 CCAAGATCGAGTAGCAGATATTGAAATTCAAACAGAAACTACTAGCTAG 3432Acc719 CCAAGATCGAGTAGCAGATATTGAAATTCAAACAGAAACTACTAGCTAG 3432Acc729 CCAAGATCGAGTAGCAGATATTGAAATTCAAACAGAAACTACTAGCTAG 3432Acc709 CCAAGATCGAGTAGCAGATATTGAAATTCAAACAGAAACTACTAGCTAG 3432Acc710 CCAAGATCGAGTAGCAGATATTGAAATTCAAACAGAAACTACTAGCTAG 3432Acc504 CCAAGATCGAGTAGCAGATATTGAAATTCAAACAGAAACTACTAGCTAG 3432Acc848 CCAAGATCGAGTAGCAGATATTGAAATTCAAACAGAAACTACTAGCTAG 3432Acc563 CCAAGATCGAGTAGCAGATATTGAAATTCAAACAGAAACTACTAGCTAG 3432Acc757 CCAAGATCGAGTAGCAGATATTGAAATTCAAACAGAAACTACTAGCTAG 3432Tsuyuake_Pik-m CCAAGATCGAGTAGCAGATATTGAAATTCAAACAGAAACTACTAGCTAG 3432Kanto51_Pik CCAAGATCGAGTAGCAGATATTGAAATTCAAACAGAAACTACTAGCTAG 3432Kusabue_Pik CCAAGATCGAGTAGCAGATATTGAAATTCAAACAGAAACTACTAGCTAG 3432Acc201 CCGGAGTT---TAACAGCTATGAAAAAGCAAAAAGAAACTAG------- 3309Acc206 CCGGAGTT---TAACAGCTATGAAAAAGCAAAAAGAAACTAG------- 3309Acc1 CCGGAGTT---TAACAGCTATGAAAAGGCAAAAAGAAACTAG------- 3378Acc101 CCGGAGTT---TAACAGCTATGAAAAAGCAAAAAGAAACTAG------- 3309Acc718 CCGGAGTT---TAACAGCTATGAAAAAGCAAAAAGAAACTAG------- 3378Acc724 CCGGAGTT---TAACAGCTATGAAAAAGCAAAAAGAAACTAG------- 3381Acc715 CCGGAGTT---TAACAGCTATGAAAAAGCAAAAAGAAACTAG------- 3381Acc706 CCGGAGTT---TAACAGCTATGAAAAAGCAAAAAGAAACTAG------- 3312Acc624 CCGGAGTT---TAACAGCTATGAAAAAGCAAAAAGAAACTAG------- 3312Acc440 CCGGAGTT---TAACAGCTATGAAAAAGCAAAAAGAAACTAG------- 3324Acc868 CCGGAGTT---TAACAGCTATGAAAAAGCAAAAAGAAACTAC------- 3324Acc220 CCGGAGTT---TAACAGCTATGAAAAAGCAAAAAGAAACTAG------- 3378Nipponbare CCGGAGTT---TAACAGCTATGAAAAAGCAAAAAGAAACTAG------- 3378AccUP3 CCGGAGTT---TAACAGCTATGAAAAAGCAAAAAGAAACTAG------- 3378AccUP1 CCGGAGTT---TAACAGCTATGAAAAGGCAAAAAGAAACTAG------- 3378Acc224 CCGGAGTT---TAACAGCTATGAAAAAGCAAAAAGAAACTAG------- 3309 **....* **.***.*** .*** ****.********

Ashikawa et al. Supplementary Fig. S1 (30/30)