1A 1B 1D Supplementary figure 1. A DArT-based genetic map of wheat

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1A 1B 1D Supplementary figure 1. A DArT-based genetic map of wheat wPt-668160 wPt-734078 wPt-4811 wPt-6280 wPt-0196 wPt-2527 wPt-3198 wPt-4676 wPt-664778 wPt-665724 wPt-666776 wPt-669484 wPt-6709 wPt-671790 wPt-7296 wPt-730213 wPt-730618 wPt-732520 wPt-741357 wPt-744290 wPt-8770 wPt-9317 wPt-1924 wPt-8455 wPt-1782_ML1 wPt-2075_ML1 wPt-7905_ML1 wPt-6269 wPt-3347 wPt-666424 wPt-730136 wPt-6358 wPt-665174 wPt-671596 wPt-729972 wPt-671823 wPt-734107 wPt-667155 wPt-731476 wPt-671698 wPt-9752 tPt-5413 wPt-665545 wPt-734027 wPt-3560 wPt-664586 wPt-731412 wPt-667458 wPt-2150 wPt-3870 wPt-4735_ML1 wPt-4177 wPt-667180 wPt-665228 wPt-672089 wPt-731994_ML1 wPt-4666 wPt-6122 wPt-666723 wPt-7872 wPt-734054 wPt-3904 wPt-5776 wPt-667172 wPt-668236 wPt-733128 wPt-5411 wPt-3698 wPt-731617 wPt-732946 wPt-8172 wPt-666822 wPt-1709 wPt-730356 wPt-668214 wPt-730148 wPt-731806 wPt-731807 wPt-732546 wPt-733007 wPt-733464 wPt-733779 wPt-733858 wPt-734216 wPt-9429 wPt-732113 wPt-734090 wPt-1426 wPt-4886 wPt-5941 wPt-6941 wPt-7951 wPt-4765 wPt-7030 wPt-8347 wPt-3107_ML1 wPt-667634 wPt-669563 wPt-6074 wPt-667984 wPt-665250 wPt-9592 wPt-731445 wPt-6654 wPt-1906 wPt-665613 wPt-665784 wPt-734301 wPt-665590 wPt-9757 wPt-730408 wPt-665259 wPt-671483 wPt-666607 wPt-743331_ML1 wPt-664666 wPt-664968 wPt-664972 wPt-731282 wPt-4801 wPt-668087_ML1 wPt-667252 wPt-667153 wPt-4408 wPt-5660 wPt-9938 tPt-1012_ML1 wPt-0128_ML1 wPt-2847 wPt-730885 wPt-733811 wPt-733904 wPt-669499 wPt-4897 wPt-5316 wPt-667809 wPt-7784 wPt-8016 wPt-5367 wPt-7339 wPt-731090 wPt-734074 wPt-744613 tPt-6091_ML1 wPt-0164 wPt-2976 wPt-5274 wPt-666087 wPt-667288 wPt-669294 wPt-669800 wPt-730902 wPt-732377 wPt-732881 wPt-733820 wPt-734285 wPt-734288 wPt-1786_ML1 wPt-664593_ML1 wPt-664703_ML1 tPt-1419 tPt-7724 wPt-0432 wPt-0497 wPt-0769 wPt-1010 wPt-1011 wPt-2497 wPt-3712 wPt-3836_ML1 wPt-4065 wPt-5077 wPt-5160 wPt-6005 wPt-6754 wPt-6853 wPt-7147 wPt-9985 wPt-732616 wPt-0864_ML1 wPt-668205 wPt-7215 1.3 1.5 2.4 2.5 2.7 3.1 3.7 5.7 6.7 7.1 7.5 9.8 11.4 12.0 12.4 13.4 13.5 13.7 14.8 15.4 17.5 18.3 18.4 19.6 19.7 19.8 22.2 22.3 23.8 26.2 27.2 35.0 35.7 35.9 36.9 40.2 44.1 44.4 53.4 53.8 56.5 57.9 59.3 59.9 60.7 61.5 63.5 63.6 64.8 64.9 67.6 68.2 68.4 68.7 69.1 69.7 70.8 74.5 75.1 76.6 84.3 85.2 87.8 88.1 110.1 111.2 113.3 115.3 117.1 118.7 118.8 120.1 120.5 125.4 126.6 132.0 134.1 135.2 135.5 135.6 135.9 136.2 136.4 145.1 1A 1B wPt-4647 wPt-4971 wPt-666986 wPt-730758 wPt-730783 wPt-665480 wPt-6979 wPt-3855 wPt-3738 wPt-7953 wPt-4735_ML3 wPt-731994_ML2 wPt-2206 wPt-3707 wPt-3790 wPt-4196 wPt-4942 wPt-6461 wPt-8960 wPt-9664 wPt-666174 wPt-666411 wPt-741323 wPt-1387 wPt-671990 wPt-731267 wPt-664824 wPt-731920 wPt-732845 rPt-4471 wPt-5320 wPt-0413 wPt-666414 wPt-665814 wPt-9380 wPt-5503 wPt-4671 wPt-664609 wPt-666832 wPt-668040 wPt-671545 wPt-734229 wPt-671653 wPt-666719 wPt-3743 wPt-732602 wPt-667287 wPt-733835 wPt-734057 wPt-734081 wPt-732556 wPt-6059 wPt-7437_ML1 10.7 13.4 17.9 19.4 21.3 36.0 41.5 45.6 49.7 49.9 50.4 50.9 51.3 51.5 55.7 59.0 60.6 62.0 64.2 65.3 66.1 66.3 66.9 67.0 67.2 83.0 83.2 83.7 84.6 86.4 89.9 91.1 92.7 94.7 141.5 1D wPt-3465 wPt-2654 wPt-9639 wPt-2075_ML2 wPt-7905_ML2 tPt-5249 wPt-4863_ML1 wPt-0328 tPt-5675 wPt-3176 wPt-4366 wPt-4735_ML2 wPt-1139 wPt-8240 wPt-5801 wPt-5347 wPt-741980 wPt-0655 wPt-5006 wPt-6592 wPt-741094 wPt-4726 wPt-8744 wPt-2019 wPt-733882 wPt-8682 wPt-7242_ML1 tPt-8929 wPt-4325 wPt-5899 wPt-5385 wPt-5562 wPt-1726 wPt-2744 wPt-3787 wPt-740897 wPt-744960 wPt-1684 wPt-3103 wPt-6012_ML1 wPt-3266 wPt-5246 wPt-8622 wPt-8779_ML1 wPt-666564 wPt-8168 wPt-1573 wPt-1248 wPt-2461 wPt-9792 wPt-3566 wPt-5485 wPt-3451 wPt-3579 wPt-8280 wPt-0705 wPt-669577 rPt-7906 wPt-9857 wPt-9032 wPt-6975 wPt-1403 tPt-7980 wPt-7066 wPt-9809 wPt-5034 wPt-5061 wPt-0944 wPt-2526 wPt-4532 wPt-664593_ML2 wPt-664703_ML2 wPt-3950 wPt-667092 wPt-734314 wPt-1770 tPt-6091_ML2 wPt-1786_ML2 wPt-1070 wPt-5253 wPt-9028 0.0 2.8 4.8 5.3 6.7 7.2 7.3 8.5 9.1 9.7 wPt-1782_ML2 wPt-2751 wPt-741297 wPt-9524 wPt-8320 wPt-1560 wPt-744437 wPt-2052 wPt-2395 wPt-0983 wPt-7138 wPt-2988 wPt-742230 wPt-7422 wPt-3477 wPt-6370 wPt-668076 wPt-731699 wPt-9490 10.9 10.9 wPt-7094_ML1 11.2 wPt-7359 wPt-8267_ML1 11.7 11.6 wPt-0308 wPt-6442 11.9 12.3 12.3 tPt-0283 wPt-9605 wPt-0044 12.3 12.3 wPt-3098 13.5 12.3 wPt-8488 wPt-3942 wPt-742499 14.5 14.2 14.9 14.9 14.5 16.2 15.6 17.7 17.7 17.3 17.7 18.0 23.0 22.3 20.9 23.3 23.7 23.7 23.3 25.2 23.7 25.6 25.5 28.6 28.4 26.9 29.5 30.6 30.6 30.9 31.1 30.9 30.9 31.6 31.6 34.1 34.1 34.7 34.7 34.6 35.6 38.4 38.4 39.4 40.2 43.6 42.3 41.0 44.3 44.9 44.3 44.9 45.5 57.2 54.4 48.8 61.8 72.9 67.1 65.7 75.7 73.8 76.4 75.8 78.0 88.2 83.8 83.8 88.2 88.2 96.7 95.9 95.9 98.9 96.7 106.5 111.2 111.2 111.8 111.8 111.8 Supplementary figure 1. A DArT-based genetic map of wheat

2B 2A 2D Supplementary figure 1.Continued wPt-8132_ML1 wPt-3565_ML1 tPt-5584 wPt-0115 wPt-6570 tPt-6183_ML1 wPt-2087 wPt-3976 wPt-4450 wPt-4533 wPt-6207 wPt-9958 wPt-8004_ML1 wPt-9070_ML1 wPt-9432_ML1 tPt-1041 wPt-5647 wPt-0128_ML2 wPt-669245 wPt-7187 wPt-743061 wPt-744782 tPt-1012_ML2 tPt-6504_ML1 tPt-9405_ML1 wPt-8490 wPt-740658 wPt-664128 wPt-0003 wPt-0568 wPt-6711 wPt-8068 wPt-1657 wPt-0553 wPt-5029 wPt-5498 wPt-664251 wPt-743211 wPt-667820_ML1 wPt-4394 wPt-742997_ML1 wPt-1142 wPt-669755 wPt-7306 wPt-8596 tPt-8937 wPt-3114 wPt-665330 wPt-9320 wPt-2435 wPt-5251 wPt-3244 wPt-8826 wPt-7024_ML1 wPt-5865_ML1 wPt-1615_ML1 wPt-2858_ML1 wPt-9586 wPt-669355 wPt-741201 wPt-741584 wPt-7739_ML1 wPt-799683 wPt-800788 wPt-1499_ML1 wPt-0071 wPt-6687 wPt-6775_ML1 wPt-729945_ML1 wPt-7901 wPt-9277 wPt-9793 wPt-1480 4.0 8.3 10.2 10.8 12.1 15.3 17.6 18.8 19.5 19.9 20.0 20.5 21.0 25.2 28.8 31.6 34.3 37.0 43.1 45.7 45.9 48.0 62.1 62.4 63.5 64.3 65.4 70.9 71.9 74.4 77.7 79.0 80.0 81.1 93.5 95.0 98.5 103.8 108.9 109.4 110.1 2A tPt-4248 wPt-665550 wPt-1505_ML1 wPt-2397 wPt-0948 wPt-741382 wPt-7506 rPt-6122 wPt-6643 wPt-8916 wPt-0471 wPt-732040 wPt-0049 wPt-7360 wPt-2135 wPt-2274 wPt-2724 wPt-3378 wPt-732666_ML1 wPt-743307_ML1 wPt-6775_ML2 wPt-729945_ML2 wPt-2425 wPt-4368 wPt-4917 wPt-5736 wPt-6522_ML1 wPt-4773 wPt-741530_ML1 wPt-742929_ML1 wPt-3695 wPt-669273 wPt-733641 0.0 0.2 4.2 4.8 5.2 6.0 6.1 7.4 8.0 9.3 9.9 10.6 10.8 14.5 14.6 14.9 21.0 24.7 29.2 29.3 31.1 31.7 34.1 35.5 37.8 39.3 44.3 46.5 47.0 47.7 50.8 51.4 51.6 52.3 53.3 wPt-6311 wPt-0100 wPt-6271 wPt-1919 wPt-0643 wPt-8004_ML3 wPt-9070_ML3 wPt-3812 wPt-665644 wPt-730889 wPt-734280 wPt-731409 wPt-733567 wPt-667312 wPt-740836 wPt-666987 wPt-665342 wPt-6531_ML1 wPt-8393_ML1 wPt-6574 wPt-6850 wPt-2644 wPt-664520 wPt-667584 wPt-731148 wPt-731941 wPt-733674 wPt-1554 wPt-5586 wPt-665694 wPt-667476 wPt-6704 wPt-671737 wPt-730744 wPt-731134 wPt-731406 wPt-732270 wPt-732603 wPt-671778 wPt-4144 wPt-733932 wPt-1902 wPt-729860 wPt-732942 wPt-734230 wPt-2781 wPt-6847 wPt-8713_ML2 wPt-4413 wPt-668120 wPt-5865_ML2 wPt-664745 wPt-667406 wPt-665317 wPt-665868 wPt-666332 wPt-666887 wPt-668044 wPt-664805 wPt-730613_ML1 wPt-731130 wPt-666464 wPt-9749 wPt-3728 wPt-7466 wPt-669517 wPt-733725 wPt-1991 wPt-666809 wPt-667266 wPt-671650 wPt-6452 wPt-665836 wPt-732052 wPt-732923 wPt-667765 wPt-730677 wPt-667054 wPt-732666_ML2 wPt-743307_ML2 wPt-731220 wPt-731336 wPt-665102 wPt-668261 wPt-671742 wPt-730080 wPt-730757 wPt-3757 wPt-0153 wPt-1301 wPt-4329 wPt-6064 wPt-7825 wPt-7921 wPt-9848 wPt-667485 wPt-741208 wPt-730427 wPt-8319 wPt-1615_ML2 wPt-2858_ML2 wPt-666518 wPt-1499_ML2 15.3 15.9 48.9 52.9 53.5 56.7 58.0 60.2 67.3 69.0 70.1 70.9 71.5 72.9 73.0 74.2 75.3 75.5 75.7 77.7 79.5 79.6 79.9 80.3 81.0 81.1 82.2 83.4 83.5 84.1 85.0 86.3 86.5 88.6 89.0 90.5 95.6 95.8 96.6 98.1 99.0 99.5 100.3 101.0 101.2 101.3 102.6 102.7 103.5 103.6 104.2 112.6 114.0 114.7 2D wPt-3592 wPt-3459 wPt-3807 wPt-5934 wPt-6120 wPt-5960 wPt-6627 wPt-6575 wPt-6970 wPt-7312 wPt-7672 wPt-8424 wPt-8263 wPt-9274 wPt-8737 wPt-4350 wPt-4916 wPt-1024 tPt-1663 wPt-8918 wPt-8058 wPt-3565_ML2 wPt-9230 wPt-6158_ML2 wPt-667472 wPt-5195 tPt-4602 wPt-744022 wPt-744643 wPt-3949 wPt-9859 wPt-6706_ML1 wPt-5188_ML1 wPt-2106 tPt-7321 tPt-4246 wPt-4453 wPt-8398 53.6 58.6 59.7 63.2 64.6 68.5 69.9 70.4 72.1 72.8 74.8 74.9 75.5 76.2 76.6 76.9 77.1 77.7 78.8 79.0 79.8 80.4 80.8 81.0 81.3 81.5 82.0 85.1 86.2 86.5 86.9 87.8 87.9 88.3 88.5 89.1 89.3 90.2 90.7 93.1 93.6 96.5 97.2 97.6 100.3 100.7 101.6 102.0 102.7 104.1 105.0 105.9 106.4 106.6 107.3 107.8 111.1 117.9 118.6 119.5 122.4 123.3 125.2 125.4 126.1 126.9 129.9 wPt-1964 tPt-4627 wPt-733214 wPt-5250 wPt-665014 wPt-5374 tPt-6504_ML2 wPt-8004_ML2 wPt-9070_ML2 wPt-4134_ML1 wPt-1489 wPt-4664 wPt-8404 wPt-8349 wPt-4997 wPt-3561 wPt-7619 wPt-9402 wPt-7985 wPt-9423 wPt-4301 wPt-8072 wPt-743630 wPt-3983 wPt-9668 wPt-6932 wPt-7320 wPt-2600 wPt-666389 wPt-668087_ML2 wPt-0408_ML1 wPt-6477 wPt-6242 wPt-6471 tPt-9065 wPt-8548 wPt-6174 wPt-730172 wPt-669681 wPt-2430 wPt-1140 wPt-9350 wPt-2327 wPt-4889 wPt-800425 wPt-800707 wPt-3132 wPt-8460 wPt-1294 wPt-9131_ML1 wPt-3569_ML1 wPt-3272 wPt-741721 wPt-733572 wPt-0079 wPt-8521 wPt-4199 wPt-5878 wPt-7200 wPt-2854 wPt-0694 wPt-0473 wPt-0189 wPt-0950 wPt-9654 wPt-8340 wPt-0489 tPt-4125_ML1 wPt-5242 wPt-7305 wPt-745051 wPt-8629 wPt-4133 wPt-0906 wPt-8713_ML1 wPt-8693 wPt-1646 wPt-0697 wPt-3755 wPt-9257 wPt-3383 wPt-742206 wPt-5128 tPt-5438 wPt-5989 wPt-9336 wPt-3898 wPt-9190 wPt-7004 wPt-666931 wPt-732386 wPt-744808 wPt-7161 Supplementary figure 1.Continued

3D 3B 3A Supplementary figure 1. Continued wPt-667495 wPt-741190_ML2 2.2 10.9 11.0 14.5 16.3 16.5 18.5 21.5 22.5 26.2 37.5 39.4 41.2 43.0 46.4 48.8 49.8 50.9 51.6 52.6 3D wPt-5209 wPt-5522 wPt-8446 wPt-1162 wPt-742172 wPt-733477 wPt-9496_ML1 wPt-734202 wPt-741739 wPt-741817 wPt-742052 wPt-742337 wPt-742715 wPt-10291_ML1 wPt-742222_ML1 wPt-3260 wPt-3609 wPt-3761 wPt-3921_ML1 wPt-7984 wPt-666738_ML1 wPt-2557 wPt-666139 wPt-10006 wPt-11419 wPt-742528 tPt-9267 wPt-0264 wPt-6132 wPt-10311_ML2 wPt-741750 wPt-798970 wPt-744251 wPt-9066 wPt-2757 wPt-3094 wPt-3536 wPt-741331 wPt-741413 wPt-800213 wPt-9012 wPt-743847 wPt-7212 wPt-3231 wPt-5916 wPt-10991 tPt-6487 wPt-0571 wPt-10945 wPt-4842 wPt-7132 wPt-2748_ML2 wPt-5432 wPt-8855_ML2 wPt-7271_ML2 wPt-0013 wPt-0895 wPt-2193 wPt-2298 wPt-2766 wPt-5836 wPt-732330 wPt-733544 wPt-0610_ML1 wPt-8140 wPt-8238 wPt-731754 wPt-8356_ML2 wPt-0672 wPt-6802_ML1 wPt-6239 wPt-10948 wPt-664393 wPt-732044 wPt-7486 wPt-10005 wPt-1191 wPt-1484 wPt-2936 wPt-3046 wPt-6216 wPt-9579 tPt-1366 wPt-5105 wPt-6945 wPt-6973 wPt-7015 wPt-9170 wPt-10642 wPt-4209 wPt-1158 wPt-669328 rPt-5396 wPt-0327 wPt-11295 wPt-2091 wPt-4608 wPt-5390 wPt-5939 wPt-7152 wPt-8915 wPt-9432_ML2 wPt-9510 wPt-10458 wPt-10323_ML1 wPt-743661 wPt-4048_ML1 wPt-6020 wPt-6047 wPt-11218 wPt-3078 wPt-9443 wPt-668152_ML1 wPt-668181_ML1 wPt-741571 wPt-743775 wPt-9310 wPt-9433 tPt-6872 wPt-10033 wPt-11024 wPt-7142 wPt-7024_ML2 tPt-5281 wPt-4364 wPt-731910 wPt-2372 rPt-7068_ML1 wPt-10462_ML1 wPt-5786 wPt-2202_ML2 wPt-7254 wPt-10546 wPt-0644_ML1 tPt-7068 wPt-5020 wPt-7688 wPt-1171_ML1 wPt-11400 wPt-5906 wPt-8096 wPt-11278 wPt-3107_ML2 wPt-0896 wPt-10276_ML1 wPt-10455_ML1 wPt-8056 wPt-0065 wPt-5769 wPt-2904 wPt-664981 wPt-672088 wPt-1804 wPt-3725 wPt-10179 wPt-10176 wPt-9049_ML2 wPt-4974 wPt-5704 tPt-3621_ML1 wPt-6436 wPt-11049 wPt-4933 wPt-0345 wPt-2491 wPt-0912 wPt-666728 wPt-0367 wPt-10537 wPt-9368 wPt-6834 wPt-0324 wPt-8513 wPt-10758 wPt-0751 wPt-742982 wPt-2559_ML1 wPt-5072 wPt-6131 wPt-7614_ML1 wPt-0343 wPt-10874 tPt-4541 wPt-10071 wPt-6961 wPt-7158 wPt-2416 wPt-734141 wPt-1306 wPt-7354_ML1 wPt-7739_ML2 wPt-4412 wPt-8412_ML1 wPt-9788_ML1 wPt-0280 wPt-0438 wPt-0995 wPt-5825 wPt-7266 wPt-8141 wPt-8352 wPt-8983 11.3 12.0 13.0 13.7 14.1 14.2 16.1 17.0 19.0 20.0 20.3 20.7 23.0 23.3 24.6 24.9 25.1 25.4 25.6 26.5 26.7 27.4 27.6 28.8 29.2 30.2 33.8 34.6 37.1 37.2 37.8 39.0 42.9 43.1 44.2 44.9 45.2 47.6 49.0 49.7 51.5 53.1 53.7 54.3 56.5 57.1 57.7 58.3 58.7 59.9 61.3 63.1 65.2 65.3 65.4 65.7 66.5 66.7 67.5 68.5 70.7 71.0 74.3 74.4 75.0 75.4 77.4 78.9 79.0 79.2 81.1 83.0 84.6 85.4 85.8 86.0 87.1 87.3 92.2 94.7 94.9 95.5 97.6 98.3 101.2 105.3 106.3 107.3 110.4 113.0 115.4 119.4 122.6 123.3 124.6 127.4 128.7 128.9 129.2 131.3 131.4 131.8 132.1 132.4 132.5 133.2 135.4 135.5 136.3 136.8 3B wPt-6012_ML2 wPt-8356_ML1 wPt-7217 wPt-743723 wPt-664488 wPt-2253 wPt-729938_ML1 wPt-730115_ML1 wPt-733405 wPt-740590_ML1 wPt-741190_ML1 wPt-741484 wPt-9634 wPt-6854 wPt-9369 wPt-671711_ML1 wPt-732029 wPt-740544 wPt-741816 wPt-741848 wPt-741976 wPt-741986 wPt-742039 wPt-742118 wPt-742486 wPt-742665 wPt-743858 wPt-743909 wPt-2748_ML1 wPt-8855_ML1 wPt-1353 wPt-7890 wPt-10311_ML1 wPt-9928 wPt-2938 wPt-0836 wPt-1688 wPt-2478 wPt-1464 wPt-7341 wPt-7812 wPt-7992 tPt-0519 tPt-6949 wPt-0951 wPt-1655 wPt-7271_ML1 wPt-8779_ML2 wPt-0714 wPt-745076 wPt-0797 wPt-1923 wPt-4407 wPt-8593 tPt-1143 wPt-1681 wPt-2755 wPt-7608_ML1 wPt-7756 tPt-2603 wPt-744743 wPt-2202_ML1 wPt-2740 wPt-0286 wPt-1562 wPt-3816 wPt-9049_ML1 wPt-2127 wPt-733571 wPt-9422 wPt-4725 wPt-2698 wPt-5173 wPt-7340 tPt-7492 wPt-730156 wPt-5133 wPt-9761 wPt-9268 wPt-8892_ML1 wPt-743015 tPt-9901 wPt-4128 wPt-4398 tPt-6376 wPt-3195 wPt-3978 wPt-1694 wPt-1888 wPt-8876 wPt-5476 wPt-4545 wPt-2942 wPt-2144 wPt-8146 wPt-0398 wPt-9160 0.0 29.5 33.5 35.1 35.8 38.8 40.7 44.1 45.7 46.5 46.7 48.1 50.4 52.2 53.0 56.2 56.9 58.7 58.9 59.2 60.2 64.7 70.6 71.0 73.4 74.1 79.7 80.8 96.0 98.8 130.1 131.6 132.2 132.7 146.7 155.2 158.0 158.4 166.7 168.1 168.9 176.4 180.7 182.9 185.8 186.0 186.3 188.3 188.9 199.9 201.7 202.4 204.0 204.7 204.9 206.8 207.8 209.1 212.1 213.2 213.3 3A Supplementary figure 1. Continued

4B 4A 4D Supplementary figure 1.Continued wPt-4537 wPt-4280 wPt-744595 wPt-3439_ML1 wPt-6869_ML1 wPt-1272 wPt-5559 wPt-732448 wPt-733363 wPt-734310 wPt-1046 wPt-7233 wPt-730068 wPt-731583 wPt-8555 wPt-0246 wPt-4607 wPt-667593 tPt-5519 wPt-9393 wPt-744434 wPt-3991 wPt-5497 wPt-8892_ML2 wPt-5334 wPt-732423 wPt-8796 wPt-1505_ML2 tPt-4125_ML2 wPt-7062 wPt-9067 wPt-6209 wPt-733038 wPt-6016 wPt-1101 wPt-5303 wPt-730303 wPt-731869 tPt-4214 wPt-3608 wPt-3917 wPt-5265 wPt-8292 wPt-4962 wPt-5338 wPt-1115 0.0 14.9 15.5 16.6 19.9 20.4 20.7 22.6 39.2 55.4 57.8 58.5 61.3 65.0 65.3 67.8 68.0 68.7 68.9 70.9 94.1 97.0 99.3 104.9 108.3 110.7 114.5 119.5 4B wPt-9445 wPt-9738 wPt-2788 wPt-7612 wPt-4986_ML1 wPt-1091 wPt-3810 wPt-6728 wPt-744614 wPt-0162 wPt-0817 wPt-800147 wPt-800509 wPt-5951 tPt-9400 wPt-5428 wPt-5857 wPt-6997 wPt-7280 wPt-732259 wPt-2903 wPt-669203 wPt-671707 wPt-0538 wPt-2909_ML1 wPt-3349 wPt-8275 wPt-1743 wPt-8144 wPt-7096_ML1 wPt-7327 wPt-9901_ML1 wPt-2084 wPt-3795 wPt-5003 wPt-6440 wPt-7807 wPt-6502 wPt-9006_ML1 wPt-2780_ML1 wPt-3937 wPt-9305 wPt-2291 wPt-6404 wPt-744914_ML1 wPt-730913_ML1 wPt-1007 wPt-5578 wPt-666456_ML1 wPt-668307_ML1 wPt-669526 wPt-6900 wPt-2985 wPt-7354_ML2 wPt-8167 wPt-8271 wPt-0610_ML2 wPt-3449 wPt-7590 wPt-1155 wPt-3491 wPt-4424 wPt-9418 wPt-9641 wPt-0150 wPt-744256 wPt-669617_ML1 wPt-734161_ML1 rPt-7987_ML1 wPt-0764 wPt-4487_ML1 wPt-6390 wPt-7876 wPt-8657 wPt-742051_ML1 wPt-0023 wPt-0447 wPt-0763 wPt-1961 wPt-4064 wPt-4620_ML1 wPt-4828 wPt-5172 wPt-9675 wPt-664749 wPt-672107 wPt-742056 rPt-0238 wPt-6867 wPt-3845 wPt-4680 wPt-6757 wPt-731374 wPt-1161 wPt-2533 wPt-3250 wPt-6688 wPt-8091 wPt-3402_ML1 5.1 7.0 22.1 25.0 47.8 59.6 59.7 60.7 62.6 62.8 64.5 68.1 71.3 77.8 83.1 83.2 84.4 84.7 85.1 85.5 85.7 87.8 89.9 90.1 90.6 90.9 91.1 92.0 92.4 93.1 93.2 94.2 94.5 96.9 97.6 98.3 99.7 100.9 102.1 102.7 103.0 103.4 104.6 104.8 105.8 106.1 106.9 112.9 4A wPt-4572 wPt-0431 wPt-3058 wPt-5809 6.2 72.8 4D Supplementary figure 1.Continued

5B 5A 5D Supplementary figure 1. Continued wPt-1432 wPt-7240 wPt-1302 wPt-9006_ML2 wPt-9925_ML1 wPt-744314 wPt-9666 wPt-9724 wPt-2305_ML1 wPt-0819 wPt-8604 wPt-3833_ML1 wPt-7237 rPt-6127 wPt-3085 wPt-3873_ML1 wPt-6372_ML1 wPt-798756 wPt-5175 wPt-665267 wPt-0312_ML1 wPt-1149_ML1 wPt-5120 wPt-7029 wPt-5346 wPt-6348 wPt-7653 wPt-1784 tPt-8942 wPt-4736 wPt-2041_ML2 tPt-0228 wPt-8132_ML2 wPt-9814 wPt-5737 wPt-0963ML1 wPt-666323 wPt-3569_ML2 wPt-3995 tPt-4875 wPt-0929 wPt-1457 wPt-1951 wPt-6498_ML1 wPt-3439_ML2 wPt-1505_ML3 wPt-669837 wPt-744750 wPt-744851 wPt-9467_ML1 wPt-6706_ML2 wPt-3289 wPt-8637 wPt-0103 wPt-5514 tPt-7755 wPt-3012 wPt-5792 wPt-8163 wPt-742141 wPt-7167 wPt-1409 wPt-9613_ML1 wPt-4628 wPt-2607 wPt-7101 wPt-3503 wPt-666939 tPt-3719 wPt-1548 wPt-3457 wPt-6531_ML2 wPt-8393_ML2 wPt-4246 wPt-6135 wPt-3661 wPt-5896 wPt-3763 wPt-5604 wPt-5928 wPt-2707 wPt-4577 wPt-6191 wPt-0935 wPt-8094 wPt-9205_ML1 wPt-1304 wPt-9103 wPt-9598 wPt-730613_ML2 rPt-7889 wPt-3329 tPt-1253 wPt-3076 wPt-664788 wPt-1179_ML1 wPt-9504 tPt-3144 wPt-4418 wPt-7006 wPt-1348 wPt-667015 wPt-3402_ML2 wPt-0927 wPt-2804 wPt-4091 wPt-730313 wPt-4986_ML2 wPt-664746_ML1 wPt-6971 wPt-7238 wPt-2373 wPt-7665 wPt-9116 wPt-0484 wPt-3922 wPt-6465 wPt-4551 wPt-666215 wPt-7400 wPt-5118 wPt-0295 wPt-4402 tPt-3621_ML2 wPt-8449 0.0 0.6 1.2 6.2 17.3 20.9 24.4 25.5 26.4 27.3 27.9 28.2 28.4 29.4 31.9 32.7 33.0 35.0 36.7 37.5 37.9 38.8 42.1 42.9 43.2 43.4 43.6 43.8 44.5 44.8 48.4 48.5 48.8 52.5 53.5 54.2 60.3 64.8 67.6 69.2 69.3 69.9 71.3 72.2 72.4 73.0 73.9 76.4 82.6 93.7 97.3 98.5 108.4 111.6 112.9 114.9 117.5 118.1 120.0 120.6 122.4 125.1 132.6 137.7 138.1 139.6 140.7 141.4 144.6 148.5 150.5 151.8 151.9 154.4 154.7 155.3 155.9 156.3 158.4 158.8 160.6 162.3 5B wPt-9748 wPt-1165 wPt-666142 tPt-9702 wPt-2041_ML1 wPt-3620 wPt-5787 tPt-6183_ML2 wPt-4131 wPt-9452 wPt-5588 wPt-742925 wPt-744567 wPt-7769 wPt-7185 wPt-3884 wPt-3187 wPt-3509 wPt-733649 wPt-800634 wPt-800131 wPt-8226 wPt-3563 wPt-9094 wPt-667213 wPt-797301 wPt-797380 wPt-797381 wPt-797382 wPt-797581 wPt-798198 wPt-798459 wPt-798280 wPt-8794 wPt-1038 wPt-3334_ML1 wPt-5096 tPt-4184 tPt-6495 wPt-733461 tPt-2429 wPt-734145 wPt-4351 wPt-7061 wPt-1200 wPt-2873 wPt-4203 wPt-6462 23.3 35.1 35.6 36.8 37.7 37.9 38.7 40.1 40.6 40.8 41.1 41.2 41.4 42.3 42.7 44.8 45.3 46.1 48.4 48.5 50.5 111.4 112.4 117.1 118.4 118.8 122.8 123.5 123.7 123.9 5A wPt-7323 wPt-2256 wPt-0400 wPt-9788_ML2 30.1 57.8 161.7 5D Supplementary figure 1. Continued

6D 6A 6B Supplementary figure 1.Continued wPt-0864_ML2 wPt-730591 rPt-9065 tPt-0877 wPt-666574 wPt-671855 wPt-6904 wPt-741547 wPt-9679 wPt-669315 wPt-8266 wPt-5652 wPt-732062_ML1 wPt-733856_ML1 wPt-733976 wPt-731250 wPt-666074 tPt-2833 wPt-3524_ML1 wPt-731842 wPt-731934 wPt-9205_ML2 tPt-6278 tPt-7399 wPt-3605_ML1 wPt-665036_ML1 wPt-665782 wPt-666988 wPt-730631 wPt-734004 wPt-9113 wPt-667405 wPt-668000 wPt-671638 wPt-730460 wPt-733322 wPt-734157 wPt-741290 wPt-7663 wPt-2822 wPt-3965 wPt-7623 wPt-9584 wPt-664552 wPt-664733 wPt-666208 wPt-667170 wPt-667780 wPt-671799 wPt-730729 wPt-731010 wPt-732760 wPt-733764 wPt-8539 wPt-9131_ML2 wPt-2573 wPt-9690 wPt-9692 wPt-9132 wPt-671766 wPt-730168 wPt-0139 wPt-3091 wPt-7599 wPt-3308_ML1 wPt-671708 wPt-730109 wPt-730368 wPt-730456 wPt-730711 wPt-731413 wPt-733151 wPt-741037 wPt-7445 wPt-733115 wPt-733357 wPt-0357 wPt-666224_ML1 wPt-729806 wPt-667844 wPt-1981 wPt-729839 wPt-732263 wPt-0902 wPt-7857 wPt-664792 wPt-730772 wPt-732355 tPt-8557 wPt-7572 wPt-1695_ML1 wPt-665169 wPt-667261 wPt-671568 wPt-666773 wPt-666964 wPt-7809 wPt-9089 wPt-731592 wPt-732951 wPt-734140 wPt-8954 wPt-6829 tPt-9048_ML1 wPt-5480_ML1 wPt-669617_ML2 wPt-731524 wPt-741026 wPt-3127_ML1 rPt-6189 rPt-9324 tPt-6716 wPt-5696 wPt-671558 wPt-672030 wPt-730608 wPt-743435 wPt-7548 wPt-1375 wPt-1642 wPt-5572 wPt-6995 wPt-731120 wPt-9000 wPt-666494 wPt-665805 wPt-666724 wPt-730338 tPt-3786 wPt-668031 wPt-734345 wPt-734346 wPt-731002 wPt-732975 wPt-667607 wPt-9976 wPt-730629 wPt-732324 wPt-733051 wPt-733699 wPt-2632 wPt-3247 wPt-4145 wPt-4229 wPt-8124 wPt-9474 wPt-2582 wPt-664937_ML1 wPt-744786 tPt-6661 wPt-1661 wPt-731854 wPt-732328 wPt-6696 0.2 0.7 1.3 1.8 2.5 3.2 3.8 4.1 4.4 6.2 6.3 6.7 6.9 7.6 7.9 8.2 8.8 10.8 11.2 12.6 14.8 15.5 15.6 16.2 16.3 16.7 16.9 17.0 17.5 20.2 21.0 21.2 21.5 22.7 22.8 23.2 23.5 24.1 24.2 27.0 29.0 29.4 29.6 30.3 31.5 32.1 36.7 36.9 42.2 45.3 48.2 48.7 49.1 50.0 73.9 81.6 82.7 83.6 84.5 85.4 86.4 87.3 89.7 92.3 93.0 93.8 94.8 95.2 95.5 96.3 99.0 99.7 104.0 105.5 107.1 107.7 107.9 108.3 108.9 109.0 6A wPt-5188_ML2 wPt-6282 wPt-4012_ML2 wPt-667662_ML2 wPt-734331_ML2 wPt-7662 wPt-741533 wPt-7642_ML1 wPt-5234 wPt-8015 wPt-5971 wPt-7203 wPt-1547 wPt-3116 wPt-8894 wPt-2964 wPt-7437_ML2 wPt-7711 wPt-6585 wPt-742417 wPt-743215_ML1 wPt-744632_ML1 wPt-0245 wPt-0882 wPt-1089 wPt-1852 wPt-3130 wPt-3304 wPt-4283 wPt-7207 wPt-7582 wPt-8239 wPt-8563 wPt-9255_ML1 wPt-9990 wPt-730892 wPt-1756 wPt-0151 wPt-4142 wPt-664276 wPt-1474 wPt-4900 wPt-1437 wPt-2095 wPt-4930 wPt-743200 wPt-744407 wPt-744581 wPt-3524_ML2 wPt-4706 wPt-732062_ML2 wPt-733856_ML2 wPt-6674 wPt-4119 wPt-5256 wPt-741515 wPt-8814 wPt-666793 wPt-667798 wPt-745052 wPt-663764 wPt-2175 wPt-7745 tPt-4887 wPt-3605_ML2 wPt-664250 tPt-3506 wPt-0554 wPt-4858 wPt-7576 wPt-5333 wPt-5408 wPt-8412_ML2 wPt-3203 wPt-665036_ML2 wPt-669130 wPt-3308_ML2 wPt-666224_ML2 wPt-7540 wPt-4742 wPt-2899 wPt-4218 wPt-2218 wPt-744396 wPt-745110 wPt-4893 wPt-6247 wPt-7616_ML2 wPt-8721 wPt-9195 wPt-3402_ML3 wPt-3733 wPt-9784 wPt-2000 wPt-8183 wPt-8560 wPt-7489 wPt-6744 rPt-1040 wPt-2564 wPt-7935 wPt-9791 wPt-6522_ML2 wPt-741530_ML2 wPt-742929_ML2 wPt-0644_ML2 wPt-4648 wPt-2424 wPt-10462_ML2 wPt-664174_ML1 wPt-3439_ML3 wPt-6869_ML2 wPt-741804 wPt-743231 wPt-1730 wPt-3060 wPt-5037 wPt-2559_ML2 wPt-7614_ML2 wPt-3581 wPt-3168 wPt-743099 tPt-8161 wPt-5211 wPt-9881 wPt-4048_ML2 wPt-10323_ML2 wPt-8892_ML3 tPt-3689 wPt-1307 wPt-2498 wPt-3284 wPt-6802_ML2 wPt-6039 wPt-1171_ML2 wPt-9930 wPt-10276_ML2 wPt-10455_ML2 wPt-3107_ML3 wPt-1048 wPt-669607 wPt-1325 tPt-9048_ML2 wPt-5480_ML2 wPt-2162 wPt-664937_ML2 wPt-3207 wPt-0171 wPt-4164 wPt-1541 wPt-6116 wPt-9952 wPt-9256 wPt-8493 wPt-0406 wPt-8059 wPt-1761_ML1 wPt-4662 wPt-732061 0.0 3.2 4.2 6.0 6.1 6.5 6.9 7.7 9.2 9.5 10.0 10.3 11.7 11.9 12.0 12.7 12.8 13.8 14.2 15.0 15.2 15.9 16.5 21.0 21.2 23.2 23.4 24.1 25.7 26.4 30.1 31.6 32.6 33.1 33.9 36.1 37.6 38.5 39.6 42.7 43.4 46.2 47.5 47.9 48.0 49.3 50.5 50.9 51.5 54.3 54.8 55.4 55.5 55.6 56.6 57.2 57.6 58.0 58.9 60.3 61.2 62.0 62.5 63.0 63.8 64.4 65.7 66.4 66.6 67.3 68.7 69.0 69.4 71.7 74.6 80.7 82.2 83.0 83.8 84.7 100.7 101.5 106.9 107.1 107.9 108.7 111.9 112.2 113.3 113.9 115.2 116.7 117.1 119.8 127.8 133.1 6B wPt-1519 wPt-1695_ML2 wPt-5114 wPt-664719 wPt-672044 wPt-666615 wPt-732847 wPt-732892 wPt-2864 wPt-667005 wPt-1314 wPt-3350 wPt-3334_ML2 wPt-731816 wPt-4602 wPt-6978 wPt-729831 wPt-733655 wPt-3127_ML2 wPt-665675 wPt-2782 wPt-668152_ML2 wPt-6661 wPt-1761_ML2 wPt-732626 rPt-7068_ML2 wPt-668181_ML2 wPt-9863 wPt-730539 wPt-731329 0.0 1.6 2.3 2.7 3.1 3.2 97.2 102.4 103.8 106.9 108.2 108.5 114.5 125.0 127.7 128.4 128.9 129.0 131.0 132.5 6D Supplementary figure 1.Continued

7A 7D 7B Supplementary figure 1. Continued wPt-6417 wPt-9496_ML2 rPt-7987_ML2 wPt-4487_ML2 wPt-668307_ML2 tPt-6794 wPt-666456_ML2 tPt-9405_ML2 wPt-2523 wPt-664558 wPt-665253 wPt-672051 wPt-672075 wPt-672171 wPt-8300 wPt-3836_ML2 wPt-6273 wPt-0008 wPt-6967 wPt-7151 wPt-8043 wPt-734161_ML2 wPt-4172 wPt-4960 wPt-7113_ML1 wPt-742051_ML2 wPt-8149 wPt-9255_ML2 wPt-2371 wPt-669103_ML1 wPt-3572 wPt-0303_ML1 wPt-665927_ML1 wPt-6959 wPt-8192 wPt-7608_ML2 wPt-6668 wPt-3135 wPt-3648 wPt-7034 wPt-5964_ML2 wPt-730913_ML2 wPt-9901_ML2 wPt-2780_ML2 wPt-731311 wPt-9207 wPt-740561 wPt-742244 wPt-7096_ML2 wPt-1179_ML2 wPt-8473 wPt-2909_ML2 wPt-4835 wPt-6447 wPt-7734 wPt-9796 wPt-3883 wPt-9314 wPt-744715 tPt-6221 wPt-4515 wPt-7785 wPt-1080_ML1 wPt-0321 wPt-744937 wPt-4051 wPt-7076_ML1 wPt-5232 wPt-4023 wPt-4744 tPt-2230 wPt-3992 wPt-2100 wPt-4637 wPt-4796 wPt-6083 wPt-0205 wPt-0514 wPt-3002 wPt-3393 wPt-9555 wPt-4877 wPt-6217 wPt-0275 wPt-667817_ML2 wPt-4721 wPt-4009 wPt-7053 wPt-3425 wPt-4831 wPt-6620 wPt-671471 wPt-6768 wPt-671548 wPt-8375 wPt-5524 wPt-5558 wPt-6013 wPt-2083 wPt-3782 tPt-9518 wPt-1557 wPt-744897 wPt-0745 wPt-0961 wPt-0971_ML1 wPt-1706 wPt-2246 wPt-2260 wPt-3226 wPt-4553 wPt-5641 wPt-7122 wPt-741686 wPt-7763_ML1 wPt-1023 wPt-6019 wPt-1958 wPt-6495 wPt-9813_ML1 wPt-4038_ML1 wPt-0494_ML1 wPt-2316 wPt-5533 wPt-7947 wPt-2501 9.7 9.8 10.0 10.2 10.3 10.5 10.6 10.8 10.9 11.2 11.5 11.7 12.0 12.3 12.5 12.6 12.8 12.9 13.0 13.5 13.6 14.0 15.1 23.3 23.5 44.1 52.4 55.1 56.7 65.0 67.2 68.1 69.2 75.9 84.3 85.7 85.8 86.5 87.1 88.4 90.1 91.6 91.8 110.2 122.3 124.0 126.1 128.1 131.5 134.3 145.1 147.1 150.6 153.3 153.4 158.3 160.2 162.3 163.4 164.3 164.5 165.8 168.6 179.9 7A wPt-7076_ML2 wPt-1080_ML2 wPt-666104 wPt-743790 wPt-664320 wPt-664368 wPt-731269 wPt-743102 wPt-743491 wPt-743601 wPt-744347 wPt-744521 wPt-744644 wPt-744841 wPt-1269 wPt-5150 wPt-667820_ML2 wPt-742997_ML2 wPt-664478 wPt-668026 wPt-731305 wPt-731831 wPt-743620 wPt-743632 wPt-2565 wPt-663820 wPt-663918 wPt-733104 wPt-743698 wPt-743749 wPt-743999 wPt-744148 wPt-744346 wPt-744444 wPt-744784 wPt-744889 wPt-745067 wPt-0366 wPt-663792 wPt-742840 wPt-742858 wPt-742911 wPt-743140 wPt-743306 wPt-743384 wPt-743666 wPt-743671 wPt-744124 wPt-744736 wPt-744866 wPt-745068 wPt-745070 wPt-745121 wPt-5049 wPt-663989 wPt-664047 wPt-664309 wPt-664317 wPt-664412 wPt-664971 wPt-665471 wPt-666850 wPt-669154 wPt-733729 wPt-743380 wPt-743589 wPt-743651 wPt-743860 wPt-744265 wPt-744271 wPt-744512 wPt-744675 wPt-744976 wPt-745008 wPt-745062 wPt-663849 wPt-663992 wPt-664020 wPt-743269 wPt-744388 wPt-744656 wPt-743331_ML2 wPt-669103_ML2 wPt-665730 wPt-744914_ML2 wPt-664286 wPt-0303_ML2 wPt-665927_ML2 wPt-0934 wPt-744596 wPt-798604 wPt-665260 wPt-743096 wPt-743549 wPt-743551 wPt-3359 wPt-1100 wPt-0789 wPt-7508 wPt-0231 wPt-4555 wPt-666095 wPt-1859 wPt-664400 wPt-665687 wPt-2258 wPt-7642_ML2 wPt-7763_ML2 wPt-4315 wPt-7251_ML2 wPt-663934 wPt-664044 wPt-664174_ML2 0.0 0.2 0.8 1.0 1.3 1.6 1.9 2.1 2.2 3.3 4.0 4.5 5.0 5.1 37.2 55.9 93.5 115.0 116.9 138.3 169.3 170.5 171.7 175.8 7D wPt-664746_ML2 wPt-4309 wPt-6936 wPt-8211 wPt-8920 wPt-5283 wPt-7318 wPt-0137 wPt-4230 wPt-4863_ML2 wPt-2737 wPt-743486 wPt-8283 wPt-7925 wPt-1149_ML2 wPt-9467_ML2 wPt-3676 wPt-3873_ML2 wPt-6372_ML2 wPt-3833_ML2 wPt-6498_ML2 wPt-7934 wPt-4025 wPt-7242_ML2 wPt-0312_ML2 wPt-2572 wPt-8981 wPt-9665 wPt-2305_ML2 wPt-3447 wPt-0963_ML2 wPt-6463 wPt-2273 wPt-2994 wPt-1826 wPt-3723 wPt-9925_ML2 wPt-0635 wPt-4045 wPt-2407 wPt-9987 wPt-5892 wPt-7887 rPt-3887 wPt-8615 wPt-6156 wPt-8938 wPt-0194 wPt-4814 wPt-3093 wPt-0971_ML2 wPt-8007 wPt-2356 wPt-4300 wPt-4038_ML2 wPt-7720 wPt-0408_ML2 wPt-5646 wPt-8040 wPt-1075 wPt-3004 wPt-3190 wPt-6484 wPt-744769 wPt-744987 wPt-0600 wPt-7094_ML2 wPt-8267_ML2 wPt-1957 wPt-5462 wPt-4875 wPt-5138 wPt-7108 wPt-8387 wPt-3445 wPt-8246 wPt-8803 wPt-3710 tPt-8504 wPt-9515 wPt-2933 wPt-733669 wPt-1196 wPt-669693 wPt-2878 wPt-4120 wPt-4743 wPt-9877 wPt-6276 wPt-7113_ML2 wPt-665293 wPt-5816 wPt-4134_ML2 wPt-7080 wPt-7241 wPt-7471 wPt-8598 wPt-9613_ML2 wPt-9904 wPt-4620_ML2 wPt-2677 wPt-3402_ML4 wPt-1533 wPt-4644 wPt-6320 wPt-7251_ML1 wPt-9813_ML2 wPt-0126 wPt-3785 wPt-5069 wPt-0494_ML2 wPt-6869_ML3 wPt-744187 wPt-800156 wPt-743215_ML2 wPt-744632_ML2 wPt-3439_ML4 53.0 69.6 84.5 106.8 134.4 136.6 137.6 138.5 138.9 141.7 142.4 144.9 145.0 145.4 146.4 147.6 148.5 149.4 149.9 152.3 153.4 155.1 158.0 163.8 165.6 166.5 185.5 187.5 190.9 192.4 192.9 195.7 199.4 200.5 200.7 201.6 205.0 210.4 210.8 210.9 212.2 212.5 212.6 212.8 213.0 214.1 214.2 214.8 215.3 215.4 217.4 218.2 218.3 218.7 219.3 219.7 219.9 220.2 220.3 221.3 221.4 221.7 222.1 223.1 223.2 223.9 224.0 224.3 224.8 225.5 227.5 227.6 228.4 233.4 234.8 7B Supplementary figure 1. Continued

Supplementary figure 2. PAUP generated dendrogram of the germplasm set.

(a) Supplementary figure 3. Germination % arising from STGs conducted in 1978, 1998 and 2008 of (a) the whole germplasm collection, (b) Q1 accessions, (c) Q2 accessions, (d) Q3 accessions, (e) Q4 accessions, (f) Q5 accessions, (g) Q6 accessions, (h) ‘Mixed’ accessions, (i) accessions from Asia, (j) accessions from southern Europe, (k) accessions from the rest of Europe, (l) accessions from the Americas, (m) var. aestivum accessions, (n) var. lutescens accessions (o) var. ferrugineum accessions, (p) var. ‘others’ accession, (q) spring type accessions, (r) winter type accessions.

(b) Supplementary figure 3. Continued

(c) Supplementary figure 3. Continued

(d) Supplementary figure 3. Continued

(e) Supplementary figure 3. Continued

(f) Supplementary figure 3. Continued

(g) Supplementary figure 3. Continued

(h) Supplementary figure 3. Continued

(i) Supplementary figure 3. Continued

(j) Supplementary figure 3. Continued

(k) Supplementary figure 3. Continued

(l) Supplementary figure 3. Continued

(m) Supplementary figure 3. Continued

(n) Supplementary figure 3. Continued

(o) Supplementary figure 3. Continued

(p) Supplementary figure 3. Continued

(q) Supplementary figure 3. Continued

(r) Supplementary figure 3. Continued

1.3 1.5 2.4 2.5 2.7 3.1 9.8 17.5 18.3 19.7 19.8 22.2 22.3 23.8 35.7 35.9 36.9 44.1 53.8 56.5 59.9 60.7 74.5 87.8 111.2 135.6 1A wPt-668160, 1978*, 2008 wPt-734078, 1978* wPt-4811, 2010 wPt-8455, PHS wPt-6358, PHS wPt-664586, 1978* wPt-667458, 1978* wPt-4735_ML1, 2008* wPt-731994_ML1, 2008 (wPt-4666, -6122), 1978 wPt-5776, 2010 (wPt-667172, -668236), PHS wPt-733128, 2010 wPt-3698, 1978 wPt-666822, AA wPt-1709, CD wPt-734090, PHS wPt-1426, 2010 wPt-4886, PHS* wPt-5941, DI, PHS wPt-730408, 1978 wPt-4801, CD wPt-667153, 1978, 2008* wPt-0497, AA wPt-0196, 1978 (wPt-8770, -669484), 1978 wPt-6709, CD, PHS wPt-9317, 1978*, 2008, DI, PHS* wPt-4177, 2008 wPt-672089, AA (wPt-2527, -6280), 1978* wPt-731412, 1978 wPt-741297, CD* wPt-9490, 1978 wPt-6442, 1978 tPt-0283, 1978 wPt-742499, PHS* wPt-3465, 2008 wPt-4863_ML1, 1978*, 2008* wPt-4735_ML2, 2008* wPt-733882, AA*, CD wPt-7242_ML1, PHS wPt-1726, 2008, AA wPt-3787, PHS (wPt-740897, -740960), 2008, AA wPt-3103, 2008 (wPt-5246, -8622), 2008 wPt-666564, 1978, 2008* wPt-5485, 2008* wPt-8280, 2008 wPt-0705, PHS wPt-669577, AA wPt-9032, 2010 wPt-7066, 2010 wPt-5034, 1978* wPt-5061, 1978, 2010 wPt-3950, 2010, DI*, PHS* wPt734314, 2010, DI 1B 4.8 11.7 12.3 13.5 14.2 16.2 18.0 28.4 29.5 31.1 31.6 34.1 38.4 40.2 44.9 54.4 57.2 61.8 72.9 76.4 96.7 98.9 9.7 34.7 83.8 wPt-4971, 2010 wPt-665480, CD wPt-3738, 1978* wPt-7953, 1978 wPt-4735_ML3, 2008 wPt-731994_ML2, 2008 wPt-2206, AA wPt-1387, 2010 wPt-671990, AA wPt-731267, AA rPt-4471, CD wPt-5320, CD wPt-5503, 2010, CD 10.7 17.9 36.0 41.5 45.6 50.4 50.9 51.3 59.0 60.6 66.3 1D Supplementary figure 4. Markers in significant association (p<0.05) or highly significant association (p<0.01) (bold with asterisk) with 1978 (purple), 2008 (red), 2010, RAA (AA in green), RCD (CD in blue), DI (brown) and PHS (navy blue). Red regions on chromosomes indicate areas where 2008 and AA or CD MTAs lie within 5 cM on either side of each other. Black squares are approximate centromere positions where known. Trait descriptions are provided in text. 12.1 15.3 17.6 18.8 20.0 20.5 28.8 37.0 43.1 45.9 62.4 65.4 77.7 79.0 81.1 95.0 108.9 109.4 2A wPt-6207, DI*, PHS* wPt-8490, PHS wPt-0003, 2010 wPt-5029, PHS (wPt -0568, -6711, -8068), 2008* wPt-5245, DI wPt-744900, CD wPt-6570, 1978 (tPt-1041, wPt-5647), 2008 wPt-669245, 1978 wPt-4394, 1978 wPt-8596, 1978, DI, PHS wPt-5251, AA* wPt-3244, CD wPt-7024_ML1, 1978 wPt-9586, 1978 wPt-0071, AA wPt-9277, AA wPt-7306, 1978, DI (wPt-6687, -6775_ML1), 1978 wPt-729945_ML1, 1978

2B 2D 3A 3B Supplementary figure 4. Continued wPt-6271, 2010* wPt-1919, AA, DI wPt-8424, 1978 wPt-4350, 1978 tPt-4602, 1978 wPt-744643, 2010, DI wPt-4453, 2008* tPt-4627, CD wPt-5250, DI* wPt-733214, AA wPt-665014, 2008 wPt-4134_ML1, 2008 wPt-8349, AA wPt-4301, DI wPt-7320, PHS wPt-666389, 2010 wPt-0408_ML1, 2010*, CD tPt-9065, 2008 wPt-6174, AA, CD wPt-8548, AA wPt-669681, 2008, 2010 wPt-2430, 2008*, CD* wPt-9350, PHS wPt-800425, 1978*, PHS* wPt-800707, 1978, PHS* wPt-8460, 1978, PHS* wPt-741721, AA, CD wPt-733572, 1978, 2008* wPt-7200, PHS wPt-0473, 2008 wPt-0189, PHS tPt-4125_ML1, 2008 wPt-0489, 2010 wPt-7305, PHS wPt-0906, PHS* wPt-8693, 2008, AA, CD* wPt-1646, 2010, wPt-5128, DI, PHS wPt-5989, 2010 tPt-5438, AA, PHS wPt-9190, PHS wPt-732386, 1978 wPt-665550, 1978* wPt-2397, 1978 wPt-0948, 1978 (wPt-0471, -732040), DI wPt-732666_ML1, 1978*, DI wPt-743307_ML1, 1978* wPt-6775_ML2, 1978 wPt-729945_ML2, 1978 (wPt-3695, -669273), 1978*, DI wPt-733641, DI 0.2 4.2 5.2 10.6 14.5 24.7 29.3 31.1 31.7 34.1 44.3 47.0 52.3 59.7 63.2 64.6 72.8 74.8 74.9 76.6 77.1 80.4 81.3 82.0 85.1 86.5 86.9 87.8 89.1 89.3 96.5 97.2 97.6 101.6 102.7 106.4 106.6 107.3 118.6 123.3 125.2 126.9 129.9 Supplementary figure 4. Continued 48.9 60.2 69.0 73.0 80.3 82.2 95.6 98.1 99.0 101.0 101.2 101.3 102.6 103.5 104.2 2D wPt-734280, 2010* wPt-665342, 2008 wPt-6574, PHS (wPt-730744, -732270), PHS wPt-665694, 2010, PHS* wPt-731134, PHS wPt-6847, PHS* wPt-668120, PHS* wPt-669517, AA wPt-6452, PHS wPt-665836, PHS wPt-730677, PHS wPt-667054, 1978*, DI wPt-732666_ML2, 1978* wPt-743307_ML2, 2008 wPt-731220, PHS wPt-731336, 2010*, AA (wPt-665102,-671742, -730757), PHS wPt-8319, PHS wPt-665644, 2010* wPt-730889, 2010 wPt-731406, PHS* wPt-5586, PHS* wPt- 668261, PHS* (wPt-4329, -6064),PHS 3A 33.5 35.1 35.8 40.7 44.1 46.7 50.4 56.2 56.9 71.0 79.7 80.8 98.8 132.2 158.4 176.4 186.0 188.9 213.2 213.3 52.2 wPt-7217, 2010 wPt-664488, 2010 wPt-2253, 2010, DI wPt-9634, 1978 wPt-6854, AA wPt-2748_ML1, CD wPt-8855_ML1 , CD wPt-10311_ML1, AA wPt-9928, AA* wPt-1464, AA* wPt-7341, CD wPt-0951, 2008 wPt-0714, AA*, CD wPt-745076,AA, CD wPt-4407, 2010 wPt-8593, 2010 (wPt-1681,-2755, -7756), 2010, DI* wPt-7608_ML1, DI*, PHS wPt-2202_ML1, 2010, CD, PHS* wPt-733571, DI wPt-7340, CD wPt-8892_ML1, 2010, AA, CD (tPt-9901, wPt-4128), 1978, 2008 wPt-0398, 2008 wPt-9160, 2008 3B 133.2 20.3 24.9 34.6 37.2 39.0 49.0 51.5 53.1 53.7 54.3 56.5 57.7 58.3 67.5 75.0 75.4 79.0 79.2 85.4 86.0 132.1 135.5 58.7 136.8 136.3 94.7 wPt-666139, 2010, PHS wPt-10311_ML2, AA wPt-2748_ML2, CD (wPt-0013, -0895, -2298, -2766, - 5836), AA, CD (wPt-2193, -732330), CD wPt-6239, 2008 wPt-732044, 2008, PHS wPt-7486, AA, CD wPt-10005, 1978 wPt-1191, 2010 (wPt-1484, -6216, -9579), 2008 tPt-1366, CD, PHS wPt-5105, 2008, PHS wPt-6945, PHS* wPt- 7015, 2008, PHS wPt-9170, 2008, 2010, PHS* wPt-1158, AA, CD, PHS wPt-0327, AA*, CD (wPt-5939, -7152), AA* wPt-9432_ML2, 1978 wPt-10458, CD wPt-7024_ML2, 1978 wPt-2372, DI, PHS wPt-5786, 2010, CD, DI, PHS wPt-2202_ML2, 2010, CD, PHS* wPt-0644_ML1, 1978 wPt-7688, PHS* (wPt-10276_ML1, -10455), 2008 wPt-0065, AA wPt-3725, DI wPt-5704, PHS (tPt-4541, wPt-10071), AA wPt-4412, DI wPt-734141, AA* wPt-8352, AA wPt-8412_ML1, CD wPt-9788_ML1, CD wPt-8855_ML2, CD wPt-664393, 2008, PHS wPt-6973, 2008, PHS

3D 4A 4B 4D 5A Supplementary figure 4. Continued 11.0 16.5 18.5 26.2 37.5 39.4 41.2 43.0 49.8 50.9 52.6 3D wPt-1516, 2008 wPt-9810, 2010 wPt-742463, 2010 wPt-742329, 2010 wPt-740873, 2010 wPt-664771, CD (wPt-740564, -742365), CD wPt -742810, CD wPt-740930, CD wPt-741446, CD wPt-666681, CD wPt-671740, CD (wPt-4292, -5215), CD wPt-4476, CD wPt-7334, CD 68.1 83.1 84.4 84.7 87.8 90.6 91.1 100.9 102.7 103.0 103.4 104.6 105.8 106.9 4A tPt-9400, 2008, DI wPt-2903, PHS wPt-671707, PHS wPt-2909_ML1, DI (wPt-2084 -3795, -5003), PHS wPt-2780_ML1, 2010* wPt-9305, DI, PHS* wPt-669617_ML1, 2010*, CD (wPt-6390, -7876), 2010 wPt-742051_ML1,1978, 2010 wPt-0023, 2010 wPt-0447, 1978, 2010 rPt-0238, 2010 wPt-731374, AA wPt-1161, 1978 14.9 15.5 16.6 57.8 61.3 67.8 68.7 94.1 97.0 4B (wPt-4280, -744595), AA wPt-9118, AA (wPt-1272, -732448, -733363), AA wPt-8892_ML2, 2010, AA, CD wPt-732423, 2008 tPt-4125_ML2, 2008 wPt-6209, PHS wPt-733038, DI, PHS* wPt-5303, 2010 (wPt-730303, -731869), AA wPt-4572, 1978 6.2 4D 23.3 35.6 40.6 40.8 41.1 42.3 45.3 50.5 112.4 122.8 123.7 5A wPt-9748, DI wPt-666142, PHS wPt-742925, 2008*, AA wPt-744567, 2008* wPt-7769, 2008* wPt-3187, 1978, 2010 wPt-3509, 1978* wPt-8226, DI wPt-8794, 2008 wPt-3334_ML1, 1978, CD wPt-5096, CD wPt-734145, 2008* wPt-1200, 1978* wPt-2873, 1978 Supplementary figure 4. Continued

5D 5B 6A 6B Supplementary figure 4. Continued wPt-7323, 1978, CD wPt-2256, DI wPt-9788_ML2, CD 30.1 57.8 161.7 5D 29.4 37.5 43.2 44.5 53.5 54.2 60.3 69.3 69.9 73.0 73.9 76.4 93.7 97.3 150.5 154.7 155.3 156.3 162.3 5B (wPt-5120, -7029), PHS tPt-0228, 2008 wPt-6498_ML1, DI (wPt-744750, -744851), AA wPt-5514, 1978* tPt-7755, PHS wPt-742141, 1978* wPt-4628, DI*, PHS* wPt-2607 , DI*, PHS wPt-7101 , DI wPt-3457, PHS wPt-4246, AA, CD wPt-6135, DI*, PHS wPt-5896, PHS wPt-3763, DI (wPt-2804, -4091, -730313), PHS wPt-7238, 1978, PHS wPt-7665, 1978 wPt-9116, 1978 (wPt-4551, -7400, -666215), 2008* wPt-8449, DI (wPt-5604, -5928), DI* 1.3 3.2 6.3 10.8 15.5 15.6 16.2 17.0 20.2 22.7 23.5 24.1 27.0 30.3 31.5 36.7 36.9 45.3 48.2 48.7 49.1 50.0 92.3 93.0 96.3 99.7 104.0 105.5 107.7 107.9 108.3 6A wPt-665021, CD* wPt-669498, 2010 wPt-9832, DI wPt-7840, CD wPt-665398, AA wPt-8719, 2010 (rPt-9065, -671855, -741547), 2008* wPt-9679, 2008*; wPt-666574, 2008 wPt-731250, CD (tPt-2833, wPt-731842), 2008, 2010 wPt-3605_ML1, 2008, DI, PHS* (wPt-2822, -3965), 1978 (wPt-730729, -733764), 1978 wPt-9132, DI*, PHS* wPt-671708, 1978 wPt-730711, 2010, DI, PHS wPt-731413, DI, PHS* wPt-741037, PHS wPt-733357, DI, PHS wPt-729806, DI, PHS wPt-667844, DI, PHS* wPt-729839, CD, PHS wPt-732263, 2010 (wPt-0902, -7857), DI (wPt-664792 , -730772, -732355), DI tPt-8557, PHS wPt-732975, 2010 wPt-669617_ML2, 2010*, CD (wPt-5696, -671558), 2010 wPt-668031, AA*, CD* (wPt-734345, -734346), 2010 (wPt-667607, -9976), 2010 wPt-730629, 2010 wPt-4229, 2010, CD* wPt-8124, 2008, AA, CD* wPt-664937_ ML1, -744786), AA tPt-6661, 2010*, CD wPt-1661, CD wPt-733151, DI*, PHS* (wPt-8539, -9131_ML2), 1978* 9.2 11.7 12.0 12.8 15.9 21.2 23.4 33.9 36.1 37.6 50.5 51.5 57.2 64.4 65.7 66.4 68.7 82.2 83.0 100.7 111.9 113.9 117.1 119.8 127.8 133.1 6B wPt-5971, 2008 wPt-7711, 2010 (wPt-742417, -743215_ML1), 2010 wPt-1756, CD, PHS wPt-4900, PHS wPt-4706, 2010 wPt-6674, 2010, CD wPt-4119, 1978 wPt-3605_ML2, 2008, DI, PHS * (wPt-4858, -7576), DI wPt-5333, 2010 (wPt-5408, - 8412_ML2), CD (wPt-8721, -9195), 2008* wPt-9784, PHS wPt-0644_ML2, 1978 wPt-3581, 2010 wPt-3168, 2008*, 2010 wPt-9881, 2010, DI wPt-8892_ML3, 2010, AA, CD wPt-10276_ML2, 2008 wPt-10455_ML2, 2008 wPt-669607, 2010 wPt-664937_ML2, AA wPt-4164, 2008 wPt-9952, 2008 wPt-0406, 1978 wPt-1761_ML1, 2008, DI* wPt-4662, 2008 wPt-732061, 2008 Supplementary figure 4. Continued

6D 7A 7B 7D Supplementary figure 4. Continued 3.1 3.2 97.2 102.4 106.9 108.2 128.4 6D wPt-2864, 1978, 2008 wPt-667005, 1978, 2008 wPt-1314, CD wPt-3334_ML2, 1978, CD wPt-731816, CD* wPt-6978, CD (wPt-729831, -733655), CD wPt-1761_ML2, 2008, DI* wPt-732626, AA wPt-3350, CD* 7A wPt-6417, 2008 tPt-9405_ML2, PHS wPt-6967, 1978 (wPt-7113_ML1, -8149), 1978* wPt-742051_ML2, 1978*, 2010 wPt-2371, , 2010 wPt-0303_ML1, 2008 wPt-7608_ML2, DI* wPt-744715, 1978 wPt-4515, CD, DI, PHS wPt-0321, 1978 wPt-744937, 1978 tPt-2230, DI (wPt-2100, -4637), DI (wPt-4796, -6083), DI wPt-0205, CD wPt-0514, 2010 wPt-0275, CD wPt-4009, PHS wPt-7053, CD* wPt-4831, 2010 wPt-6620, 2010 wPt-744897, 2008 wPt- 8043, 1978* wPt-2780_ML2, 2010* 9.7 10.3 10.5 10.6 10.8 11.5 12.0 52.4 55.1 67.2 68.1 85.8 86.5 90.1 91.8 110.2 122.3 158.3 87.5 13.0 69.6 106.8 137.6 145.4 147.6 149.4 155.1 158.0 185.5 190.9 201.6 210.9 212.6 212.8 214.1 214.2 214.8 218.2 218.3 219.3 220.3 221.7 233.4 7B wPt-6936, 1978 wPt-7318, 2010, PHS wPt-4863_ML2, 1978*, 2008* wPt-2737, DI wPt-6498_ML2, DI wPt-7242_ML2, PHS wPt-8981, DI wPt-6463, 2010, DI, PHS* (wPt-2273, -2994), 2008*, DI* wPt-4045, PHS wPt-9987, 2008*, CD wPt-3093, 1978 wPt-7720, AA wPt-0408_ML2, 2010*, CD wPt-3190, CD wPt-6484, CD* wPt-744987, CD wPt-1957, CD wPt-5462, CD wPt-8246, AA wPt-8803, AA wPt-2933 , AA wPt-7113_ML2, 1978* (wPt-4134_ML2, -7471), 2008 wPt-743215_ML2, 2010 1.0 4.0 4.5 5.0 55.9 115.0 7D wPt-664478, AA wPt-0303_ML2, 2008 wPt-0934, 2008 wPt-744596, 2008 wPt-743096, 2010 wPt-743551, 2010 wPt-0789, 1978 (wPt-0231, -666095), CD Supplementary figure 4. Continued

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