Table S1 Basic Information of Rice Accessions Used in This Study

Table S1 Basic information of rice accessions used in this study

No / Name / Origin / AccNo / Subspecies / Q indica /
1 / Heijing 2 / Heilongjiang, China / ZD-01001 / japonica / 0.001
2 / Laoguangtou83 / Heilongjiang, China / 07-00010 / japonica / 0.002
3 / Erjiunan 1 / Zhejiang, China / ZD-00474 / indica / 0.987
4 / Chaoyang 1 B / Henan, China / indica / 0.999
5 / Aijiaonante / Guangdong, China / ZD-00141 / indica / 0.999
6 / L301B / Henan, China / indica / 0.999
7 / Guangluai 4 / Guangdong, China / ZD-00002 / indica / 0.999
8 / Xiangaizao10 / Hunan, China / indica / 0.999
9 / Jinnante43B / Hunan, China / indica / 0.999
10 / Xiangzaoxian 7 / Hunan, China / ZD-02715 / indica / 0.997
11 / 80B / Hunan, China / indica / 0.996
12 / Guangluai-15 / Guangxi, China / indica / 0.999
13 / ZhuzhenB / Hunan, China / indica / 0.999
14 / Baoxie123B / Hunan, China / indica / 0.99
15 / Heimangdao / Ningxia, China / 28-00005 / japonica / 0.002
16 / Baoxie-7B / Hunan, China / indica / 0.9
17 / JinnanteB / Hunan, China / indica / 0.999
18 / Funingzipi / Hebei, China / japonica / 0.001
19 / Zhenshan97B / Jiangxi, China / indica / 0.998
20 / Gzhenshan97B / Sichuan, China / indica / 0.999
21 / Qingsiai16B / Guangdong, China / indica / 0.902
22 / LimingB / Liaoning, China / japonica / 0.001
23 / IR661-1 / Philippines / indica / 0.82
24 / Nanjing 11 / Jiangsu, China / ZD-00560 / indica / 0.999
25 / Weiguo / Liaoning, China / ZD-00907 / japonica / 0.001
26 / Gui630 / Guiana / indica / 0.988
27 / Dianrui409B / Yunnan, China / indica / 0.996
28 / Liaojing287 / Liaoning, China / ZD-02324 / japonica / 0.026
29 / Huhui628 / (Unknown) / japonica / 0.208
30 / JinghuB / Anhui, China / japonica / 0.001
31 / 88B / Jiangsu, China / indica / 0.997
32 / Gu154 / Cuba / WD-12711 / indica / 0.999
33 / Ninghui21 / Jiangsu, China / japonica / 0.268
34 / Xianghui91269 / Hunan, China / indica / 0.867
35 / Longhuamaohu / Hebei, China / japonica / 0.129
36 / Lucaihao / Fujian, China / ZD-00290 / indica / 0.999
37 / Yelicanghua / Tianjin, China / 02-00295 / japonica / 0.002
38 / Chengduai 3 / Sichuan, China / ZD-00743 / indica / 0.999
39 / Gongju 73 / Yunnan, China / 21-01899 / indica / 0.998
40 / Jiabala / Xizang, China / 26-00008 / indica / 0.999
41 / Xugunuo / Hunan, China / 18-01829 / indica / 0.997
42 / Huke 3 / Sichuan, China / indica / 0.999
43 / Taichung Native 1 / Taiwan, China / 30-00210 / indica / 0.999
44 / Huangsiguizhan / Guangdong, China / ZD-02431 / indica / 0.998
45 / Aituogu151 / Sichuan, China / ZD-02032 / indica / 0.999
46 / Xiangwanxian 3 / Hunan, China / ZD-02694 / indica / 0.982
47 / Taichung65 / Taiwan, China / 30-00205 / japonica / 0.118
48 / Zaoshunonghu6 / Hunan, China / japonica / 0.001
49 / Chengnongshuijing / Sichuan, China / indica / 0.984
50 / Guihuahuang / Jiangsu, China / ZD-00587 / japonica / 0.055
51 / Momi / Guangxi, China / ZD-02547 / indica / 0.99
52 / Xiushui115 / Zhejiang, China / ZD-01559 / japonica / 0.025
53 / Sanbaili / Jiangxi, China / 30-00591 / indica / 0.985
54 / Jindao 1 / Shanxi, China / ZD-02277 / japonica / 0.002
55 / Xingguo / Jilin, China / 06-00035 / japonica / 0.001
56 / Dandongludao / Liaoning, China / 05-00052 / japonica / 0.005
57 / Zhonghua 8 / Beijing, China / ZD-02261 / japonica / 0.006
58 / Liusha 1 / Guangxi, China / ZD-00213 / indica / 0.995
59 / Bawangbian1 / Hubei, China / 17-01470 / indica / 0.999
60 / Aimakang / Sichuan, China / ZD-00747 / indica / 0.999
61 / Dongtingwanxian / Hubei, China / 17-00502 / indica / 0.987
62 / Yangdao 2 / Jiangsu, China / ZD-01820 / indica / 0.999
63 / Zhengdao 5 / Henan, China / ZD-03525 / japonica / 0.001
64 / Zhenxian232 / Jiangsu, China / ZD-02944 / indica / 0.998
65 / Jing87-304 / Hunan, China / ZD-02685 / japonica / 0.001
66 / Hongwan 1 / Fujian, China / ZD-01328 / indica / 0.998
67 / Liushizao / Anhui, China / 11-00322 / indica / 0.981
68 / Taidongludao / Taiwan, China / japonica / 0.179
69 / Taizhongxianxuan2 / Taiwan, China / indica / 0.999
70 / Dangyu 5 / Anhui, China / ZD-03115 / indica / 0.997
71 / Youmangzaojing / Shanghai, China / japonica / 0.001
72 / Maguzi / Shanxi (SHX), China / 24-00195 / japonica / 0.004
73 / Menjiading2 / Hainan, China / 31-00042 / indica / 0.98
74 / Aimi / Jiangxi, China / 12-02373 / indica / 0.988
75 / Haobayong1 / Yunnan, China / 21-01853 / japonica / 0.045
76 / Wanlixian / Hunan, China / 18-03459 / indica / 0.993
77 / Esiniu / Guangdong, China / 15-01740 / indica / 0.998
78 / Jiefangxian / Jiangxi, China / 12-00644 / indica / 0.999
79 / Huanghezaoer / Jiangsu, China / 09-00530 / japonica / 0.002
80 / Nantiangangjiu / Sichuan, China / 20-01734 / japonica / 0.001
81 / Hengxianliangchun / Guangxi, China / 16-00163 / indica / 0.999
82 / Hanmagu / Henan, China / 19-00204 / indica / 0.999
83 / Leihuozhan / Anhui, China / 11-00403 / indica / 0.994
84 / Baihezaohe / Hunan, China / indica / 0.999
85 / Aihechi / Jiangxi, China / 12-02280 / indica / 0.999
86 / Haomake (K) / Yunnan, China / 21-00083 / japonica / 0.002
87 / Sanbangqishiluo / Yunnan, China / 21-00529 / japonica / 0.209
88 / Shanjiugu / Sichuan, China / 20-03215 / japonica / 0.004
89 / Lixinjing / Sichuan, China / ZD-00806 / japonica / 0.001
90 / Xiangnuo / Guizhou, China / 22-00570 / japonica / 0.002
91 / Nianhenuo / Guizhou, China / 22-01439 / japonica / 0.001
92 / Tieganwu / Zhejiang, China / 10-00463 / japonica / 0.001
93 / Yienchangtan / Hubei, China / 17-00966 / indica / 0.999
94 / Xiangdao / Henan, China / 19-00022 / indica / 0.994
95 / Meihuanuo / Sichuan, China / 20-02073 / indica / 0.999
96 / Xiaohonggu / Yunnan, China / 21-01165 / indica / 0.999
97 / Zhongnong 4 / Sichuan, China / 09-01020 / indica / 0.998
98 / Laohongdao / Shanxi (SHX), China / 24-00215 / japonica / 0.186
99 / Wuzidui / Yunnan, China / 21-01577 / japonica / 0.001
100 / Xibaizhan / Sichuan, China / 20-01262 / indica / 0.831
101 / Minbeiwanxian / Fujian, China / 13-00737 / indica / 0.998
102 / Qiyuexian / Guangxi, China / 16-06887 / indica / 0.998
103 / Zegu / Guizhou, China / 22-00040 / indica / 0.994
104 / Maweizhan / Guizhou, China / 22-01615 / indica / 0.999
105 / Mamagu / Sichuan, China / 20-01452 / indica / 0.999
106 / Zinuo / Yunnan, China / 21-02223 / indica / 0.844
107 / Qingke / Yunnan, China / 21-01257 / indica / 0.693
108 / Beizinuo / Yunnan, China / 21-05171 / indica / 0.999
109 / Wuzuihonggu / Yunnan, China / 21-05061 / indica / 0.999
110 / Nangaogu / Yunnan, China / 21-03113 / indica / 0.999
111 / Mowanggunei / Yunnan, China / 21-02768 / indica / 0.953
112 / Qitougu / Yunnan, China / 21-02171 / indica / 0.92
113 / Yizhixiang / Fujian, China / 13-00411 / indica / 0.998
114 / Guanghexiangnuo / Guangxi, China / japonica / 0.007
115 / Wenxiangnuo / Yunnan, China / 21-00272 / indica / 0.997
116 / Ximaxian / Yunnan, China / 21-05093 / japonica / 0.006
117 / Xiaobaimi / Guizhou, China / 22-04637 / indica / 0.991
118 / Qianxibendidaozi / Hebei, China / 02-00025 / japonica / 0.001
119 / Lulongdabaimang / Hebei, China / 02-00044 / japonica / 0.001
120 / Tangshanchaoxiandao / Hebei, China / 02-00078 / japonica / 0.001
121 / Miziwan / Shanghai, China / 08-00027 / japonica / 0.001
122 / Huangsanbai / Shanghai, China / 08-00047 / japonica / 0.08
123 / Xiaofeilaifeng / Jiangsu, China / 09-00315 / japonica / 0.001
124 / Yanzinuo / Jiangsu, China / 09-00628 / japonica / 0.001
125 / Youmangtiehe / Jiangsu, China / 09-00705 / japonica / 0.001
126 / Wunuodao / Jiangsu, China / 09-01656 / japonica / 0.014
127 / Xiaohuangmang / Jiangsu, China / 09-01634 / indica / 0.997
128 / Tutounuodao / Jiangsu, China / 09-01635 / indica / 0.999
129 / Gailiangwu / Zhejiang, China / 10-00524 / indica / 0.998
130 / Heitouhong / Zhejiang, China / 10-00140 / japonica / 0.002
131 / Zihong / Zhejiang, China / 10-00841 / japonica / 0.001
132 / Mazhan / Jiangxi, China / 12-00001 / indica / 0.882
133 / Liangguozao / Jiangxi, China / 12-01638 / indica / 0.998
134 / Shangraozao / Jiangxi, China / 12-01720 / indica / 0.978
135 / Jianyangzao / Jiangxi, China / 12-02303 / japonica / 0.001
136 / Zhushituo / Sichuan, China / 20-01882 / japonica / 0.033
137 / Hongguzi / Sichuan, China / 20-02928 / japonica / 0.001
138 / Madaozi / Shanxi (SHX), China / 24-00306 / japonica / 0.001
139 / Sichengoujiangmidao / Shanxi (SHX), China / 24-00322 / japonica / 0.001
140 / Laomangdao / Shanxi (SHX), China / 24-00360 / japonica / 0.136
141 / Susuidao / Shandong, China / 14-00014 / japonica / 0.001
142 / Yingqiunuo / Anhui, China / 11-00250 / japonica / 0.018
143 / Nanfengzao / Anhui, China / 11-00378 / indica / 0.991
144 / Qiuqianbai / Anhui, China / 11-00389 / indica / 0.999
145 / Banmaozhan / Anhui, China / 11-00398 / indica / 0.999
146 / Jiangxizao / Anhui, China / 11-00435 / indica / 0.999
147 / Peiai64 / Hunan, China / indica / 0.999
148 / Niangunuo / Hunan, China / 18-03942 / indica / 0.999
149 / Muguanuo / Hunan, China / 18-03950 / indica / 0.999
150 / Lanzaonuo / Hunan, China / 18-04228 / indica / 0.994
151 / Zaojiugu / Sichuan, China / 20-02084 / indica / 0.999
152 / Baiheshangu / Guizhou, China / 22-02611 / indica / 0.999
153 / Qingshuidao / Shandong, China / 14-00068 / indica / 0.999
154 / Lucaihao / Guangdong, China / indica / 0.999
155 / Teqing / Guangdong, China / indica / 0.995
156 / Chiminei / Guangdong, China / 15-00658 / indica / 0.999
157 / BG951 / Sri Lanka / indica / 0.999
158 / IAC1300 / Brazil / indica / 0.999
159 / IRAT10 / Cote d’Ivoire / indica / 0.929
160 / IRAT216 / Cote d’Ivoire / indica / 0.996
161 / Kasalath / India / indica / 0.982
162 / 9311 / Jiangsu, China / indica / 0.999
163 / Nipponbare / Japan / WD-10576 / japonica / 0.001
164 / Lemont / USA / WD-18407 / japonica / 0.152
165 / ITA408 / Nigeria / japonica / 0.001
166 / Nongken57 (Kinmaze) / Japan / WD-11065 / japonica / 0.053
167 / Suweon352 / South Korea / japonica / 0.001
168 / Cypress / USA / japonica / 0.001
169 / AUS43 / Bengal / japonica / 0.001
170 / ITA82 / Nigeria / japonica / 0.001

AccNo is the ID number of each rice accession in China National Gene Bank, available in Chinese Crop Germplasm Resources Information System (CGRIS, http://icgr.caas.net.cn/cgris_english.html).

Table S2 List of SSR and InDel markers used in this study

Chr. / Name / Physical position (bp) / Allele number / Population structure /
1 / RM495 / 213758 / 3 / *
1 / RM576 / 8136666 / 4 / *
1 / RM583 / 8326662 / 8 / *
1 / RM582 / 9188491 / 4 / *
1 / R1M20 / 18513516 / 2 / *
1 / R1M30 / 24757297 / 2 / *
1 / RM246 / 27663068 / 5 / *
1 / R1M37 / 29918593 / 2 / *
1 / RM104 / 40494732 / 3 / *
2 / RM110 / 1326947 / 5 / *
2 / RM423 / 3836866 / 3 / *
2 / RM341 / 19336265 / 7 / *
2 / RM475 / 20399300 / 5 / *
2 / RM6 / 29579845 / 5 / *
2 / RM166 / 34346727 / 6 / *
3 / RM523 / 1298834 / 3 / *
3 / RM282 / 12387497 / 4 / *
3 / RM16 / 23082184 / 7 / *
3 / RM520 / 30870212 / 3 / *
4 / RM551 / 168620 / 6 / *
4 / RM335 / 679893 / 6 / *
4 / RM252 / 25145162 / 8 / *
5 / RM153 / 167824 / 6 / *
5 / RM13 / 1989212 / 7 / *
5 / RM592 / 2774918 / 14 / *
5 / RM169 / 7477291 / 7 / *
5 / RM430 / 18670780 / 5 / *
6 / RM586 / 1476793 / 5 / *
6 / RM276 / 6230045 / 10 / *
6 / RM541 / 19513541 / 8 / *
6 / RM340 / 28599181 / 10 / *
7 / RM427 / 2677960 / 2
7 / RM298 / 2768240 / 2
7 / RM481 / 2908317 / 7
7 / RM5711 / 3140480 / 6
7 / RM4098 / 3155071 / 4
7 / RM7418 / 3187047 / 2
7 / RM1353 / 3311066 / 5 / *
7 / RM1243 / 3553941 / 6
7 / RM21070 / 3994570 / 2
7 / RM6111 / 4090238 / 2
7 / RM8263 / 4654105 / 5
7 / RM6872 / 4658715 / 2
7 / RM21108 / 4682232 / 4
7 / RM8262 / 5297682 / 2
7 / RM125 / 5478758 / 2
7 / RM6081 / 5597494 / 3
7 / RM7121 / 5622107 / 8
7 / RM6338 / 5657919 / 4
7 / RM180 / 5734495 / 11
7 / RM5672 / 6379286 / 8
7 / RM1253 / 6966985 / 3
7 / RM8006 / 7684246 / 9
7 / RM501 / 8005319 / 11
7 / RM8022 / 8131699 / 2
7 / RM3859 / 8876434 / 6
7 / RM1186 / 8962151 / 4 / *
7 / RM3767 / 9037380 / 4
7 / RM5436 / 9074011 / 7
7 / RM21367 / 10275458 / 9
7 / R7M20 / 11393310 / 2
7 / RM542 / 12659488 / 8
7 / RM3832 / 12659573 / 7
7 / RM214 / 12782791 / 7
7 / RM1377 / 12782829 / 7
7 / RM500 / 15909894 / 5
7 / RM2 / 16020982 / 5
7 / RM1135 / 16931296 / 5
7 / RM445 / 17461575 / 2
7 / RM533 / 17511357 / 3
7 / RM21598 / 17739086 / 3
7 / RM418 / 18131530 / 11
7 / RM3186 / 18629302 / 5
7 / RM432 / 18957898 / 4
7 / RM11 / 19256213 / 4
7 / R7M30 / 19363756 / 2
7 / RM560 / 19582282 / 7
7 / RM21716 / 19965797 / 6
7 / RM21734 / 20364431 / 3
7 / RM2420 / 20592303 / 2
7 / RM346 / 20991661 / 6
7 / RM21772 / 21264872 / 4
7 / RM3799 / 21630136 / 7
7 / RM336 / 21870504 / 9 / *
7 / RM10 / 22187108 / 5
7 / RM455 / 22349892 / 3
7 / RM21854 / 23083213 / 3
7 / RM5508 / 23557850 / 12
7 / R7M37 / 23565667 / 2
7 / RM1365 / 23788938 / 10
7 / RM351 / 23924184 / 3
7 / RM1132 / 23983788 / 7
7 / RM505 / 24525712 / 2
7 / RM234 / 25471987 / 6
7 / RM21976 / 25589679 / 8
7 / RM18 / 25651810 / 3
7 / RM47 / 25806035 / 3
7 / RM478 / 25948820 / 4
7 / RM3552 / 26354048 / 4
7 / RM1209 / 26464125 / 4
7 / RM134 / 26635833 / 4
7 / RM118 / 26635903 / 2
7 / RM1364 / 26773305 / 9
7 / RM429 / 26805311 / 5
7 / RM6063 / 27612675 / 4
7 / RM2715 / 28645602 / 6
7 / RM5720 / 28668341 / 10
7 / RM1362 / 28923297 / 5
7 / RM1306 / 28946226 / 9
7 / RM7601 / 29037860 / 4 / *
7 / RM2789 / 29222369 / 3
7 / RM248 / 29339144 / 4