Table S2: List of 408 SSR markers used for parental polymorphism screening and QTL mapping of Basmati quality traits along with their respective physical positions in the 12 rice chromosome pseudomolecules (build 4). The 111 green shaded markers were genetically mapped while 7 yellow shaded markers though polymorphic showed highly distorted segregation (P< 0.001). Markers with unknown physical position are listed in the end for each chromosome.
Chromosome 1 / Chromosome 2 / Chromosome 3S. No. / Maker / Position (bp) / S. No. / Maker / Position (bp) / S. No. / Maker / Position (bp)
1. / RM499 / 386708 / 44. / RM109 / 183338 / 93. / RM60 / 85199
2. / RM1254 / 2120682 / 45. / RM154 / 1083895 / 94. / RM132 / 993694
3. / RM84 / 3942474 / 46. / RM233A / 2069848 / 95. / RM569 / 1888209
4. / RM220 / 4422194 / 47. / RM236 / 2105542 / 96. / RM81A / 1925952
5. / RM1 / 4633595 / 48. / RM279 / 2882052 / 97. / RM231 / 2433371
6. / RM283 / 4883717 / 49. / RM423 / 3836866 / 98. / RM5474 / 3783230
7. / RM522 / 5242654 / 50. / RM3732 / 4407865 / 99. / RM489 / 4313795
8. / RM272 / 5939266 / 51. / RM3294 / 5204941 / 100. / RM2326 / 6523196
9. / RM259 / 7443429 / 52. / RM6247 / 5797966 / 101. / RM218 / 8385483
10. / RM243 / 7968524 / 53. / RM174 / 7006088 / 102. / RM157 / 9471847
11. / RM578 / 8407910 / 54. / RM322 / 7433419 / 103. / RM7 / 9808692
12. / RM572 / 9863371 / 55. / RM145 / 7706893 / 104. / RM563 / 11050785
13. / RM294 / 10074717 / 56. / RM5699 / 8981409 / 105. / RM554 / 12136585
14. / RM23 / 10702372 / 57. / RM452 / 9563306 / 106. / RM282 / 12387497
15. / RM493 / 12263624 / 58. / RM290 / 10807179 / 107. / RM338 / 13201597
16. / RM140 / 12284300 / 59. / RM324 / 11389741 / 108. / RM156 / 17669794
17. / RM329 / 15984638 / 60. / RM1211 / 18450427 / 109. / RM564 / 18543554
18. / RM24 / 19304427 / 61. / RM4499 / 18529790 / 110. / RM16 / 23082184
19. / RM129 / 19336608 / 62. / RM341 / 19336265 / 111. / RM2420 / 25278366
20. / RM6880 / 22322432 / 63. / RM262 / 20794972 / 112. / RM2334 / 26696572
21. / RM476 / 22507218 / 64. / RM106 / 25141096 / 113. / RM135 / 27367791
22. / RM3475 / 26368916 / 65. / RM263 / 25865402 / 114. / RM186 / 28762816
23. / RM246 / 27663068 / 66. / RM599 / 27109229 / 115. / RM2593 / 30327757
24. / RM443 / 28667265 / 67. / RM221 / 27609877 / 116. / RM3166 / 30627610
25. / RM403 / 29712477 / 68. / RM525 / 28267604 / 117. / RM5813 / 30931517
26. / RM128 / 31065597 / 69. / RM497 / 29027990 / 118. / RM416 / 31194667
27. / RM297 / 32427458 / 70. / RM53 / 29470224 / 119. / RM8203 / 31338236
28. / RM302 / 33315126 / 71. / RM6 / 29579845 / 120. / RM3867 / 31692330
29. / RM212 / 33381420 / 72. / RM318 / 29631532 / 121. / RM1352 / 32292762
30. / RM238 / 33975695 / 73. / RM530 / 30532212 / 122. / RM143 / 33130300
31. / RM319 / 34005652 / 74. / RM240 / 31497147 / 123. / RM3564 / 33370442
32. / RM226 / 34360812 / 75. / RM8255 / 31980076 / 124. / RM227 / 34871262
33. / RM265 / 35524465 / 76. / RM112 / 32013785 / 125. / RM570 / 35534495
34. / RM315 / 37062027 / 77. / RM561 / 32682777 / 126. / RM3586 / 36087130
35. / RM431 / 39221782 / 78. / RM250 / 32774365 / 127. / RM36 / -
36. / RM104 / 40494732 / 79. / RM5607 / 33264381 / 128. / RM55 / -
37. / RM568 / 41033683 / 80. / RM5300 / 33858507 / 129. / RM251 / -
38. / RM414 / 41084024 / 81. / RM5916 / 34057002 / 130. / RM293 / -
39. / RM34 / - / 82. / RM166 / 34346727
40. / RM35 / - / 83. / RM1251 / 34509971
41. / RM237 / - / 84. / RM213 / 34652341
42. / RM306 / - / 85. / RM208 / 35135799
43. / RM428 / - / 86. / RM482 / 35272373
87. / RM266 / 35425869
88. / RM48 / 35529323
89. / RM138 / 35674147
90. / RM27 / -
91. / RM29 / -
92. / RM475 / -
Chromosome 4 / Chromosome 5 / Chromosome 6
S. No. / Maker / Position (bp) / S. No. / Maker / Position (bp) / S. No. / Maker / Position (bp)
131. / RM335 / 679893 / 158. / RM153 / 167824 / 192. / RM133 / 226944
132. / RM3471 / 6294626 / 159. / RM2494 / 169915 / 193. / RM170 / 1360570
133. / RM261 / 6558964 / 160. / RM159 / 466069 / 194. / RM190 / 1764586
134. / RM2530 / 6997540 / 161. / RM2010 / 1158994 / 195. / RM5199 / 2270164
135. / RM5633 / 13059370 / 162. / RM3345 / 1989762 / 196. / RM197 / 3085625
136. / RM307 / 13126513 / 163. / RM1366 / 2893916 / 197. / RM204 / 3168377
137. / RM401 / 13138740 / 164. / RM405 / 3051448 / 198. / RM225 / 3416533
138. / RM1100 / 17768559 / 165. / RM574 / 3428912 / 199. / RM115 / 4182749
139. / RM6314 / 18429511 / 166. / RM2422 / 7002251 / 200. / RM217 / 4234184
140. / RM185 / 18564328 / 167. / RM7293 / 7506144 / 201. / RM111 / 5096744
141. / RM417 / 19410814 / 168. / RM289 / 7787118 / 202. / RM253 / 5425408
142. / RM1359 / 19845162 / 169. / RM516 / 8283515 / 203. / RM2126 / 5905238
143. / RM142 / 20503509 / 170. / RM249 / 10755867 / 204. / RM50 / 6375949
144. / RM119 / 21227137 / 171. / RM598 / 16730510 / 205. / RM6359 / 6434836
145. / RM3337 / 21,912,977 / 172. / RM1237 / 17935443 / 206. / RM3125 / 6949292
146. / RM1869 / 22886592 / 173. / RM164 / 19175845 / 207. / RM121 / 7592048
147. / RM273 / 23825125 / 174. / RM3695 / 19570575 / 208. / RM136 / 8751256
148. / RM252 / 25145164 / 175. / RM440 / 19891890 / 209. / RM564 / 11767249
149. / RM241 / 26823436 / 176. / RM305 / 20923630 / 210. / RM3183 / 12447059
150. / RM5320 / 27795920 / 177. / RM3575 / 21370956 / 211. / RM238 / 13155585
151. / RM303 / 28540846 / 178. / RM5642 / 22163763 / 212. / RM193 / 18085431
152. / RM1703 / 29395899 / 179. / RM3295 / 22249363 / 213. / RM3187 / 20925676
153. / RM3217 / 30083436 / 180. / RM188 / 22650583 / 214. / RM3827 / 22297202
154. / RM255 / 30738432 / 181. / RM178 / 25081202 / 215. / RM3628 / 23737032
155. / RM131 / 34389697 / 182. / RM6972 / 25325414 / 216. / RM162 / 24035491
156. / RM280 / 34955602 / 183. / RM274 / 26827527 / 217. / RM275 / 24324733
157. / RM559 / 35117645 / 184. / RM6200 / 26905037 / 218. / RM2062 / 24944560
185. / RM26 / 27321395 / 219. / RM343 / 25993420
186. / RM3170 / 27933431 / 220. / RM528 / 26554756
187. / RM6313 / 28257221 / 221. / RM30 / 27252300
188. / RM334 / 28464262 / 222. / RM340 / 28599181
189. / RM31 / 28590085 / 223. / RM6224 / 29162764
190. / RM1054 / 29144016 / 224. / RM103 / 30889151
191. / RM39 / - / 225. / RM494 / 31088151
226. / RM3 / -
227. / RM238 / -
Chromosome 7 / Chromosome 8 / Chromosome 9
S. No. / Maker / Position (bp) / S. No. / Maker / Position (bp) / S. No. / Maker / Position (bp)
228. / RM51 / 237988 / 263. / RM337 / 146952 / 293. / RM4413 / 1172554
229. / RM4584 / 493986 / 264. / RM152 / 677616 / 294. / RM8219 / 1546867
230. / RM2381 / 2418000 / 265. / RM1235 / 1203398 / 295. / RM5688 / 1715785
231. / RM427 / 2677966 / 266. / RM38 / 2109496 / 296. / RM2855 / 3838869
232. / RM5711 / 3140480 / 267. / RM4955 / 2953435 / 297. / RM2705 / 4740026
233. / RM2006 / 4196305 / 268. / RM1270 / 3075143 / 298. / RM444 / 5925291
234. / RM8263 / 4654194 / 269. / RM25 / 4372113 / 299. / RM1328 / 9205384
235. / RM125 / 5478776 / 270. / RM4085 / 4443929 / 300. / RM325 / 10536929
236. / RM6081 / 5597570 / 271. / RM126 / 5216035 / 301. / RM1817 / 10620258
237. / RM3718 / 7955501 / 272. / RM7057 / 5849960 / 302. / RM1896 / 11767417
238. / RM214 / 12782791 / 273. / RM2584 / 7559239 / 303. / RM524 / 12922558
239. / RM1377 / 12782829 / 274. / RM3395 / 10288317 / 304. / RM5657 / 14366733
240. / RM3755 / 14732790 / 275. / RM44 / 11753077 / 305. / RM409 / 14372051
241. / RM2530 / 15568565 / 276. / RM339 / 17812339 / 306. / RM219 / 14503902
242. / RM7110 / 16852605 / 277. / RM3153 / 18856800 / 307. / RM6567 / 14617631
243. / RM445 / 17461575 / 278. / RM342 / 19827403 / 308. / RM3700 / 15427214
244. / RM432 / 18957898 / 279. / RM42 / 19964404 / 309. / RM434 / 15662582
245. / RM11 / 19256213 / 280. / RM223 / 20519970 / 310. / RM1189 / 16271090
246. / RM336 / 21870504 / 281. / RM556 / 22209691 / 311. / RM7424 / 16580768
247. / RM428 / 22047165 / 282. / RM210 / 22341749 / 312. / RM257 / 17719660
248. / RM70 / 22775157 / 283. / RM5353 / 23988913 / 313. / RM2190 / 17846091
249. / RM505 / 24526057 / 284. / RM256 / 24140506 / 314. / RM41 / 18075857
250. / RM473 / 25456532 / 285. / RM80 / 24348513 / 315. / RM288 / 18562723
251. / RM234 / 25471987 / 286. / RM149 / 24591236 / 316. / RM6570 / 18576133
252. / RM47 / 25806035 / 287. / RM230 / 25704179 / 317. / RM242 / 18810120
253. / RM6650 / 27576347 / 288. / RM6070 / 26189532 / 318. / RM278 / 19320020
254. / RM3555 / 27889886 / 289. / RM447 / 26416863 / 319. / RM160 / 19788247
255. / RM1335 / 28297983 / 290. / RM281 / 27765376 / 320. / RM201 / 20174289
256. / RM2715 / 28645602 / 291. / RM4153 / 28070665 / 321. / RM1553 / 21003444
257. / RM2789 / 29222369 / 292. / RM5545 / 28141927 / 322. / RM215 / 21189110
258. / RM248 / 29339323 / 323. / RM6797 / 22712967
259. / RM172 / 29560592 / 324. / RM205 / 22720646
260. / RM82 / - / 325. / RM285 / -
261. / RM118 / -
Chromosome 10 / Chromosome 11 / Chromosome 12
S. No. / Maker / Position (bp) / S. No. / Maker / Position (bp) / S. No. / Maker / Position (bp)
326. / RM6364 / 51637 / 352. / RM181 / 201993 / 380. / RM1880 / 746975
327. / RM474 / 1804009 / 353. / RM286 / 383711 / 381. / RM20 / 970495
328. / RM222 / 2604526 / 354. / RM6288 / 2166293 / 382. / RM83 / 1734831
329. / RM7217 / 4393333 / 355. / RM1812 / 2405106 / 383. / RM19 / 2432080
330. / RM2125 / 4658655 / 356. / RM332 / 2840213 / 384. / RM247 / 3185384
331. / RM216 / 5102302 / 357. / RM5599 / 3824361 / 385. / RM6296 / 3200576
332. / RM239 / 9361257 / 358. / RM1124 / 3851094 / 386. / RM117 / 3501057
333. / RM271 / 9546849 / 359. / RM167 / 4073024 / 387. / RM512 / 5104306
334. / RM4455 / 11405822 / 360. / RM6894 / 5913975 / 388. / RM1036 / 8794524
335. / RM6868 / 14103712 / 361. / RM441 / 6080890 / 389. / RM101 / 8826702
336. / RM596 / 14950802 / 362. / RM3625 / 6664298 / 390. / RM102 / 8831676
337. / RM5304 / 16088250 / 363. / RM6115 / 8081872 / 391. / RM155 / 10078774
338. / RM184 / 16100732 / 364. / RM3701 / 8100690 / 392. / RM179 / 14450698
339. / RM258 / 17756107 / 365. / RM202 / 8984931 / 393. / RM1261 / 17531126
340. / RM6100 / 18558474 / 366. / RM5731 / 9939641 / 394. / RM313 / 20839498
341. / RM171 / 18790632 / 367. / RM7303 / 16484315 / 395. / RM309 / 21454591
342. / RM1108 / 18903461 / 368. / RM6272 / 16488311 / 396. / RM2309 / 22083254
343. / RM3019 / 19503463 / 369. / RM287 / 16730846 / 397. / RM463 / 22092198
344. / RM147 / 20689755 / 370. / RM209 / 17771755 / 398. / RM277 / 22331236
345. / RM484 / 20808566 / 371. / RM229 / 18372685 / 399. / RM7376 / 23443445
346. / RM228 / 21984994 / 372. / RM21 / 19137833 / 400. / RM3331 / 23460827
347. / RM333 / 22113966 / 373. / RM2110 / 19423316 / 401. / RM1103 / 23539495
348. / RM591 / 22641454 / 374. / RM206 / 21979485 / 402. / RM6396 / 24966349
349. / RM6824 / 22785035 / 375. / RM187 / 23189237 / 403. / RM6386 / 24966354
350. / RM590 / 22785050 / 376. / RM254 / 23729167 / 404. / RM270 / 24969001
351. / RM244 / - / 377. / RM7163 / 26256534 / 405. / RM3739 / 24969014
378. / RM144 / 28246911 / 406. / RM235 / 26107904
379. / RM7443 / 28395760 / 407. / RM17 / 26954668
408. / RM12 / 27024395