Skip to main content

Table 1 Details of SSR loci used for genotyping in the 192 rice accessions and their genetic diversity parameters

From: Analysis of Population Structure and Genetic Diversity in Rice Germplasm Using SSR Markers: An Initiative Towards Association Mapping of Agronomic Traits in Oryza Sativa

S. no Marker Chromosome no. SSR MOTIF Min molecular weight Maximum molecular weight Number of alleles Gene diversity Heterozygosity PIC value
1 RM237 1 (CT)18 110 143 4 0.61 0.89 0.545
2 RM1 1 (GA)26 70 105 3 0.63 0.12 0.552
3 RM5 1 (GA)14 105 115 3 0.64 0.6 0.557
4 RM312 1 (ATTT)4(GT)9 95 105 3 0.3 0.03 0.281
5 RM283 1 (GA)18 149 155 3 0.42 0.02 0.377
6 RM452 2 (GTC)9 195 245 3 0.54 0.83 0.448
7 HvSSR0247 2   395 400 2 0.5 0.18 0.373
8 RM555 2 (AG)11 135 145 3 0.59 0.04 0.517
9 RM211 2 (TC)3A(TC)18 140 160 3 0.52 0.08 0.463
10 RM324 2 (CAT)21 135 180 5 0.74 0.06 0.695
11 RM514 3 (AC)12 245 252 2 0.19 0 0.171
12 RM55 3 (GA)17 220 225 3 0.44 0.07 0.4
13 RM231 3 (CT)16 170 200 3 0.59 0.12 0.511
14 RM416 3 (GA)9 110 115 2 0.42 0.01 0.335
15 RM442 3 (AAG)10 260 275 3 0.5 0.03 0.448
16 RM 16643 4 (GGGA)5 165 200 5 0.73 0.05 0.685
17 RM 559 4 (AACA)6 160 165 2 0.39 0.01 0.311
18 RM17377 4 (AG)25 140 175 4 0.67 0.04 0.625
19 RM7585 4 (TCTT)6 140 160 4 0.46 0.02 0.422
20 RM17616 4 (TC)14 165 180 3 0.16 0 0.146
21 RM413 5 (AG)11 75 100 4 0.59 0.25 0.548
22 RM178 5 (GA)5(AG)8 110 115 3 0.39 0.04 0.35
23 RM 161 5 (AG)20 160 180 3 0.29 0.04 0.258
24 RM7293 5 (ATGT)6 140 150 3 0.64 0.1 0.558
25 RM1024 5 (AC)13 125 140 3 0.32 0.02 0.298
26 RM 162 6 (AC)20 220 240 3 0.37 0.03 0.34
27 RM7434 6 (GTAT)10 120 145 5 0.66 0.19 0.614
28 RM19620 6 (GTG)7 160 177 3 0.21 0.03 0.204
29 RM5963 6 (CAG)9 160 175 3 0.48 0.15 0.38
30 RM11 7 (GA)17 120 150 4 0.71 0.72 0.661
31 RM118 7 (GA)8 155 185 4 0.62 0.77 0.543
32 RM125 7 (GCT)8 105 130 4 0.61 0.89 0.544
33 RM455 7 (TTCT)5 130 135 2 0.24 0.02 0.208
34 HvSSR0740 7   340 400 4 0.7 0.21 0.65
35 RM44 8 (GA)16 95 107 4 0.62 0.77 0.559
36 RM433 8 (AG)13 235 270 3 0.55 0.81 0.446
37 RM447 8 (CTT)8 105 120 4 0.64 0.16 0.572
38 RM284 8 (GA)8 140 145 2 0.21 0.02 0.189
39 RM408 8 (CT)13 120 125 3 0.52 0.01 0.465
40 RM25 8 (GA)18 120 140 4 0.73 0.37 0.679
41 RM256 8 (CT)21 125 140 4 0.73 0 0.681
42 RM105 9 (CCT)6 100 140 3 0.41 0.48 0.37
43 RM107 9 (GA)7 280 300 3 0.48 0 0.425
44 RM 215 9 (CT)16 140 150 3 0.6 0.01 0.528
45 RM 316 9 (GT)8-(TG)9(TTTG)4(TG)4 160 235 7 0.79 0.75 0.756
46 RM205 9 (CT)25 110 140 4 0.72 0 0.665
47 RM171 10 (GATG)5 320 330 2 0.24 0.02 0.211
48 RM271 10 (GA)15 90 99 3 0.66 0.19 0.588
49 RM590 10 (TCT)10 120 140 4 0.57 0.04 0.516
50 RM474 10 (AT)13 240 280 3 0.61 0 0.537
51 RM222 10 (CT)18 200 220 3 0.63 0.02 0.557
52 RM144 11 (ATT)11 160 240 5 0.69 0.18 0.644
53 RM287 11 (GA)21 95 110 5 0.75 0.2 0.706
54 RM 536 11 (CT)16 240 270 5 0.74 0.06 0.701
55 RM224 11 (AAG)8(AG)13 120 155 5 0.65 0.07 0.617
56 RM206 11 (CT)21 130 145 4 0.34 0 0.319
57 RM277 12 (GA)11 115 120 2 0.45 0.08 0.35
58 RM 5795 12 (AGC)8 140 145 2 0.5 0.03 0.374
59 RM1227 12 (AG)15 160 180 2 0.31 0.02 0.262
60 RM20A 12 (ATT)14 220 240 3 0.54 0 0.476
61 RM2197 12 (AT)23 135 140 2 0.44 0 0.341
  Average      3 0.52 0.18 0.468