Table 1. Summary statistics of the 40 SSR markers used in this study.
| Marker | Motif | Chr | Size range (bp) | AN | Major allele | H e | H o | PIC | |
|---|---|---|---|---|---|---|---|---|---|
| Size (bp) | Frequency (%) | ||||||||
| RM495* | (CTG)7 | 1 | 147–159 | 5 | 159 | 32 | 0.78 | 0.00 | 0.74 |
| RM1* † | (GA)26 | 1 | 74–118 | 12 | 94 | 21 | 0.85 | 0.03 | 0.84 |
| RM259* † | (CT)17 | 1 | 148–181 | 16 | 181 | 20 | 0.88 | 0.01 | 0.87 |
| RM5* † | (GA)14 | 1 | 104–130 | 7 | 114 | 29 | 0.77 | 0.03 | 0.73 |
| RM431* † | (AG)16 | 1 | 240–252 | 4 | 252 | 38 | 0.72 | 0.01 | 0.67 |
| RM240 | (CT)21 | 2 | 109–145 | 13 | 109 | 45 | 0.74 | 0.01 | 0.71 |
| RM213 | (CT)17 | 2 | 119–153 | 13 | 137 | 36 | 0.77 | 0.00 | 0.74 |
| RM208 † | (CT)17 | 2 | 156–178 | 8 | 164 | 56 | 0.63 | 0.00 | 0.60 |
| RM207 | (CT)25 | 2 | 69–156 | 20 | 126 | 29 | 0.84 | 0.04 | 0.82 |
| RM489* † | (ATA)8 | 3 | 235–271 | 4 | 265 | 45 | 0.67 | 0.00 | 0.61 |
| RM338* † | (CTT)6 | 3 | 179, 182 | 2 | 179 | 64 | 0.46 | 0.00 | 0.35 |
| RM55* † | (GA)17 | 3 | 217–238 | 6 | 232 | 66 | 0.53 | 0.01 | 0.50 |
| RM514* † | (AC)12 | 3 | 237–269 | 8 | 245 | 50 | 0.68 | 0.01 | 0.64 |
| RM124* † | (TC)10 | 4 | 265–271 | 4 | 267 | 47 | 0.67 | 0.00 | 0.61 |
| RM507* † | (AAGA)7 | 5 | 254, 258 | 2 | 254 | 57 | 0.49 | 0.00 | 0.37 |
| RM413* † | (AG)11 | 5 | 69–105 | 8 | 79 | 31 | 0.75 | 0.01 | 0.71 |
| RM178* † | (GA)5(AG)8 | 5 | 115–121 | 4 | 115 | 85 | 0.27 | 0.00 | 0.26 |
| RM334* † | (CTT)20 | 5 | 143–207 | 12 | 143 | 18 | 0.87 | 0.00 | 0.86 |
| RM26 | (GA)15 | 5 | 102–114 | 6 | 106 | 44 | 0.71 | 0.00 | 0.67 |
| RM133* † | (CT)8 | 6 | 228–232 | 3 | 228 | 57 | 0.57 | 0.00 | 0.50 |
| RM510* † | (GA)15 | 6 | 109–125 | 5 | 111 | 30 | 0.75 | 0.01 | 0.70 |
| RM190 † | (CT)11 | 6 | 105–139 | 8 | 126 | 29 | 0.80 | 0.00 | 0.77 |
| RM217 | (CT)20 | 6 | 114–200 | 16 | 120 | 31 | 0.80 | 0.05 | 0.77 |
| RM125* † | (GCT)8 | 7 | 126–147 | 4 | 126 | 49 | 0.64 | 0.01 | 0.57 |
| RM11* † | (GA)17 | 7 | 121–143 | 6 | 121 | 57 | 0.61 | 0.01 | 0.57 |
| RM118* † | (GA)8 | 7 | 142–162 | 5 | 158 | 47 | 0.64 | 0.00 | 0.57 |
| RM234 † | (CT)25 | 7 | 133–164 | 13 | 133 | 42 | 0.78 | 0.02 | 0.77 |
| RM505 † | (CT)12 | 7 | 179–207 | 5 | 179 | 68 | 0.46 | 0.00 | 0.39 |
| RM152* † | (GGC)10 | 8 | 132–155 | 5 | 144 | 71 | 0.47 | 0.01 | 0.43 |
| RM25* † | (GA)18 | 8 | 129–147 | 5 | 129 | 42 | 0.67 | 0.02 | 0.61 |
| RM284* † | (GA)8 | 8 | 142–150 | 4 | 142 | 67 | 0.49 | 0.00 | 0.44 |
| RM433* † | (AG)13 | 8 | 219–233 | 8 | 223 | 74 | 0.45 | 0.00 | 0.43 |
| RM223 | (CT)25 | 8 | 142–165 | 9 | 152 | 28 | 0.82 | 0.00 | 0.80 |
| RM80 | (CTC)25 | 8 | 98–172 | 12 | 127 | 50 | 0.71 | 0.00 | 0.68 |
| RM242 | (CT)26 | 9 | 186–225 | 11 | 186 | 68 | 0.51 | 0.02 | 0.48 |
| RM171* † | (GATG)5 | 10 | 324–344 | 5 | 336 | 67 | 0.49 | 0.00 | 0.44 |
| RM552* † | (TAT)13 | 11 | 157–248 | 17 | 157 | 42 | 0.71 | 0.01 | 0.67 |
| RM144* † | (ATT)11 | 11 | 220–274 | 8 | 220 | 51 | 0.64 | 0.00 | 0.59 |
| RM209 | (CT)18 | 11 | 121–155 | 9 | 125 | 21 | 0.84 | 0.05 | 0.81 |
| RM19* † | (ATC)10 | 12 | 205–251 | 10 | 214 | 49 | 0.70 | 0.05 | 0.66 |
| Mean | - | - | 8 | - | 46 | 0.67 | 0.01 | 0.62 | |
Notes:
*Taken from panel of 50 standard SSR markers: http://archive.gramene.org/markers/microsat/50_ssr.html.
†SSR markers selected for combined analysis of current genotyping data and global rice germplasm data reported in Garris et al. [3].
Chr, Rice chromosome; AN, Number of allele per locus; H e, Gene diversity or expected heterozygosity; H o, Observed heterozygosity; PIC, Polymorphism information content.