Table 2

Parameters of 48 microsatellite markers assembled into 24 duplexes (Sets 1-24) in switchgrass
Set SSR IDa Typeb Repeat motif LGc Positiond NAe Lmin-max(bp)f Dmin(bp)g PICh NE-1Pi Primer (pmol)j
1 PVAAG-3163/4 gSSR (ACA)29 5b 63.5 19 211-293 16 0.925 0.248 1
PVGA-1143/4 gSSR (GA)7-(GA)8 5a 29.3 20 156-195 0.926 0.246 1
2 PVCAG-2397/8 gSSR (CAG)12 3b 36.3 9 161-189 73 0.822 0.484 2
PVCAG-2517/8 gSSR (GCT)8 9a 6.9 15 213-234 0.879 0.362 2
3 PVCAG-2147/8 gSSR (CAG)7 6b 150.5 12 285-306 68 0.836 0.454 1
SWW-1394 eSSR (GGT)n 7a,VIIa 60.4 8 194-217 0.651 0.709 0.5
4 SWW-463 eSSR (TG)n 9a 58.3 7 253-273 108 0.762 0.58 0.5
PVAAG-3017/8 gSSR (AAG)11 6b 58.8 8 132-145 0.787 0.539 0.5
5 PVAAG-3091/2 gSSR (TTC)13 9a 79.5 13 304-346 71 0.867 0.39 1
PVAAG-3245/6 gSSR (TTC)9 2a 91.4 19 102-233 0.929 0.237 0.25
6 NFSG-112 gSSR (GA)n 8b,VIIIb 48 4 189-195 22 0.65 0.472 0.5
NFSG-036 gSSR (GA)n 4a,IVa 0 17 120-167 0.91 0.289 0.5
7 SWW-573 eSSR (CAG)n 2b 39.5 11 229-247 60 0.767 0.561 1
PVCAG-2473/4 gSSR (GCA)12 3a 60.8 13 138-169 0.896 0.325 4
8 PVAAG-2895/6 gSSR (GAA)10 5b 118 23 310-413 82 0.936 0.215 4
PVCAG-2527/8 gSSR (GCT)9 4b 60.8 12 206-228 0.867 0.392 4
9 NFSG-200 gSSR (GA)n 9b,IXb 76.4 15 107-146 19 0.884 0.35 1
NFSG-219 gSSR (GA)n 8b,VIIIb 26.6 19 165-199 0.928 0.243 1
10 SWW-387 eSSR (CT)n 9b 46.5 5 154-159 44 0.622 0.49 2
PVGA-1663/4 gSSR (AG)13 9b 34.1 17 203-230 0.89 0.332 2
11 PVAAG-3051/2 gSSR (GAA)29 7a 31.8 15 185-254 10 0.851 0.418 1
PVCAG-2209/10 gSSR (GC)8 4a 13.4 9 264-274 0.839 0.452 1
12 PVCAG-2207/8 gSSR (CTG)5 2b 40.3 7 221-238 29 0.677 0.685 0.125
PVCAG-2289/90 gSSR (TGC)5 4b 61 16 157-192 0.886 0.343 0.25
13 PVCAG-2187/8 gSSR (GCA)7 8b 69.4 13 152-179 99 0.859 0.404 1
PVGA-1549/50 gSSR (GAA)6 1b 83.5 11 278-331 0.85 0.428 1
14 SWW-2662 eSSR (AGG)n 2b, IIb 73.5 10 178-197 43 0.774 0.555 1
5211_B07 eSSR (AGC)8 2a 17.2 7 240-253 0.799 0.525 1
15 PVGA-1357/8 gSSR (AC)7-(GA)22 5a 59.5 22 229-337 3 0.938 0.211 1
PVGA-1301/2 gSSR (TC)22 9b 50.5 17 163-226 0.914 0.279 1.5
16 PVGA-1243/4 gSSR (TC)23 5b 69.3 25 280-317 62 0.945 0.191 2
PVCAG-2297/8 gSSR (CAG)6 3a 66.6 15 177-218 0.866 0.386 0.5
17 PVAAG-3311/2 gSSR (CTT)28 2a 29.6 12 140-170 66 0.883 0.353 0.5
PVGA-1813/4 gSSR (GA)7 5a 72.2 18 236-276 0.915 0.277 1
18 NFSG-035 gSSR (GA)n 3a, IIIa 129.2 13 117-151 52 0.897 0.325 1
SWW-125 gSSR (GA)n 2b, IIb 45.5 5 203-220 0.629 0.487 1
19 PVCA-893/4 gSSR (AC)19 3b 65.3 9 297-336 81 0.78 0.546 1
SWW-1615 eSSR (GGC)n 1a, Ia 109.8 17 185-216 0.873 0.368 1
20 SWW-1622 eSSR (GCG)n 2b, IIb 56.3 6 233-246 15 0.77 0.576 1
SWW-1889 eSSR (GCT)n 6b, VIb 72 4 211-218 0.624 0.484 1
21 PVCA-415/6 gSSR (TG)16 6a 68.1 20 137-172 5 0.93 0.236 1
SWW-1643 eSSR (GA)n 3b 136 12 177-207 0.881 0.361 2
22 PVCA-979/80 gSSR (GT)30 8a 50.2 8 283-310 60 0.678 0.679 2
SWW-2376 eSSR (CTG)n 5b, Vb 111.5 9 204-223 0.655 0.703 2
23 PVCAG-2269/70 gSSR (CAG)8 4b 0 17 209-262 6 0.906 0.298 0.5
PVCAG-2361/2 gSSR (AGC)8 1b 25.9 8 268-277 0.705 0.648 1
24 PVCAG-2279/80 gSSR (GCT)8 5a 11.7 11 236-248 14 0.83 0.46 0.25
PVGA-1963/4 gSSR (GA)9-(AG)6 5b 66.5 17 191-222 0.908 0.294 2

Footnote: a The sequences of primer pairs are available in previous studies [15-19]; b gSSR, genomic SSR; eSSR, EST-SSR; c The linkage group (LG) with an Arabic number indicates the map developed by Liu et al.[24], while Roman number by Okada et al.[18]; d The position indicated genetic distance of linkage map by Liu et al.[24]; e Number of alleles (NA); f Minimum and maximum allele lengths (L); g Minimum difference (D) between non-allelic bands; h Polymorphic information content (PIC); i Average non-exclusion probability for one known parent (NE-1P); j Each primer quantity.

Liu and Wu

Liu and Wu BMC Genomics 2012 13:522   doi:10.1186/1471-2164-13-522

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