Genetic Diversity of Shanlan Upland Rice (Oryza sativa L.) and Association Analysis of SSR Markers Linked to Agronomic Traits

Table 2

SSR markers used in study.

No.	SSR marker	Sequence (5 to 3)	Annealing temperature (°C)	Size of common polymorphic fragments (bp)
1	RM583	Forward: agatccatccctgtggagag; Reverse: gcgaactcgcgttgtaatc	55	179, 189, 192, 195, 198
2	RM7l	Forward: ctagaggcgaaaacgagatg; Reverse: gggtgggcgaggtaataatg	55	121, 139, 148, 213
3	RM85	Forward: ccaaagatgaaacctggattg; Reverse: gcacaaggtgagcagtcc	55	79, 94, 100, 103
4	RM471	Forward: acgcacaagcagatgatgag; Reverse: gggagaagacgaatgtttgc	55	104, 106, 114
5	RM274	Forward: cctcgcttatgagagcttcg; Reverse: cttctccatcactcccatgg	55	149, 161
6	RM190	Forward: ctttgtctatctcaagacac; Reverse: ttgcagatgttcttcctgatg	55	107, 119, 121
7	RM336	Forward: cttacagagaaacggcatcg; Reverse: gctggtttgtttcaggttcg	55	141, 144, 151, 154, 160, 163, 165, 192
8	RM72	Forward: ccggcgataaaacaatgag; Reverse: gcatcggtcctaactaaggg	55	149, 159, 162, 165
9	RM2l9	Forward: cgtcggatgatgtaaagcct; Reverse: catatcggcattcgcctg	55	194, 196, 215, 221
10	RM311	Forward: tggtagtataggtactaaacat; Reverse: tcctatacacatacaaacatac	55	160, 166, 170, 182
11	RM209	Forward: atatgagttgctgtcgtgcg; Reverse: caacttgcatcctcccctcc	55	125, 132, 151, 153, 160
12	RM19	Forward: caaaaacagagcagatgac; Reverse: ctcaagatggacgccaaga	55	216, 247, 250, 253
13	RM1195	Forward: atggaccacaaacgaccttc; Reverse: cgactcccttgttcttctgg	55	142, 144, 146, 148, 150, 152
14	RM208	Forward: tctgcaagccttgtctgatg; Reverse: taagtcgatcattgtgtggacc	55	162, 164, 172, 176, 178
15	RM232	Forward: ccggtatccttcgatattgc; Reverse: ccgacttltcctcclgacg	55	141, 150, 156, 159, 161
16	RM119	Forward: catccccctgctgctgctgctg; Reverse: cgccggatgtgtgggactagcg	67	166, 169
17	RM267	Forward: tgcagacatagagaaggaagtg; Reverse: agcaacagcacaacttgatg	55	136, 138, 153, 155
18	RM253	Forward: tccttcaagagtgcaaaacc; Reverse: gcattgtcatgtcgaagcc	55	213, 245
19	RM481	Forward: tagctagccgattgaatggc; Reverse: ctccacctcctatgttgttg	55	135, 138, 141, 144, 147, 177, 188
20	RM339	Forward: gtaatcgatgctgtgggaag; Reverse: gagtcatgtgatagccgatatg	55	140, 146, 158
21	RM278	Forward: gtagtgagcctaacaataatc; Reverse: tcaactcagcatctctgtcc	55	59, 139, 141, 143
22	RM258	Forward: tgctgtatgtagctcgcacc; Reverse: tggcctttaaagctgtcgc	55	128, 132, 136, 146
23	RM224	Forward: atcgatcgatcttcacgagg; Reverse: tgctataaaaggcattcggg	55	120, 128, 131, 143, 153, 155, 157
24	RM17	Forward: tgccctgttattttcttctctc; Reverse: ggtgatcctttcccatttca	55	153, 158, 182, 184
25	RM493	Forward: tagctccaacaggatcgacc; Reverse: gtacgtaaacgcggaaggtg	55	221, 236, 245
26	RM561	Forward: gagctgttttggactacggc; Reverse: gagtagctttctcccacccc	55	60, 185, 187, 193, 268, 270
27	RM8277	Forward: agcacaagtaggtgcatttc; Reverse: atttgcctgtgatgtaatagc	55	165, 187, 190, 193, 196
28	RM551	Forward: agcccagactagcatgattg; Reverse: gaaggcgagaaggatcacag	55	182, 184, 186, 188, 192, 194, 196
29	RM598	Forward: gaatcgcacacgtgatgaac; Reverse: atgcgactgatcggtactcc	55	153, 156, 162
30	RMl76	Forward: cggctcccgctacgacgtctcc; Reverse: agcgatgcgctggaagaggtgc	67	133, 136
31	RM432	Forward: ttctgtctcacgctggattg; Reverse: agctgcgtacgtgatgaatg	55	166, 178, 186
32	RM331	Forward: gaaccagaggacaaaaatgc; Reverse: catcatacatttgcagccag	55	63, 92, 150, 152, 158, 172
33	OSR28	Forward: agcagctatagcttagctgg; Reverse: actgcacatgagcagagaca	55	136, 174, 177, 180, 183
34	RM590	Forward: catctccgctctccatgc; Reverse: ggagttggggtcttgttcg	55	136, 143
35	RM21	Forward: acagtattccgtaggcacgg; Reverse: gctccatgagggtggtagag	55	128, 132, 147, 158, 160
36	RM3331	Forward: cctcctccatgagctaatgc; Reverse: aggaggagcggatttctctc	50	110, 122, 124, 126
37	RM443	Forward: gatggttttcatcggctacg; Reverse: agtcccagaatgtcgtttcg	55	115, 119, 121, 123
38	RM490	Forward: atctgcacactgcaaacacc; Reverse: agcaagcagtgctttcagag	55	93, 99, 103
39	RM424	Forward: tttgtggctcaccagttgag; Reverse: tggcgcattcatgtcatc	55	240, 277, 280
40	RM423	Forward: agcacccatgccttatgttg; Reverse: cctttttcagtagccctccc	55	269, 286, 293, 299
41	RM571	Forward: ggaggtgaaagcgaatcatg; Reverse: cctgctgctctttcatcagc	55	54, 180, 189, 191
42	RM231	Forward: ccagattatttcctgaggtc; Reverse: cacttgcatagttctgcattg	55	178, 180, 182, 184, 186, 188
43	RM567	Forward: atcagggaaatcctgaaggg; Reverse: ggaaggagcaatcaccactg	55	244, 246, 248, 250, 252
44	RM289	Forward: ttccatggcacacaagcc; Reverse: ctgtgcacgaacttccaaag	55	87, 106
45	RM542	Forward: tgaatcaagcccctcactac; Reverse: ctgcaacgagtaaggcagag	55	87, 89, 111
46	RM316	Forward: ctagttgggcatacgatggc; Reverse: acgcttatatgttacgtcaac	55	165, 182, 184, 186, 196, 198, 200, 213
47	RM332	Forward: gcgaaggcgaaggtgaag; Reverse: catgagtgatctcactcaccc	55	164, 167, 169, 176
48	RM7102	Forward: taggagtgtttagagtgcca; Reverse: tcggtttgcttatacatcag	55	170, 175, 187