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

Nachimuthu, Vishnu Varthini; Muthurajan, Raveendran; Duraialaguraja, Sudhakar; Sivakami, Rajeswari; Pandian, Balaji Aravindhan; Ponniah, Govinthraj; Gunasekaran, Karthika; Swaminathan, Manonmani; K K, Suji; Sabariappan, Robin

doi:10.1186/s12284-015-0062-5

Rice

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

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