Table 2.

Details of primers used for genotyping 120 rice genotypes and their estimated molecular genetic diversity parameters.

S. no	Marker	Allele no	Min. size of alleles (bp)	Max. size of alleles (bp)	Major allele frequency	Gene diversity (He)	Heterozygosity (Ho)	PIC	Shannon's index (I)	Nei's genetic diversity index (Nei)	Average heterozygosity
1	RM1112	3	100	110	0.601	0.487	0.020	0.378	0.714	0.488	0.460
2	RM1272	4	100	140	0.524	0.537	0.124	0.433	0.846	0.532	0.500
3	RM16	2	190	210	0.876	0.217	0.035	0.194	0.373	0.216	0.211
4	RM169	2	165	175	0.646	0.457	0.053	0.353	0.672	0.479	0.421
5	RM200	3	100	120	0.789	0.341	0.256	0.296	0.587	0.339	0.350
6	RM219	3	190	210	0.688	0.456	0.625	0.388	0.724	0.429	0.417
7	RM224	3	130	155	0.745	0.406	0.204	0.363	0.756	0.430	0.394
8	RM229	3	115	125	0.835	0.283	0.073	0.256	0.538	0.293	0.262
9	RM2334	3	130	200	0.471	0.565	0.291	0.468	0.932	0.577	0.543
10	RM235	3	125	140	0.573	0.551	0.227	0.471	0.914	0.563	0.458
11	RM237	3	125	135	0.797	0.332	0.052	0.292	0.570	0.316	0.299
12	RM242	3	195	230	0.753	0.393	0.021	0.346	0.696	0.408	0.370
13	RM254	2	150	165	0.991	0.018	0.000	0.018	0.045	0.015	0.011
14	RM259	2	150	160	0.767	0.357	0.008	0.294	0.547	0.361	0.343
15	RM26	2	100	120	0.885	0.204	0.010	0.183	0.350	0.198	0.177
16	RM261	2	130	135	0.902	0.177	0.000	0.161	0.496	0.316	0.244
17	RM28073	2	550	580	0.881	0.209	0.031	0.187	0.375	0.217	0.224
18	RM28102	3	160	180	0.775	0.366	0.112	0.326	0.637	0.352	0.349
19	RM283	3	145	160	0.845	0.275	0.176	0.257	0.574	0.297	0.265
20	RM287	3	100	125	0.722	0.418	0.085	0.354	0.693	0.416	0.372
21	RM297	4	140	180	0.525	0.570	0.238	0.484	0.984	0.577	0.527
22	RM30	4	70	100	0.569	0.572	0.413	0.503	1.025	0.572	0.537
23	RM306	2	155	170	0.806	0.313	0.012	0.264	0.526	0.343	0.310
24	RM3166	4	105	160	0.970	0.058	0.020	0.057	0.166	0.061	0.085
25	RM3295	4	80	120	0.505	0.585	0.263	0.502	1.003	0.590	0.560
26	RM3307	3	170	185	0.500	0.624	1.000	0.553	1.035	0.623	0.612
27	RM3343	2	140	150	0.626	0.468	0.748	0.359	0.652	0.459	0.383
28	RM335	5	100	150	0.505	0.642	0.476	0.585	1.215	0.655	0.631
29	RM3688	2	100	115	0.842	0.266	0.010	0.231	0.441	0.270	0.284
30	RM410	4	170	250	0.446	0.649	0.522	0.581	1.159	0.654	0.626
31	RM439	2	245	260	0.787	0.336	0.027	0.279	0.522	0.338	0.325
32	RM47	2	225	230	0.947	0.101	0.000	0.096	0.221	0.109	0.101
33	RM481	5	110	180	0.474	0.604	0.295	0.525	1.055	0.594	0.553
34	RM510	2	120	130	0.849	0.849	0.023	0.224	0.440	0.269	0.158
35	RM514	3	250	260	0.521	0.588	0.300	0.507	0.946	0.576	0.528
36	RM521	2	240	270	0.861	0.861	0.008	0.210	0.365	0.210	0.212
37	RM5349	3	110	125	0.583	0.506	0.052	0.402	0.776	0.509	0.477
38	RM5463	3	155	175	0.720	0.420	0.095	0.357	0.712	0.433	0.361
39	RM5485	2	140	160	0.945	0.103	0.000	0.098	0.199	0.095	0.059
40	RM553	2	155	165	0.754	0.371	0.026	0.302	0.548	0.362	0.333
41	RM574	2	150	155	0.828	0.285	0.031	0.244	0.451	0.278	0.258
42	RM5814	2	100	130	0.500	0.500	1.000	0.375	0.693	0.500	0.500
43	RM589	3	155	175	0.715	0.432	0.169	0.374	0.758	0.440	0.418
44	RM590	2	130	140	0.763	0.362	0.030	0.297	0.572	0.383	0.374
45	RM5926	3	110	160	0.818	0.312	0.106	0.286	0.603	0.319	0.288
46	RM6911	2	130	150	0.649	0.456	0.447	0.352	0.663	0.470	0.447
47	RM6966	3	140	180	0.663	0.468	0.071	0.387	0.776	0.478	0.476
48	RM7555	3	100	120	0.943	0.108	0.021	0.104	0.276	0.122	0.120
49	RM9	4	120	160	0.668	0.495	0.239	0.442	0.911	0.499	0.478
50	SSR12-17.4	2	450	480	0.788	0.334	0.047	0.278	0.519	0.336	0.330
51	K20-1	2	240	243	0.782	0.331	0.000	0.281	0.521	0.342	0.312
52	K20-2	2	982	995	0.606	0.478	0.000	0.364	0.693	0.500	0.500
53	K29-3	2	248	236	0.784	0.338	0.000	0.281	0.534	0.350	0.324
54	K29-1	2	206	212	0.630	0.466	0.043	0.357	0.641	0.449	0.328
55	PAP1	2	520	590	0.775	0.348	0.014	0.288	0.543	0.358	0.357
56	PAP3	2	260	500	0.539	0.497	0.713	0.373	0.690	0.496	0.493
57	PAP4	2	320	350	0.644	0.458	0.115	0.353	0.674	0.481	0.440
	Average	2.7	–	–	0.717	0.407	0.175	0.326	0.641	0.392	0.364

Additional primers evaluated: K41, K42, K43, K45, K46-1, and K46-2 (dominant markers); PAP5, RM142, RM164, RM184, RM24386, RM247, RM291, RM322, RM444, RM492, RM5314, RM536, RM538, SSR12-12.8, and ESSR12-20.2 (monomorphic primers).