Table 1.

List of HvSSR primers used for genotyping of 729 rice varieties along with their chromosomal position, product size, No. of alleles amplified, gene diversity, heterozygosity and PIC value

Chr. No.	Primer ID	Size (bp)	Forward primer	Reverse primer	Major allele frequency	Allele no	Gene diversity	Heterozygosity	PIC
1	HvSSR01-32	250	AAACTGGAGATGAACTCGAA	GTAACGAACTAGAGCATGGG	0.9445	2.0000	0.1048	0.0340	0.0993
	HvSSR01-41	348	TGAGTGAGACTTGACAGTGC	AGTTAACACCAATGCTGACC	0.5943	3.0000	0.5405	0.2340	0.4638
	HvSSR01-53	274	TGTCGTCCACGTAGTAGGAG	ACACTCCTCCTCTGTTCTCA	0.8894	2.0000	0.1968	0.0030	0.1774
2	HvSSR02-01	312	AAGAGATGAGAAGAGCAATGA	CAACTTAGAGGAAGAAGGAGG	0.7813	2.0000	0.3417	0.0892	0.2834
	HvSSR02-33	355	TAATGCACGCACAACTTTAC	TATAGAATGCTGACTGGGCT	0.7976	2.0000	0.3228	0.0923	0.2707
	HvSSR02-50	195	TTTCAGGAATCTGATGCTTT	TTAATCAAAGCCCTAACAGC	0.6579	3.0000	0.5077	0.1445	0.4547
3	HvSSR03-02	228	TAGCGGAGTTGGAATAACAC	CTGCACTGCATACCTCATAA	0.5346	4.0000	0.5737	0.9224	0.4922
	HvSSR03-10	280	GTACACAACGTCACAACAGC	ACTGTGGCATATGTTCGATT	0.7566	2.0000	0.3683	0.1468	0.3005
	HvSSR03-19	230	AATTCAGTTCACGCATTCTT	AGCTGTTCGTCTGCATAGTT	0.8968	2.0000	0.1851	0.0577	0.1680
	HvSSR03-37	386	GGAAATCGTCAAGAACGTC	TAATTGTATACCACTCCGCC	0.3780	3.0000	0.6610	0.3013	0.5868
	HvSSR03-54	352	GCCTATCAGGCTATCATCAC	GTGATCGACATTGAGGAGTT	0.8168	2.0000	0.2993	0.0049	0.2545
4	HvSSR04-19	265	TCGTGGAGTATCCTGTATCC	TTATAACTTGGAGCTCAGGC	0.9127	3.0000	0.1631	0.1041	0.1566
	HvSSR04-27	318	ATGGATTTAGGCTTGTTTGA	ATACTGCGAAGGTGAAGAGA	0.7150	4.0000	0.4609	0.2629	0.4319
	HvSSR04-46	179	GGCGCGCTTATATATGTACT	CGATTGCGTGGTGTAACTAT	0.7774	4.0000	0.3712	0.1475	0.3413
5	HvSSR05-09	335	CTCTCCATCTTGCAATCTTC	TGCATGACTCTATCAACCAG	0.5331	3.0000	0.5509	0.0768	0.4558
	HvSSR05-15	275	CCATGTCAAACGGTTACTTT	GGGAGAAGTGAGAAAGAGGT	0.9366	3.0000	0.1205	0.0975	0.1166
	HvSSR05-30	353	TACGACGGACGATTAAAGTT	GCTAACTCATTCATCTCGCT	0.7962	2.0000	0.3245	0.0000	0.2719
6	HvSSR06-03	212	CTAGGGAATCAGCGGTTAG	GCTCTCTTGTCCTTCTTCTTC	0.9582	3.0000	0.0802	0.0099	0.0771
	HvSSR06-16	368	TCTGAAATGCTGTCATCAAG	GAGCAGAGTAGGACATGAGC	0.9767	2.0000	0.0454	0.0186	0.0444
	HvSSR06-40	385	CTCTTCCGTGGTTAAAGAAA	CACTGGTATGATCTCCGACT	0.5405	3.0000	0.5285	0.2859	0.4232
7	HvSSR07-18	343	GGTGTGTTGTCGAATCTCTC	ATGCCATTGTCCTTACATTC	0.5436	3.0000	0.5383	0.1317	0.4392
	HvSSR07-51	341	CGAGCATGTCTGTCAAGTAA	GTTCGAATGTAATGTTGGCT	0.8503	3.0000	0.2645	0.0349	0.2464
8	HvSSR08-14	295	TCCACTTTACATCGTCACAA	CTACCTCTTAACCGCACATT	0.5996	3.0000	0.5401	0.0736	0.4661
	HvSSR08-19	221	CATCTCTTGAGAAATCTGCC	TGTGCATTTCGTCTTTCATA	0.4944	4.0000	0.5183	0.1278	0.4022
9	HvSSR09-11	366	TGCAGAATTTCTTCCTTCAT	ACCAGAATCTCCCAAATGTA	0.7632	5.0000	0.3981	0.0371	0.3752
	HvSSR09-26	331	TGGGCATCTGGTACTATCTT	AGCTCATTCCACAGGTTAGA	0.9594	2.0000	0.0779	0.0056	0.0749
	HvSSR09-55	382	TTACTCCGCATATATCCATGT	ATTTGACACCAAGTTGATCC	0.5925	4.0000	0.5090	0.7326	0.4105
10	HvSSR10-03	289	TCTTTCCCAAATTCCAGATA	CATTAGTTGTTTGTGGCAGA	0.9081	3.0000	0.1711	0.0883	0.1641
	HvSSR10-13	169	CAGGGAATCAACATCAAAGT	AGCAAGGCAAGTCATCTCTA	0.5795	4.0000	0.5292	0.4003	0.4378
	HvSSR10-34	202	TAGACCGAGGAATTGAAAGA	TTTGGGCTTATTGTCAGTTT	0.9060	4.0000	0.1749	0.0982	0.1681
11	HvSSR11-13	285	TGAAACCACAATGAGTCAAA	GCCCTAAACCCAAATAGAAG	0.7532	2.0000	0.3718	0.1062	0.3027
	HvSSR11-21	291	TACGCTATAACCATGAAGCA	CTCCCGTTATTGTCCTTACA	0.8305	5.0000	0.2962	0.2161	0.2766
	HvSSR11-58	371	ACTGAATCCTTACTGGAGCA	GGAGATAAGCATTTGGAAGA	0.7881	5.0000	0.3639	0.1607	0.3451
12	HvSSR12-01	271	GATTTGCAACACGTACGATA	GATCATCCACTCTGAGCAAT	0.9203	2.0000	0.1467	0.0986	0.1360
	HvSSR12-13	388	ACCTTAGGGCTGAGTTCTTT	TTAGGCTTGTCTCTTCCTCA	0.9048	5.0000	0.1782	0.0710	0.1733
	HvSSR12-39	289	ATCTAACAACAACAATCCCG	CATCTTCATCCCTCGTGTAT	0.8793	4.0000	0.2211	0.1142	0.2124
	Mean				0.7630	3.1111	0.3346	0.1536	0.2917