Development of EST-based SNP and InDel markers and their utilization in tetraploid cotton genetic mapping

BMC Genomics

Table 1 Polymorphic rates of the SNP and InDel markers

Primers	No. markers	No. polymorphic markers/loci	Polymorphic rate (%)	Classes	Subclasses⁵⁾	No. Markers	No. Polymorphic markers/loci	Polymorphic rate (%)
HAU-SNP¹⁾	356	47/50	13.20		4	27	6/6	22.22
				inter	5	21	4/5	19.05
				23/134	6	16	2/3	12.50
				17.16%	7	11	0/0	0.00
					≥8	59	11/11	18.64
					4	0	0/0	--
				hemi	5	8	1/1	12.50
				24/222	6	9	2/2	22.22
				10.81%	7	10	0/0	0.00
					≥8	195	21/22	10.77
HAU-SNP²⁾	455	43/43	9.45		4	171	15/15	8.77
					5	89	12/12	13.48
					6	97	6/6	6.19
					7	38	3/3	7.89
					≥8	60	7/7	11.67
HAU-InDel³⁾	415	41/42	9.88
HAU-InDel⁴⁾	123	6/7	4.88
Total	1,349	137/142	10.16

¹⁾HAU-SNP001 ~ 356, which were developed by comparing ESTs between G. hirsutum and G. barbadense.
²⁾HAU-SNP357 ~ 811, which were developed by mining G. hirsutum unigenes.
³⁾HAU-InDel001 ~ 415, which were developed by mining the 3′UTRs of public G. hirsutum sequences.
⁴⁾HAU-InDel416 ~ 538, which were developed by blasting putative 3′UTRs of G. hirsutum against the 3′UTRs of Arabidopsis.
⁵⁾Subclasses mean different types of clusters/unigenes classified by the number of sequences contained in a cluster/unigene.

ISSN: 1471-2164