Skip to main content

Table 1 Polymorphic rates of the SNP and InDel markers

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

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