Table 4.
Polymorphism observed in terms of SNPs and InDels between sequences of KMR3 and IL50-13 for the DEGs and reported yield related genes.
| S. No. | Category | Gene Name | No. of variants | No. of SNPs | No. of SNPs (CDS) | No. of SNPs (UTRs) | No. of SNPs (Introns) | No.of InDels | No.of InDels (CDS) | No.of InDels (UTRs) | No.of InDels (Introns) |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | A28 | Os02t0589000-01 | 13 | 10 | 0 | 0 | 10 | 3 | 0 | 0 | 3 |
| 2 | A61 | Os02t0626400-03 | 86 | 84 | 84 | 0 | 0 | 2 | 2 | 0 | 0 |
| 3 | A11 | Os02t0569800-00 | 118 | 100 | 4 | 0 | 96 | 18 | 0 | 0 | 18 |
| 4 | A51 | Os02t0616600-01 | 123 | 108 | 0 | 5 | 103 | 15 | 0 | 1 | 14 |
| 5 | A32 | Os02t0592000-00 | 230 | 195 | 0 | 0 | 195 | 35 | 0 | 0 | 35 |
| 6 | A16 | Os02t0574800-01 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| 7 | A1 | Os02t0552500-00 | 3 | 3 | 3 | 0 | 0 | 0 | 0 | 0 | 0 |
| 8 | A12 | Os02t0569900-01 | 36 | 34 | 34 | 0 | 0 | 2 | 2 | 0 | 0 |
| 9 | A62 | Os02t0626400-01 | 195 | 184 | 184 | 0 | 0 | 11 | 11 | 0 | 0 |
| 10 | A63 | Os02t0627100-01 | 218 | 205 | 205 | 0 | 0 | 13 | 13 | 0 | 0 |
| 11 | B8 | Os08t0468100-03 | 7 | 1 | 0 | 0 | 1 | 6 | 0 | 0 | 6 |
| 12 | B21 | Os08t0487301-00 | 11 | 9 | 5 | 0 | 4 | 2 | 2 | 0 | 0 |
| 13 | B23 | Os08t0490100-01 | 23 | 17 | 17 | 0 | 0 | 6 | 6 | 0 | 0 |
| 14 | C1 | Os01t0314800-01 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| 15 | C4 | Os02t0831500-01 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 1 |
| 16 | C10 | Os06t0229800-01 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| 17 | D6 | Os03t0407400-00 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| 18 | D8 | Os03t0117900-01 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| 19 | D19 | Os08t0509600-01 | 4 | 4 | 0 | 0 | 4 | 0 | 0 | 0 | 0 |
| Total | 1073 | 959 | 541 | 5 | 413 | 114 | 36 | 1 | 77 |
Category A refers to genes within qyld2.1, B refers to genes within qyld8.2, C refers to genes showing high fold expression and D refers to reported yield related genes. The candidate genes (PAL) showing maximum SNPs in CDS and within qyld2.1 are shown in bold.