Table 6.
Nine identified SNPs in the 500-kb mapping region containing the GmDW1 allele in the dw genome and marker development
| The ID of developed markers based on the corresponding SNP locus | SNP | The wild-type pool | The mutant pool | SNP effect and target gene | ||||
|---|---|---|---|---|---|---|---|---|
| Physical position in Gm08 (bp) | Referencea | Variationb | Genotypec | Reads depthd | Genotypec | Reads depthd | ||
| 12,598,498 | G | A | G, A | 24, 15 | G, G | 28, 0 | Intergenic | |
| SNP08-1 | 12,613,790 | C | T | C, T | 18, 5 | T, T | 0, 26 | Nonsynonymous, Glyma.08G162100 |
| SNP08-2 | 12,686,354 | G | T | G, G | 26, 0 | G, T | 9, 6 | Upstream |
| SNP08-3 | 12,847,120 | T | A | T, A | 50, 6 | A, A | 0, 63 | Upstream |
| SNP08-4 | 12,903,104 | T | A | T, T | 43, 0 | A, A | 0, 41 | Nonsynonymous, Glyma.08G163900 |
| 12,969,978 | G | A | G, A | 10, 3 | G, G | 13, 0 | Downstream | |
| SNP08-5 | 13,012,790 | C | A | C, C | 37, 3 | C, A | 26, 5 | Nonsynonymous, Glyma.08G165100 |
| 13,055,558 | G | A | G, A | 32, 18 | G, G | 24, 0 | Upstream | |
| SNP08-6 | 13,077,287 | C | T | C, C | 34, 0 | T, T | 0, 37 | Nonsynonymous, Glyma.08G165800 |
aThe genotypes of the SNP locus in the Williams 82 reference genome, while b represents the genotypes of the corresponding mutated locus present in the mutant- or wild-type pool genome. c Homozygous or heterozygous genotype (e.g., “G,G” vs “G,A”) of the SNP locus was identified in the wild-type pool and mutant-type pool genome
dThe number of clean reads covering each of genotypes at the SNP locus