Table 4.
Summary of the genome-wide association study for pod shattering in the BC4/F4 IL population
| Phenotyping approach | Shattering trait | Sample size (no. of ILs) |
Ch | Associated SNPs (n) | Genomic region | Three best-associated SNPs |
|---|---|---|---|---|---|---|
| Shattering occurrence | ||||||
| Sh y/n | Dehiscent versus indehiscent | 1183 | Pv 05 | 52 | 38322754–39384267 | S5_38611412 (4.35E-30) S5_38792327 (6.71E-24) S5_39120955 (1.03E-27) |
| Sh y/n | Dehiscent versus indehiscent (only accurate phenotypic scores) | 1165 | Pv 05 | 54 | 38322754–39384267 | S5_38611412 (3.21E-27) S5_38792327 (5.06E-25) S5_39120955 (2.7E-27) |
| Sh y/n | All classes (dehiscent, intermediate, indehiscent) | 1196 | Pv 05 | 52 | 38322754–39384267 | S5_38611412 (1.32E-31) S5_38792327 (5.77E-25) S5_39120955 (5.04E-27) |
| Field | Dehiscent versus indehiscent | 1192 | Pv 05 | 38 | 38322754–39182106 | S5_38611085 (9.10E-20) S5_38611412 (2.73E-23) S5_38611464 (5.34E-19) |
| Post-harvest | Putative dehiscent versus putative indehiscent | 1165 | Pv 05 | 43 | 38322754–39379952 | S5_38611085 (2.82E-27) S5_38611412 (2.79E-30) S5_38612876 (1.23E-26) |
| Shattering modulation | ||||||
| Post-harvest | Quantitative (all classes) | 1192 | Pv 05 | 20 | 38348010–39120955 | S5_38611412 (1.05E-15) S5_38611464 (5.43E-14) S5_38612876 (5.27E-15) |
| Field | % Twisting pods/plant | 1002 | Pv 05 | 7 | 38611085–38792327 | S5_38611412 (3.51E-10) S5_38612876 (4.63E-08) S5_38792327 (4.77E-08) |