Table 3.
List of significant markers associated with multiple phenotypic traits (pleiotropy), in the SWAMP obtained from GWAS using three datasets: BLUEC (Citra), BLUEQ (Quincy), and BLUEA (combined).
| SNP | Trait | Dataset | −log10(p) | Effect | PVE |
|---|---|---|---|---|---|
| S1B_597446331 | SF | BLUEA | 4.18 | −4.85 | 0.09 |
| SHI | BLUEA | 4.88 | −0.87 | 0.11 | |
| S3A_12525847 | GY | BLUEC | 4.75 | 149.89 | 0.28 |
| HI | BLUEC | 4.29 | 1.37 | 0.21 | |
| S3A_12554700 | GY | BLUEC | 5.10 | −148.37 | 0.29 |
| TGW | BLUEQ | 4.55 | −0.92 | 0.28 | |
| S3A_12915079 | GN | BLUEC | 4.60 | 324.68 | 0.15 |
| GY | BLUEC | 4.87 | 151.80 | 0.28 | |
| S3A_625236830 | GFR | BLUEC | 4.86 | 8.36 | 0.25 |
| GY | BLUEC | 4.69 | 309.94 | 0.29 | |
| HI | BLUEC | 4.63 | 2.97 | 0.23 | |
| S3B_605293365 | GFR | BLUEA | 4.38 | 3.39 | 0.19 |
| GY | BLUEA | 4.14 | 123.54 | 0.26 | |
| S5A_605144047 | GN | BLUEQ | 4.14 | 643.69 | 0.12 |
| TGW | BLUEA | 4.10 | −1.71 | 0.30 | |
| TGW | BLUEQ | 5.05 | −1.64 | 0.28 |
SF, spike fertility (grains g−1 chaff weight); GY, grain yield (kg h−1); GN, grain number m−2; TGW, thousand grain weight (g); GFR, grain filling rate (kg h−1 days); SHI, spike harvest index; HI, harvest index; PVE, phenotypic variance explained.