Table 1 QTLs for morpho-agronomic traits identified in GWAS using principal components in 181 aus rice germplasm
Trait | QTL | Chr | Flanking region (Mb) | Peak SNP position | Ref allele | -Log10(P) | MAF | Effect | PVE |
|---|---|---|---|---|---|---|---|---|---|
PC1 (DtF, Ht, PnL, PnW, SpkN) | qPC1-1.1 | 1 | 4.36–4.68 | 4,521,776 | G | 9.30 | 0.10 | -0.69 | 5.06 |
|  | qPC1-1.2 | 1 | 29.49–29.81 | 29,651,634 | C | 8.38 | 0.21 | 0.53 | 1.47 |
|  | qPC1-2.1 | 2 | 24.78–24.90 | 24,835,927 | G | 7.18 | 0.30 | -0.38 | 2.05 |
|  | qPC1-4.1 | 4 | 27.76–27.85 | 27,801,414 | G | 8.59 | 0.20 | 0.37 | 2.05 |
|  | qPC1-5.1 | 5 | 19.42–19.81 | 19,616,683 | G | 7.32 | 0.23 | 0.42 | 5.80 |
|  | qPC1-7.1 | 7 | 0.73–1.05 | 888,054 | A | 15.81 | 0.16 | -1.04 | 7.97 |
|  | qPC-8.1 | 8 | 17.81–18.19 | 18,001,305 | A | 7.63 | 0.16 | -0.56 | 5.13 |
|  | qPC1-8.2 | 8 | 21.12–21.51 | 21,316,516 | T | 9.30 | 0.13 | 0.76 | 1.11 |
PC2 (PnW, Yld, HI) | qPC2-1.1 | 1 | 27.93–28.25 | 28,087,887 | T | 9.85 | 0.15 | 0.44 | 10.53 |
|  | qPC2-7.1 | 7 | 21.54–21.86 | 21,700,005 | T | 7.61 | 0.27 | 0.33 | 2.58 |
|  | qPC2-7.2 | 7 | 26.45–26.77 | 26,611,742 | C | 7.62 | 0.12 | 0.50 | 1.23 |
|  | qPC2-11.1 | 11 | 3.35–3.48 | 3,412,660 | G | 10.30 | 0.48 | -0.34 | 3.98 |
|  | qPC2-11.2 | 11 | 4.49–4.62 | 4,552,359 | T | 7.99 | 0.15 | -0.54 | 1.60 |
PC3 (Tn, GW, Yld) | qPC3-1.1 | 1 | 4.62–4.94 | 4,789,451 | G | 7.69 | 0.07 | 0.46 | 6.20 |
|  | qPC3-1.2 | 1 | 41.66–41.98 | 41,821,709 | A | 7.45 | 0.33 | 0.39 | 6.51 |
|  | qPC3-3.1 | 3 | 17.99–18.45 | 18,218,891 | C | 7.18 | 0.06 | -0.55 | 2.07 |
|  | qPC3-5.1 | 5 | 13.96–14.35 | 14,156,143 | G | 10.16 | 0.17 | 0.48 | 5.86 |
|  | qPC3-5.2 | 5 | 27.71–28.10 | 27,904,519 | C | 7.04 | 0.35 | 0.26 | 0.37 |