Table 4.
Favorable alleles and effects of 12 SNP loci validated in the RIL population.
| SNP name | Chr. | Environment | Allele | Mean ± SE | Allele effect | P-value |
|---|---|---|---|---|---|---|
| GENE-1086_1111 | 2A | 15YZ | AA | 58.67 ± 0.57 | 1.26 | 2.00 × 10−3 |
| Others | 56.34 ± 0.48 | |||||
| 16YZ | AA | 59.16 ± 0.58 | 1.29 | 1.41 × 10−3 | ||
| Others | 56.76 ± 0.47 | |||||
| Average | AA | 53.78 ± 0.39 | 0.84 | 3.29 × 10−3 | ||
| Others | 52.22 ± 0.34 | |||||
| BS00022896_51 | 2A | 15YZ | TT | 59.30 ± 0.69 | 2.09 | 3.56 × 10−4 |
| Others | 56.37 ± 0.43 | |||||
| 16JZ | TT | 44.55 ± 0.61 | 1.05 | 4.30 × 10−2 | ||
| Others | 43.09 ± 0.38 | |||||
| 16YZ | TT | 59.05 ± 0.64 | 1.28 | 3.10 × 10−2 | ||
| Others | 57.25 ± 0.46 | |||||
| Average | TT | 54.09 ± 0.49 | 1.22 | 5.00 × 10−3 | ||
| Others | 52.38 ± 0.32 | |||||
| BS00014345_51 | 2B | 16JZ | CC | 44.05 ± 0.37 | 0.59 | 3.70 × 10−2 |
| Others | 42.69 ± 0.56 | |||||
| 16YZ | CC | 58.61 ± 0.47 | 0.81 | 1.20 × 10−3 | ||
| Others | 56.71 ± 0.60 | |||||
| Average | CC | 53.36 ± 0.31 | 0.49 | 3.40 × 10−2 | ||
| Others | 52.20 ± 0.47 | |||||
| wsnp_JD_c12346_12606967 | 2B | 15YZ | AA | 57.76 ± 0.43 | 0.45 | 4.00 × 10−3 |
| Others | 54.44 ± 0.96 | |||||
| 16YZ | AA | 58.10 ± 0.41 | 0.32 | 4.20 × 10−2 | ||
| Others | 55.74 ± 1.26 | |||||
| Average | AA | 53.25 ± 0.31 | 0.34 | 3.00 × 10−3 | ||
| Others | 50.77 ± 0.64 | |||||
| BobWhite_c10539_201 | 2D | 15YZ | AA | 57.71 ± 0.43 | 0.43 | 8.00 × 10−3 |
| Others | 54.70 ± 0.96 | |||||
| 16JZ | AA | 43.96 ± 0.35 | 0.36 | 3.00 × 10−3 | ||
| Others | 41.12 ± 0.65 | |||||
| 16YZ | AA | 58.44 ± 0.39 | 0.57 | 4.80 × 10−5 | ||
| Others | 53.79 ± 1.00 | |||||
| Average | AA | 53.23 ± 0.31 | 0.31 | 8.00 × 10−3 | ||
| Others | 51.08 ± 0.69 | |||||
| wsnp_Ex_c12223_19533198 | 2D | 15YZ | GG | 58.10 ± 0.41 | 0.46 | 4.00 × 10−3 |
| Others | 55.04 ± 0.99 | |||||
| 16YZ | GG | 43.96 ± 0.35 | 0.33 | 3.90 × 10−2 | ||
| Others | 42.42 ± 0.78 | |||||
| Average | GG | 53.56 ± 0.28 | 0.35 | 1.00 × 10−3 | ||
| Others | 51.23 ± 0.68 | |||||
| Excalibur_c73633_120 | 3B | 15YZ | GG | 57.83 ± 0.43 | 0.46 | 6.00 × 10−3 |
| others | 54.83 ± 0.89 | |||||
| 16JZ | GG | 43.93 ± 0.36 | 0.46 | 1.00 × 10−3 | ||
| others | 40.76 ± 0.67 | |||||
| 16YZ | GG | 58.51 ± 0.40 | 0.59 | 7.87 × 10−5 | ||
| others | 54.16 ± 0.90 | |||||
| Average | GG | 53.33 ± 0.31 | 0.38 | 1.00 × 10−3 | ||
| others | 50.83 ± 0.62 | |||||
| tplb0051b16_1324 | 4A | 15YZ | GG | 58.52 ± 0.52 | 1.17 | 1.00 × 10−3 |
| others | 56.10 ± 0.54 | |||||
| 16JZ | GG | 44.50 ± 0.40 | 1.06 | 1.00 × 10−3 | ||
| others | 42.35 ± 0.47 | |||||
| Average | GG | 53.77 ± 0.38 | 0.80 | 2.00 × 10−3 | ||
| others | 52.12 ± 0.37 | |||||
| RAC875_c84991_116 | 5A | 15YZ | CC | 58.59 ± 0.62 | 1.30 | 3.00 × 10−3 |
| others | 56.30 ± 0.48 | |||||
| 16YZ | CC | 59.36 ± 0.62 | 1.52 | 1.00 × 10−3 | ||
| others | 56.69 ± 0.46 | |||||
| Average | CC | 53.87 ± 0.42 | 0.95 | 2.00 × 10−3 | ||
| others | 52.20 ± 0.35 | |||||
| wsnp_BF474379A_Ta_2_2 | 7A | 15YZ | CC | 58.68 ± 0.55 | 1.32 | 3.48 × 10−4 |
| others | 56.06 ± 0.46 | |||||
| 16YZ | CC | 58.85 ± 0.51 | 0.98 | 9.00 × 10−3 | ||
| others | 56.93 ± 0.52 | |||||
| Average | CC | 53.68 ± 0.38 | 0.72 | 8.00 × 10−3 | ||
| others | 52.28 ± 0.36 | |||||
| BS00003630_51 | 7B | 15YZ | TT | 57.94 ± 0.43 | 0.41 | 7.00 × 10−3 |
| others | 54.87 ± 0.77 | |||||
| 16JZ | TT | 43.94 ± 0.34 | 0.36 | 5.00 × 10−3 | ||
| others | 41.29 ± 0.78 | |||||
| Average | TT | 53.44 ± 0.29 | 0.32 | 2.00 × 10−3 | ||
| others | 51.05 ± 0.55 | |||||
| Kukri_c35508_426 | 7D | 15YZ | TT | 59.43 ± 0.57 | 1.97 | 1.24 × 10−6 |
| others | 55.77 ± 0.46 | |||||
| 16JZ | TT | 44.38 ± 0.39 | 0.82 | 1.90 × 10−2 | ||
| others | 42.85 ± 0.49 | |||||
| 16YZ | TT | 58.99 ± 0.54 | 1.23 | 3.00 × 10−3 | ||
| others | 56.69 ± 0.52 | |||||
| Average | TT | 54.10 ± 0.35 | 1.16 | 6.16 × 10−5 | ||