Table 2.
The GWAS results at genome significant level for FI of different parities using GBS data in pigs.
| Trait | Chr | Range of SNP (Mb) | Number of SNP | Top SNP position (bp) | n_miss | Allele | Allele frequency | Candidate gene | P |
|---|---|---|---|---|---|---|---|---|---|
| FI_L12 | 1 | 91.98–92.02 | 1 | 92,003,527 | 22 | A/T | 0.028 | 1.88E-08 | |
| FI_L12 | 1 | 94.76–94.80 | 1 | 94,779,648 | 22 | A/T | 0.012 | 9.18E-08 | |
| FI_L12 | 1 | 193.57–193.61 | 1 | 193,593,040 | 22 | A/G | 0.021 | 2.10E-07 | |
| FI_L12 | 5 | 60.57–60.61 | 1 | 60,589,650 | 23 | T/G | 0.045 | ETV6 | 2.02E-07 |
| FI_L12 | 11 | 22.40–22.44 | 1 | 22,424,991 | 19 | G/A | 0.042 | 1.45E-07 | |
| FI_L12 | 12 | 24.86–24.90 | 1 | 24,879,958 | 13 | G/T | 0.027 | HOXB7/HOXB8/HOXB9/MIR196A-1 | 2.04E-11 |
| FI_L12 | 14 | 4.88–4.92 | 1 | 4,904,707 | 10 | C/A | 0.011 | 2.73E-09 | |
| FI_L12 | 14 | 97.23–97.27 | 2 | 97,251,403 | 19 | A/G | 0.026 | 6.52E-08 | |
| FI_L23 | 7 | 46.65–46.69 | 1 | 46,665,496 | 6 | G/A | 0.017 | GSTA4/RF00100/ICK | 2.24E-09 |
| FI_L34 | 2 | 135.91–135.95 | 1 | 135,932,694 | 5 | C/A | 0.022 | 8.09E-10 | |
| FI_L34 | 5 | 55.26–55.30 | 1 | 55,275,110 | 7 | T/A | 0.013 | 6.38E-15 | |
| FI_L34 | 10 | 65.05–65.09 | 1 | 65,071,338 | 2 | C/A | 0.017 | FBH1 | 3.87E-10 |
| FI_L34 | 11 | 9.67–9.71 | 1 | 9,688,680 | 8 | T/C | 0.022 | 2.35E-08 | |
| FI_L34 | 11 | 45.04–45.08 | 1 | 45,058,333 | 5 | G/T | 0.03 | BORA/DIS3/PIBF1 | 5.34E-08 |
| FI_L34 | 14 | 59.76–59.80 | 1 | 59,780,380 | 9 | C/T | 0.022 | 1.83E-08 | |
| FI_L34 | 16 | 60.14–60.18 | 1 | 60,161,199 | 9 | C/T | 0.022 | 2.30E-08 | |
| FI_L34 | 17 | 63.80–63.84 | 1 | 63,824,477 | 6 | C/T | 0.017 | 3.25E-11 | |
| FI_Y12 | 1 | 162.16–162.20 | 2 | 162,179,241 | 6 | C/T | 0.016 | ALPK2 | 1.91E-08 |
| FI_Y12 | 1 | 162.20–162.24 | 3 | 162,222,395 | 0 | A/G | 0.016 | ALPK2 | 2.22E-08 |
| FI_Y12 | 1 | 162.36–162.40 | 1 | 162,375,129 | 0 | G/A | 0.016 | NEDD4L | 2.22E-08 |
| FI_Y12 | 1 | 162.39–162.43 | 2 | 162,406,916 | 18 | G/A | 0.015 | RF00100 | 2.61E-08 |
| FI_Y12 | 1 | 162.44–162.48 | 1 | 162,458,116 | 4 | G/A | 0.016 | 2.45E-08 | |
| FI_Y12 | 1 | 162.51–162.55 | 1 | 162,528,642 | 1 | T/G | 0.016 | 2.29E-08 | |
| FI_Y12 | 1 | 162.55–162.59 | 1 | 162,569,732 | 17 | G/A | 0.015 | 2.12E-08 | |
| FI_Y12 | 1 | 162.90–162.94 | 1 | 162,919,642 | 1 | T/C | 0.016 | ATP8B1 | 2.23E-08 |
| FI_Y12 | 2 | 136.11–136.15 | 1 | 136,127,645 | 1 | A/G | 0.012 | 6.04E-11 | |
| FI_Y12 | 3 | 106.83–106.87 | 3 | 106,849,597 | 10 | G/A | 0.011 | TTC27 | 1.89E-11 |
| FI_Y12 | 3 | 107.26–107.30 | 4 | 107,281,336 | 0 | G/A | 0.011 | BIRC6 | 2.13E-11 |
| FI_Y12 | 3 | 109.38–109.42 | 3 | 109,400,403 | 2 | T/C | 0.012 | 2.00E-11 | |
| FI_Y12 | 4 | 111.53–111.57 | 1 | 111,553,999 | 12 | C/T | 0.013 | 1.09E-09 | |
| FI_Y12 | 4 | 38.34–38.38 | 1 | 38,362,147 | 23 | T/G | 0.013 | KCNS2 | 3.68E-08 |
| FI_Y12 | 5 | 103.41–103.45 | 1 | 103,426,443 | 9 | A/C | 0.013 | 5.22E-16 | |
| FI_Y12 | 5 | 55.47–55.51 | 1 | 55,486,024 | 13 | A/C | 0.013 | RF00026 | 1.11E-09 |
| FI_Y12 | 6 | 27.78–27.82 | 4 (including 27,811,226) | 27,804,546 | 0 | T/C | 0.022 | HSF4/B3GNT9/TRADD/NOL3/KIAA0895L/C16orf70 | 2.56E-08 |
| FI_Y12 | 7 | 2.04–2.08 | 9 | 2,061,622 | 0 | A/G | 0.012 | SLC22A23 | 3.32E-10 |
| FI_Y12 | 7 | 2.14–2.18 | 3 | 2,161,296 | 3 | T/A | 0.016 | 6.46E-11 | |
| FI_Y12 | 7 | 2.20–2.24 | 1 | 2,216,046 | 4 | G/A | 0.02 | 6.08E-08 | |
| FI_Y12 | 7 | 2.20–2.24 | 13 | 2,221,168 | 0 | G/A | 0.014 | PXDC1 | 9.60E-09 |
| FI_Y12 | 7 | 2.27–2.31 | 4 | 2,289,143 | 18 | G/C | 0.024 | FAM50B | 1.55E-07 |
| FI_Y12 | 7 | 2.54–2.58 | 1 | 2,557,543 | 3 | T/C | 0.014 | 9.93E-09 | |
| FI_Y12 | 7 | 2.72–2.76 | 1 | 2,737,334 | 2 | A/G | 0.014 | 9.94E-09 | |
| FI_Y12 | 7 | 2.77–2.81 | 2 | 2,790,067 | 21 | G/A | 0.015 | 1.33E-08 | |
| FI_Y12 | 7 | 2.93–2.97 | 2 | 2,946,286 | 7 | C/A | 0.014 | CDYL | 1.12E-08 |
| FI_Y12 | 7 | 2.96–3.00 | 2 | 2,984,884 | 6 | G/A | 0.014 | PPP1R3G/RPP40 | 1.07E-08 |
| FI_Y12 | 7 | 3.09–3.13 | 1 | 3,113,873 | 1 | A/G | 0.014 | 9.62E-09 | |
| FI_Y12 | 7 | 3.25–3.29 | 2 | 3,273,858 | 5 | G/A | 0.014 | FARS2 | 9.82E-09 |
| FI_Y12 | 7 | 3.34–3.38 | 1 | 3,358,876 | 2 | G/T | 0.014 | FARS2 | 2.36E-08 |
| FI_Y12 | 7 | 4.34–4.38 | 1 | 4,362,436 | 0 | C/G | 0.016 | 7.90E-08 | |
| FI_Y12 | 7 | 4.44–4.48 | 3 | 4,463,468 | 12 | T/C | 0.025 | 7.57E-08 | |
| FI_Y12 | 7 | 4.83–4.87 | 1 | 4,847,230 | 1 | T/A | 0.016 | DSP | 8.17E-08 |
| FI_Y12 | 7 | 126.22–126.26 | 1 | 126,240,205 | 0 | A/G | 0.012 | 7.36E-10 | |
| FI_Y12 | 7 | 133.35–133.39 | 1 | 133,368,593 | 0 | A/G | 0.498 | 3.00E-20 | |
| FI_Y12 | 8 | 144.75–144.79 | 1 | 144,770,928 | 21 | T/C | 0.018 | 9.09E-08 | |
| FI_Y12 | 10 | 3.59–3.63 | 2 | 3,609,429 | 24 | C/T | 0.031 | 3.40E-12 | |
| FI_Y12 | 10 | 43.64–43.68 | 1 | 43,663,373 | 17 | C/A | 0.017 | ST8SIA6 | 4.56E-08 |
| FI_Y12 | 11 | 73.33–73.37 | 1 | 73,353,457 | 9 | C/A | 0.017 | 1.26E-07 | |
| FI_Y12 | 12 | 2.80–2.84 | 1 | 2,824,213 | 15 | A/G | 0.026 | RBFOX3 | 4.59E-08 |
| FI_Y12 | 13 | 209.06–209.10 | 3 | 209,081,546 | 1 | A/C | 0.011 | 5.01E-11 | |
| FI_Y12 | 14 | 15.45–15.49 | 2 | 15,472,751 | 1 | A/G | 0.018 | GLRA3 | 1.14E-09 |
| FI_Y12 | 14 | 15.18–15.22 | 1 | 15,199,253 | 3 | A/T | 0.024 | 8.60E-09 | |
| FI_Y12 | 15 | 4.07–4.11 | 2 | 4,094,589 | 0 | A/G | 0.026 | ORC4 | 5.84E-09 |
| FI_Y12 | 15 | 4.10–4.14 | 1 | 4,121,092 | 4 | A/G | 0.02 | 2.40E-07 | |
| FI_Y12 | 15 | 4.47–4.51 | 1 | 4,487,592 | 24 | C/G | 0.02 | 2.49E-08 | |
| FI_Y12 | 15 | 4.88–4.92 | 1 | 4,895,899 | 0 | T/A | 0.022 | 6.28E-08 | |
| FI_Y12 | 15 | 5.22–5.26 | 6 | 5,235,766 | 6 | G/A | 0.023 | 7.35E-08 | |
| FI_Y12 | 15 | 134.32–134.36 | 1 | 134,340,038 | 21 | C/A | 0.013 | 2.74E-10 | |
| FI_Y12 | 15 | 150.28–150.32 | 1 | 150,297,519 | 6 | T/C | 0.019 | 4.32E-13 | |
| FI_Y12 | 16 | 65.60–65.64 | 1 | 65,618,538 | 14 | A/G | 0.023 | LSM11/THG1L | 2.26E-07 |
| FI_Y12 | 17 | 16.52–16.56 | 3 | 16,543,976 | 20 | G/T | 0.015 | 3.76E-09 | |
| FI_Y12 | 17 | 63.20–63.24 | 1 | 63,224,611 | 18 | T/G | 0.058 | 6.51E-08 | |
| FI_Y12 | 18 | 0.05–0.09 | 1 | 65,826 | 2 | C/T | 0.038 | 1.92E-07 | |
| FI_Y23 | 4 | 81.79–81.83 | 1 | 81,813,944 | 18 | T/G | 0.011 | NME7 | 6.99E-10 |
| FI_Y23 | 4 | 73.90–73.94 | 1 | 73,919,093 | 14 | A/C | 0.011 | TOX | 3.35E-08 |
| FI_Y23 | 4 | 127.80–127.84 | 1 | 127,815,487 | 9 | C/A | 0.013 | 1.51E-07 | |
| FI_Y23 | 6 | 114.17–114.21 | 1 | 114,189,381 | 23 | T/C | 0.011 | 1.38E-07 | |
| FI_Y23 | 7 | 46.65–46.69 | 1 | 46,665,504 | 22 | G/T | 0.014 | GSTA4/RF00100/ICK | 8.67E-10 |
| FI_Y23 | 9 | 46.50–46.54 | 1 | 46,524,685 | 16 | G/T | 0.018 | CBL/MCAM/RNF26 | 8.49E-08 |
| FI_Y23 | 11 | 65.25–65.29 | 1 | 65,267,206 | 8 | C/A | 0.011 | DNAJC3 | 5.23E-09 |
| FI_Y23 | 15 | 123.50–123.54 | 1 | 123,522,220 | 18 | G/A | 0.044 | EPHA4 | 3.29E-09 |
| FI_Y34 | 2 | 62.61–62.65 | 1 | 62,633,529 | 3 | T/C | 0.498 | SLC1A6/LOC100736663/LOC100523890 | 1.00E-07 |
| FI_Y34 | 7 | 133.40–133.44 | 5 | 133,416,643 | 1 | T/C | 0.498 | 9.88E-08 | |
| FI_Y34 | 9 | 33.26–33.30 | 1 | 33,275,594 | 3 | T/C | 0.041 | MMP20 | 3.58E-08 |
| FI_Y34 | 11 | 0.60–0.64 | 1 | 616,632 | 20 | C/A | 0.013 | ZMYM5 | 1.89E-08 |
| FI_Y34 | 15 | 35.81–35.85 | 1 | 35,828,705 | 1 | G/A | 0.498 | 9.89E-08 |
Chr, chromosome; range of SNP, range of significant chromosome region; number of SNP, number of SNP involved; n_miss, number of missing values of the SNP; alleles, alleles of top SNP.
The bolded text shown that the common SNPs detected in both GBS data and imputed WGS data.