Table 3.
The GWAS results at genome significant level for FI of different parities using imputed WGS data (allelic R 2 > 0.3) in pigs.
| Trait | Chr | Range of SNP (Mb) | Number of SNP | Top SNP position (bp) | Allelic R 2 | n_miss | Alleles | Allele frequency | Candidate gene | P |
|---|---|---|---|---|---|---|---|---|---|---|
| FI_Y12 | 1 | 39.39–39.43 | 2 | 39,407,333 | 0.65 | 0 | A/G | 0.014 | 6.08E-12 | |
| FI_Y12 | 2 | 136.11–136.15 | 19 | 136,127,645 | 1.00 | 0 | A/G | 0.012 | 5.81E-11 | |
| FI_Y12 | 5 | 103.41–103.45 | 3 | 103,426,443 | 0.96 | 0 | A/C | 0.012 | 4.29E-16 | |
| FI_Y12 | 6 | 23.29–23.33 | 6 | 23,313,531 | 0.75 | 0 | T/C | 0.044 | CDH8 | 2.88E-09 |
| FI_Y12 | 6 | 27.79–27.83 | 1 | 27,811,226 | 0.93 | 0 | A/G | 0.02 | C16orf70/B3GNT9/TRADD/HSF4/NOL3/KIAA0895L/EXOC3L1 | 3.68E-09 |
| FI_Y12 | 7 | 2.14–2.18 | 35 | 2,160,719 | 0.61 | 0 | T/C | 0.018 | 6.93E-11 | |
| FI_Y12 | 10 | 3.59–3.63 | 4 | 3,609,429 | 0.88 | 0 | T/C | 0.026 | 2.81E-13 | |
| FI_Y12 | 14 | 10.67–10.71 | 22 | 10,694,678 | 0.74 | 0 | C/T | 0.068 | ADRA1A | 2.00E-09 |
| FI_Y12 | 14 | 15.18–15.22 | 6 | 15,199,253 | 0.99 | 0 | A/G | 0.024 | 8.07E-09 | |
| FI_Y12 | 15 | 150.28–150.32 | 3 | 150,297,519 | 0.98 | 0 | T/C | 0.018 | 3.82E-13 | |
| FI_Y12 | 15 | 134.32–134.36 | 1 | 134,340,038 | 0.90 | 0 | C/A | 0.012 | 3.18E-10 | |
| FI_Y34 | 12 | 43.71–43.75 | 11 | 43,730,214 | 0.69 | 0 | G/A | 0.014 | NF1 | 6.79E-09 |
| FI_Y34 | 15 | 154.76–154.80 | 1 | 154,777,447 | 0.61 | 0 | T/G | 0.159 | 2.17E-09 | |
| FI_Y34 | 15 | 154.77–154.81 | 1 | 154,788,901 | 0.62 | 0 | T/C | 0.159 | 2.17E-09 | |
| FI_Y34 | 15 | 154.91–154.95 | 10 | 154,933,940 | 0.75 | 0 | C/T | 0.212 | 1.72E-09 |
Chr, chromosome; range of SNP, range of significant chromosome region; number of SNP, number of SNP involved; allelic R2, estimated correlation between the imputed and true genotypes; 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.