Table 2.
Chromosome wide significant associations identified in the whole data set for boar taint and testes size parameters
| Trait 1 | SNP | SSC 2 | Pos 3 | Mut 4 | MAF 5 | eEff (se) 6 | Chi2 | Emp. P-value 7 | Var 8 |
|---|---|---|---|---|---|---|---|---|---|
| lnSKA | ASGA0047791 | 10 | 46867278 | G/A | 0.45 | −0.10 (0.03) | 14.32 | 1.93E-05* | 2.35% |
| lnSKA | ALGA0064494 | 12 | 7132733 | G/A | 0.23 | 0.13 (0.03) | 14.84 | 1.36E-05* | 2.43% |
| lnSKA | ASGA0077381 | 17 | 54986042 | G/A | 0.04 | 0.28 (0.07) | 14.03 | 2.35E-05* | 2.30% |
| lnIND | ALGA0056841 | 10 | 10002850 | G/A | 0.24 | 0.13 (0.03) | 15.54 | 1.38E-05* | 2.55% |
| lnIND | H3GA0031761 | 11 | 31230971 | A/G | 0.43 | −0.11 (0.03) | 15.72 | 1.24E-05* | 2.58% |
| lnIND | M1GA0020074 | 14 | 152454616 | A/C | 0.26 | 0.16 (0.03) | 26.94 | 1.05E-08*** | 4.33% |
| lnIND | MARC0028756 | 14 | 152480709 | A/G | 0.26 | 0.16 (0.03) | 26.94 | 1.05E-08*** | 4.33% |
| lnIND | SIRI0000194 | 14 | 153477507 | A/G | 0.32 | 0.15 (0.03) | 24.63 | 4.48E-08*** | 3.97% |
| lnIND | ASGA0068311 | 14 | 153593360 | A/G | 0.32 | 0.15 (0.03) | 24.70 | 4.29E-08*** | 3.99% |
| lnIND | MARC0059044 | NA | NA | A/G | 0.28 | 0.13 (0.03) | 18.92 | 1.62E-06# | 3.08% |
| length | ASGA0018288 | 4 | 11933017 | A/G | 0.24 | −2.99 (0.73) | 16.62 | 1.09E-05* | 2.80% |
| length | H3GA0016069 | 5 | 23313949 | A/G | 0.32 | −2.82 (0.66) | 18.00 | 4.74E-06** | 3.03% |
| length | ASGA0025083 | 5 | 23646360 | A/G | 0.33 | −2.54 (0.65) | 15.42 | 2.28E-05* | 2.60% |
| length | H3GA0044665 | 15 | 91511319 | G/A | 0.43 | −2.59 (0.66) | 15.29 | 2.46E-05* | 2.58% |
| length | CASI0001308 | 18 | 60484331 | G/A | 0.03 | −7.17 (1.78) | 16.23 | 1.39E-05* | 2.74% |
| length | MARC0003381 | NA | NA | A/G | 0.43 | −2.62 (0.60) | 19.22 | 2.26E-06 | 3.22% |
| width | ALGA0097186 | 18 | 16444813 | A/G | 0.45 | 1.52 (0.39) | 15.05 | 2.45E-05* | 2.54% |
| width | ALGA0098863 | 18 | 57260307 | A/G | 0.35 | −1.63 (0.42) | 15.03 | 2.48E-05* | 2.54% |
| weight | ALGA0031253 | 5 | 23002609 | A/G | 0.33 | −7.19 (1.70) | 17.88 | 1.29E-06** | 3.00% |
| weight | ASGA0025080 | 5 | 23190382 | A/C | 0.40 | −6.81 (1.71) | 15.76 | 5.49E-06** | 2.65% |
| weight | H3GA0016069 | 5 | 23313949 | A/G | 0.32 | −7.62 (1.75) | 19.05 | 5.84E-07*** | 3.20% |
| weight | ASGA0025083 | 5 | 23646360 | A/G | 0.33 | −8.20 (1.70) | 23.36 | 3.14E-08*** | 3.88% |
| weight | ALGA0031261 | 5 | 23662089 | G/A | 0.10 | −10.12 (2.76) | 13.45 | 2.67E-05* | 2.27% |
| weight | H3GA0016074 | 5 | 23737420 | A/G | 0.24 | −7.41 (1.94) | 14.61 | 1.21E-05* | 2.47% |
| weight | ASGA0103650 | 5 | 24057900 | G/A | 0.24 | −7.44 (1.94) | 14.73 | 1.12E-05* | 2.48% |
| weight | ALGA0098863 | 18 | 57260307 | A/G | 0.35 | −6.65 (1.80) | 13.61 | 2.40E-05* | 2.30% |
| weight | MARC0003381 | NA | NA | A/G | 0.44 | −7.70 (1.57) | 23.98 | 2.06E-08# | 7.50% |
| GSI | ALGA0031253 | 5 | 23002609 | A/G | 0.33 | −0.0089 (0.0021) | 18.52 | 4.51E-07*** | 3.26% |
| GSI | H3GA0016069 | 5 | 23313949 | A/G | 0.32 | −0.0085 (0.0021) | 16.12 | 2.50E-06** | 2.86% |
| GSI | ASGA0025083 | 5 | 23646360 | A/G | 0.33 | −0.0096 (0.0021) | 21.38 | 5.90E-08*** | 3.75% |
| GSI | H3GA0016074 | 5 | 23737420 | A/G | 0.24 | −0.0088 (0.0024) | 13.94 | 1.19E-05* | 2.48% |
| GSI | ASGA0103650 | 5 | 24057900 | G/A | 0.24 | −0.0089 (0.0024) | 14.20 | 9.95E-06* | 2.52% |
1: androstenone, log-transformed (lnAND); skatole, log-transformed (lnSKA); indole, log-transformed (lnIND); testis length, width and weight (length, width and weight); gonadosomatic index (GSI); 2: sus scrofa chromosome (SSC); 3: position in Mb; 4: mutation (Mut); 5: minor allele frequency (MAF); 6: substitution effect and standard error (se), 7: empirical p-value and significant thresholds, Bonferroni corrected - ***p< 0.05 genome-wide,**p<0.01 chromosome-wide and *p<0.05 chromosome-wide significance level, #p<0.05 significance level of not annotated SNPs; 8: proportion of the explained variation (Var, %).