Table 3.
Chromosome wide significant associations identified in subset B1 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 |
|---|---|---|---|---|---|---|---|---|---|
| lnAND | ALGA0039432 | 7 | 23184219 | G/A | 0.48 | 0.13 (0.03) | 14.73 | 1.27E-05* | 5.80% |
| lnAND | MARC0059955 | 7 | 24223914 | G/A | 0.37 | 0.13 (0.03) | 14.40 | 1.59E-05* | 5.68% |
| lnAND | MARC0097446 | 18 | 3346636 | C/A | 0.03 | 0.36 (0.10) | 13.55 | 2.83E-05* | 5.36% |
| lnAND | ASGA0104833 | NA | NA | G/A | 0.23 | 0.15 (0.04) | 15.61 | 7.01E-06# | 6.13% |
| lnAND | ASGA0094873 | NA | NA | A/G | 0.48 | −0.12 (0.03) | 15.29 | 8.64E-06# | 6.02% |
| lnSKA | H3GA0000454 | 1 | 6764028 | A/C | 0.45 | −0.20 (0.05) | 18.66 | 1.45E-06** | 7.24% |
| lnSKA | ASGA0048539 | 10 | 63586433 | G/A | 0.13 | 0.24 (0.06) | 14.05 | 2.91E-05* | 5.55% |
| lnSKA | ASGA0077381 | 17 | 54986042 | G/A | 0.06 | 0.37 (0.09) | 16.10 | 7.61E-06** | 6.31% |
| lnIND | H3GA0000454 | 1 | 6764028 | A/C | 0.45 | −0.22 (0.05) | 17.27 | 5.55E-06* | 6.74% |
| lnIND | H3GA0012922 | 4 | 77217709 | G/A | 0.36 | −0.20 (0.05) | 16.44 | 9.30E-06* | 6.44% |
| lnIND | ALGA0025735 | 4 | 77249057 | G/C | 0.36 | −0.20 (0.05) | 16.44 | 9.30E-06* | 6.44% |
| width | ASGA0098931 | 18 | 56634280 | A/G | 0.02 | −12.76 (2.95) | 18.74 | 7.88E-06** | 7.75% |
| GSI | ALGA0108818 | 12 | 49085493 | G/A | 0.13 | 0.0003 (0.0001) | 15.83 | 2.04E-05* | 7.54% |
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<0.01 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, %).