Boar taint is an offensive urine or faecal-like odour, affecting the smell and taste of cooked pork from
some mature non-castrated male pigs. Androstenone and skatole in fat are the molecules responsible. In most pig
production systems, males, which are not required for breeding, are castrated shortly after birth to reduce the risk
of boar taint. There is evidence for genetic variation in the predisposition to boar taint.
A genome-wide association study (GWAS) was performed to identify loci with effects on boar taint. Five hundred
Danish Landrace boars with high levels of skatole in fat (>0.3 μg/g), were each matched with a litter mate with low
levels of skatole and measured for androstenone. DNA from these 1,000 non-castrated boars was genotyped using
the Illumina PorcineSNP60 Beadchip. After quality control, tests for SNPs associated with boar taint were performed on
938 phenotyped individuals and 44,648 SNPs. Empirical significance thresholds were set by permutation (100,000). For
androstenone, a ‘regional heritability approach’ combining information from multiple SNPs was used to estimate the
genetic variation attributable to individual autosomes.