A combined GWAS approach reveals key loci for socially-affected traits in Yorkshire pigs

Socially affected traits in pigs are controlled by direct genetic effects and social genetic effects, which can make elucidation of their genetic architecture challenging. We evaluated the genetic basis of direct genetic effects and social genetic effects by combining single-locus and haplotype-based GWAS on imputed whole-genome sequences. Nineteen SNPs and 25 haplotype loci are identified for direct genetic effects on four traits: average daily feed intake, average daily gain, days to 100 kg and time in feeder per day. Nineteen SNPs and 11 haplotype loci are identified for social genetic effects on average daily feed intake, average daily gain, days to 100 kg and feeding speed. Two significant SNPs from single-locus GWAS (SSC6:18,635,874 and SSC6:18,635,895) are shared by a significant haplotype locus with haplotype alleles 'GGG' for both direct genetic effects and social genetic effects in average daily feed intake. A candidate gene, MT3, which is involved in growth, nervous, and immune processes, is identified. We demonstrate the genetic differences between direct genetic effects and social genetic effects and provide an anchor for investigating the genetic architecture underlying direct genetic effects and social genetic effects on socially affected traits in pigs.