GWAS for Direct and Indirect Effect on Androstenone

In Europe castration of pigs will no longer take place after January 2018; in the Netherlands already 80% of the male piglets is no longer castrated and therefore the risk for boar taint, an unpleasant odor to the meat when cooked or heated, is increasing. One of the components causing boar taint is androstenone (AND), a pheromone that is released from saliva in boars, and attracts estrous females. As interaction between animals is important for the expression of AND, the AND phenotype of an animal can be affected by the genotype of another (referred to as an indirect genetic effect; IGE). In a previous study we estimated the contribution of IGE to the total genetic variance of AND. The estimated indirect genetic variance was small (0.002) but significant, and contributed 12% of the total genetic variance. Thereafter, an association study on AND was performed where direct SNP effects and indirect SNP effects were estimated. The dataset consisted of 1,282 non-castrated boars (993 boars genotyped), from 184 groups of pen members and 46,421 SNPs were included in the analysis. One QTL on SSC6 was chromosome-wide significant for the direct effect which was the same region as described in a previous study. A single SNP on SSC9 and two regions and a single SNP on SSC14 were found for the indirect effect. In addition to the newly discovered QTL and the confirmation of known QTL, this study also presents a methodology to model SNPs for indirect genetic effects.