SNP effects depend on genetic and environmental context

Bastiaansen, J.W.M.; Bovenhuis, H.; Lopes, M.S.; Silva, F.; Megens, H.J.W.C.; Calus, M.P.L.


Effects that are estimated for SNP markers depend on LD with the QTL, and interactions of the QTL with other genetic and environmental factors. These factors are often mentioned but rarely studied. Breeding for crossbred performance both brings the need and supplies data for studying these interactions. SNPs with different effects on litter size in pigs between low and high production environments were identified from a genomic reaction norm model. Clustering of these SNPs lead to candidate genes related to bacterial defense that are expressed in reproductive tracts and regulated by the estrous cycle. To study interaction of SNPs with genetic background, a method to determine breed origin of alleles in crossbreds was implemented using long range phasing with AlphaPhase software. With more genotypes and phenotypes on crossbreds, estimation of interactions with genetic background and the environment will become feasible.