The importance of population structure on the accuracy of genomic prediction in a multi-breed sheep population

Abstract

Population structure, due to breed, strains and sire family, influences the accuracy of genomic prediction. We investigated principle component analysis as a way to account for population structure in within and across breed genomic prediction of greasy fleece weight and eye muscle depth in multi-breed sheep data. Population structure (including for example half sib family relationships) is responsible for a large proportion of the accuracy of genomic prediction. Correcting for it increased accuracy of greasy fleece weight across breed prediction, but reduced accuracy of across breed prediction for eye muscle depth for breeds not in the reference set. However, the correction reduced within breed accuracy.