Partitioning the genetic variance into genomic and pedigree components for parasite resistance in sheep

Abstract

In this study, we estimated the additive genetic variance explained by genomic markers for parasite resistance in a large mixed population of sheep and compared this estimate to the additive genetic variance explained by pedigree. Furthermore, we partitioned the total genetic variance by fitting both of genomic relationship matrix (GRM) and numerator relationship matrix (NRM) simultaneously into a genomic component explained by genomic relationships and a polygenic component explained by pedigree relationships. In this analysis, all the genetic variation explained by pedigree could be captured by the 50K SNP chip markers. When both of GRM and NRM were fitted simultaneously, 73.7% of total genetic variance was explained by genomic effects while the remaining variance (26.3%) was explained by pedigree effects. The proportion of genetic variance explained by genomic effects was further partitioned into 26 chromosomes. A significant relationship was found between chromosome-specific variance and the length of the chromosome (R² = 0.26). This indicates that disease resistance is a largely polygenic trait with a large number of genes involved in the mechanisms of resistance but there are some chromosomal regions that explain a larger proportion of the variation.