Genomic and pedigree methods to analyse inbreeding depression in Basco-Bearnaise rams
Résumé
Inbreeding depression is caused by increased homozygosity of individuals and it is involved in the decrease of performance and fitness of the animals. The goal of this study is to estimate inbreeding depression for semen traits in Basco-Béarnaise rams. Genomic (e.g. using SNP-by-SNP approach) or pedigree-based inbreeding can be used to obtain inbreeding coefficients (f). It is possible to detect inbreeding depression (b) from the regression of the phenotype (y) on f, as y=Xβ+fb+u+e, where u is the vector of breeding values. In sheep, inbreeding from pedigree tends to be underestimated due to missing pedigrees. Inbreeding coefficients, f, were estimated using four methods. The first method used the traditional pedigree-based inbreeding. The second used pedigree-based inbreeding but accounting for non-zero relationships for unknown parents. The third method used the metafounder relationships in pedigree-based inbreeding. The fourth method calculates inbreeding from a combined relationship matrix using pedigree and genotypes with metafounder relationships. Breeding values, u, for the first three methods were estimated with the classical BLUP using phenotypes and pedigree information and the fourth method was Single Step GBLUP with metafounders.