Experiences in estimation of metafounders ancestral relationships of dairy sheep
Résumé
Metafounders are representations of inbred and related base populations. Dairy sheep breeding schemes have steady genetic progress but also unrecorded parentships of 10 to 80% of the individuals depending on the breed. Thus,use of genetic groups is essential to obtain unbiased breeding values and correct genetic trends. However, fitting genetic groups as fixed effects is not tenable in view of genomic information and metafounders are a theoretically appealing solution. This involves estimation of relationships within and across metafounders (Gamma: Γ) using genotyped of individuals that may be several generations removed from them. Here, we present experiences in estimating Gamma in Manech Tete Rousse by a pseudo-EM maximum likelihood method. The number of genotyped individuals is 2,111, and a pedigree with their ancestors included 15,270 individuals and 11 metafounders (Gamma is a 11×11 matrix) defined every 3-4 years from 1975 to 2009. These metafounders only model missing pedigrees, there is no introduction of foreign animals in this breed. The pseudo-EM algorithm always maximized the likelihood and different initial points ended up in the same estimates of Gamma. Results show a self-relationship of 0.47 to 0.54, increasing with time, and high relationships (correlations ranging from 0.89 to 0.98) across metafounders.Closer metafounders are more related, as expected. Results are coherent with a priori knowledge of the dynamics of the breed.