Within- and across-breed genomic predictions and genomic relationships for Western Pyrenees dairy sheep breeds Latxa, Manech, and Basco-Béarnaise.

Genotypes, phenotypes and pedigrees of 6 breeds of dairy sheep (including subdivisions of Latxa, Manech, and Basco-Béarnaise) from the Spain and France Western Pyrenees were used to estimate genetic relationships across breeds (together with genotypes from the Lacaune dairy sheep) and to verify by forward cross-validation single-breed or multiple-breed genetic evaluations. The number of rams genotyped fluctuated between 100 and 1,300 but generally represented the 10 last cohorts of progeny-tested rams within each breed. Genetic relationships were assessed by principal components analysis of the genomic relationship matrices and also by the conservation of linkage disequilibrium patterns at given physical distances in the genome. Genomic and pedigree-based evaluations used daughter yield performances of all rams, although some of them were not genotyped. A pseudo-single step method was used in this case for genomic predictions. Results showed a clear structure in blond and black breeds for Manech and Latxa, reflecting historical exchanges, and isolation of Basco-Béarnaise and Lacaune. Relatedness between any 2 breeds was, however, lower than expected. Single-breed genomic predictions had accuracies comparable with other breeds of dairy sheep or small breeds of dairy cattle. They were more accurate than pedigree predictions for 5 out of 6 breeds, with absolute increases in accuracy ranging from 0.05 to 0.30 points. They were significantly better, as assessed by bootstrapping of candidates, for 2 of the breeds. Predictions using multiple populations only marginally increased the accuracy for a couple of breeds. Pooling populations does not increase the accuracy of genomic evaluations in dairy sheep; however, single-breed genomic predictions are more accurate, even for small breeds, and make the consideration of genomic schemes in dairy sheep interesting.

Genetic parameters and trends for milk production of blond-faced Latxa sheep using Bayesian analysis.

The genetic progress attained with the breeding scheme of the blond-faced Latxa dairy sheep in the Spanish Basque Country was assessed by a Bayesian approach based on the marginal posterior distributions of parameters achieved via Gibbs sampling. The data file included 49,056 milk yield records of 22,363 ewes. Normal distributions were assumed for EBV and fixed effects, and scaled inverted chi-square distributions were assumed for variance components or additive, permanent environment, and residual effects. Under vague priors for variance components, the posterior means (SD) for heritability and permanent environment coefficient for milk yield at 120 d were 0.22(0.01) and 0.20(0.01). An important effect on the milk yield (41.6% of the mean) was evident for a genetic group of imported rams. Selection was effective for sheep that were bred by AI and that had known parents. The robustness of results for effect of genetic group and genetic trends was validated using a mildly informative prior constructed from variance components estimated with the related black-faced Latxa breed.