Développement d'évaluations génomiques multiraciales chez les bovins laitiers

Abstract : Within-breed genomic selection is now implemented in a number of large cattle breeds. However, building reference populations large enough remains a major challenge for smaller breeds. Combining reference populations and implementing a multi-breed approach appears to be an appealing alternative for small breeds.Such an approach requires conserved linkage disequilibrium across breeds to maintain the association between QTL and markers. Therefore, the use of a high density chip is generally needed. Error rates for high density imputation from medium density genotypes, classically used in cattle, were estimated. The mean error rate was below 1% in most dairy cattle breed which implies that a large high density imputed reference populations can be available for genomic selection at low cost. Reference populations from the three major French dairy breeds were imputed to high density and used to develop a multi-breed genomic evaluation.Several alternative genomic selection approaches (within-breed or multi-breed, based on medium or high density genotypes) were compared for breeds with different sizes of reference population. Improvement of genomic prediction accuracy due to the multi-breed evaluation was observed for breeds with 500 animals or less in their reference population. Accuracy of a third alternative using multi-breed evaluation based on medium density genotypes of closely related breeds was investigated. The benefit of multi-breed genomic evaluation was then three times higher in this situation than in the one where populations from major dairy cattle breeds were pooled. It can be noted that in both situations, using within-breed genomic information allowed a significant gain in accuracy compared to pedigree-based evaluations even for a small breed, when all sires of selection candidates belong to the reference population.These results suggest that implementation of genomic selection is feasible in small dairy cattle breeds. However further work is required to determine which optimal strategy can/must be implemented in a given breed.
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Chris Hozé. Développement d'évaluations génomiques multiraciales chez les bovins laitiers. Génétique animale. AgroParisTech, 2014. Français. ⟨NNT : 2014AGPT0024⟩. ⟨tel-01127472⟩

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