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Utilisation des données de contrôles élémentaires pour la modélisation et l'estimation des interactions génotype x milieu : Etude en bovins laitiers

Abstract : Because of the diversity of pedoclimatic conditions in France, dairy farms have very diversified herd management systems. For this reason, some breeders question the efficiency of the existing breeding schemes for their own management system. To overcome these concerns, a genotype by environment interaction study at the French national level has been considered necessary. The aim of this thesis is to assess the presence of genotype by environment interactions in Normande, Montbéliarde and Holstein breeds for production and functional traits.A tricky point in genotype by environment interaction studies is the environmentdefinition. The innovation of this thesis deals with the use of Herd-Test Day profiles.They are co-products of the French test day model. They reflect the production dueto herd management over time. They are available in national databases and only reflect herd management effect contrary to other definitions in which there is a confusion between genetic and environmental effects in the environment definition or which focus on specific features of the herd management without taking into account its global effect. Herd Test Day profiles of more than 15,000 herds have been studied through time series smoothing, factor analysis and clustering methods. It led to 2 definitions of the environment for the genotype by environment interaction study : environments defined as herd groups or one to several environmental gradients.Genotype by environment interactions were assessed with 2 models : the multitrait model and the reaction norm model. The first one uses herd groups as definition of the environment whereas reaction norm model considers the environment as a gradient. Several methodological improvements have been suggested for reaction norm models : taking into account several environmental gradients in a reaction norm model and summarizing them through a reduced rank genetic matrix.No reranking has been shown : the best parents are the same whatever the herd management system. Consequently, current breeding schemes are relevant. However, a scale effect exists : the variability of animal breeding values is higher in intensive herds. Genetic models will not account for this scale effect. However, a tool useful for breeders could indicate the deviation between expected performances and actual performances due to this scale effect.
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Bérénice Huquet. Utilisation des données de contrôles élémentaires pour la modélisation et l'estimation des interactions génotype x milieu : Etude en bovins laitiers. Génétique animale. AgroParisTech, 2012. Français. ⟨NNT : 2012AGPT0060⟩. ⟨pastel-00947191⟩



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