The aim of the project is to give the information necessary to the implementation genomic selection in pyramid schemes which concern : selection of purebred animals to produce crossbred animals; selection in high health environment but production under commercial conditions. Experimental approach will be carried out in pig and in chicken. Resource populations, purebred and crossbred, controlled in different environments, will be created and controlled for a large number of traits. Genotyping will be carried out thanks to high density SNP Chips (64K already available). Different methods of genomic evaluaation will be compared according to their ability to predict accurately the genetic values of the reproducers in these situations (genetic type, environment). Data sets will be also exploit to optimize the breeding schemes. Results will be presented to the breeders' community of concerned species.

The most important congenital genetic defects that occur in piglets are hernias (umbilical hernia and inguinal or scrotal hernias), cryptorchidism and splay legs, and to a lesser extent intersexuality, hermaphrodism and anal atresia. They affect on average 3% of the commercial pig populations worldwide. It is important to stress out that, besides the direct economic loss, these defects have a serious impact on animal welfare and health. Some of the defects cause direct piglet mortality, while others lead to culling of piglets showing the disorder. For most of these defects there are strong indications for a genetic component. In SwAn project, we propose to focus on the identification of genes underlying congenital / hereditary disorders in pigs. We propose (1) to enrich the collection of affected samples, (2) to use genome-wide association studies (GWA) with a SNP panel comprising 60 000 markers covering the entire genome at a density which is appropriate for population-based association studies, (3) to identify some of the causal mutations and genes of these congenital diseases and (4) to propose effective marker assisted selection (MAS) against genetic defects.