Genetic variability, structure and assignment of Spanish and French pig populations based on a large sampling

The Spanish and French pig populations share the common practice of quasi systematic paternity control of pure breed and composite line males. Ten microsatellite markers are in common between Spain and France controls, among the 17 markers used in France and the 13 used in Spain. After the adjustment of allele sizes, it is possible to merge the two datasets and to obtain a set of 5791 animals, including the vast majority of the males in the Duroc, Landrace, Large White and Pietrain French and Spanish breeds. Twelve French composite lines are also available. The genetic diversity analysis of these pig populations is presented, as well as the assignment of an individual to its breed. The effects of heterogeneous sampling across time and of relatedness among animals are also assessed. Consistent with the results of the previous studies, we found that different populations from the same breed clearly clustered together. In addition, all populations of this study, whether purebred or composite, are quite well differentiated from the other ones. As a result, we note that the 10 microsatellites commonly used for paternity control ensure a powerful detection of the breed of origin, with the power of detection being 95-99%. The detection of the exact population within breed is more difficult, but the power exceeds 70% for most of the populations. Practical implications include, for instance, the detection of outlier animals, crosses and admixture events.