Genetic structure of the European Charolais and Limousin cattle metapopulations using pedigree analyses

Pedigree collected by the Interbeef ser- vice allowed genetic diversity to be assessed by using pedigree analyses for the European Charolais (CHA) and Limousin (LIM) cattle populations registered in national herdbooks in Denmark (DNK), France (FRA), Ireland (IRL), Sweden (SWE), and, solely for the LIM breed, the United Kingdom (UK). The CHA data set included 2,563,189 calves with weaning performance, of which 96.1% were recorded in FRA, 3.0% in SWE, 0.5% in IRL, and 0.4% in DNK. The LIM data set in- cluded 1,652,734 calves with weaning performance, of which 91.9% were recorded in FRA, 4.9% in UK, 1.8% in DNK, 0.9% SWE, and 0.5% in IRL. Pedigree files included 3,191,132 CHA and 2,409,659 LIM animals. Gene flows were rather limited between populations, except from FRA toward other countries. Pedigree completeness was good in all subpopulations for both breeds and allowed the pedigree to be traced back to the French population. A relatively high level of genetic diversity was assessed in each CHA and LIM subpopu- lation by estimating either effective population sizes (Ne >244 and Ne >345 in the CHA and LIM subpopu- lations, respectively), relationship coefficients within subpopulations (<1.3% in both breeds), or probability of gene origins. However, in each subpopulation, it was shown that founders and also ancestors had unbalanced genetic contributions, leading to a moderate but con- tinuous reduction in genetic diversity. Analyses between populations suggested that all European CHA and LIM populations were differentiated very little. The Swedish CHA population was assessed as genetically more dis- tant from the other CHA populations because of fewer gene flows from other countries and because of the use of North American sires to introgress the polled phe- notype. In each European subpopulation, most of the main ancestors, which explained 50% of gene origin, were born in FRA. However, those main ancestors were different between countries. Moreover, in both breeds, the main ancestors, which explained 50% of the gene origin in DNK, IRL, SWE, and UK for the LIM breed, were found to be infrequently used in FRA. Those re- sults were consistent with the low relationship coef- ficients estimated between subpopulations (<0.6% in both the CHA and LIM breeds). Therefore, in both breeds, each subpopulation may constitute a reservoir of genetic diversity for the other ones.