Historical and Contemporary Management of Genetic Diversity in French Local Horse Breeds: Insights from Genomic Data

The phenotypic and genetic diversity of horses worldwide today likely resulted from two main events: (i) domestication and, afterwards, (ii) breed creation. While many studies discuss the origin and domestication of horses, very few focus on the second important event, which has largely shaped the genetic architecture of horses at present. This study exhaustively examined all 18 local horse breeds from France, all of which are endangered by small census sizes, making them prone to suffer from genetic drift, loss of diversity, and inbreeding depression. While pedigrees are available, they are often incomplete or error-prone. Thus, we used molecular markers to reconstruct the history of French local breeds and to monitor the evolution of genetic diversity and its link to management practices. The study was based on 976 animals (approx. 50 per breed), spanning two time periods corresponding to the change in management from public stud farms to privatization. The samples were genotyped using a 10K SNP array dedicated to genetic resources characterization. French local horses can be classified not only phenotypically but also genetically into two categories: the light 'territory' breeds and heavier 'draft' breeds, with regular gene flow observed between the two groups that are linked to historical records. The evolution of kinship and inbreeding over the two time periods exhibited distinct patterns between the cohorts and across the breeds, reflecting various consequences of different management practices. To conclude, this study was the first to exhaustively depict the evolution of French local horses, while it also demonstrated the usefulness of genomic data in monitoring genetic diversity and evaluating the effectiveness of management programs.