Genetic structure and connectivity analysis in a large domestic livestock meta-population: The case of the Pura Raza Español horses

The Pura Raza Español (PRE) is an autochthonous Spanish horse population distributed in 65 countries and managed by a single association. Since 1960s, breeding animals have been steadily exported to other countries to establish local subpopulations. We analysed the genetic structure of a PRE horse meta-population (MP) of 215,500 animals from countries with at least 80 active animals (27 countries comprising 77% of the total animals in the complete pedigree). Genotypes from active animals (59% of the total animals in the complete pedigree) were also studied. Genetic analysis of the MP was performed using classical parameters such as inbreeding (F), coancestry, founder contribution, effective number of founders/ancestors (fe/fa) and gene flow between countries. Results showed that the MPF coefficient decreased in the last two decades (1990-2013), indicating an explicit management against F. Founder contribution to genetic variability across countries mainly came from females (73.6%). In general, unbalanced contributions of founders reflected the high loss of genetic diversity along generations (fe/fa as low as 32/19 for the whole MP). Despite this differential contribution, the proportional contribution to the global diversity of each country was similar. The highest within-country coancestry value corresponded to Cuba (0.1509), being the only country with highly inbred individuals (over 12%), and the lowest value corresponded to Spain (0.0574). These results should help to avoid further declines in genetic variability and increases in F levels, especially in small countries like Cuba. In parallel, only nine countries presented descendants in a single population, suggesting a common origin for all countries and/or a substantial exchange of genetic material between populations. Spain and the US showed the highest gene flow rates. These results support the need of a coordinated management strategy, especially promoting the exchange of genetic material to increase the effective population size and maintain the levels of genetic diversity in the PRE horse population.