Genetic diversity and substructuring of the Hungarian merino sheep breed using microsatellite markers

The Hungarian Merino sheep breed (Ovis aries) is the most significant animal resource of the Hungarian sheep sector which, unfortunately, has gone through a huge reduction in number during the last decades and became endangered in 2014. A modern molecular genetic survey is now becoming more than necessary in order to characterize the within-breed genetic diversity and structure. For that reason, six Hungarian Merino flocks were genotyped in 16 microsatellite markers. In total, 144 different alleles were found and the mean values of observed and expected heterozygosity were 0.714 and 0.705, respectively, suggesting a noticeable genetic variability of the breed. The genetic differentiation of the Hungarian flocks was generally low, as reflected by the estimated total F value (0.036), the extended pattern of admixture in Structure analysis, as well as, by the noticeable level of genetic clustering in UPGMA and FCA analyses. However, two out of the six studied flocks tended to be genetically more distant. The outcome of our study could be a starting point for a planned breeding strategy of the Hungarian Merino breed, by keeping the within-flock genetic variability in priority, as well as, by preserving the potential genetic uniqueness with close monitoring of the inbreeding.