Genetic diversity of Estonian horse breeds and their genetic affinity to northern European and some Asian breeds

Abstract

Sixteen microsatellite markers were used to assess the genetic diversity in native and imported transboundary horse breeds and populations from the Baltic Sea region, North-Eastern Europe and Asia (Mongolia and Yakutia, the Russian Federation), with a special focus on Estonian horse breeds. Testing for within-breed genetic variation, Hardy-Weinberg proportions, linkage disequilibrium between genotypes across loci, molecular variance, genetic relationships and population structure was performed.The current microsatellite data indicated that the horse breeds in the Baltic Sea region, including all local Estonian, Finnhorse and Latvian horse breeds, have high within-breed variation. In terms of allelic richness and heterozygosity, the within-breed diversity was higher in the Estonian local breeds than in the Norwegian horse breeds.On the basis of genetic distances, a distinguishable polarization amongst the breeds was observed in two breeds, the Arabian and the Døle, being the most distant and defining of the warm-blooded and the Norwegian breed groups, respectively. The local Estonian breeds, together with the Finnhorse, Mezen, Mongolian and Yakutian breeds, formed a sparse intermediate aggregate with a low variability, attributed to the differences among the breeds. The population structure analysis showed admixed ancestry in this small-size (pony type) breed group. Our study suggests that the local Nordic (Northern European) breeds (N = 11) formed three genetic clusters.The introgression of genes from warm-blooded breeds was considerable in one of the Estonian local horse breeds, the Tori, as well as in the Latvian horse. Compared to the Tori and Latvian Horse, the Estonian Native, the Estonian Heavy Draught and the Finnhorse have preserved a unique gene pool to a larger extent and are more distinct.