Indigenous Greek Horse Breeds: Genetic Structure and the Influence of Foreign Breeds

This study aims to examine the genetic structure and diversity levels of seven indigenous Greek horse breeds: Andravida, Pindos, Thessaly, Skyros, Penia, Messara and Rodos, using 15 microsatellites. Phenotypic traits were combined with factorial correspondence analyses to create two datasets: one “Baseline” containing typical samples, and one “Unknown” with non-typical or of disputed origin samples. In the Greek “Baseline” horses, 142 alleles were found. The mean observed and effective number of alleles, the polymorphism information content and the allelic richness were 6.75, 4.14, 0.63 and 5.12, respectively. The expected and observed heterozygosity and inbreeding coefficient varied between 0.81 and 0.29 and 0.79 and 0.24. The above dataset was enriched with data from 41 foreign horse breeds and 40 Przewalski samples to perform a breed assignment. The highest percentage of successfully assigned samples was for Skyros, Messara and Rodos, with rates of 93%, 89% and 100%, respectively, suggesting their considerable homogeneity, while Andravida, Pindos, Thessaly and Penia scored 32.5, 34.1, 44.0 and 45.7%, respectively. Structural analysis confirmed the results of FCA and showed the genetic similarities of the above breeds. The results revealed the influence of foreign breeds (mainly Garrano, Turkoman, Irish Draft, Hanoverian and Belgian Draft). There is an urgent need to implement management measures for the pure homogeneous breeds and selection strategies for the remaining breeds which are genetically similar.