The genotyping efficiency and polymorphism of 7 microsatellite markers (AHT084, COR006, COR017, COR018, COR040, COR055, COR088) was evaluated in order to apply them to parentage testing among a number of warm-blooded, cold-blooded and primitive horse breeds and to illustrate genetic differences between the breeds investigated. The amplification and sequence structure of these STR markers was also verified in other Equidae like zebra, kulan, donkey and Przewalski horse. Microsatellite allelic differentiation was similar to the allele numbers reported, with an extremely wide allelic range observed at AHT084 locus. However, due to genotyping difficulties AHT084 is not a suitable marker for parentage testing. The use of the other 6 STR markers among most of the horse breeds studied allows excluding wrongly assigned parentage with a probability of 0.99. Fragment analysis and sequencing of STR alleles confirmed the presence of investigated tandem repeats in other Equidae species. Clustering of investigated horse breeds on the tree of Fst distance was consistent with their breeding history, clearly separating breeds into 3 horse types mentioned above.
