A study of patrilineal genetic diversity in Iranian indigenous horse breeds

Autosomal markers and mtDNA have been used in horse phylogenetic studies. These studies display evolutionary events that happened in both sexes or only in females. It is necessary to investigate genetic diversity in Y-specific markers for clarifying contribution of males in horse domestication. The Y chromosome, excluding the pseudoautosomal region, is inherited as a single nonrecombinant unit and, therefore, it warrants that mutational events in patrilines are preserved as single haplotypes. Six Y-specific microsatellites were used to study patrilineal genetic variation in 405 male horses from 8 Iranian native horse breeds, one wild population and an exotic breed. These markers displayed no variation in all populations. The lack of polymorphisms could be as a result of lower contribution of stallions to the gene pools of the domestic horses compared to the mares because a sex bias is towards females due to a special breeding strategy (in which a few selected stallions mate with many mares each), a strong tendency to upgrade many breeds by crossing between champion stallions from particular breeds and mares from different breeds; also due to a bias in the early utilization of male horses as food source, a bias towards stallions in migrations and lack of detailed maps on horse Y chromosome.