The domestic horse harbours Y‐chromosomal microsatellite polymorphism only on two widely distributed male lineages

Abstract

Source/description: Mitochondrial DNA (mtDNA) and the paternally inherited portion of the Y chromosome (NRY) are inherited uniparentally and do not recombine. They provide a tool for constructing female and male genealogical histories and have therefore been widely analysed in a broad range of wild and domesticated animals. In livestock, mtDNA and NRY markers act as an informative tool to elucidate the origin of breeds and to trace maleand female-mediated gene flow. Paradoxically, horses (Equus caballus) have the largest mtDNA diversity among domestic species, and mtDNA has been widely used to investigate the origin of domestic horse breeds, but only limited sequence diversity has been described on the NRY. In a recent paper, we presented the first polymorphic Y-chromosomal markers for paternal lineage analysis in modern domestic horses. They resulted in only six haplotypes, all clearly distinct from the Przewalski horse (Equus przewalskii). Only single mutational steps separate the modern horse Y-chromosomal haplotypes from each other. Horse paternal lineages seem therefore closely related, but Y-chromosomal diversity might be underestimated on the sequence level due to ascertainment bias. Highly mutable microsatellite markers may help to increase the resolution, as shown in cattle. An initial investigation of five Y-chromosomal microsatellites revealed no polymorphism and thus supported a very close relationship and recent origin of the modern horse haplotypes. In this study, we investigate Y-chromosomal lineages in greater depth using eight newly identified Y-chromosomal microsatellite markers in a comprehensive sample set containing all modern and Przewalski horse Y-chromosomal haplotypes.