Paternal genetic diversity, differentiation and phylogeny of three white yak breeds/populations in China

Abstract

The white yak, a unique and valuable farm animal of the Qinghai-Tibetian Plateau, is mainly distributed in Tianzhu (County of Gansu Province), Menyuan, Huzhu and Ledu (three Counties of Qinghai Province) in China. In the present study, the Y-chromosomal based genetic diversity, differentiation and phylogeny of three Chinese white yak breeds/populations (Tianzhu, Huzhu and Menyuan) were comprehensively explored using five Y-SNPs (SRY4, USP9Y, UTY19, AMELY3 and OFD1Y10) and one Y-STR (INRA189) markers. The results of this study showed that six Y-haplotypes (H1Y1, H9Y1, H10Y1, H11Y2, H12Y2 and H13Y2) were identified in 97 male yaks from three white yak breeds/populations. Among haplotypes, H1Y1, H10Y1 and H11Y2 were shared haplotypes for all of breeds/populations and H12Y2 was shared by Tianzhu and Huzhu populations. However, H9Y1 and H13Y2 haplotypes were only detected in Menyuan and Tianzhu white yak populations, respectively. The Y-haplotype diversity was maximum in Huzhu white yak (0.7500±0.0349), the medium in Tianzhu white yak (0.6881±0.0614) and lowest in Menyuan white yak (0.5720±0.0657), respectively. The total Y-haplotype diversity of three white yak breeds/populations was 0.7567±0.0233, indicating rich paternal genetic diversity in white yak. The FST values showed a moderate differentiation between Tianzhu and Menyuan (FST =0.0763, P<0.05) populations, weak differentiation between Huzhu and Tianzhu white yak breeds/populations (FST =0.0186, P>0.05) and Huzhu and Menyuan (FST =-0.005, P>0.05) populations. The clustering analysis showed a close genetic relationship between Huzhu and Menyuan white yaks and far from Tianzhu white yak breed. The phylogenetic analyses showed that white yak had two Y-haplogroups/lineages (Y1 and Y2) with two potential paternal origins. The data of present study could contribute to the conservation and utilization of special white yak genetic resources.