Rich maternal and paternal genetic diversity and divergent lineage composition in wild yak (Bos mutus)

Wild yak (Bos mutus) is a vulnerable bovine species on the Qinghai–Tibetan Plateau (QTP). So far, most studies on molecular genetic diversity of wild yak have focused on autosomal and mtDNA variations based on small number of samples. In this study, we analyzed 84 D-loop and 24 whole mitogenome sequences of wild yak to further comprehensively explore its maternal genetic diversity and lineage composition. Meanwhile, using six yak Y-specific polymorphic markers (i.e., SRY4, USP9Y, UTY19, AMELY3, OFD1Y10 and INRA189), we assessed the paternal genetic diversity and lineage composition based on eight wild yak. Our results showed that wild yak exhibited abundant maternal genetic diversity with haplotype diversities of 0.9621 ± 0.0078 and 0.9928 ± 0.0144 in the D-loop and whole mitogenome sequences, respectively. Maternal phylogenetic analysis of wild yak uncovered three defined lineages (mt-I, mt-II and mt-III). Similarly, profuse paternal genetic diversity was observed in wild yak with Y-haplotype diversity (Hd) at 0.8214 ± 0.1007. Two Y-haplogroups (Y1 and Y2) with four Y-haplotypes (yH1-yH4) were identified in paternal phylogenetic analysis, indicating wild yak to be of two paternal lineages. This study of genetic diversity and lineage composition of wild yak would provide useful information for the genetic resource conservation and utilization of this vulnerable wild species.

野生牦牛（Bos mutus）是分布于青藏高原（Qinghai–Tibetan Plateau，QTP）的易危牛科物种。迄今为止，针对野生牦牛分子遗传多样性的多数研究均基于少量样本，聚焦于常染色体与线粒体DNA（mtDNA）的变异分析。本研究共分析了84条野生牦牛D-loop序列与24条全线粒体基因组序列，以期全面解析其母系遗传多样性与谱系构成。与此同时，本研究借助6个牦牛Y染色体特异性多态性标记（即SRY4、USP9Y、UTY19、AMELY3、OFD1Y10与INRA189），基于8头野生牦牛样本评估了其公系遗传多样性与谱系构成。研究结果显示，野生牦牛拥有丰富的母系遗传多样性：其D-loop序列与全线粒体基因组序列的单倍型多样性分别为0.9621 ± 0.0078与0.9928 ± 0.0144。野生牦牛的母系系统发育分析揭示了3个明确的谱系（mt-I、mt-II与mt-III）。同理，野生牦牛亦表现出丰富的公系遗传多样性，其Y染色体单倍型多样性（Hd）为0.8214 ± 0.1007。公系系统发育分析共鉴定出2个Y染色体单倍群（Y1与Y2）以及4个Y染色体单倍型（yH1~yH4），表明野生牦牛存在2个公系谱系。本研究对野生牦牛遗传多样性与谱系构成的解析，可为这一易危野生物种的遗传资源保护与利用提供重要参考依据。