A genetically unique Chinese cattle population shows evidence of common ancestry with wild species when analysed with a reduced ascertainment bias SNP panel

In Hong Kong, there is a cattle population of ~1,200 individuals of uncertain origin and genetic diversity. This population shows heterogeneous morphology, both in body type and pigmentation. Once used as draught animals by the local farmers, they were abandoned around the 1970s due to changes in the economy, and since then have lived as feral populations. To explore the origins of these cattle, we analysed ~50k genotype data of 21 Hong Kong feral cattle, along with data from 703 individuals of 36 cattle populations of European, African taurine, and Asian origin, the wild x domestic hybrid gayal, plus two wild bovine species, gaur and banteng. To reduce the effect of ascertainment bias ~4k loci that are polymorphic in the two wild species were selected for further analysis. The stringent SNP selection we applied resulted in increased heterozygosity across all populations studies, compared with the full panel of SNP, thus reducing the impact of ascertainment bias and facilitating the comparison of divergent breeds of cattle. Our results showed that Hong Kong feral cattle have relatively high levels of genetic distinctiveness, possibly due to the low level of artificial selection, and a likely common ancestry with wild species. We found signs of a putative taurine introgression, probably dating to the import of north European breeds during the British colonialism of Hong Kong. We showed that Hong Kong feral cattle, are distinct from Bos taurus and Bos indicus breeds. Our results highlight the distinctiveness of Hong Kong feral cattle and stress the conservation value of this indigenous breed that is likely to harbour adaptive genetic variation, which is a fundamental livestock resource in the face of climate change and diversifying market demands.

香港地区现存约1200头来源与遗传多样性均不明的牛种群。该种群在体型与毛色上均表现出异质性形态特征。此前当地农户曾将其作为役用家畜，后因经济结构变革于20世纪70年代左右遭到弃养，自此以野生化种群的形式存续至今。为探究该种群的起源，我们对21头香港野生化牛的约50k基因型数据进行了分析，同时纳入了源自欧洲、非洲普通牛（taurine）与亚洲起源的36个牛种群共703个个体的基因型数据，以及野生与家养杂交的大额牛（gayal），外加两种野生牛科动物：印度野牛（gaur）与爪哇野牛（banteng）的相关数据。为降低确定偏差（ascertainment bias）的影响，我们选取了在两种野生牛科动物中呈多态性的约4k个基因座开展后续分析。相较于全部单核苷酸多态性（Single Nucleotide Polymorphism，SNP）检测面板，本次严格的SNP筛选策略使所有研究种群的杂合度均有所提升，从而削弱了确定偏差的影响，更便于对不同分化程度的牛品种进行比较分析。研究结果显示，香港野生化牛具备相对较高的遗传独特性，这可能源于较低水平的人工选择，且其与野生牛科物种可能拥有共同的祖先。我们还发现了疑似普通牛基因渐渗的痕迹，其发生时间大概率与英国殖民香港时期引入北欧牛品种的事件相吻合。研究证实，香港野生化牛与普通牛（Bos taurus）及瘤牛（Bos indicus）品种均存在显著差异。本研究结果凸显了香港野生化牛的独特性，并强调了这一本土种群的保护价值——该种群或携带适应性遗传变异，是应对气候变化与市场需求多元化的重要家畜遗传资源。