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

Mario Barbato,Matilde Passamonti,John L Williams,Rick Tearle,Paolo Ajmone Marsan,Licia Colli,Michael P Reichel,Wai Yee Low,Alessandro Achilli

doi:10.1371/journal.pone.0231162

Mario Barbato, Matilde Passamonti + Show 7 more

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https://doi.org/10.1371/journal.pone.0231162

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Abstract

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.

Highlights

Livestock domestication started ~12,000 years ago (YA) and marked the most significant transition in human history, providing nutrients, traction, fertilizer, leather, fuel and provisions
As expected, when we tested the ability of the ancestral SNP panel to reduce ascertainment bias via resampling by permutation, the distance from the Ho computed using the ancestral set and the mean the Ho distribution for each bread was proportional to the phylogenetic distance between that breed and the taurine breeds used for SNP discovery (S3 Fig)
Using this ancestral SNP set we identified the Hong Kong feral cattle (HKF) population as genetically distinct from other taurine, indicine and crossbred cattle populations, and showed evidence of a significant contribution of wild bovine species to the genetics of the HKF

Summary

Introduction

Livestock domestication started ~12,000 years ago (YA) and marked the most significant transition in human history, providing nutrients, traction, fertilizer, leather, fuel and provisions. The actual number of extant breeds is likely to be larger as a significant proportion of indigenous livestock populations, which are present in the developing world, have yet to be described at genotypic and phenotypic level [1,2]. Indigenous domestic populations (often referred to as native breeds) are typically unmanaged genetically, or managed through traditional husbandry. These native breed generally show high levels of phenotypic variation [3,4,5,6,7] and are better adapted to local environments than specialised dairy and beef breeds, which are mostly of European taurine origin [8,9,10]. Indigenous populations have been reported for the major livestock species, including sheep, goat, pig, and cattle [7,11,12,13]

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