Whole-genome resequencing provides insights into the evolution and divergence of the native domestic yaks of the Qinghai
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RESEARCH ARTICLE
Open Access
Whole‑genome resequencing provides insights into the evolution and divergence of the native domestic yaks of the Qinghai–Tibet Plateau Zhi‑xin Chai1†, Jin‑wei Xin2†, Cheng‑fu Zhang2, Dawayangla2, Luosang2, Qiang Zhang2, Pingcuozhandui2, Chao Li2, Yong Zhu2, Han‑wen Cao2, Hui Wang1, Jian‑lin Han3, Qiu‑mei Ji2* and Jin‑cheng Zhong1*
Abstract Background: On the Qinghai–Tibet Plateau, known as the roof ridge of the world, the yak is a precious cattle species that has been indispensable to the human beings living in this high-altitude area. However, the origin of domestica‑ tion, dispersal route, and the divergence of domestic yaks from different areas are poorly understood. Results: Here, we resequenced the genome of 91 domestic yak individuals from 31 populations and 1 wild yaks throughout China. Using a population genomics approach, we observed considerable genetic variation. Phylogenetic analysis suggested that the earliest domestications of yak occurred in the south-eastern QTP, followed by dispersal to the west QTP and northeast to SiChuang, Gansu, and Qinghai by two routes. Interestingly, we also found potential associations between the distribution of some breeds and historical trade routes such as the Silk Road and Tang-Tibet Ancient Road. Selective analysis identified 11 genes showing differentiation between domesticated and wild yaks and the potentially positively selected genes in each group were identified and compared among domesticated groups. We also detected an unbalanced pattern of introgression among domestic yak, wild yak, and Tibetan cattle. Conclusions: Our research revealed population genetic evidence for three groups of domestic yaks. In addition to providing genomic evidence for the domestication history of yaks, we identified potential selected genes and introgression, which provide a theoretical basis and resources for the selective breeding of superior characters and high-quality yak. Keywords: Domestication, Plateau adaptability, Gene exchange, Bovidae, Hybrids, Selective
*Correspondence: [email protected]; [email protected] † Zhi-xin Chai and Jin-wei Xin contributed equally to this work 1 Key Laboratory of Qinghai‑Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, China 2 State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Institute of Animal Science and Veterinary Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China Full list of author information is available at the end of the article
Background The domestication of animals provided a stable source of food, labor, and hides, which played an important role in the lifestyle changes of humans from hunter gatherer to agricultural settlement [1]. On the Qinghai–Tibet Plateau (QTP), known as the roof ridge of the world, the average altitude is over 4000 m, where most plants and animals cannot survive because of the harsh climate, hyp
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