Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia

Ningbo Chen, Yudong Cai, Qiuming Chen, Ran Li, Kun Wang, Yongzhen Huang, Songmei Hu, Shisheng Huang, Hucai Zhang, Zhuqing Zheng, Weining Song, Zhijie Ma, Yun Ma, Ruihua Dang, Zijing Zhang, Lei Xu, Yutang Jia, Shanzhai Liu, Xiangpeng Yue, Weidong Deng, Xiaoming Zhang, Zhouyong Sun, Xianyong Lan, Jianlin Han, Hong Chen, Daniel G Bradley, Yu Jiang () and Chuzhao Lei ()
Additional contact information
Ningbo Chen: Northwest A&F University
Yudong Cai: Northwest A&F University
Qiuming Chen: Northwest A&F University
Ran Li: Northwest A&F University
Kun Wang: Northwestern Polytechnical University
Yongzhen Huang: Northwest A&F University
Songmei Hu: Shaanxi Provincial Institute of Archaeology
Shisheng Huang: Northwest A&F University
Hucai Zhang: Yunnan University
Zhuqing Zheng: Northwest A&F University
Weining Song: Northwest A&F University
Zhijie Ma: Northwest A&F University
Yun Ma: Ningxia University
Ruihua Dang: Northwest A&F University
Zijing Zhang: Henan Academy of Agriculture Science
Lei Xu: Anhui Academy of Agriculture Science
Yutang Jia: Anhui Academy of Agriculture Science
Shanzhai Liu: National Beef Cattle and Yak Industrial Technology System
Xiangpeng Yue: Lanzhou University
Weidong Deng: Yunnan Agricultural University
Xiaoming Zhang: Chinese Academy of Sciences
Zhouyong Sun: Shaanxi Provincial Institute of Archaeology
Xianyong Lan: Northwest A&F University
Jianlin Han: Chinese Academy of Agriculture Sciences (CAAS)
Hong Chen: Northwest A&F University
Daniel G Bradley: Trinity College Dublin
Yu Jiang: Northwest A&F University
Chuzhao Lei: Northwest A&F University

Nature Communications, 2018, vol. 9, issue 1, 1-13

Abstract: Abstract Cattle domestication and the complex histories of East Asian cattle breeds warrant further investigation. Through analysing the genomes of 49 modern breeds and eight East Asian ancient samples, worldwide cattle are consistently classified into five continental groups based on Y-chromosome haplotypes and autosomal variants. We find that East Asian cattle populations are mainly composed of three distinct ancestries, including an earlier East Asian taurine ancestry that reached China at least ~3.9 kya, a later introduced Eurasian taurine ancestry, and a novel Chinese indicine ancestry that diverged from Indian indicine approximately 36.6–49.6 kya. We also report historic introgression events that helped domestic cattle from southern China and the Tibetan Plateau achieve rapid adaptation by acquiring ~2.93% and ~1.22% of their genomes from banteng and yak, respectively. Our findings provide new insights into the evolutionary history of cattle and the importance of introgression in adaptation of cattle to new environmental challenges in East Asia.

Date: 2018
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DOI: 10.1038/s41467-018-04737-0

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