Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing

Ningbo Chen, Xiaoting Xia, Quratulain Hanif, Fengwei Zhang, Ruihua Dang, Bizhi Huang, Yang Lyu, Xiaoyu Luo, Hucai Zhang, Huixuan Yan, Shikang Wang, Fuwen Wang, Jialei Chen, Xiwen Guan, Yangkai Liu, Shuang Li, Liangliang Jin, Pengfei Wang, Luyang Sun, Jicai Zhang, Jianyong Liu, Kaixing Qu, Yanhong Cao, Junli Sun, Yuying Liao, Zhengzhong Xiao, Ming Cai, Lan Mu, Amam Zonaed Siddiki, Muhammad Asif, Shahid Mansoor, Masroor Ellahi Babar, Tanveer Hussain, Gamamada Liyanage Lalanie Pradeepa Silva, Neena Amatya Gorkhali, Endashaw Terefe, Gurja Belay, Abdulfatai Tijjani, Tsadkan Zegeye, Mebrate Genet Gebre, Yun Ma, Yu Wang, Yongzhen Huang, Xianyong Lan, Hong Chen, Nicola Rambaldi Migliore, Giulia Colombo, Ornella Semino, Alessandro Achilli, Mikkel-Holger S. Sinding, Johannes A. Lenstra, Haijian Cheng, Wenfa Lu, Olivier Hanotte (), Jianlin Han (), Yu Jiang () and Chuzhao Lei ()
Additional contact information
Ningbo Chen: Northwest A&F University
Xiaoting Xia: Northwest A&F University
Quratulain Hanif: National Institute for Biotechnology and Genetic Engineering
Fengwei Zhang: Northwest A&F University
Ruihua Dang: Northwest A&F University
Bizhi Huang: Yunnan Academy of Grassland and Animal Science
Yang Lyu: Northwest A&F University
Xiaoyu Luo: Northwest A&F University
Hucai Zhang: Yunnan University
Huixuan Yan: Northwest A&F University
Shikang Wang: Northwest A&F University
Fuwen Wang: Northwest A&F University
Jialei Chen: Northwest A&F University
Xiwen Guan: Northwest A&F University
Yangkai Liu: Northwest A&F University
Shuang Li: Northwest A&F University
Liangliang Jin: Northwest A&F University
Pengfei Wang: Northwest A&F University
Luyang Sun: Northwest A&F University
Jicai Zhang: Yunnan Academy of Grassland and Animal Science
Jianyong Liu: Yunnan Academy of Grassland and Animal Science
Kaixing Qu: Chuxiong Normal University
Yanhong Cao: Guangxi Vocational University of Agriculture
Junli Sun: Guangxi Vocational University of Agriculture
Yuying Liao: Guangxi Key Laboratory of Veterinary Biotechnology
Zhengzhong Xiao: Guangxi Vocational University of Agriculture
Ming Cai: Yunnan Academy of Grassland and Animal Science
Lan Mu: Southwest Forestry University
Amam Zonaed Siddiki: Chattogram Veterinary and Animal Sciences University (CVASU)
Muhammad Asif: National Institute for Biotechnology and Genetic Engineering
Shahid Mansoor: National Institute for Biotechnology and Genetic Engineering
Masroor Ellahi Babar: The University of Agriculture
Tanveer Hussain: Virtual University of Pakistan
Gamamada Liyanage Lalanie Pradeepa Silva: University of Peradeniya
Neena Amatya Gorkhali: Nepal Agriculture Research Council, Khumaltar
Endashaw Terefe: Arsi University
Gurja Belay: Addis Ababa University
Abdulfatai Tijjani: International Livestock Research Institute (ILRI)
Tsadkan Zegeye: Mekelle Agricultural Research Center
Mebrate Genet Gebre: Haramaya University
Yun Ma: Ningxia University
Yu Wang: Northwest A&F University
Yongzhen Huang: Northwest A&F University
Xianyong Lan: Northwest A&F University
Hong Chen: Northwest A&F University
Nicola Rambaldi Migliore: University of Pavia
Giulia Colombo: University of Pavia
Ornella Semino: University of Pavia
Alessandro Achilli: University of Pavia
Mikkel-Holger S. Sinding: University of Copenhagen
Johannes A. Lenstra: Utrecht University
Haijian Cheng: Northwest A&F University
Wenfa Lu: Jilin Agricultural University
Olivier Hanotte: International Livestock Research Institute (ILRI)
Jianlin Han: Chinese Academy of Agricultural Sciences (CAAS)
Yu Jiang: Northwest A&F University
Chuzhao Lei: Northwest A&F University

Nature Communications, 2023, vol. 14, issue 1, 1-13

Abstract: Abstract Indicine cattle, also referred to as zebu (Bos taurus indicus), play a central role in pastoral communities across a wide range of agro-ecosystems, from extremely hot semiarid regions to hot humid tropical regions. However, their adaptive genetic changes following their dispersal into East Asia from the Indian subcontinent have remained poorly documented. Here, we characterize their global genetic diversity using high-quality whole-genome sequencing data from 354 indicine cattle of 57 breeds/populations, including major indicine phylogeographic groups worldwide. We reveal their probable migration into East Asia was along a coastal route rather than inland routes and we detected introgression from other bovine species. Genomic regions carrying morphology-, immune-, and heat-tolerance-related genes underwent divergent selection according to Asian agro-ecologies. We identify distinct sets of loci that contain promising candidate variants for adaptation to hot semi-arid and hot humid tropical ecosystems. Our results indicate that the rapid and successful adaptation of East Asian indicine cattle to hot humid environments was promoted by localized introgression from banteng and/or gaur. Our findings provide insights into the history and environmental adaptation of indicine cattle.

Date: 2023
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DOI: 10.1038/s41467-023-43626-z

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