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

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.

Bibliographic Details

Main Authors:	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, Zonaed Siddiki, Amam, Asif, Muhammad, Mansoor, Shahid, Babar, M.E., Hussain, Tanveer, Silva, G.L.L.P., Gorkhali, N.A., Terefe, E., Belay, G., Tijjani, Abdulfatai, Zegeye, T., Gebre, M., Yun Ma, Yu Wang, Yongzhen Huang, Xianyong Lan, Hong Chen, Migliore, N.R., Colombo, G., Semino, O., Achilli, A., Sinding, M.-H.S., Lenstra, J.A., Haijian Cheng, Wenfa Lu, Hanotte, Olivier H., Jianlin Han, Yu Jiang, Chuzhao Lei
Format:	Journal Article biblioteca
Language:	English
Published:	2023
Subjects:	animal breeding, genetics, livestock,
Online Access:	https://hdl.handle.net/10568/135197 https://doi.org/10.1038/s41467-023-43626-z
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