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

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Title Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing
 
Creator 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
 
Subject animal breeding
genetics
livestock
 
Description 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
2023-12-11T15:27:21Z
2023-12-11T15:27:21Z
 
Type Journal Article
 
Identifier 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, Terefe, E., Belay, G., Tijjani, A., 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, O., Jianlin Han, Yu Jiang and Chuzhao Lei. 2023. Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing. Nature Communications 14:7803.
2041-1723
https://hdl.handle.net/10568/135197
https://doi.org/10.1038/s41467-023-43626-z
 
Language en
 
Rights CC-BY-4.0
Open Access
 
Source Nature Communications