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

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  • 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
  • Johannes A. Lenstra
  • Haijian Cheng
  • Wenfa Lu
  • Olivier Hanotte
  • Jianlin Han
  • Yu Jiang
  • Chuzhao Lei
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.
OriginalsprogEngelsk
Artikelnummer7803
TidsskriftNature Communications
Vol/bind14
Udgave nummer1
Antal sider13
ISSN2041-1723
DOI
StatusUdgivet - 2023

Bibliografisk note

Funding Information:
This project was supported by grants from the National Key Research and Development Program of China (2021YFD1200400, SQ2021YFF1000041, and 2022YFF1000100) (W.L., N.C., and Y.J.), the earmarked fund for China Agriculture Research System of MOF and MARA (CARS-37) (C.L. and B.H.), the Yunnan Expert Workstations (202305AF150156), the National Natural Science Foundation of China (31872317), Foreign Young Talents Program (QN2022172008L) (C.L.), fellowships of the China Postdoctoral Science Foundation (2021T140564 and 2020M683587), the National Natural Science Foundation of China (32102523), the Shaanxi Youth Science and Technology New Star (2022KJXX-77), and High-end Foreign Experts Recruitment Plan (G2022172032L) (N.C.), Shaanxi Postdoctoral Science Foundation (2023BSHEDZZ132) (X.X.), the Program of Yunling Scholar and Yunling Cattle Special Program of Yunnan Joint Laboratory of Seeds and Seeding Industry (202205AR070001) and Construction of Yunling Cattle Technology Innovation Center and Industrialization of Achievements (2019ZG007) (B.H.), the National Natural Science Foundation of China (32072720) (Y.M.), the Chinese Government’s contribution to the CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources in Beijing (2023-YWF-ZX-02) (J.H.), the International Livestock Research Institute’s Livestock Genetics Program that was supported by the CGIAR Research Program on Livestock (CRP livestock) and sponsored by the CGIAR funding contributors to the Trust Fund ( http://www.cgiar.org/about-us/our-funders/ ), partly by the Bill and Melinda Gates Foundation and UK aid from UK Foreign, Commonwealth and Development Office (Grant Agreement OPP1127286) under the auspices of the Centre for Tropical Livestock Genetics and Health (CTLGH), established jointly by the University of Edinburgh, SRUC (Scotland’s Rural College) and ILRI (O.H.). This project was also supported by the Addis Ababa University, Ethiopia, the Italian Ministry of Education for Universities and Research (MUR) for PRIN2017 20174BTC4R (A.A.), the “Fondazione Adriano Buzzati–Traverso for the Luigi Luca Cavalli-Sforza fellowship (N.R.M.), the Carlsberg Foundation (CF20-0355) (M.H.S.S.), and the National Natural Science Foundation of China International Cooperative Research and Exchange Program (31861143014) (W.L.). Finally, we thank the High-Performance Computing (HPC) Center of Northwest A&F University (NWAFU) and Hefei Advanced Computing Center for providing computing resources and Lucia Mazzocchi for her contribution to the Y chromosome computational analysis.

Funding Information:
This project was supported by grants from the National Key Research and Development Program of China (2021YFD1200400, SQ2021YFF1000041, and 2022YFF1000100) (W.L., N.C., and Y.J.), the earmarked fund for China Agriculture Research System of MOF and MARA (CARS-37) (C.L. and B.H.), the Yunnan Expert Workstations (202305AF150156), the National Natural Science Foundation of China (31872317), Foreign Young Talents Program (QN2022172008L) (C.L.), fellowships of the China Postdoctoral Science Foundation (2021T140564 and 2020M683587), the National Natural Science Foundation of China (32102523), the Shaanxi Youth Science and Technology New Star (2022KJXX-77), and High-end Foreign Experts Recruitment Plan (G2022172032L) (N.C.), Shaanxi Postdoctoral Science Foundation (2023BSHEDZZ132) (X.X.), the Program of Yunling Scholar and Yunling Cattle Special Program of Yunnan Joint Laboratory of Seeds and Seeding Industry (202205AR070001) and Construction of Yunling Cattle Technology Innovation Center and Industrialization of Achievements (2019ZG007) (B.H.), the National Natural Science Foundation of China (32072720) (Y.M.), the Chinese Government’s contribution to the CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources in Beijing (2023-YWF-ZX-02) (J.H.), the International Livestock Research Institute’s Livestock Genetics Program that was supported by the CGIAR Research Program on Livestock (CRP livestock) and sponsored by the CGIAR funding contributors to the Trust Fund (http://www.cgiar.org/about-us/our-funders/), partly by the Bill and Melinda Gates Foundation and UK aid from UK Foreign, Commonwealth and Development Office (Grant Agreement OPP1127286) under the auspices of the Centre for Tropical Livestock Genetics and Health (CTLGH), established jointly by the University of Edinburgh, SRUC (Scotland’s Rural College) and ILRI (O.H.). This project was also supported by the Addis Ababa University, Ethiopia, the Italian Ministry of Education for Universities and Research (MUR) for PRIN2017 20174BTC4R (A.A.), the “Fondazione Adriano Buzzati–Traverso for the Luigi Luca Cavalli-Sforza fellowship (N.R.M.), the Carlsberg Foundation (CF20-0355) (M.H.S.S.), and the National Natural Science Foundation of China International Cooperative Research and Exchange Program (31861143014) (W.L.). Finally, we thank the High-Performance Computing (HPC) Center of Northwest A&F University (NWAFU) and Hefei Advanced Computing Center for providing computing resources and Lucia Mazzocchi for her contribution to the Y chromosome computational analysis.

Publisher Copyright:
© 2023, The Author(s).

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