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

Author

Listed:
  • Ningbo Chen

    (Northwest A&F University)

  • Xiaoting Xia

    (Northwest A&F University)

  • Quratulain Hanif

    (National Institute for Biotechnology and Genetic Engineering
    Chinese Academy of Agricultural Sciences (CAAS))

  • 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
    International Livestock Research Institute (ILRI))

  • Gurja Belay

    (Addis Ababa University)

  • Abdulfatai Tijjani

    (International Livestock Research Institute (ILRI)
    The Jackson Laboratory)

  • 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
    Shandong Key Lab of Animal Disease Control and Breeding)

  • Wenfa Lu

    (Jilin Agricultural University)

  • Olivier Hanotte

    (International Livestock Research Institute (ILRI)
    University of Nottingham)

  • Jianlin Han

    (Chinese Academy of Agricultural Sciences (CAAS)
    International Livestock Research Institute (ILRI)
    Yazhouwan National Laboratory)

  • Yu Jiang

    (Northwest A&F University
    Northwest A&F University)

  • Chuzhao Lei

    (Northwest A&F University)

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.

Suggested Citation

  • 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 & Y, 2023. "Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43626-z
    DOI: 10.1038/s41467-023-43626-z
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    References listed on IDEAS

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