Nature Communications (Nov 2023)
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,
- Chuzhao Lei
Affiliations
- Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
- Xiaoting Xia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
- Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering
- Fengwei Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
- Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
- Bizhi Huang
- Yunnan Academy of Grassland and Animal Science
- Yang Lyu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
- Xiaoyu Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
- Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environment Science, Yunnan University
- Huixuan Yan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
- Shikang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
- Fuwen Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
- Jialei Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
- Xiwen Guan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
- Yangkai Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
- Shuang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
- Liangliang Jin
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
- Pengfei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
- Luyang Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
- Jicai Zhang
- Yunnan Academy of Grassland and Animal Science
- Jianyong Liu
- Yunnan Academy of Grassland and Animal Science
- Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University
- Yanhong Cao
- Guangxi Vocational University of Agriculture
- Junli Sun
- Guangxi Vocational University of Agriculture
- Yuying Liao
- Guangxi Veterinary Research Institute, Guangxi Key Laboratory of Veterinary Biotechnology
- Zhengzhong Xiao
- Guangxi Vocational University of Agriculture
- Ming Cai
- Yunnan Academy of Grassland and Animal Science
- Lan Mu
- College of Landscape and Horticulture, Southwest Forestry University
- Amam Zonaed Siddiki
- Genomics Research Group, Department of Pathology and Parasitology, Faculty of Veterinary Medicine, 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
- Department of Molecular Biology, Virtual University of Pakistan
- Gamamada Liyanage Lalanie Pradeepa Silva
- Department of Animal Science, University of Peradeniya
- Neena Amatya Gorkhali
- National Animal Breeding and Genetics Centre, National Animal Science Research Institute, Nepal Agriculture Research Council, Khumaltar
- Endashaw Terefe
- College of Agriculture and Environmental Science, Department of Animal Science, Arsi University
- Gurja Belay
- College of Natural and Computational Sciences, The School of Graduate Studies, Addis Ababa University
- Abdulfatai Tijjani
- International Livestock Research Institute (ILRI)
- Tsadkan Zegeye
- Mekelle Agricultural Research Center
- Mebrate Genet Gebre
- School of Animal and Rangeland Science, College of Agriculture, Haramaya University
- Yun Ma
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University
- Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
- Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
- Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
- Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
- Nicola Rambaldi Migliore
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia
- Giulia Colombo
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia
- Ornella Semino
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia
- Alessandro Achilli
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia
- Mikkel-Holger S. Sinding
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen
- Johannes A. Lenstra
- Faculty of Veterinary Medicine, Utrecht University
- Haijian Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
- Wenfa Lu
- College of Animal Science and Technology, Jilin Agricultural University
- Olivier Hanotte
- International Livestock Research Institute (ILRI)
- Jianlin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS)
- Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
- Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
- DOI
- https://doi.org/10.1038/s41467-023-43626-z
- Journal volume & issue
-
Vol. 14,
no. 1
pp. 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.
