ArticleNature communications2023
Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing.
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58 citing papers in PubMed.
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- Genomic solutions to metadata challenges: a case study on the 1000 Bull Genomes Project.Genetics, selection, evolution : GSE · 2026Article
- Genome-wide variation landscape reveals temperature adaptation in Chinese indigenous cattle.Journal of animal science and biotechnology · 2026Article
- The First Ancient DNA Evidence of Zebu Husbandry in Thailand During the Prehistoric Through the Historic Periods.Animals : an open access journal from MDPI · 2026Article
- Whole-Genome Resequencing Reveals Deep Genomic Differentiation and Highly Differentiated Segments Between a Composite Domestic Cattle Population and Yak from the Ili River Valley and Other Xinjiang Regions.Animals : an open access journal from MDPI · 2026Article
- Whole-genome resequencing data of 200 domestic yaks from China.Scientific data · 2026Article
- Runs of homozygosity reveal population dynamics and selection across global cattle.Journal of animal science and biotechnology · 2026Article
- Population Genomics Reveals Genetic Diversity, Introgression, and Genetic Differentiation in Tianshan Mountains Western Honeybees (Evolutionary applications · 2026Article
- Large-Scale Comparative Genomics of European and Chinese Cattle Breeds Reveals Population Structure, Breeding History, and Adaptive Divergence.Animals : an open access journal from MDPI · 2026Article
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- Distinct adaptation and ancestral retention signals in African and European indigenous cattle genomes.Communications biology · 2026Article
- The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution.Animals : an open access journal from MDPI · 2026Review
- Genomic Insights into the Origins, Population Structure, and Local Adaptation of Philippine Visayan Native Cattle.Animals : an open access journal from MDPI · 2026Article
- The chromosome-level genome of Chinese indicine cattle breed provides insights into bovine adaptation and immunity.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- Genetic admixture and adaptive signatures of Guanling cattle revealed by whole-genome sequence.BMC genomics · 2026Article
- Genetic diversity and population structure of Mexican Gir cattle using genome-wide SNP data.Translational animal science · 2026Article
- Genome-wide characterization of copy number variants and their functional relevance in indigenous draught cattle of South Asia.PloS one · 2026Article
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Authors and funding
57 authors.
Ningbo Chen *Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.ORCID 0000-0001-6624-5885
Xiaoting Xia *Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Quratulain Hanif *National Institute for Biotechnology and Genetic Engineering, Faisalabad, 38000, Pakistan.ORCID 0000-0002-9841-8055
Fengwei Zhang *Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Ruihua Dang *Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Bizhi Huang *Yunnan Academy of Grassland and Animal Science, Kunming, 650212, China.
Yang LyuKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Xiaoyu LuoKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Hucai ZhangInstitute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environment Science, Yunnan University, Kunming, 650500, China.
Huixuan YanKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Shikang WangKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Fuwen WangKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Jialei ChenKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Xiwen GuanKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Yangkai LiuKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Shuang LiKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Liangliang JinKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.ORCID 0000-0002-4084-2638
Pengfei WangKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Luyang SunKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Jicai ZhangYunnan Academy of Grassland and Animal Science, Kunming, 650212, China.
Jianyong LiuYunnan Academy of Grassland and Animal Science, Kunming, 650212, China.
Kaixing QuAcademy of Science and Technology, Chuxiong Normal University, Chuxiong, 675000, China.
Yanhong CaoGuangxi Vocational University of Agriculture, Nanning, 530007, China.
Junli SunGuangxi Vocational University of Agriculture, Nanning, 530007, China.
Yuying LiaoGuangxi Veterinary Research Institute, Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, 530001, China.
Zhengzhong XiaoGuangxi Vocational University of Agriculture, Nanning, 530007, China.
Ming CaiYunnan Academy of Grassland and Animal Science, Kunming, 650212, China.ORCID 0000-0002-2416-374X
Lan MuCollege of Landscape and Horticulture, Southwest Forestry University, Kunming, 650224, China.
Amam Zonaed SiddikiGenomics Research Group, Department of Pathology and Parasitology, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University (CVASU), Chattogram, 4225, Bangladesh.
Muhammad AsifNational Institute for Biotechnology and Genetic Engineering, Faisalabad, 38000, Pakistan.
Shahid MansoorNational Institute for Biotechnology and Genetic Engineering, Faisalabad, 38000, Pakistan.
Masroor Ellahi BabarThe University of Agriculture, Dera Ismail Khan, Khyber Pakhtunkhwa, 29050, Pakistan.
Tanveer HussainDepartment of Molecular Biology, Virtual University of Pakistan, Islamabad, 44100, Pakistan.ORCID 0000-0002-2522-2406
Gamamada Liyanage Lalanie Pradeepa SilvaDepartment of Animal Science, University of Peradeniya, Peradeniya, 20400, Sri Lanka.
Neena Amatya GorkhaliNational Animal Breeding and Genetics Centre, National Animal Science Research Institute, Nepal Agriculture Research Council, Khumaltar, Lalitpur, 45200, Nepal.
Endashaw TerefeCollege of Agriculture and Environmental Science, Department of Animal Science, Arsi University, Asella, Ethiopia.ORCID 0000-0002-9152-8382
Gurja BelayCollege of Natural and Computational Sciences, The School of Graduate Studies, Addis Ababa University, 1000, Addis Ababa, Ethiopia.
Abdulfatai TijjaniInternational Livestock Research Institute (ILRI), P.O. Box 5689, 1000, Addis Ababa, Ethiopia.
Tsadkan ZegeyeMekelle Agricultural Research Center, P.O. Box 258, 7000, Mekelle, Tigray, Ethiopia.ORCID 0000-0003-2679-880X
Mebrate Genet GebreSchool of Animal and Rangeland Science, College of Agriculture, Haramaya University, 2040, Haramaya, Oromia, Ethiopia.
Yun MaKey Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, 750000, China.
Yu WangKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Yongzhen HuangKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Xianyong LanKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Hong ChenKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Nicola Rambaldi MiglioreDepartment of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100, Pavia, Italy.ORCID 0000-0003-1523-0450
Giulia ColomboDepartment of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100, Pavia, Italy.ORCID 0000-0002-5423-4844
Ornella SeminoDepartment of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100, Pavia, Italy.ORCID 0000-0002-9675-9403
Alessandro AchilliDepartment of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100, Pavia, Italy.ORCID 0000-0001-6871-3451
Mikkel-Holger S SindingSection for Computational and RNA Biology, Department of Biology, University of Copenhagen, DK-1350, Copenhagen, Denmark.ORCID 0000-0003-1371-219X
Johannes A LenstraFaculty of Veterinary Medicine, Utrecht University, 3584 CM, Utrecht, The Netherlands.ORCID 0000-0003-1745-7739
Haijian ChengKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Wenfa LuCollege of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China.
Olivier HanotteInternational Livestock Research Institute (ILRI), P.O. Box 5689, 1000, Addis Ababa, Ethiopia. o.hanotte@cgiar.org.ORCID 0000-0002-2877-4767
Jianlin HanCAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), 100193, Beijing, China. h.jianlin@cgiar.org.ORCID 0000-0002-1527-3963
Yu JiangKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China. yu.jiang@nwafu.edu.cn.ORCID 0000-0003-4821-3585
Chuzhao LeiKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China. leichuzhao1118@nwafu.edu.cn.ORCID 0000-0003-1647-1037
Funding
Earmarked Fund for China Agriculture Research System CARS-37Earmarked Fund for Modern Agro-industry Technology Research System CARS-37National Natural Science Foundation of China (National Science Foundation of China) 32072720National Natural Science Foundation of China (National Science Foundation of China) 32102523
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.
Indexed as
Biological EvolutionEcosystemAllelesAnimalsCattleGenetic VariationPolymorphism, Single NucleotideWhole Genome Sequencing
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