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Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia
Open accessAbstract
Cattle domestication and the complex histories of East Asian cattle breeds warrant further investigation. Through analysing the genomes of 49 modern breeds and eight East Asian ancient samples, worldwide cattle are consistently classified into five continental groups based on Y-chromosome haplotypes and autosomal variants. We find that East Asian cattle populations are mainly composed of three distinct ancestries, including an earlier East Asian taurine ancestry that reached China at least ~3.9 kya, a later introduced Eurasian taurine ancestry, and a novel Chinese indicine ancestry that diverged from Indian indicine approximately 36.6-49.6 kya. We also report historic introgression events that helped domestic cattle from southern China and the Tibetan Plateau achieve rapid adaptation by acquiring ~2.93% and ~1.22% of their genomes from banteng and yak, respectively. Our findings provide new insights into the evolutionary history of cattle and the importance of introgression in adaptation of cattle to new environmental challenges in East Asia.
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“strongly supporting the two independent domestication events involving distinct aurochs subspecies.”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [9]
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“Molecular divergence of taurine and indicine (also referred to as zebu) lineages is estimated to have occurred at approximately 201,000–301,200 years ago [5,7,8,9,10], strongly supporting the two independent domestication events involving distinct aurochs subspecies.”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [9]
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“The Y2 haplogroup is distributed across Eurasia and Africa, whiel Y2a sub-haplogroup is dominant in Eurasian cattle and Y2b sub-haplogroup is found having a higher proportion in Northeast Asian and Qinghai-Tibetan Plateau cattle [9,34].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [9]
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“The divergence of Y3a from Y3b, as well as sub-haplogroups within indicine mitogenomes, occurred approximately 23,100–24,800 years ago, while South Asian indicine ancestry diverged from East Asian and African indicine ancestry approximately 10,300–40,100 and 11,800 years ago, respectively [9,10].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [9]
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“The mtDNA I1 haplogroup and Y3b sub-haplogroup are widely distributed in India and other parts of the world, while Y3a sub-haplogroup predominates in southern China and Southeast Asia [6,9,36,37].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [9]
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“The autosomal genetic structure of modern cattle is primarily divided into six ancestries (Table 1): European taurine, East Asian taurine, African taurine, South Asian or Indian indicine, East Asian or Chinese indicine, and African indicine ancestry [9,10,31].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [9]
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“The introgression proportions of banteng (Bos javanicus), gaur (Bos gaurus), and yak (Bos mutus) ancestries into East Asian indicine or Tibetan taurine cattle ranged from 1.13% to 10.21%, 2.06% to 9.98%, and 0.05% to 2.94%, respectively [9,10].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [9]
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“During the late Neolithic (4000–5000 years ago), taurine cattle were introduced to East Asia from West Asia, carrying T3 and the East Asian-specific T4 haplogroups [9,33,55,56,57].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [9]
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“Studies based on Y-chromosome microsatellites or SNP markers classify modern cattle paternal origins into taurine Y1, Y2 (Y2a and Y2b), and indicine Y3 (Y3a and Y3b) haplogroups [9,10].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [9]
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“Tibetan and Northeast Asian cattle breeds share an East Asian taurine ancestry component, and the Y2b sub-haplogroup was likely maintained by geographical barriers [9].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [9]
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“In contrast, Eurasian taurine ancestry and the Y2a sub-haplogroup predominated in cattle from Northwest China and south-central Europe [9].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [9]
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High-throughput long paired-end sequencing of a Fosmid library by PacBio
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Self-citation
Metadata
- Authors
- Chen, N., Cai, Y., Chen, Q., Li, R., Wang, K., Huang, Y., Hu, S., Huang, S., Zhang, H., Zheng, Z., Song, W., Ma, Z., Ma, Y., Dang, R., Zhang, Z., Xu, L., Jia, Y., Liu, S., Yue, X., Deng, W., Zhang, X., Sun, Z., Lan, X., Han, J., Chen, H., Bradley, D. G., Jiang, Y., & Lei, C.
- Affiliations
- Northwest A&F University (CN)
- Northwestern Polytechnical University (CN)
- Yunnan University (CN)
- Qinghai University (CN)
- Ningxia University (CN)
- Henan Academy of Agricultural Sciences (CN)
- Anhui Academy of Agricultural Sciences (CN)
- National Beef Cattle Industrial Technology System (CN)
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems (CN)
- Yunnan Agricultural University (CN)
- Kunming Institute of Zoology (CN)
- Chinese Academy of Agricultural Sciences (CN)
- Trinity College Dublin (IE)
- Corresponding author
- Jiang, Yu
- Lei, Chuzhao
- ORCID
- Chen, Ningbo
- Cai, Yudong
- Chen, Qiuming
- Li, Ran
- Wang, Kun
- Huang, Yongzhen
- Hu, Songmei
- Huang, Shisheng
- Zhang, Hucai
- Zheng, Zhuqing
- Song, Weining
- Ma, Zhijie
- Dang, Ruihua
- Zhang, Zijing
- Xu, Lei
- Jia, Yutang
- Yue, Xiangpeng
- Deng, Weidong
- Zhang, Xiaoming
- Lan, Xianyong
- Han, Jianlin
- Chen, Hong
- Bradley, Daniel G
- Jiang, Yu
- Lei, Chuzhao
- Venue
- Nature Communications
- Published
- 2018-06-14
- Volume
- 9
- Issue
- 1
- Pages
- 2337-2337
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC6002414
- OpenAlex
- W2805177757
- Cited by
- 403
- References
- 60
- Citations by year
- 2026: 26 · 2025: 49 · 2024: 66 · 2023: 56 · 2022: 52 · 2021: 74 · 2020: 38 · 2019: 29 · 2018: 12
- FWCI
- 23.77
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Lanzhou University Institutional Repository (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- CGSPace A Repository of Agricultural Research Outputs (Consultative Group for International Agricultural Research) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Trinity's Access to Research Output (TARA) (Trinity College Dublin) (submittedVersion)
- Funders
- Natural Science Foundation of Qinghai Province of China
- National Natural Science Foundation of China (31501918)
- Yunnan Modern Agriculture Beef Cattle Industry Technology System
- National Thousand Youth Talents Plan
- National Beef Cattle and Yak Industrial Technology System
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Keywords
- cattle domestication, population ancestry, adaptive introgression, banteng, yak, Y-chromosome haplotypes
- MeSH terms
- Domestication, Animals, Breeding, Cattle, China, Chromosomes, Female, Genetics, Population, Geography, Haplotypes, Male, Mitochondria, Phylogeny, Species Specificity, Genetic Variation, Models, Statistical, Genome, Tibet, Polymorphism, Single Nucleotide
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