Population Structure, and Selection Signatures Underlying High-Altitude Adaptation Inferred From Genome-Wide Copy Number Variations in Chinese Indigenous Cattle
Open accessAbstract
Copy number variations (CNVs) have been demonstrated as crucial substrates for evolution, adaptation and breed formation. Chinese indigenous cattle breeds exhibit a broad geographical distribution and diverse environmental adaptability. Here, we analyzed the population structure and adaptation to high altitude of Chinese indigenous cattle based on genome-wide CNVs derived from the high-density BovineHD SNP array. We successfully detected the genome-wide CNVs of 318 individuals from 24 Chinese indigenous cattle breeds and 37 yaks as outgroups. A total of 5,818 autosomal CNV regions (683 bp - 4,477,860 bp in size), covering ~14.34% of the bovine genome (UMD3.1), were identified, showing abundant CNV resources. Neighbor-joining clustering, principal component analysis (PCA), and population admixture analysis based on these CNVs support that most Chinese cattle breeds are hybrids of Bos taurus taurus (hereinafter to be referred as Bos taurus) and Bos taurus indicus (Bos indicus). The distribution patterns of the CNVs could to some extent be related to the geographical backgrounds of the habitat of the breeds, and admixture among cattle breeds from different districts. We analyzed the selective signatures of CNVs positively involved in high-altitude adaptation using pairwise Fst analysis within breeds with a strong Bos taurus background (taurine-type breeds) and within Bos taurus×Bos indicus hybrids, respectively. CNV-overlapping genes with strong selection signatures (at top 0.5% of Fst value), including LETM1 (Fst = 0.490), TXNRD2 (Fst=0.440) and STUB1 (Fst=0.420) within taurine-type breeds, and NOXA1 (Fst = 0.233), RUVBL1 (Fst=0.222) and SLC4A3 (Fst=0.154) within hybrids, were potentially involved in the adaptation to hypoxia. Thus, we provide a new profile of population structure from the CNV aspects of Chinese indigenous cattle and new insights into high-altitude adaptation in cattle.
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In Apeijiaza and Shigatse Humped cattle, genes associated with cardiovascular function (NOXA1, RUVBL1, SLC4A3) underwent intense selection.
“In Apeijiaza cattle and Shigatse Humped cattle, both of which carry indicine ancestry, genes associated with cardiovascular function (NOXA1, RUVBL1, SLC4A3) underwent intense selection [95].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [95]
Tibetan taurine cattle displayed significant selection signals in LETM1, TXNRD2, and STUB1, which may promote hypoxia adaptation by modulating mitochondrial function and HIF-1α stability.
“Tibetan taurine cattle displayed significant selection signals in LETM1, TXNRD2, and STUB1, which may promote hypoxia adaptation by modulating mitochondrial function and HIF-1α stability [95].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [95]
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Flagged first, then by citations
Research works printed but not linked: 1
- National Bureau of Statistics (2016). China Statistical Yearbook 2016 (Beijing: China Statistics Press).
Cited by
Sorted by citations
Evolution and Domestication of the Bovini Species
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The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution
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- Authors
- Zhang, Y., Hu, Y., Wang, X., Jiang, Q., Zhao, H., Wang, J., Ju, Z., Yang, L., Gao, Y., Wei, X., Bai, J., Zhou, Y., & Huang, J.
- Affiliations
- Shandong Academy of Agricultural Sciences (CN)
- Huazhong Agricultural University (CN)
- Corresponding author
- Zhou, Yang
- Huang, Jinming
- ORCID
- Venue
- Frontiers in Genetics
- Publisher
- Frontiers Media SA
- Published
- 2020-02-14
- Volume
- 10
- Pages
- 1404-1404
- ISSN
- 1664-8021 (ISSN-L)
- PMC
- PMC7033542
- OpenAlex
- W3006074903
- Cited by
- 42
- References
- 101
- Citations by year
- 2026: 1 · 2025: 5 · 2024: 8 · 2023: 8 · 2022: 7 · 2021: 3 · 2020: 8 · 2018: 1 · 2017: 1
- FWCI
- 3.96
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Frontiers in Genetics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Natural Science Foundation of China (2019LZGC011, 31771374)
- Natural Science Foundation of Hubei Province (2018CFB363)
- Natural Science Foundation of Shandong Province (2019LZGC011, JQ201709)
- Agricultural Variety Improvement Project of Shandong Province (2019LZGC011)
- Fundamental Research Funds for the Central Universities (2662017QD016)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Agricultural and Biological Sciences › Agronomy and Crop Science › Livestock Farming and Management
- Keywords
- copy number variation, high-altitude adaptation, population structure, Bos taurus taurus, Bos indicus, admixture, selection signatures, hypoxia, FST, LETM1, TXNRD2, STUB1, NOXA1, RUVBL1, yak
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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