Genome-wide scan for selection signatures reveals novel insights into the adaptive capacity characteristics in three Chinese cattle breeds
Open accessAbstract
BACKGROUND: Cattle have evolved genetic adaptations to a diverse range of agroecological zones, such as plateaus and arid zones. However, little is known about its genetic basis of adaptation to harsh environments within a short period of time after domestication. Here, we analyzed whole-genome sequence data from three indigenous cattle breeds (Anxi, Qaidam and Zhangmu) in northwest China and five worldwide cattle breeds (Angus, Holstein, Jersey, Gir and N'Dama) to explore their genetic composition and identify selective sweeps in the Chinese cattle breeds. RESULTS: Analyses of phylogenetic and population structure revealed that three indigenous cattle breeds share genomic components from Bos taurus and Bos indicus. A novel set of candidate genes was identified through comparative genomic analyses of cattle from contrasting environments based on SNP and copy number variation (CNV) data. These candidate genes are potentially associated with adaptive phenotypes, including high-altitude adaptability (e.g., ANGPT1, PPARGC1A, RORA), cold climate adaptation (e.g., TSHR, PRKG, OXCT1), and dryland adaptation (e.g., PLEKHA7, NFATC1, PLCB1). CONCLUSIONS: This study unravels the unique adaptive diversity of three Chinese indigenous cattle breeds, providing a valuable resource for future research on sustainable livestock breeding strategies to response to climate change.
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Compared with low-altitude breeds such as Angus, strong selection signals were identified in ANGPT1 and PPARGC1A in high-altitude cattle.
“Compared with low-altitude breeds such as Angus, Wu et al. [96] identified strong selection signals in ANGPT1 and PPARGC1A, two genes functionally related to hypoxia adaptation.”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [96]
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References 71 · Cited by 10
- Authors
- Wu, X., Pei, J., Xiong, L., Ge, Q., Bao, P., Liang, C., Yan, P., & Guo, X.
- Affiliations
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences (CN)
- Agricultural Genomics Institute at Shenzhen (CN)
- Corresponding author
- Yan, Ping
- Guo, Xian
- Venue
- BMC Genomics
- Published
- 2025-02-28
- Volume
- 26
- Issue
- 1
- Pages
- 206-206
- ISSN
- 1471-2164 (ISSN-L)
- PMC
- PMC11871715
- OpenAlex
- W4408071430
- Cited by
- 10
- References
- 71
- Citations by year
- 2026: 6 · 2025: 4
- FWCI
- 5.88
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- BMC Genomics (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- Shenzhen Science and Technology Innovation Program (KCXFZ20201221173205015)
- Agricultural Science and Technology Innovation Program (25-LZIHPS-01)
- China Agriculture Research System of MOF and MARA (CARS-37)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Effects of Environmental Stressors on Livestock
- Keywords
- cattle, adaptive evolution, selection signatures, selective sweeps, indigenous cattle breeds, high-altitude adaptation, cold climate adaptation, dryland adaptation, Bos indicus, copy number variation, candidate genes, angiopoietin-1, PGC-1α, RORA, TSHR, OXCT1, PLEKHA7, NFATc1, PLCB1, population structure, phylogenetic analysis, climate change adaptation
- MeSH terms
- Whole Genome Sequencing, Adaptation, Physiological, Animals, Breeding, Cattle, China, Phenotype, Phylogeny, Selection, Genetic, Genome, Polymorphism, Single Nucleotide, Genomics, Genome-Wide Association Study, DNA Copy Number Variations
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