Whole genome insights into genetic diversity, introgression, and adaptation of Yunnan indigenous cattle of Southwestern China
Open accessAbstract
BACKGROUND: Yunnan Province, located in Southwestern China, the intricate geography, variable climate, and abundant vegetation of the region have collectively contributed to shaping the distinctive germplasm characteristics observed in Yunnan indigenous cattle through prolonged domestication. The different breeds of Yunnan cattle exhibit distinct advantageous characteristics and traits, which are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. However, a comprehensive genomic landscape of genetic resources has yet to be delineated. RESULTS: Herein, we employed 140 whole-genome sequencing data from Yunnan indigenous cattle across eight breeds to elucidate their genetic diversity and population structure. Utilizing both uniparental and biparental markers, we elucidated the intricate genetic composition of Yunnan indigenous cattle, which is closely correlated with the geographic environment. A predominant East Asian indicine ancestry which gradually diminishes towards the north. The analysis revealed a high genetic diversity among populations and a low-to-moderate inbreeding coefficient, underscoring the rich genetic reservoir of Yunnan cattle breeds. Additionally, gene flow between Yunnan indicine and wild Bos species in and around Yunnan was verified, highlighting localized introgression from Yunnan Gayal as a critical factor in the successful adaptation of Yunnan indicine cattle to the local hot and humid environments. CONCLUSIONS: Our findings established the SNPs database for facilitating resource conservation and selective breeding. Moreover, these valuable insights into the genomic diversity and adaptive history of Yunnan indigenous cattle breeds contribute significantly to our understanding of their evolutionary dynamics and offer a foundation for future genetic improvement and conservation strategies.
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The rapid adaptation of East Asian cattle to hot and humid environments and high-altitude environments was promoted by localized introgression from other bovine species.
“The rapid adaptation of East Asian cattle to hot and humid environments and high-altitude environments was promoted by localized introgression from other bovine species [65,66].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [66]
The Discussion (page unavailable) says that introgressed regions from Yunnan gayal may have helped Yunnan cattle adapt to humid tropical conditions and disperse rapidly. The paper does not establish that such introgression promoted high-altitude adaptation, and its finding concerns Yunnan cattle rather than East Asian cattle generally. (LLM, conf=0.86)
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The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution
Liu, Y., Dao, W., Gao, R., Fan, X., Yang, R., & Miao, Y. (2026) · Animals · doi:10.3390/ani16050776 · Cited by 1 · see citing works
- Authors
- Guan, X., Xiang, W., Qu, K., Ahmed, Z., Liu, J., Cai, M., Zhang, J., Chen, N., Lei, C., & Huang, B.
- Affiliations
- Northwest A&F University (CN)
- Chuxiong Normal University (CN)
- University of Poonch Rawalakot (PK)
- Corresponding author
- Lei, Chuzhao
- Huang, Bizhi
- ORCID
- Venue
- BMC Genomics
- Published
- 2025-03-04
- Volume
- 26
- Issue
- 1
- Pages
- 216-216
- ISSN
- 1471-2164 (ISSN-L)
- PMC
- PMC11881512
- OpenAlex
- W4408152085
- Cited by
- 10
- References
- 50
- Citations by year
- 2026: 7 · 2025: 3
- 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, cc-by-sa)
- Funders
- Chuxiong Science and Technology Leading Talents (CXKJLJRC2023-07)
- Yunnan Expert Workstations (202305AF150156)
- the China Agriculture Research System of MOF and MARA (CARS-37)
- the Program of Yunling Scholar and Yunling Cattle Special Program of Yunnan Joint Laboratory of Seeds and Seeding Industry (202205AR070001)
- the Construction of Yunling Cattle Technology Innovation Center and Industrialization of Achievements (2019ZG007)
- 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 › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- genetic diversity, introgression, adaptation, population structure, gene flow, Bos, inbreeding coefficient, cattle breeds, germplasm conservation, hot and humid environment
- MeSH terms
- Whole Genome Sequencing, Genetic Introgression, Adaptation, Physiological, Animals, Breeding, Cattle, China, Genetics, Population, Phylogeny, Genetic Variation, Genome, Polymorphism, Single Nucleotide, Genomics, Gene Flow
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