Discovery of Genomic Characteristics and Selection Signatures in Southern Chinese Local Cattle
Open accessAbstract
Chinese local cattle with a high level of genetic diversity mainly originate from two subspecies; the cattle in northern China are primarily Bos Taurus, and the cattle in southern China are primarily Bos indicus. Cattle from southern China are characterized by a specific phenotype and adapted to the local environment. This study explored the genetic diversity, degree of admixture, and selection signature in eight local cattle breeds in southern China. The lowest level of heterozygosity was found in Hainan and Nandan cattle from Hainan and Guangxi province, respectively, whereas the highest level of heterozygosity was detected in Zhaotong cattle from Yunnan province. A neighbor-joining phylogenetic tree analysis clearly separated Lufeng cattle from other breeds, whereas Leiqiong and Hainan cattle have some crossover. Based on linkage disequilibrium-filtered single nucleotide polymorphisms (SNPs), the admixture analysis revealed two clusters corresponding to the taurine and indicine cattle lineages, and the local cattle breeds from southern China showed a certain degree of admixture. When K= 4 and 9, we found a slight separation among Leiqiong, Lufeng, and Hainan cattle. Meanwhile, we performed a selection signature analysis in Hainan, Leiqiong, and Lufeng cattle distributed in the extreme south of China, using the integrated haplotype score (iHS), Rsb statistic, and BayeScan software. Using the iHS approach, we identified 251, 270, and 256 candidate regions in Lufeng, Leiqiong, and Hainan cattle, respectively. Moreover, we identified 184, 174, and 146 candidate regions in pairwise comparisons of Leiqiong vs. Lufeng, Leiqiong vs. Hainan, and Hainan vs. Lufeng cattle using the Rsb approach. In addition, we identified 76 loci with a total of 48 genes under selection, based on the FSTapproach. Several candidate genes under selection were found to be related to meat quality, immunity, and adaptation to the local environment in southern China. Our results provide significant information about the genetic differences among the cattle breeds from southern China and the possible cause of difference in breed-specific characteristics. Selection signature analysis identified a few candidate SNPs and genes related to certain important traits of these cattle. In general, our results provide valuable insights into the genetic basis of specific traits under selection in certain local cattle breeds.
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In southern Chinese cattle, genes related to tick and bacterial resistance (LTF, TGM3, BCAR3) show evidence of being under selection.
“Similarly, in southern Chinese cattle, genes related to tick and bacterial resistance (LTF, TGM3, BCAR3) show evidence of being under selection [105].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [105]
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- Authors
- Liu, Y., Xu, L., Yang, L., Zhao, G., Li, J., Liu, D., & Li, Y.
- Affiliations
- South China Agricultural University (CN)
- Chinese Academy of Agricultural Sciences (CN)
- Sichuan Agricultural University (CN)
- Corresponding author
- Liu, Dewu
- Li, Yaokun
- Venue
- Frontiers in Genetics
- Publisher
- Frontiers Media SA
- Published
- 2020-12-18
- Volume
- 11
- Pages
- 533052-533052
- ISSN
- 1664-8021 (ISSN-L)
- PMC
- PMC7775540
- OpenAlex
- W3113095523
- Cited by
- 27
- References
- 69
- Citations by year
- 2026: 4 · 2025: 5 · 2024: 5 · 2023: 5 · 2022: 5 · 2021: 3
- FWCI
- 1.91
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Frontiers in Genetics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Key Research and Development Program of China (CARS-37, 2018YFD0501706)
- National Beef Cattle Industrial Technology System (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 diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- cattle, Bos indicus, admixture, selection signatures, genetic diversity, heterozygosity, indigenous cattle breeds, integrated haplotype score, FST, candidate genes, meat quality, immunity, phylogenetic analysis
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