Genetic Diversity and Origin of Chinese Cattle Revealed by mtDNA D-Loop Sequence Variation
Abstract
To determine the origin and genetic diversity of Chinese cattle, we analyzed the complete mtDNA D-loop sequences of 84 cattle from 14 breeds/populations from southwest and west China, together with the available cattle sequences in GenBank. Our results showed that the Chinese cattle samples converged into two main groups, which correspond to the two species Bos taurus and Bos indicus. Although a dominant lineage was clearly discerned in both B. taurus and B. indicus mtDNAs, network analysis of the lineages in each of the two species further revealed multiple clades that presented regional difference. The B. taurus samples in China could be grouped into clades T2, T3, and T4, whereas B. indicus harbored two clades I1 and I2. Age estimation of these discerned clades showed a time range of 14,100-44,500 years before present (YBP). The phylogenetic pattern of Chinese cattle was consistent with the recently described cattle matrilineal pool from northeast Asia, but suggested that B. indicus contributed more to the cattle from south and southwest China. The genetic diversity of Chinese cattle varied among the breeds studied.
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The mitochondrial indicine I1 haplogroup spread east from northwestern India, with the I2 haplogroup sparsely distributed in India and southern China.
“The mitochondrial indicine I1 haplogroup spread east from northwestern India, with the I2 haplogroup sparsely distributed in India and southern China [7,29,30].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [30]
Cites
Molecular Evolutionary Genetics
Nei, M. (1987) · Columbia University Press eBooks · doi:10.7312/nei-92038 · Cited by 16,583 · see citing works
Fu, Y. (1997) · Genetics · doi:10.1093/genetics/147.2.915 · Cited by 7,195 · see citing works
MEGA2: molecular evolutionary genetics analysis software
Kumar, S., Tamura, K., Jakobsen, I. B., & Nei, M. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.12.1244 · Cited by 6,046 · see citing works
Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations.
Slatkin, M., & Hudson, R. R. (1991) · Genetics · doi:10.1093/genetics/129.2.555 · Cited by 2,380 · see citing works
Molecular evolutionary genetics
Felsenstein, J. (1987) · Cell · doi:10.1016/0092-8674(87)90630-1 · Cited by 2,189 · see citing works
Anderson, S., de Bruijn, M. H. L., Coulson, A. R., Eperon, I. C., Sanger, F., & Young, I. G. (1982) · Journal of Molecular Biology · doi:10.1016/0022-2836(82)90137-1 · Cited by 1,472 · see citing works
Mitochondrial portraits of human populations using median networks.
Bandelt, H. J., Forster, P., Sykes, B. C., & Richards, M. B. (1995) · Genetics · doi:10.1093/genetics/141.2.743 · Cited by 1,071 · see citing works
Genetic Evidence for an East Asian Origin of Domestic Dogs
Savolainen, P., Zhang, Y.-P., Luo, J., Lundeberg, J., & Leitner, T. (2002) · Science · doi:10.1126/science.1073906 · Cited by 960 · see citing works
Worldwide Phylogeography of Wild Boar Reveals Multiple Centers of Pig Domestication
Larson, G., Dobney, K. M., Albarella, U., Fang, M., Matisoo-Smith, E. A., Robins, J. H., Lowden, S., Finlayson, H. A., Brand, T. B., Willerslev, E., et al. (2005) · Science · doi:10.1126/science.1106927 · Cited by 912 · see citing works
Evidence for Two Independent Domestications of Cattle
Loftus, R. T., MacHugh, D. E., Bradley, D. G., Sharp, P. M., & Cunningham, P. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.7.2757 · Cited by 812 · see citing works
Origin and evolution of Native American mtDNA variation: a reappraisal.
Forster, P., Harding, R. M., Torroni, A., & Bandelt, H. J. (1996) · PubMed Central · Cited by 730 · see citing works
The Origin of the Domestic Pig: Independent Domestication and Subsequent Introgression
Giuffra, E., Kijas, J. M. H., Amarger, V., Carlborg, Ö., Jeon, J.-T., & Andersson, L. (2000) · Genetics · doi:10.1093/genetics/154.4.1785 · Cited by 712 · see citing works
Genetic Evidence for Near-Eastern Origins of European Cattle
Troy, C. S., MacHugh, D. E., Bailey, J. F., Magee, D. A., Loftus, R. T., Cunningham, P., Chamberlain, A. T., Sykes, B. C., & Bradley, D. G. (2001) · Nature · doi:10.1038/35074088 · Cited by 627 · see citing works
Mitochondrial diversity and the origins of African and European cattle
Bradley, D. G., MacHugh, D. E., Cunningham, P., & Loftus, R. T. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.10.5131 · Cited by 584 · see citing works
Multiple maternal origins and weak phylogeographic structure in domestic goats
Luikart, G., Gielly, L., Excoffier, L., Vigne, J., Bouvet, J., & Taberlet, P. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.091591198 · Cited by 564 · see citing works
mtDNA Variation among Greenland Eskimos: The Edge of the Beringian Expansion
Saillard, J., Forster, P., Lynnerup, N., Bandelt, H., & Nørby, S. (2000) · The American Journal of Human Genetics · doi:10.1086/303038 · Cited by 494 · see citing works
Bandelt, H., Macaulay, V. A., & Richards, M. B. (2000) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.2000.0792 · Cited by 214 · see citing works
Phylogeography and Origin of Indian Domestic Goats
Joshi, M. B. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msh038 · Cited by 197 · see citing works
Mannen, H., Kohno, M., Nagata, Y., Tsuji, S., Bradley, D. G., Yeo, J. S., Nyamsamba, D., Zagdsuren, Y., Yokohama, M., Nomura, K., et al. (2004) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2004.01.010 · Cited by 187 · see citing works
Mitochondrial DNA variation in cattle of South China: origin and introgression
Yu, Y., Nie, L., He, Z.-Q., Wen, J., Jian, C.-S., & Zhang, Y. (1999) · Animal Genetics · doi:10.1046/j.1365-2052.1999.00483.x · Cited by 61 · see citing works
Kim, K.-I., Lee, J. H., Lee, S.-S., & Yang, Y.-H. (2003) · Biochemical Genetics · doi:10.1023/a:1022021900205 · Cited by 28 · see citing works
Genetic Diversity of Cattle in South China as Revealed by Blood Protein Electrophoresis
Nie, L., Yu, Y., Zhang, X., Yang, G.-F., Ji-kun, W., & Zhang, Y. (1999) · Biochemical Genetics · doi:10.1023/a:1018798924778 · Cited by 18 · see citing works
Breeding distribution and maternal genetic lineages in Lulu, a dwarf cattle population in Nepal
Fujise, H., Murakami, M., Devkota, B., Dhakal, I. P., Takeda, K., Hanada, H., FUJITANI, H., SASAKI, M., & KOBAYASHI, K. (2003) · Animal Science Journal · doi:10.1046/j.1344-3941.2003.00078.x · Cited by 16 · see citing works
Mitochondrial DNA analysis of Nepalese domestic dwarf cattle Lulu*
Takeda, K., Satoh, M., Neopane, S. P., et al. (2004) · Animal Science Journal · doi:10.1111/j.1740-0929.2004.00163.x · Cited by 16 · see citing works
[Study on mitochondrial DNA genetic diversity of some cattle breeds in China].
Lei, C., Chen, H., Yang, G.-S., et al. (2004) · PubMed · Cited by 14 · see citing works
KOMATSU, M., Yasuda, Y., Matias, J. M., et al. (2004) · Cited by 2 · see citing works
General situation of domestic animal diversity in China
Yue-hui, M., You-chun, C., & Wei-qi, F. (2000) · Europe PMC (PubMed Central) · Cited by 2 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Chen, N., Cai, Y., Chen, Q., Li, R., Wang, K., Huang, Y., Hu, S., Huang, S., Zhang, H., Zheng, Z., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04737-0 · Cited by 403 · see citing works
On the Origin of Cattle: How Aurochs Became Cattle and Colonized the World
Ajmone‐Marsan, P., Garcia, J. F., & Lenstra, J. A. (2010) · Evolutionary Anthropology Issues News and Reviews · doi:10.1002/evan.20267 · Cited by 287 · see citing works
Zebu Cattle Are an Exclusive Legacy of the South Asia Neolithic
Chen, S., Lin, B.-Z., Baig, M., Mitra, B., Lopes, R. J., Santos, A. M., Magee, D. A., Azevedo, M., Tarroso, P., Sasazaki, S., et al. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msp213 · Cited by 248 · see citing works
The Multifaceted Origin of Taurine Cattle Reflected by the Mitochondrial Genome
Achilli, A., Bonfiglio, S., Olivieri, A., Malusà, A., Pala, M., Kashani, B. H., Perego, U. A., Ajmone-Marsan, P., Liotta, L., Semino, O., et al. (2009) · PLoS ONE · doi:10.1371/journal.pone.0005753 · Cited by 212 · see citing works
Genomic clues of the evolutionary history of <i>Bos indicus</i> cattle
Utsunomiya, Y. T., Milanesi, M., Fortes, M. R. S., Porto‐Neto, L. R., Utsunomiya, A. T. H., Silva, M. V. G. B., Garcia, J. F., & Ajmone‐Marsan, P. (2019) · Animal Genetics · doi:10.1111/age.12836 · Cited by 128 · see citing works
Origin of mitochondrial DNA diversity of domestic yaks
Guo, S., Savolainen, P., Su, J., Zhang, Q., Qi, D., Zhou, J., Zhong, Y., Zhao, X., & Liu, J. (2006) · BMC Evolutionary Biology · doi:10.1186/1471-2148-6-73 · Cited by 116 · see citing works
Bonfiglio, S., Achilli, A., Olivieri, A., Negrini, R., Colli, L., Liotta, L., Ajmone-Marsan, P., Torroni, A., & Ferretti, L. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015760 · Cited by 113 · see citing works
Ginja, C., Penedo, M. C. T., Melucci, L., Quiroz, J., Martínez López, O. R., Revidatti, M. A., Martínez‐Martínez, A., Delgado, J. V., & Gama, L. T. (2010) · Animal Genetics · doi:10.1111/j.1365-2052.2009.01976.x · Cited by 113 · see citing works
Species Composition and Environmental Adaptation of Indigenous Chinese Cattle
Gao, Y., Gautier, M., Ding, X., Zhang, H., Wang, Y., Wang, X., Faruque, M. O., Li, J., Ye, S., Gou, X., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-16438-7 · Cited by 112 · see citing works
Origin and Phylogeographical Structure of Chinese Cattle
Lei, C. Z., Chen, H., Zhang, H. C., Cai, X., Liu, R. Y., Luo, L. Y., Wang, C. F., Zhang, W., Ge, Q. L., Zhang, R. F., et al. (2006) · Animal Genetics · doi:10.1111/j.1365-2052.2006.01524.x · Cited by 98 · see citing works
The Origins of Chinese Domestic Cattle as Revealed by Ancient DNA Analysis
Cai, D., Sun, Y., Tang, Z., Hu, S., Li, W., Zhao, X., Xiang, H., & Zhou, H. (2014) · Journal of Archaeological Science · doi:10.1016/j.jas.2013.09.003 · Cited by 85 · see citing works
Evolution and Domestication of the Bovini Species
Zhang, K., Lenstra, J. A., Zhang, S., Liu, W., & Liu, J. (2020) · Animal Genetics · doi:10.1111/age.12974 · Cited by 82 · see citing works
Zhang, W., Gao, X., Zhang, Y., Zhao, Y., Zhang, J., Jia, Y., Zhu, B., Xu, L., Zhang, L., Gao, H., et al. (2018) · BMC Genetics · doi:10.1186/s12863-018-0705-9 · Cited by 66 · see citing works
Ancient DNA Reveals Evidence of Abundant Aurochs (Bos Primigenius) in Neolithic Northeast China
Cai, D., Zhang, N., Zhu, S., Chen, Q., Wang, L., Zhao, X., Ma, X., Royle, T. C. A., Zhou, H., & Yang, D. Y. (2018) · Journal of Archaeological Science · doi:10.1016/j.jas.2018.08.003 · Cited by 55 · see citing works
Comprehensive analysis of the mitochondrial <scp>DNA</scp> diversity in Chinese cattle
Xia, X., Qu, K., Zhang, G., Jia, Y., Ma, Z., Zhao, X., Huang, Y., Chen, H., Huang, B., & Lei, C. (2019) · Animal Genetics · doi:10.1111/age.12749 · Cited by 48 · see citing works
Zhang, Y., Hu, Y., Wang, X., Jiang, Q., Zhao, H., Wang, J., Ju, Z., Yang, L., Gao, Y., Wei, X., et al. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2019.01404 · Cited by 42 · see citing works
Paternal Origins of Chinese Cattle
Li, R., Zhang, X. M., Campana, M. G., Huang, J. P., Chang, Z. H., Qi, X. B., Shi, H., Su, B., Zhang, R. F., Lan, X. Y., et al. (2013) · Animal Genetics · doi:10.1111/age.12022 · Cited by 40 · see citing works
Discovery of Genomic Characteristics and Selection Signatures in Southern Chinese Local Cattle
Liu, Y., Xu, L., Yang, L., Zhao, G., Li, J., Liu, D., & Li, Y. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.533052 · Cited by 27 · see citing works
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Zeng, L., Qu, K., Zhang, J., Huang, B., & Lei, C. (2023) · Animal Biotechnology · doi:10.1080/10495398.2022.2047995 · Cited by 13 · see citing works
Guan, X., Xiang, W., Qu, K., Ahmed, Z., Liu, J., Cai, M., Zhang, J., Chen, N., Lei, C., & Huang, B. (2025) · BMC Genomics · doi:10.1186/s12864-024-11033-3 · Cited by 10 · see citing works
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Liu, Y., Dao, W., Gao, R., Fan, X., Yang, R., & Miao, Y. (2026) · Animals · doi:10.3390/ani16050776 · Cited by 1 · see citing works
Self-citation
- Authors
- Lai, S.-J., Liu, Y.-P., Liu, Y.-X., Li, X.-W., & Yao, Y.-G.
- Affiliations
- Kunming Institute of Zoology (CN)
- Corresponding author
- Yao, Yong-Gang
- ORCID
- Yao, Yong-Gang
- Venue
- Molecular Phylogenetics and Evolution
- Publisher
- Elsevier BV
- Published
- 2006-01
- Volume
- 38
- Issue
- 1
- Pages
- 146-154
- ISSN
- 1055-7903 (ISSN-L)
- OpenAlex
- W1998875937
- Cited by
- 143
- References
- 27
- Citations by year
- 2026: 2 · 2025: 1 · 2024: 4 · 2023: 2 · 2022: 7 · 2021: 12 · 2020: 13 · 2019: 8 · 2018: 13 · 2017: 10 · 2016: 4 · 2015: 5 · 2014: 5 · 2013: 7 · 2012: 4
- FWCI
- 3.24
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Molecular Phylogenetics and Evolution (publishedVersion)
- PubMed (publishedVersion)
- 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
- Chinese cattle, mtDNA D-loop, genetic diversity, cattle origin, cattle, Bos indicus, cattle breeds, phylogeography, divergence time estimation, cattle domestication
- MeSH terms
- Animals, Base Sequence, Cattle, China, DNA, Mitochondrial, Haplotypes, Molecular Sequence Data, Phylogeny, Genetic Variation
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