Haplogroup Classification of Korean Cattle Breeds Based on Sequence Variations of mtDNA Control Region

  • Received : 2015.08.24
  • Accepted : 2016.01.05
  • Published : 2016.05.01


Many studies have reported the frequency and distribution of haplogroups among various cattle breeds for verification of their origins and genetic diversity. In this study, 318 complete sequences of the mtDNA control region from four Korean cattle breeds were used for haplogroup classification. 71 polymorphic sites and 66 haplotypes were found in these sequences. Consistent with the genetic patterns in previous reports, four haplogroups (T1, T2, T3, and T4) were identified in Korean cattle breeds. In addition, T1a, T3a, and T3b sub-haplogroups were classified. In the phylogenetic tree, each haplogroup formed an independent cluster. The frequencies of T3, T4, T1 (containing T1a), and T2 were 66%, 16%, 10%, and 8%, respectively. Especially, the T1 haplogroup contained only one haplotype and a sample. All four haplogroups were found in Chikso, Jeju black and Hanwoo. However, only the T3 and T4 haplogroups appeared in Heugu, and most Chikso populations showed a partial of four haplogroups. These results will be useful for stable conservation and efficient management of Korean cattle breeds.


Grant : Cooperative Research Program for Agriculture Science & Technology Development

Supported by : Rural Development Administration


  1. Achilli, A., A. Olivieri, M. Pellecchia, C. Uboldi, L. Colli, N. Al-Zahery, M. Accetturo, M. Pala, B. H. Kashani, U. A. Perego, V. Battaglia, S. Fornarino, J. Kalamati, M. Houshmand, R. Negrini, O. Semino, M. Richards, V. Macaulay, L. Ferretti, H. J. Bandelt, P. Ajmone-Marsan, and A. Torroni. 2008. Mitochondrial genomes of extinct aurochs survive in domestic cattle. Curr. Biol. 18:R157-R158.
  2. Anderson, S., M. H. L. Debrujin, A. R. Coulson, I. C. Eperson, F. Sanger, and I. G. Young. 1982. Complete sequence of bovine mitochondrial DNA conserved features of the mammalian mitochondrial genome. J. Mol. Biol. 156:683-717.
  3. Dadi, H., S. H. Lee, K. S. Jung, J. W. Choi, M. S. Ko, Y. J. Han, J. J. Kim, and K. S. Kim. 2012. Effect of population reduction on mtDNA diversity and demographic history of Korean cattle populations. Asian Australas. J. Anim. Sci. 25:1223-1228.
  4. Gou, X., Y. Wang, S. Yang, W. Deng, and H. Mao. 2010. Genetic diversity and origin of Gayal and cattle in Yunnan revealed by mtDNA control region and SRY gene sequence variation. J. Anim. Breed. Genet. 127:154-160.
  5. Gravlund, P., K. Aaris-Sorensen, M. Hofreiter, M. Meyer, J. P. Bollback, and N. Noe-Nygaard. 2012. Ancient DNA extracted from Danish aurochs (Bos primigenius): Genetic diversity and preservation. Ann. Anat. 194:103-111.
  6. Hall, T. A. 1999. BioEdit: A user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp. Ser. 41:95-98.
  7. Horsburgh, K. A., S. Prost, A. Gosling, J. A. Stanton, C. Rand, and E. A. Matisoo-Smith. 2013. The genetic diversity of the Nguni breed of African cattle (Bos spp.): Complete mitochondrial genomes of haplogroup T1. PLoS One 8:e71956.
  8. Hristov, P., D. Teofannova, B. Neov, and G. Radoslavov. 2015. Haplotype diversity in autochthonous Balkan cattle breeds. Anim. Genet. 46:92-94.
  9. Jia, S., Y. Zhou, C. Lei, R. Yao, Z. Zhang, X. Fang, and H. Chen. 2010. A new insight into cattle's maternal origin in six Asian countries. J. Genet. Genomics 37:173-180.
  10. Kim, J. B. and C. Lee. 2000. Historical look at the genetic improvement in Korean cattle - Review -. Asian Australas. J. Anim. Sci. 13:1467-1481.
  11. Kim, J. H., M. J. Byun, M. J. Kim, S. W. Suh, Y. G. Ko, C. W. Lee, K. S. Jung, E. S. Kim, D. J. Yu, W. Y. Kim, and S. B. Choi. 2013a. mtDNA diversity and phylogenetic state of Korean cattle breed, Chikso. Asian Australas. J. Anim. Sci. 26:163-170.
  12. Kim, J. H., M. J., Byun, M. J. Kim, S. W. Suh, Y. S. Kim, Y. G. Ko, S. W. Kim, K. S. Jung, D. H. Kim, and S. B. Choi. 2013b. Phylogenetic analysis of Korean black cattle Based on the Mitochondrial cytochrome b gene (in Korean). J. Life Sci. 23:24-30.
  13. Lai, S. J., Y. P. Liu, Y. X. Liu, X. W. Li, and Y. G. Yao. 2006. Genetic diversity and origin of Chinese cattle revealed by mtDNA D-loop sequence variation. Mol. Phylogenet. Evol. 38:146-154.
  14. Lei, C. Z., H. Chen, H. C. Zhang, X. Cai, R. Y. Liu, L. Y. Luo, C. F. Wang, W. Zhang, Q. L. Ge, R. F. Zhang, X. Y. Lan, and W. B. Sun. 2006. Origin and phylogeographical structure of Chinese cattle. Anim. Genet. 37:579-582.
  15. Librado, P. and J. Rozas. 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451-1452.
  16. Ludwig, A., L. Alderson, E. Fandrey, D. Liekfeldt, T. K. Soederlund, and K. Froelich. 2013. Tracing the genetic roots of the indigenous White Park cattle. Anim. Genet. 44:383-386.
  17. Mannen, H., M. Kohno, Y. Nagata, S. Tsuji, D. G. Gradley, J. S. Yeo, D. Nyamsamba, Y. Zagdsuren, M. Yokohama, K. Nomura, and T. Amano. 2004. Independent mitochondrial origin and historical genetic differentiation in North Eastern Asian cattle. Mol. Phylogenet. Evol. 32:539-544.
  18. Na, G. J. 2008. Characteristics of Korean native cattle (in Korean). Korea Animal Improvement Association Bulletin 1:42-52.
  19. San, A., I. Martin-Burriel, C. Cons, M. Reta, A. Poblador, C. Rodellar, and P. Zaraqoza. 2014. Genetic diversity, structure and individual assignment of Casta Navarra cattle: a welldifferentiated fighting bull population. J. Anim. Breed. Genet. 131:11-18.
  20. Saitou, N. and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
  21. Sasazaki, S., S. Odahara, C. Hiura, F. Mukai, and H. Mannen. 2006. Mitochondrial DNA variation and genetic relationships in Japanese and Korean cattle. Asian Australas. J. Anim. Sci. 19:1394-1398.
  22. Suh, S. W., Y. S. Kim, C. Y. Cho, M. J. Byun, S. B. Choi, Y. G. Ko, C. W. Lee, K. S. Jung, K. H. Bae, and J. H. Kim. 2014. Assessment of genetic diversity, relationships and structure among Korean native cattle breeds using microsatellite markers. Asian Australas. J. Anim. Sci. 27:1548-1553.
  23. Tamura, K. and M. Nei. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10:512-526.
  24. Tamura, K., D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar. 2011. MEGA5: Molecular evolutionary genetic analysis using maximum likelihood evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28:2731-2739.
  25. Thompson, J. D., D. G. Higgins, and T. I. Gibson. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:4673-4680.
  26. Troy, C. S., D. E. MacHugh, J. F. Bailey, D. A. Maqee, R. T. Loffus, P. Cunningham, A. T. Chamberlain, B. C. Sykes, and D. G. Bradley. 2001. Genetic evidence for Near-Eastern origins of European cattle. Nature 410:1088-1091.
  27. Tu, P. A., D. Y. Lin, G. F. Li, J. C. Huang, D. C. Wang, and P. H. Wang. 2014. Characterization of the genetic diversity and population structure for the yellow cattle in Taiwan based on microsatellite markers. Anim. Biotechnol. 25:234-249.
  28. Xin, Y. P., L. S. Zan, Y. F. Liu, W. Q. Tian, H. B. Wang, G. Cheng, A. N. Li, and W. C. Yang. 2014. Genetic diversity of Y-short tandem repeats in Chinese native cattle breeds. Genet. Mol. Res. 13:9578-9587.

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