Phylogenetic analysis and characterization of mitochondrial DNA for Korean native cattle

DOI: 10.4236/ojgen.2013.31003   PDF   HTML   XML   5,454 Downloads   8,602 Views   Citations


This study was aimed to preserve mitochondria from liver tissues of Korean native cattle (KNC) as genetic resources and to analyze phylogenetic relationships among cattle breeds using the whole sequences of mtDNA. Mitochondria of KNC has been isolated with the alkaline lysis procedure using1 gof liver tissues, and measurements showed numbers of cells (2.64 × 1010), concentration (114.6 ug/ml), proteins (0.278 ug/ml), and absorbance (0.029) in 260 nm. Mitochondrial DNAs (mtDNA) were extracted from the isolated mitochondria to determine whole sequences that can be used to estimate genetic distances among cattle breeds. Designing of primers based on the bovine mtDNA sequence was resulted in 16 primer sets covering the whole mtDNA regions. The analysis of 40 KNC mtDNA sequences revealed 69 polymorphic sites that were less than the average number of SNP (single nucleotide polymorphism) for other populations (82 sites) in this study. As expected, the highest observation of SNPs was found in the D-loop region, and a total of 29 SNPs were shared between cattle populations. The haplotype analysis, which used 13 SNPs located in D-loop, COX2, ND5, CYTB, and non coding regions, revealed that KNC showed clearly different haplotypes that may be used to distinguish KNC from other breeds as well as to characterize individual identifications. The phylogenetic analysis revealed that KNC showed a relatively close genetic distance with Japanese black cattle (JBC) comparing with other breeds. Estimations of the average nucleotide diversity (0.0008) and the ratio of transition/ transversion (0.1050) of KNC were placed somewhere in the middle of genetic diversity among cattle breeds. The identified genetic variants and results of phylogenetic analysis will help understanding the phylogenetic relationships of KNC and provide useful genetic information for further studies regarding SNPs in mtDNA regions.

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Chung, H. (2013) Phylogenetic analysis and characterization of mitochondrial DNA for Korean native cattle. Open Journal of Genetics, 3, 12-23. doi: 10.4236/ojgen.2013.31003.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] Pfeiffer, I., Voelkel, I. and Brenig, B. (2005) Phylogenetics of the European Dahomey miniature cattle based on mitochondrial D-loop region DNA sequence. Animal Genetics, 36, 160-190. doi:10.1111/j.1365-2052.2005.01245.x
[2] Mannen, H., Kohno, M., Nagata, Y., Tsuji, S., Bradley, D. G., Yeo, J.S., Nyamsamb, D., Zagdsuren, Y.M., Nomura, K. and Amanof, T. (2004) Independent mitochondrial origin historical genetic differentiation in North Eastern Asian cattle. Molecular Phylogenetics and Evolution, 32, 539-544.
[3] Anderson, S., Bankier, A.T., Barrell, B.G., De Bruijn, M.H., Coulson, A.R., Drouin, J., Eperon, I.C., Nierlich, D.P., Roe, B.A., Sanger, F., Schreier, P.H., Smith, A.J., Staden, R. and Young, I.G. (1981) Sequence and organization of the human mitochondrial genome. Nature, 290, 457-465. doi:10.1038/290457a0
[4] Brown, W.M. (1980) Polymorphism in mitochondrial DNA of human as revealed by restriction endonuclease analysis. Proceedings of the National Academy of Sciences, 77, 3605-3609. doi:10.1073/pnas.77.6.3605
[5] Christopher, S.T., David, E.M., Jillian, F.B., David, A.M., Ronan, T.L., Patrick, C., Andrew, T.C., Bryan, C.S. and Daniel, G.B. (2001) Genetic evidence for Near-Eastern origins of European cattle. Nature, 410, 1088-1091. doi:10.1038/35074088
[6] Hassanin, A. and Douzery, E. J. (1999) The tribal radiation of the family Bovidae Artiodactyla and the evolution of the mitochondrial cytochrome b gene. Molecular Phylogenetics and Evolution, 13, 227-243. doi:10.1006/mpev.1999.0619
[7] Cai, X., Chen, H., Lei, C., Wang, S., Xue, K. and Zhang, B. (2007) mtDNA diversity and genetic lineages of eighteen cattle breeds from Bos taurus and Bos indicus in China. Genetica, 131, 175-183. doi:10.1007/s10709-006-9129-y
[8] Graham, J.M. (2001) Unit 3.3. isolation of mitochondria from tissues and cells by differential centrifugation. Current Protocols Cell Biology, Chapter 3. doi:10.1002/0471143030.cb0303s04
[9] Keller, I., Bensasson, D. and Nichols, R.A. (2007) Transition-transversion bias is not universal, a counter example from grasshopper pseudogenes. PLoS Genetics, 3, e22. doi:10.1371/journal.pgen.0030022
[10] Laipis, P.J., Wilcox, C.J. and Hauswirth, W.W. (1982) Nucleotide sequence variation in mitochondrial deoxyribonucleic acid from bovine liver. Journal of Dairy Science, 65, 1655-1662.
[11] Watanabe, T., Masangkay, T.S., Wakana, S., Saitou, N. and Tomita, T. (1989) Mitochondrial DNA polymorphism in native Philippine cattle based on restriction endonuclease cleavage patterns. Biochemical Genetics, 27, 431-438. doi:10.1007/BF02399672
[12] Bhat, P.P., Mishar, B.P. and Bhat, P.N. (1990) Polymorphism of mitochondrial DNA in cattle and buffaloes. Biochemical Genetics, 28, 311-318.
[13] Amano, T., Miyakoshi, Y., Tokada, T., Kikkawa, T. and Suzuki, M. (1994) Genetic variants of ribosomal DNA and mitochondrial DNA between swamp and river buffaloes. Animal Genetics, 25, 29-36.
[14] Laipis, P.J., Hauswirth, W.W., O’Brien, T.W. and Michaels G.S. (1979) A physical map of bovine mitochondrial DNA from a single animal. Biochimica et Biophysica Acta, 565, 22-32. doi:10.1016/0005-2787(79)90080-7
[15] Torroni, A., Achilli, A., Macaulay, V., Richards, M. and Bandelt, H.J. (2006) Harvesting the fruit of the human mtDNA tree. Trends in Genetics, 22, 339-345. doi:10.1016/j.tig.2006.04.001
[16] Loftus, R.T., MacHugh, D.E., Ngere, L.O., Balain, D.S., Badi, A.M., Bradley, D.G. and Cunningham, E.P. (1994) Mitochondrial genetic variation in European, African and Indian cattle populations. Animal Genetics, 25, 265-271. doi:10.1111/j.1365-2052.1994.tb00203.x

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