Asian-Australasian Journal of Animal Sciences

Asian Australasian Association of Animal Production Societies (아세아태평양축산학회)
권호 표지
DOI QR코드

DOI QR Code

Determination of Phylogenetic Relationships of Turkish Native Cattle Breeds with Other Cattle Breeds Using Mitochondrial DNA D-loop Sequence Polymorphism

  • Ozdemir, Memis (Department of Animal Science, Faculty of Agriculture, Ataturk University) ;
  • Dogru, Unsal (Department of Animal Science, Faculty of Agriculture, Ataturk University)
  • Received : 2007.09.26
  • Accepted : 2009.04.02
  • Published : 2009.07.01
Download PDF
⟨ Previous Next ⟩

Abstract

The aim of this study was to determine the specific polymorphic sites in cattle breeds and inter- and interbreed genetic variation among breeds and to develop a databank of Turkish native cattle mtDNA using sequence analysis. The entire D-loop region was analyzed based on DNA sequences in Turkish Grey, East Anatolian Red, South Anatolian Red, and Anatolian Black native breeds. In total, 68 nucleotide differences were observed at 26 different sites. The variable positions consisted of 22 transitions, two transversions, and two insertions, but no deletions. Haplotype number, haplotype diversity, nucleotide diversity, and mean number of pairwise difference values were found to be 17, 0.993, 0.00478, and 4.275, respectively. In addition, a phylogeny was developed by comparison among cattle populations for which the entire D-loop sequence was available. A high level of genetic variation was observed within and among the native cattle breeds.

Keywords

References

  1. Anderson, S., M. H. De Bruijn, A. R. Coulson, I. C. Eperon, 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 https://doi.org/10.1016/0022-2836(82)90137-1
  2. Bradley, D. G., D. E. MacHugh, P. Cunningham and R. T. Loftus. 1996. Mitochondrial diversity and the origins of African and European cattle. Proc. Natl. Acad. Sci. USA. 93:5131-5135 https://doi.org/10.1073/pnas.93.10.5131
  3. Bruford, M. W., D.G. Bradley and G. Luikart. 2003. DNA markers reveal the complexity of livestock domestication. Nat. Rev. Genet. 4:900-910 https://doi.org/10.1038/nrg1203
  4. Carracedo, A., W. Bar, P. Lincoln, W. Mayr, N. Morling, B. Olaisen, P. Schneider, B. Budowle, B. Brinkman, P. Gill, M. Holland, G. Tully and M. Wilson. 2000. DNA Commission of the International Society for Forensic Genetics: guidelines for mitochondrial DNA typing. Forensic Sci. Int. 110:79-85 https://doi.org/10.1016/S0379-0738(00)00161-4
  5. 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
  6. Kim, K., J. H. Lee, S. S. Lee and Y. H. Yang. 2003. Phylogenetic relationships of Northeast Asian cattle to other cattle populations determined using mitochondrial DNA D-loop sequence polymorphism. Biochem. Genet. 41:91-98 https://doi.org/10.1023/A:1022021900205
  7. Kumar, S., K. Tamura and M. Nei. 2004. MEGA 3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinformatics 5:150-163 https://doi.org/10.1093/bib/5.2.150
  8. Lai, S. J., P. Y. Liu, X. Y. Liu, W. X. Li and G. Y. Yao. 2006. Genetic diversity and origin of Chinese cattle revealed by mtDNA D-loop sequence variation. Mol. Phylogenet. Evol. 38(1):146-154 https://doi.org/10.1016/j.ympev.2005.06.013
  9. Loftus, R. T., D. E. Machugh, D. G. Bradley, P. M. Sharp and P. Cunningham. 1994a. Evidence for two independent domestications of cattle. Proc. Natl. Acad. Sci. USA. 91:2757-2761 https://doi.org/10.1073/pnas.91.7.2757
  10. Loftus, R. T., D. E. Machugh, L. O. Ngere, D. S. Balain, A. M. Badi, D. G. Bradley and P. Cunningham. 1994b. Mitochondrial genetic variation in European, African and Indian cattle populations. Anim. Genet. 25:265-271 https://doi.org/10.1111/j.1365-2052.1994.tb00203.x
  11. Loftus, R. T., O. Ertugrul, A. H. Harba, M. A. A. El-Barody, D. E. Machugh, S. D. E. Park and D. G. Bradley. 1999. A microsatellite survey of cattle from a centre of origin: the Near East. Mol. Ecol. 8:2015-2022 https://doi.org/10.1046/j.1365-294x.1999.00805.x
  12. MacHugh, D. E., M. D. Shriver, R. T. Loftus, P. Cunningham and D. G. Bradley. 1997. Microsatellite DNA variation and the evolution, domestication and phylogeography of taurin and zebu cattle (Bos taurus and Bos Indicus). Genetics 146:1076-1086
  13. Mannen, H., M. Morimoto, K. Oyama, F. Mukai and S. Tsuji. 2003. Identification of mitochondrial DNA substitions related to meat quality in Japanese Black cattle. J. Anim. Sci. 81:68-73
  14. Mannen, H., S. Tsuji, R. T. Loftus and D. G. Bradley. 1998. Mitochondrial DNA variation and evolution of Japanese Black cattle. Genetics 150:1169-1175
  15. Mirol, P. M., G. Giovambattista, J. P. Liron and F. N. Dulout. 2003. African and European mitochondrial haplotypes in South American Creole cattle. Heredity 91:248-254 https://doi.org/10.1038/sj.hdy.6800312
  16. Pfeiffer, I., I. Voelkel and B. Breing. 2005. Phylogenetics of the European Dahomey miniature cattle based on mitochondrial D-loop region DNA sequence. Anim. Genet. 36:179-181 https://doi.org/10.1111/j.1365-2052.2005.01245.x
  17. Rokas, A., E. Ladoukakis and E. Zouros. 2003. Animal mitochondrial recombination revisited. Trends Ecol. Evol. 18:411-417 https://doi.org/10.1016/S0169-5347(03)00125-3
  18. Saitou, N. and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic tree. Mol. Biol. Evol. 4:406-425
  19. Soysal, M. I., I. Togan, M. Nizamlıoglu, A. Erguven, V. Altunok, Y. T. Tuna, E. Ozkan, K. Gurcan, Z. Bulut and E. Koban. 2001. Examination of the genetic structures of Turkish native and hybrid sheep with microsatellites. VHAG-1553, TUBITAK
  20. Soysal, M. I. 2004. Autochthonous Breeds of Domestic Animals in Türkiye. Department of Animal Science, Faculty of Agriculture, Trakya University, Tekirdag, Turkey
  21. Steinborn, R, M. Muler and G. Brem. 1998. Genetic variation in functionally important domains of the bovine mtDNA control region. Biochim. Biophys. Acta. 1397:295-304 https://doi.org/10.1590/S1415-47572005000100011
  22. 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
  23. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin and D. G. Higgins. 1997. The Clustal X Windows İnterface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24:4876-4882 https://doi.org/10.1093/nar/25.24.4876
  24. Troy, C. S., D. E. MacHugh, J. F. Balley, D. A. Magee, T. R. Loftus, P. Cunningham, A. T. Chamberlain, B. C. Sykes and D. G. Bradley. 2001. Genetic evidance for Near-Eastern origins of European cattle. Nature 410:1088-1091 https://doi.org/10.1038/35074088

Cited by

  1. An independent event of Neolithic cattle domestication on the South-eastern Balkans: evidence from prehistoric aurochs and cattle populations vol.28, pp.3, 2009, https://doi.org/10.3109/19401736.2015.1127361