Asian-Australasian Journal of Animal Sciences

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

DOI QR Code

Phylogenetic Analysis of a Privately-owned Korean Native Chicken Population Using mtDNA D-loop Variations

  • Hoque, M.R. (Department of Animal Science and Biotechnology, Chungnam National University) ;
  • Choi, N.R. (Department of Animal Science and Biotechnology, Chungnam National University) ;
  • Sultana, H. (Department of Animal Science and Biotechnology, Chungnam National University) ;
  • Kang, B.S. (Poultry Science Division, National Institute of Animal Science, RDA) ;
  • Heo, K.N. (Poultry Science Division, National Institute of Animal Science, RDA) ;
  • Hong, S.K. (Hyunin Farm) ;
  • Jo, C. (Department of Animal Science and Biotechnology, Chungnam National University) ;
  • Lee, Jun-Heon (Department of Animal Science and Biotechnology, Chungnam National University)
  • Received : 2012.08.27
  • Accepted : 2012.10.06
  • Published : 2013.02.01
Download PDF
⟨ Previous Next ⟩

Abstract

The use of Korean native chicken is increasing, and the discovery of new genetic resources is very important from both economic and genetic conservation points of view. In this study, mtDNA D-loop sequences from 272 privately-owned Korean native chickens from a Hyunin farm were investigated. Seventeen nucleotide substitutions were identified from the sequence analysis and they were classified as 6 haplotypes. Previously investigated haplotypes in five Korean native chicken populations have been compared with the Hyunin chicken population. The results indicated that two haplotypes, H10 and H15, in the Hyunin chicken population were not previously identified in other Korean native chicken populations, representing 33.09% (90/272) and 1.1% (3/272) of the Hyunin population, respectively. On the other hand, four other haplotypes were identical to those of a previous study of Korean native chicken populations. This result is indicative of conservation strategies of Hyunin chicken populations for expanding the genetic diversity in the Korean native chicken population.

Keywords

References

  1. Aquadro, C. F. and B. D. Greenberg. 1983. Human mitochondrial DNA variation and evolution: Analysis of nucleotide sequences from seven individuals. Genetics 103:287-312.
  2. Baker, A. J. and H. D. Marshall. 1997. Mitochondrial control region sequences as tools for understanding evolution. In: Avian molecular evolution and systematic (Ed. D. P. Mindell). Academic press, San Diego. 51-82.
  3. Bandelt, H. J., P. Forster and A. Rohl. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16:37-48. https://doi.org/10.1093/oxfordjournals.molbev.a026036
  4. Cann, R. L., W. M. Brown and A. C. Wilson. 1984. Polymorphic sites and the mechanism of evolution in human mitochondrial DNA. Genetics 106:479-499.
  5. Harumi, T., A. Sano, T. Minematsu and M. Naito. 2011. Allele-specific PCR typing and sequencing of the mitochondrial D-loop region in four layer breeds. Anim. Sci. J. 82:223-226. https://doi.org/10.1111/j.1740-0929.2010.00831.x
  6. Hoque, M. R., K. C. Jung, B. K. Park, K. D. Choi and J. H. Lee. 2009. Genetic variability of mtDNA D-loop region in Korean native chickens. Korean J. Poult. Sci. 37:323-328. https://doi.org/10.5536/KJPS.2009.36.4.323
  7. Hoque, M. R., S. H. Lee, K. C. Jung, B. S. Kang, M. N. Park, H. K. Lim, K. D. Choi and J. H. Lee. 2011. Discrimination of Korean native chicken populations using SNPs from mtDNA and MHC polymorphisms. Asian-Aust. J. Anim. Sci. 24:1637-1643. https://doi.org/10.5713/ajas.2011.11144
  8. Komiyama, T., K. Ikeo and T. Gojobori. 2003. Where is the origin of the Japanese gamecock? Gene 317:195-202. https://doi.org/10.1016/S0378-1119(03)00703-0
  9. Komiyama, T., K. Ikeo and T. Gojobori. 2004. The evolutionary origin of long-crowing chicken: its evolutionary relationship with fighting cocks disclosed by the mtDNA sequence analysis. Gene 333:91-99. https://doi.org/10.1016/j.gene.2004.02.035
  10. Lansman, R. A., J. C. Avise and M. D. Huettel. 1983. Critical experimental test of the possibility of 'paternal leakage' of mitochondrial DNA. Proc. Natl. Acad. Sci. USA. 80:1969-1971. https://doi.org/10.1073/pnas.80.7.1969
  11. Lei, C. Z., W. Zhang, H. Chen, F. Lu, Q. L. Ge, R. Y. Liu, R. H. Dang, Y. Y. Yao, L. B. Yao, Z. F. Lu and Z. L. Zhao. 2007. Two maternal lineages revealed by mitochondrial DNA dloop sequences in Chinese native water buffaloes (Bubalus bubalis). Asian-Aust. J. Anim. Sci. 20:471-476. https://doi.org/10.5713/ajas.2007.471
  12. Li, J. L., Y. Shi, C. Fan and D. Manglai. 2008. mtDNA diversity and origin of Chinese Mongolian horses. Asian-Aust. J. Anim. Sci. 21:1696-1702. https://doi.org/10.5713/ajas.2008.80193
  13. Liu, Y. P., G. S. Wu, Y. G. Yao, Y. W. Miao, G. Luikart, M. Baig, A. B. Pereira, Z. L. Ding, M. G. Palanichamy and Y. P. Zhang. 2006. Multiple maternal origins of chickens: Out of the Asian jungles. Mol. Phylogenet. Evol. 38:12-19. https://doi.org/10.1016/j.ympev.2005.09.014
  14. MIFAFF. 2009. Primary statistics of food. Agriculture, Forestry and Fisheries, Korea.
  15. Miller, S. A., D. D. Dykes and H. F. Polesky. 1988. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 16:1215. https://doi.org/10.1093/nar/16.3.1215
  16. Moore, W. S. and V. R. Defilippis. 1997. The window of taxonomic resolution for phylogenies based on mitochondrial cytochrome b. In: Avian molecular evolution and systematic (Ed. D. P. Mindell). Academic press, San Diego. 84-119.
  17. Nei, M. 1982. Evolution of human races at the gene level. Prog. Clin. Biol. Res. 167-181.
  18. Odahara, S., H. J. Chung, S. H. Choi, S. L. Yu, S. Sasazaki, H. Mannan, C. S. Park and J. H. Lee. 2006. Mitochondrial DNA diversity of Korean native goats. Asian-Aust. J. Anim. Sci. 19: 482-485. https://doi.org/10.5713/ajas.2006.482
  19. Oka, T., Y. Ino, K. Nomura, S. Kawashima, T. Kuwayama, H. Hanada, T. Amano, M. Takada, N. Takahata, Y. Hayashi and F. Akishinonomiya. 2007. Analysis of mtDNA sequences shows Japanese native chickens have multiple origins. Anim. Genet. 38:287-293. https://doi.org/10.1111/j.1365-2052.2007.01604.x
  20. Rozas, J., J. C. Sanchez-DelBarrio and X. Messeguer. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496-2497. https://doi.org/10.1093/bioinformatics/btg359
  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-Aust. J. Anim. Sci. 19: 1394-1398. https://doi.org/10.5713/ajas.2006.1394
  22. Tamura, K., D. Peterson, N. Peterson, G. Stecher, M. Nei and S. Kumar. 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28:2731-2739. https://doi.org/10.1093/molbev/msr121
  23. Thompson, J. D., D. G. Higgins, T. J. Gibson and W. Clustal. 1994. Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680. https://doi.org/10.1093/nar/22.22.4673
  24. Wang, X., H. Chen and C. Z. Lei. 2007. Genetic diversity and phylogenetic analysis of the mtDNA D-loop region in Tibetan sheep. Asian-Aust. J. Anim. Sci. 20:313-315. https://doi.org/10.5713/ajas.2007.313

Cited by

  1. Genetic Diversity and Phylogenetic Analysis of South-East Asian Duck Populations Based on the mtDNA D-loop Sequences vol.29, pp.12, 2016, https://doi.org/10.5713/ajas.15.1017
  2. DNA Markers for the Genetic Diversity in Korean Native Chicken Breeds: A Review vol.43, pp.2, 2016, https://doi.org/10.5536/KJPS.2016.43.2.63
  3. Genetic diversity of Guangxi chicken breeds assessed with microsatellites and the mitochondrial DNA D-loop region vol.43, pp.5, 2016, https://doi.org/10.1007/s11033-016-3976-0
  4. The genetic diversity of chicken breeds from Jiangxi, assessed with BCDO2 and the complete mitochondrial DNA D-loop region vol.12, pp.3, 2017, https://doi.org/10.1371/journal.pone.0173192
  5. Genetic diversity of mtDNA D-loop sequences in four native Chinese chicken breeds vol.58, pp.5, 2017, https://doi.org/10.1080/00071668.2017.1332403
  6. The analysis of the mtDNA D-loop polymorphism for assessing the population diversity of the Pavlov chicken breed vol.7, pp.6, 2017, https://doi.org/10.1134/S2079059717060041
  7. The breeding history and commercial development of the Korean native chicken vol.73, pp.01, 2017, https://doi.org/10.1017/S004393391600088X
  8. Genetic diversity, phylogeographic structure and effect of selection at the mitochondrial hypervariable region of Nigerian chicken populations vol.96, pp.6, 2017, https://doi.org/10.1007/s12041-017-0860-1
  9. Estimation of linkage disequilibrium and analysis of genetic diversity in Korean chicken lines vol.13, pp.2, 2018, https://doi.org/10.1371/journal.pone.0192063
  10. DNA barcoding for identification of fish species from freshwater in Enugu and Anambra States of Nigeria vol.12, pp.4, 2013, https://doi.org/10.1007/s12686-020-01155-7