Discrimination of Korean Native Chicken Populations Using SNPs from mtDNA and MHC Polymorphisms

  • Hoque, M.R. ;
  • Lee, S.H. ;
  • Jung, K.C. ;
  • Kang, B.S. ;
  • Park, M.N. ;
  • Lim, H.K. ;
  • Choi, K.D. ;
  • Lee, J.H.
  • Received : 2011.05.17
  • Accepted : 2011.07.20
  • Published : 2011.12.01


Korean native chickens are a very valuable chicken population in Korea and their prices are higher than that of commercial broilers. In order to discriminate two commercial Korean native chicken populations (CCP1 and CCP2), single nucleotide polymorphisms (SNPs) from mitochondrial (mt) DNA D-loop sequences and LEI0258 marker polymorphisms in the major histocompatibility complex (MHC) region were investigated. A total of 718 birds from nine populations were sampled and 432 mtDNA sequences were obtained. Of these, two commercial Korean native chicken populations (363 birds) were used for investigation of their genetic relationship and breed differentiation. The sequence data classified the chickens into 20 clades, with the largest number of birds represented in clade 1. Analysis of the clade distribution indicated the genetic diversity and relation among the populations. Based on the mtDNA sequence analysis, three selected SNPs from mtDNA polymorphisms were used for the breed identification. The combination of identification probability (Pi) between CCP1 and CCP2 using SNPs from mtDNA and LEI0258 marker polymorphisms was 86.9% and 86.1%, respectively, indicating the utility of these markers for breed identification. The results will be applicable in designing breeding and conservation strategies for the Korean native chicken populations and also used for the development of breed identification markers.


mtDNA;LEI0258 Marker;Discrimination;Korean Native Chicken


  1. Alves, E., C. Castellanos, C. Ovilo, L. Silio and C. Rodriguez. 2002. Differentiation of the raw material of the Iberian pig meat industry based on the use of amplified fragment length polymorphism. Meat Sci. 61:157-162.
  2. 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.
  3. 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.
  4. Bernatchez, L. and C. Landry. 2003. MHC studies in nonmodel vertebrates: what have we learned about natural selectionin 15 years? J. Evol. Biol. 16:363-377.
  5. 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.
  6. Fu, Y., D. Niu and H. Ruan. 2001. Studies of genetic diversity of native chicken breeds in Zhejiang province of China. Acta Genetica Sinica. 28:606-613.
  7. Fulton, J. E., H. R. Juul-Madsen, C. M. Ashwell, A. M. McCarron, J. A. Arthur, N. P. O'Sullivan and Jr. R. L. Taylor. 2006. Molecular genotype identification of the Gallus gallus major histocompatibility complex. Immunogenetics 58:407-421.
  8. Komiyama, T., K. Ikeo and T. Gojobori. 2003. Where is the origin of the Japanese gamecock? Gene 317:195-202.
  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.
  10. Kumar, S., M. Nei, J. Dudley and K. Tamura. 2008. MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief. Bioinform. 9:299-306.
  11. 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.
  12. 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 (Bubalusbubalis). Asian-Aust. J. Anim. Sci. 20:471-476.
  13. 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.
  14. Liu, Z. G., C. Z. Lei, J. Luo, C. Ding, G. H. Chen, H. Chang, K. H. Wang, X. X. Liu, X. Y. Zhang, X. J. Xiao and S. L. Wu. 2004. Genetic variability of mtDNA sequences in Chinese native chicken breeds. Asian-Aust. J. Anim. Sci. 17:903-909.
  15. 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.
  16. McConnell, S. K., D. A. Dawson, A. Wardle and T. Burke. 1999. The isolation and mapping of 19 tetranucleotide microsatellite markers in the chicken. Anim. Genet. 30:183-189.
  17. Mindell, D. P., M. D. Sorenson, C. J. Huddleston, H. C. Miranda, A. Knight, S. J. Sawchuk and T. Yuri. 1997. Phylogenetic relationships among and within select avian orders based on mitochondrial DNA. In: Avian molecular evolution and systematic (Ed. D. P. Mindell). Academic press, San Diego. 214-247.
  18. 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.
  19. 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.
  20. Piertney, S. B. and M. K. Oliver. 2006. The evolutionary ecology of the major histocompatibility complex. Heredity 96:7-21.
  21. Sasazaki, S., K. Itoh, S. Arimitsu, T. Imada, A. Takasuga, H. Nagaishi, S. Takano, H. Mannen and S. Tsuji. 2004. Development of breed identification markers derived from AFLP in beef cattle. Meat Sci. 67:275-280.
  22. 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.
  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.
  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.
  25. Wayne, D., H. Willem, S. Ferguson and B. Paulette. 2002. Characterization and evolution of the mitochondrial DNA control region in hornbills (Bucerotiformes). J. Mol. Evol. 54:794-806.

Cited by

  1. Mitochondrial D-Loop Variations for Discrimination of Commercial Korean Native Chicken Populations vol.39, pp.4, 2012,
  2. ISAG-recommended Microsatellite Marker Analysis Among Five Korean Native Chicken Lines vol.54, pp.6, 2012,
  3. Association of SNPs in ODC and PRDM16 with Body Weight Traits in Korean Native Chicken vol.40, pp.2, 2013,
  4. FABP3 and FABP4 Genes Are the Potential Candidates for Body Weights in Korean Native Chicken vol.40, pp.2, 2013,
  5. Analysis of Genetic Characteristics and Probability of Individual Discrimination in Korean Indigenous Chicken Brands by Microsatellite Marker vol.55, pp.3, 2013,
  6. Diversity and evolution of the highly polymorphic tandem repeat LEI0258 in the chicken MHC-B region vol.65, pp.6, 2013,
  7. Uncovering Genomic Features and Maternal Origin of Korean Native Chicken by Whole Genome Sequencing vol.9, pp.12, 2014,
  8. Genetic Diversity and Phylogenetic Analysis of South-East Asian Duck Populations Based on the mtDNA D-loop Sequences vol.29, pp.12, 2016,
  9. DNA Markers for the Genetic Diversity in Korean Native Chicken Breeds: A Review vol.43, pp.2, 2016,
  10. Genetic diversity of mtDNA D-loop sequences in four native Chinese chicken breeds vol.58, pp.5, 2017,
  11. The breeding history and commercial development of the Korean native chicken vol.73, pp.01, 2017,
  12. Estimation of linkage disequilibrium and analysis of genetic diversity in Korean chicken lines vol.13, pp.2, 2018,