Assessment of genetic diversity and phylogenetic relationships of Korean native chicken breeds using microsatellite markers

  • Seo, Joo Hee (Genomic Informatics Center, Hankyong National University) ;
  • Lee, Jun Heon (Department of Animal Science and Biotechnology, Chunam National University) ;
  • Kong, Hong Sik (Genomic Informatics Center, Hankyong National University)
  • Received : 2016.07.06
  • Accepted : 2017.03.10
  • Published : 2017.10.01


Objective: This study was conducted to investigate the basic information on genetic structure and characteristics of Korean Native chickens (NC) and foreign breeds through the analysis of the pure chicken populations and commercial chicken lines of the Hanhyup Company which are popular in the NC market, using the 20 microsatellite markers. Methods: In this study, the genetic diversity and phylogenetic relationships of 445 NC from five different breeds (NC, Leghorn [LH], Cornish [CS], Rhode Island Red [RIR], and Hanhyup [HH] commercial line) were investigated by performing genotyping using 20 microsatellite markers. Results: The highest genetic distance was observed between RIR and LH (18.9%), whereas the lowest genetic distance was observed between HH and NC (2.7%). In the principal coordinates analysis (PCoA) illustrated by the first component, LH was clearly separated from the other groups. The correspondence analysis showed close relationship among individuals belonging to the NC, CS, and HH lines. From the STRUCTURE program, the presence of 5 clusters was detected and it was found that the proportion of membership in the different clusters was almost comparable among the breeds with the exception of one breed (HH), although it was highest in LH (0.987) and lowest in CS (0.578). For the cluster 1 it was high in HH (0.582) and in CS (0.368), while for the cluster 4 it was relatively higher in HH (0.392) than other breeds. Conclusion: Our study showed useful genetic diversity and phylogenetic relationship data that can be utilized for NC breeding and development by the commercial chicken industry to meet consumer demands.


  1. Lee KW, Oh JD, Lee JA, et al. Estimation of genetic characteristic and cumulative power of discrimination using the microsatellite markers in Korean native chicken. Korean J Poult Sci 2010;37:81-7.
  2. Heo KN. The importance of the origin of genetic resources and the preservation of our Korean native chickens. Korean Poult J 2013;12: 130-3.
  3. Oh JD, Lee KW, Seo OS, et al. Estimation of genetic characteristics and cumulative power of discrimination in Korean native chicken and Korean native commercial chicken. J Life Sci 2010;20:1086-92.
  4. Lee KH, Kim HJ, Lee HJ, Kang MG, Jo CU. A study on components related to flavor and taste in commercial broiler and Korean native chicken meat. Korean J Food Preserv 2012;19:385-92.
  5. Lee MJ, Heo KN, Choi HC, Hong EC, Kim CD. The performance test in crossbreds of Korean native chickens for the establishment of new lines. Korean J Poult Sci 2014;41:39-44.
  6. Dawson DA, Ball AD, Spurgin LG, et al. High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species. BMC Genomics 2013;14:1-22.
  7. Marshall TC, Slate J, Kruuk LE, Pemberton JM. Statistical confidence for likelihood-based paternity inference in natural populations. Mol Ecol 1998;7:639-55.
  8. Park SDE. Trypanotolerance in West African cattle and the population genetic effects of selection [Ph.D. Thesis]. Dublin, Ireland: University of Dublin; 2001.
  9. Wright S. The interpretation of population structure by Fstatistics with special regard to systems of mating. Evolution 1965;19:395-420.
  10. Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics 2000;155:945-59.
  11. Saitou N, Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic tree. Mol Biol Evol 1987;4:406-25.
  12. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F. GENETIX 4.05, logiciel sous Windows TM pour la genetique des populations. Laboratoire Genome, Populations, Interactions, CNRS UMR 5000, Universite de Montpellier II, Montpellier (France) [cited 2015 Feb 7]. Available from
  13. Berthouly C, Bed'Hom B, Tixier-Boichard M, et al. Using molecular markers and multivariate methods to study the genetic diversity of local European and Asian chicken breeds. Anim Genet 2008;39:121-9.
  14. Botstein D, White RL, Skolnick M, Davis RW. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 1980;32:314-31.
  15. Korea Food Science Association. Food science technology dictionary. Gwangil Press; 2008.
  16. Seo DW, Hoque MR, Choi NR, et al. Discrimination of Korean native chicken lines using fifteen selected microsatellite markers. Asian- Australas J Anim Sci 2013;26:316-22.

Cited by

  1. Assessment of genetic diversity and phylogenetic relationship of Limousin herds in Hungary using microsatellite markers vol.32, pp.2, 2019,