Studies on Genetic Diversity and Phylogenetic Relationships of Korean Native Chicken using the Microsatellite Marker

Microsatellite Marker를 활용한 한국 토종닭 품종의 유전적 다양성 및 유연관계 분석

  • Received : 2014.11.19
  • Accepted : 2015.01.29
  • Published : 2015.03.31


In this study, genotyping was executed by using 27 microsatellite markers for genetic diversity of 469 Korean Native Chickens [20 population, each population is 24 samples but Hanhyup A line is 13 samples). in total 469 samples were collected from National Institute of Animal Science (Korean Native Chicken (NR, NY, NG, NL and NW), Ogye (NO), Leghorn F,K (NF and NK), Black and Brown cormish (NH and NS), Rhode Island Red C, D (NC and ND), Total is 12 populations] and Hanhyup [H line (HH), F line (HF), G line (HG), V line (HV), S line (HS), W line (HW), Y line (HY), A line (HA), total is 8 populations]. [The allele number were observed 5 (ADL0268) to 20 (MCW0127) each markers. Observed heterozygostiy ($H_{obs}$), expected heterozygosity ($H_{exp}$), polymorphism Information Content (PIC) were observed 0.359 to 0.677, 0.668 to 0.881 and 0.646 to 0.869, respectively. Using these markers, the calculated the heterozygote deficit within chicken line ($F_{is}$) value each population from mean 0.117. Phylogenetic tree showing the genetic relationship among 20 population using standard genetic distance calculated from 27 microsatellite markers. genetic distances revealed the closest (0.175) between NC and ND. on the other hand, Farthest genetic distances (0.710) revealed between NF and HV. STRUCTURE analysis and Principal Components Analysis (PCA) showed that results of similar phylogenetic tree. The expected probability of identity values on random individuals (Total population and only Hanhyup line) was estimated at $8.80{\times}10^{-83}$ and $3.87{\times}10^{-117}$, respectively. In conclusion, This study shows the useful data that be utilized as a basic data of Korean Native Chicken breeding and development for commercial chicken industry to meet the consumer's demand.


microsatellite marker;Korean Native Chicken;polymorphism;genetic diversity;phylogenetic relationships


  1. Choi NR, Hoque MR, Seo DW, Sultana H, Park HB, Lim HT, Heo KN, Kang BS, Jo C, Lee JH 2012 ISAG-recommended microsatellite marker analysis among five Korean native chicken lines. Journal of Animal Science and Technology 54(6):401-409.
  2. Heo KN 2013 The importance of the origin of genetic resources and the preservation of our Korean native chickens. Korean Poultry Journal 12:130-133.
  3. Ayres KL, Overall ADJ 2004 API-CALC 1.0: computer program for calculating the average probability of identity allowing for substructure, inbreeding and the presence of close relatives. Mol Ecol Notes 4(2):315-318.
  4. Barker JSF, Tan SG, Selvaraj OS, Mukherjee TK 1997 Genetic variation within and relationships among populations of Asian water buffalo (Bubalus bubalis). Anim Genet 28:1-13.
  5. Heo KN, Choo HJ, Seo BY, Park MN, Jung KC, Hwangbo J, Kim HK, Hong EC, Seo OS, Kang BS 2011 Investigation of TYR and MC1R polymorphisms in Korean native chickens and the commercial chickens. CNU Journal of Agricultural Science 38(3):465-471.
  6. Kong HS, Oh JD, Lee JH, Jo KJ, Sang BD, Choi CH, Kim SD, Lee SJ, Yeon SH, Jeon GJ, Lee HK 2006 Genetic variation and relationships of Korean native chickens and foreign breeds using 15 microsatellite markers. Asian-Aust J Anim Sci 11:1546-1550.
  7. Lee HK, Oh JD, Park CH, Lee KW, Lee JH, Jeon GJ, Kong HS 2010 Comparison for genetic diversity between Korean native commercial chicken brand groups using microsatellite markers. Korean J Poult Sci 37(4):355-360.
  8. Lee KH, Kim HJ, Lee HJ, Kang MG, Jo CU 2012 A study on components related to flavor and taste in commercial broiler and Korean native chicken meat. Korean J Food Preserv 19(3):385-392.
  9. Lee KW, Oh JD, Lee JA, Cho KH, Nam IS, Lee JH, Seo OS, Jeon GJ, Lee HK, Kong HS 2010 Estimation of genetic characteristic and cumulative power of discrimination using the microsatellite markers in Korean native chicken. Korean J Poult Sci 37(1):81-87.
  10. Lee MJ, Heo KN, Choi HC, Hong EC, Kim CD 2014 The performance test in crossbreds of Korean native chickens for the establishment of new lines. Korean J Poult Sci 41 (1):39-44.
  11. Oh JD, Lee KW, Seo OS, Cho BW, Jeon GJ, Lee HG, Kong HS 2010 Estimation of genetic characteristics and cumulative power of discrimination in Korean native chicken and Korean native commercial chicken. Journal of Life Science 20(7):1086-1092.
  12. Ota T 1993. DISPAN. Pennsylvania State University, PA. USA.
  13. Park MN, Kim TH, Lee HJ, Choi JA, Heo KN, Kim CD, Choo HJ, Han JY, Lee TH, Lee JH, Lee KT 2013 Genetic variations of chicken MC1R gene and associations with feather color of Korean native chicken (KNC) 'Woorimatdag'. Korean J Poult Sci 40(2):139-145.
  14. Peakall R, Smouse PE 2006 GenAlEx 6 : Genetic analysis in excel population genetic software for teaching and research. Mol Ecol Notes 6(1):288-295.
  15. Peelman LJ, Mortiaux F, Van Zeveren A, Dansercoer A, Mommens G, Coopman F, Bouquet Y, Burny A, Renaville R, Portetelle D 1998 Evaluation of the genetic variability of 23 bovine microsatellite markers in four Belgian cattle breeds. Anim Genet 29:161-167.
  16. Saitou N, Nei M 1987 The neighbor-joining method : A new method for reconstructing phylogenetic tree. Mol Biol Evol 4:406-425.
  17. Seo DW, Hoque MR, Choi NR, Sultana H, Park HB, Heo KN, Kang BS, Lim HT, Lee, Jo C, Lee JH 2013 Discrimination of Korean native chicken lines using fifteen selected microsatellite markers. Asian-Aust J Anim Sci 26(3):316-322.
  18. Suh SW 2014 Molecular genetic evaluation of Korean domestic animal genetic resources using microsatellite markers. Doctor's degree, Gyeongsang National University.
  19. Suh SW, Cho CY, Kim JH, Choi SB, Kim YS, Kim H, Seong HH, Lim HT, Cho JH, KoYG 2013 Analysis of genetic characteristics and probability of individual discrimination in Korean indigenous chicken brands by microsatellite marker. Journal of Animal Science and Technology 55(3): 185-194.

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