ISAG-recommended Microsatellite Marker Analysis Among Five Korean Native Chicken Lines

  • Choi, Nu-Ri (Department of Animal Science and Biotechnology, Chungnam National University) ;
  • Hoque, Md. Rashedul (Department of Animal Science and Biotechnology, Chungnam National University) ;
  • Seo, Dong-Won (Department of Animal Science and Biotechnology, Chungnam National University) ;
  • Sultana, Hasina (Department of Animal Science and Biotechnology, Chungnam National University) ;
  • Park, Hee-Bok (Department of Animal Science, Gyeongsang National University) ;
  • Lim, Hyun-Tae (Department of Animal Science, Gyeongsang National University) ;
  • Heo, Kang-Nyeong (Poultry Science Division, National Institute of Animal Science, RDA) ;
  • Kang, Bo-Seok (Poultry Science Division, National Institute of Animal Science, RDA) ;
  • Jo, Cheorun (Department of Animal Science and Biotechnology, Chungnam National University) ;
  • Lee, Jun-Heon (Department of Animal Science and Biotechnology, Chungnam National University)
  • Received : 2012.08.29
  • Accepted : 2012.12.13
  • Published : 2012.12.31


The objective of this study was to determine genetic variation of five Korean native chicken lines using 30 microsatellite (MS) markers, which were previously recommended by ISAG (International Society for Animal Genetics). The initial study indicated that two microsatellite markers, MCW0284 and LEI0192, were not amplified in these lines and excluded for further analysis. Twenty eight microsatellite markers were investigated in 83 birds from five Korean native chicken lines. The identified mean number of alleles was 4.57. Also, the expected, observed heterozygosity (He, Ho) and polymorphism information content (PIC) values were estimated in these markers and they ranged from 0.31~0.868, 0.145~0.699, and 0.268~0.847, respectively. The results were used for the discrimination of five chicken lines using genetic distance values and also neighbor-joining phylogenetic tree was constructed. Based on the He and PIC values, eighteen markers are enough for the discrimination of these Korean native chicken lines for the expected probability of identity values among genotypes of random individuals (PI), random half sibs ($PI_{half-sibs}$) and random sibs ($PI_{sibs}$). Taken together, these results will help the decision of conservation strategies and establishment of traceability system in this native chicken breed. Also, the use of ISAG-recommended microsatellite markers may indicate that the global comparison with other chicken breeds is possible.


Discrimination;Genetic diversity;Microsatellite;Korean native chicken


Supported by : Rural Development Administration


  1. Nei, M., Tajima, F. and Tateno, Y. 1983. Accuracy of estimated phylogenetic trees from molecular data. J. Mol. Evol. 19(2): 153-170.
  2. Tadano, R., Nishibori, M., Nagasaka, N. and Tsudzuki, M. 2007a. Assessing genetic diversity and population structure for commercial chicken lines based on forty microsatellite analyses. Poult. Sci. 86(11):2301-2308.
  3. Tadano, R., Sekino, M., Nishibori, M. and Tsudzuki, M. 2007b. Microsatellite marker analysis for the genetic relationships among japanese long-tailed chicken breeds. Poult. Sci. 86(3): 460-469.
  4. Tadano, R., Nishibori, M. and Tsudzuki, M. 2008. High accuracy of genetic discrimination among chicken lines obtained through an individual assignment test. Anim. Genet. 39:567-571.
  5. FAO. 2004. Guidelines for development of national management of farm animal genetic resources plans. Measurement of Domestic Animal Genetic Diversity (MoDAD): Recommended microsatellite markers. Rome, Italy.
  6. Guo, X. L., Li, X. L., Li, Y., Gu, Z. L., Zheng, C. S., Wei, Z. H., Wang, J. S., Zhou, R. Y., Li, L. H. and Zheng, H. Q. 2010. Genetic variation of chicken MC1R gene in different plumage colour populations. Br. Poult. Sci. 51(6):734-739.
  7. Hillel, J., Groenen, M. A. M., Tixier-Boichard, M., Korol, A. B., David, L., Kirzhner, V. M., Burke, T., Dirie, A. B., Crooijmans, R. P. M. A., Elo, K., Feldman, M., Freidlin, P. J., Maki-Tanila, A., Oortwijn, M., Thomson, P., Vignal, A., Wimmers, K. and Weigend, S. 2003. Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools. Genet. Sel. Evol. 35(5):533-557.
  8. Hoque, M. R., Jung, K. C., Park, B. K., Choi, K. D. and Lee, J. H. 2009. Genetic Variability of mtDNA D-loop Region in Korean Native Chickens. Korean J. Poult. Sci. 37(4):323-328.
  9. Hoque, M. R., Lee, S. H., Jung, K. C., Kang, B. S., Park, M. N., Lim, H. K., Choi, K. D. and Lee, J. H. 2011. Discrimination of Korean Native Chicken Populations Using SNPs from mtDNA and MHC Polymorphisms. Asian-Aust. J. Anim. Sci. 24(12):1637-1643.
  10. Kerje, S., Lind, J., Schutz, K., Jensen, P. and Andersson, L. 2003. Melanocortin 1- receptor (MC1R) mutations are associated with plumage colour in chicken. Anim. Genet. 34:241-248.
  11. Kong, H. S., Oh, J. D., Lee, J. H., Jo, K. J., Sang, B. D., Choi, C. H., Kim, S. D., Lee, S. J., Yeon, S. H., Jeon, G. J. and Lee, H. K. 2006. Genetic variation and relationships of Korean native chickens and foreign breeds using 15 microsatellite markers. Asian-Aust. J. Anim. Sci. 19(11):1546-1550.
  12. Liu, K. and Muse, S. 2005. Powermarker: An integrated analysis environment for genetic marker analysis. Bioinformatics. 21(9): 2128-2129.
  13. Marshall, T. C., Slate, J., Kruuk, L. E. B. and Pemberton, J. M. 1998. Statistical confidence for likelihood-based paternity inference in natural populations. J. Mol. Ecol. 7(5):639-655.
  14. MIFAFF. 2011. Primary statistics of Food, Agriculture, Forestry and Fisheries, Korea.
  15. Miller, S. A., Dykes, D. D. and Polesky, H. F. 1988. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 16(3):1215.
  16. Muchadeyi, F. C., Eding, H., Wollny, C. B. A., Groeneveld, E., Makuza, S. M., Shamseldin, R., Simianer, H. and Weigend, S. 2007. Absence of population substructuring in zimbabwe chicken ecotypes inferred using microsatellite analysis. Anim. Genet. 38(4):332-339.
  17. Muhammet, K. and Mehmet, A. Y. 2008. Genetic diversity among Turkish native chickens, Denizli and Gerze, estimated by microsatellite markers. Biochem. Genet. 46:480-491.
  18. Mwacharo, J. M., Nomura, K., Hanada, H., Jianlin, H., Hanotte, O. and Amano, T. 2007. Genetic relationships among kenyan and other east african indigenous chickens. Anim. Genet. 38 (5):485-490.
  19. Ayres, K. L. and Overall, A. D. J. 2004. API-CALC 1.0: a computer program for calculating the average probability of identity allowing for substructure, inbreeding and the presence of close relatives. Mol. Ecol. Notes. 4:315-318.
  20. Berthouly, C., Bed'Hom, B., Tixier-Boichard, M., Chen, C. F., Lee, Y. P., Laloe, D., Legros, H.,Verrier, E. and Rognon, X. 2008. Using molecular markers and multivariate methods to study the genetic diversity of local European and Asian chicken breeds. Anim. Genet. 39(2):121-129.
  21. Bodzsar, N., Eding, H., Revay, T., Hidas, A. and Weigend, S. 2009. Genetic diversity of Hungarian indigenous chicken breeds based on microsatellite markers. Anim. Genet. 40(4): 516-523.
  22. Botstein, D., White, R. L., Skolnik, M. and Davis, R. W. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32:314-331.
  23. Chang, C. S., Chen, C. F., Berthouly-Salazar, C., Chazara, O., Lee, Y. P., Chang, C. M., Chang, K. H., Bed'Hom, B. and Tixier-Boichard, M. 2011. A global analysis of molecular markers and phenotypic traits in local chicken breeds in Taiwan. Anim. Genet. 43:172-182.
  24. Cheng, H. H. and Crittenden, L. B. 1994. Microsatellite markers for genetic-mapping in the chicken. Poult. Sci. 73(4):539-546.
  25. Ding, F. X., Zhang, G. X., Wang, J. Y., Li, Y., Zhang, L. J., Wei, Y., Wang, H. H., Zhang, L. and Hou, Q. R. 2010. Genetic diversity of a Chinese native chicken breed, Bian chicken, based on twenty-nine microsatellite markers. Asian- Aust. J. Anim. Sci. 23(2):154-161.
  26. FAO. 1997. Secondary guidelines for development of national farm animal genetic resources management plans. Measurement of Domestic Animal Diversity (MoDAD): Recommended microsatellite markers linitiative for domestic animal diversity. FAO, Rome, Italy. (

Cited by

  1. Power of Variance Component Linkage Analysis to Identify Quantitative Trait Locus in Chickens vol.55, pp.2, 2013,
  2. Analysis of Genetic Characteristics and Probability of Individual Discrimination in Korean Indigenous Chicken Brands by Microsatellite Marker vol.55, pp.3, 2013,
  3. Studies on Genetic Diversity and Phylogenetic Relationships of Korean Native Chicken using the Microsatellite Marker vol.42, pp.1, 2015,
  4. DNA Markers for the Genetic Diversity in Korean Native Chicken Breeds: A Review vol.43, pp.2, 2016,
  5. The breeding history and commercial development of the Korean native chicken vol.73, pp.01, 2017,