Genetic Relationship among the Korean Native and Alien Horses Estimated by Microsatellite Polymorphism

  • Cho, G.J. (College of Veterinary Medicine, Kyungpook National University)
  • Received : 2005.10.11
  • Accepted : 2006.02.08
  • Published : 2006.06.01


Microsatellite polymorphism and the genetic relationship were estimated using genotype information of 305 horses from 11 microsatellite loci. The breeds include the indigenous Korean breeds, Korean native horse (102) and Jeju racing horse (56) together with Japan Hokkaido horse (5), Mongolian horse (19), Thoroughbred horse (108), Quarter horse (11) and Przewalskii horse (4). Allelic frequencies, the number of alleles per locus were estimated by direct counting from observed genotype, and genetic variability was computed using the CERVUX software and DISPAN. The number of alleles per locus varied from 6 (HMS6) to 18 (ASB17) with an average value of 10.45 in horse breeds. The expected total heterozygosity ($H_T$) and coefficient of gene differentiation ($G_{ST}$) ranged 0.764-0.921 (the average value was 0.830) and 0.102-0.266 (the average value was 0.180) in horse breeds, respectively. Four populations (Przewalskii horse, Japan Hokkaido horse, Quarter horse, Thoroughbred horse) showed lower heterozygosity than the average value (the average value was 0.710). The expected heterozygosity within breed ($H_S$) and mean no. of observed alleles ranged from $0.636{\pm}0.064$ (Japan Hokkaido horse) to $0.809{\pm}0.019$ (Mongolian horse), and from 2.73 (Przewalskii horse) to 8.27 (Korean native horse), respectively. The polymorphic information content (PIC) ranged from 0.490 (Przewalskii horse) to 0.761 (Mongolian horse) with an average value of 0.637 in horse breeds. The results showed three distinct clusters with high bootstrap support: the Korean native horse cluster (Korean native horse, Mongolian horse), the European cluster (Przewalskii horse, Thoroughbred horse), and other horse cluster (Jeju racing horse, Japan Hokkaido horse, and Quarter horse). A relatively high bootstrap value was observed for the Korean native horse cluster and European cluster (87%), and the Korean native horse and Mongolian horse (82%). Microsatellite polymorphism data were shown to be useful for estimating the genetic relationship between Korean native horse and other horse breeds, and also be applied for parentage testing in those horse breeds.


Supported by : Rural Development Administration


  1. Bowling, A. T., M. L. Eggleston-Scott, G. Byrns, R. S. Clark, S. Dileanis and E. Wictum. 1997. Validation of microsatellite markers for routine horse parentage testing. Anim. Genet. 28:247-252
  2. Canon, J., M. L. Checa, C. Carleos, J. L. Vega-Pla, M. Vallejo and S. Dunner. 2000. The genetic structure of Spanish Celtic horse breeds inferred from microsatellite data. Anim. Genet. 31:39- 48
  3. Cho, G. J. 2005. Microsatellite polymorphism and genetic relationship in dog breeds in Korea. Asian-Aust. J. Anim. Sci. 18:1071-1074
  4. Cho, B. W., K. W. Lee, H. S. Kang, S. K. Kim, T. S. Shin and Y. G. Kim. 2001. Application of polymerase chain reaction with short oligonucletide primers of arbitrary sequence for the genetic analysis of Cheju native horse. J. Agric. Tech. Dev. Inst. 5:109-114
  5. Cho, G. J., T. S. Kim, Y. H. Um, B. H. Kim and J. S. You. 1999. Genetic studies of blood markers in Cheju horses. I. Red blood cell types. Kor. J. Vet. Res. 39:1066-1072
  6. Cho, G. J., B. H. Kim, D. S. Lee and K. K. Lee. 2000. Genetic studies of blood markers in Cheju horse. II. Blood protein types. Kor. J. Vet. Res. 40:283-290
  7. Cho, G. J. and B. W. Cho. 2003. Validation of microsatellite markers for routine canine parentage testing in Korea. Kor. J. Genet. 25:103-108
  8. Cho, G. J. and B. W. Cho. 2004. Microsatellite DNA typing using 16 markers for parentage verification of the Korean native horse. Asian-Aust. J. Anim. Sci. 17:750-754
  9. Cho, G. J., Y. J. Yang, H. S. Kang and B. W. Cho. 2002. Genetic diversity and validation of microsatellite markers for Jeju native horse parentage testing. Kor. J. Genet. 24:359-365
  10. Kim, K. S and C. B. Choi. 2002. Genetic structure of Korean native pig using microsatellite markers. Kor. J. Genet. 24:1-7
  11. Klukkowska, J., T. Strabel, M. Mackowski and M. Switonski. 2003. Microsatellite polymorphism and genetic distances between the dog, red fox and arctic fox. J. Anim. Breed. Genet. 120:88-94
  12. Li, C., Z. Wang, B. Liu, S. Yang, Z. Zhu, B. Fan, M. Yu, S. Zhao and K. Li. 2004. Evaluation of the genetic relationship among ten Chinese indigenous pig breeds with twenty-six microsatellite markers. Asian-Aust. J. Anim. Sci. 17:441-444
  13. Marshall, T. C., J. Slate, L. Kruuk and J. M. Pemberton. 1998. Statistical confidence for likelihood-based paternity inference in natural populations. Mol. Ecol. 7:639-655
  14. Nei, M., F. Tajima and Y. Tateno. 1983. Accuracy of estimated phylogenetic trees from molecular data. J. Mol. Evol. 19:153- 170
  15. Ota, T. 1993. DISPAN. Pennsylvania State University. PA. USA
  16. Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425
  17. Sun, W., H. Chang, Z. J. Ren, Z. P. Yang, R. Q. Geng, S. X. Lu, L. Du and K. Tsunoda. 2004. Genetic differentiation between sheep and goats based on microsatellite DNA. Asian-Aust. J. Anim. Sci. 17:583-587
  18. Takezaki, N. and M. Nei. 1996. Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genet. 14:389-399
  19. Tozaki, T., H. Kakoi, S. Mashima, K. I. Hirota, T. Hasegawa, N. Ishida, N. Miura, N. H. Choi-Miura and M. Tomita. 2001. Population study and validation of paternity testing for Thoroughbred horses by 15 microsatellite loci. J. Vet. Med. Sci. 63:1191-1197
  20. Tozaki, T., N. Takezaki, T. Hasegawa, N. Ishida, M. Kurosawa, M. Tomita, N. Saitou and H. Mukoyama. 2003. Microsatellite variation in Japanese and Asian horses and their phylogenetic relationship using a European horse outgroup. J. Heredity 94:374-380
  21. Vila, C., J. A. Leonard, A. Gotherstrom, S. Marklund, K. Sandberg, K. Liden, R. K. Wayne and H. Ellegren. 2001. Widespread origins of demestic horse lineages. Sci. 291:474-477
  22. Yoon, D. H., H. S. Kong, J. D. Oh, J. H. Lee, B. W. Cho, J. D. Kim, K. J. Jeon, C. Y. Jo, G. J. Jeon and H. K. Lee. 2005. Establishment of an individual identification system based on microsatellite polymorphisms in Korean cattle (Hanwoo). Asian-Aust. J. Anim. Sci. 18:762-766
  23. Zhang, J. H., Y. Z. Xiong and C. Y. Deng. 2005. Correlations of genic heterozygosity and variances with heterosis in a pig populations revealed by microsatellites DNA marker. Asian-Aust. J. Anim. Sci. 18:620-625

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