Genetic Diversity and Population Structure in Native Chicken Populations from Myanmar, Thailand and Laos by Using 102 Indels Markers

  • Maw, A.A. (University of Veterinary Science) ;
  • Kawabe, Kotaro (Natural Science Centre for Research and Education, Kagoshima University) ;
  • Shimogiri, T. (Faculty of Agriculture, Kagoshima University) ;
  • Rerkamnuaychoke, W. (Faculty of Veterinary Medicine, Kasetsart University) ;
  • Kawamoto, Y. (Faculty of Agriculture, University of Ryukyus) ;
  • Masuda, S. (Liberal Arts Education Centre, Aso Campus, Tokai University) ;
  • Okamoto, S. (Faculty of Agriculture, Kagoshima University)
  • Received : 2014.03.24
  • Accepted : 2014.07.08
  • Published : 2015.01.01


The genetic diversity of native chicken populations from Myanmar, Thailand, and Laos was examined by using 102 insertion and/or deletion (indels) markers. Most of the indels loci were polymorphic (71% to 96%), and the genetic variability was similar in all populations. The average observed heterozygosities ($H_O$) and expected heterozygosities ($H_E$) ranged from 0.205 to 0.263 and 0.239 to 0.381, respectively. The coefficients of genetic differentiation (Gst) for all cumulated populations was 0.125, and the Thai native chickens showed higher Gst (0.088) than Myanmar (0.041) and Laotian (0.024) populations. The pairwise Fst distances ranged from 0.144 to 0.308 among populations. A neighbor-joining (NJ) tree, using Nei's genetic distance, revealed that Thai and Laotian native chicken populations were genetically close, while Myanmar native chickens were distant from the others. The native chickens from these three countries were thought to be descended from three different origins (K = 3) from STRUCTURE analysis. Genetic admixture was observed in Thai and Laotian native chickens, while admixture was absent in Myanmar native chickens.


  1. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: A laboratory manual, 2nd edition, Cold Spring Laboratory Press, Cold Spring Harbor, New York, USA.
  2. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4:Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
  3. Vali, U., M. Brandström, M. Johansson, and H. Ellegren. 2008. Insertion-deletion polymorphisms (indels) as genetic markers in natural populations. BMC Genet. 9:8.
  4. Weir, B. S. 1996. Genetic Data Analysis II. Sinauer. Sunder land, MA, USA.
  5. Weir, B. S. and C. C. Cockerham. 1984. Estimating F-statistic for the analysis of population structure. Evolution 38:1358-1370.
  6. Felsenstein, J. 2009. Phylogeny Inference Package Version 3.69.
  7. Cocks, S. W. 1919. A short history of Burma. 2nd edition. Macmillan and Co. Limited, London, UK.
  8. Dorji, N., M. Daungjinda, and Y. Phasuk. 2011. Genetic characterization of Thai indigenous chickens compared with commercial lines. Trop. Anim. Health Prod. 43:779-785.
  9. Evanno, G., S. Regnaut, and J. Goudet. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol. Ecol. 14:2611-2620.
  10. Hmannan Yazawin 2. 1829. Tabinshwehti's Ayutthaya campaign (in Burmese). 2003 edition. Ministry of Information, Yangon, Myanmar.
  11. Kawabe, K., R. Worawut, S. Taura, T. Shimogiri, T. Nishida, and S. Okamoto. 2014. Genetic diversity of mtDNA D-loop polymorphisms in Laotian native fowl populations. Asian Australas. J. Anim. Sci. 27:19-23.
  12. Kinoshita, K., S. Okamoto, T. Shimogiri, K. Kawabe, T. Nishida, R. Kakizawa, Y. Yamamoto, and Y. Maeda. 2002. Gene constitution of egg white proteins of native chicken in Asian countries. Asian Australas. J. Anim. Sci. 15:157-165.
  13. Mwacharo, J. M., H. Jianlin, and T. Amano. 2006. Native African chicken: valuable genetic resources for future breeding improvement. J. Anim. Genet. Jpn. 34:63-69.
  14. Lewontin, R. C. and J. L. Hubby. 1966. A molecular approach to the study of genetic heterozygosity in natural populations of Drosophila pseduobscura. Genetics 54:595-609.
  15. Liu, Y. P., G. S. Wu, Y. G. Yao, Y. W. Miao, G. Luikart, M. Baig, A. Beja-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. Maw, A. A., T. Shimogiri, Riztyan, K. Kawabe, Y. Kawamoto, and S. Okamoto. 2012. Genetic diversity of Myanmar and Indonesia native chickens together with two jungle fowl species by using 102 Indels polymorphisms. Asian Australas. J. Anim. Sci. 25:927-934.
  17. Nishibori, M., T. Shimogiri, T. Hayashi, and H. Yasue. 2005. Molecular evidence of hybridization of species in the genus Gallus except of Gallus varius. Anim. Genet. 36:367-375.
  18. Natalle, S. C. F, R. L. Resque, E. M. Ribeiro-Rodrigues, J. F. Guerreiro, N. P. C. Santos, A. R. Santos, and S. Santos. 2010. X-linked insertion/deletion polymorphisms: Forensic applications of a 33-markers panel. Int. J. Legal Med. 124:589-593.
  19. Nei, M. 1973. Analysis of gene diversity in subdivided populations. Proc. Natl. Acad. Sci. USA. 70:3321-3323.
  20. Nei, M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583-590.
  21. Nishida, T., W. Rerkamnuaychoke, D. G. Tung, S. Saignaleus, S. Okamoto, Y. Kawamoto, J. Kimura, K. Kawabe, N. Tsunekawa, H. Otaka, and Y. Hatashi. 2000. Morphological identification and ecology of Red Jungle Fowl in Thailand, Laos and Vietnam. Anim. Sci. J. 71:470-480.
  22. Pritchard, J. K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
  23. Okamoto, S., N. Tsunekawa, Y. Kawamoto, R. Worawut, K. Kawabe, Y. Maeda, and T. Nishida. 1999. Blood protein polymorphisms of native fowls in Laos. Asian Australas. J. Anim. Sci. 12:1011-1014.
  24. Okamoto, S., K. Kinoshita, Y. Yamamoto, K. Tsunoda, H. Okabayashi, H. Mannen, K. Tanaka, T. Yamagata, K. Nozawa, M. Nishibori, Y. Kurosawa, Maung Maung Nyunt, Than Daing, Than Hla, Nay Win, and Y. Maeda. 2004. Blood protein variations of native fowls in Myanmar. Researches Report of the Society for Native Livestock. 21:237-242.
  25. Okumura, F., T. Shimogiri, K. Kawabe, S. Okamoto, M. Nishibori, Y. Yamamoto, and Y. Maeda. 2006. Gene constitution of South-East Asian native Chickens, commercial chickens and jungle fowl using polymorphisms of four Calpain genes. Anim. Sci. J. 77:188-195.
  26. Riztyan, T. Katano, T. Shimogiri, K. Kawabe, and S. Okamoto. 2011. Genetic diversity and population structure of Indonesian native chickens based on single nucleotide polymorphism makers. Poult. Sci. 90: 2471-2478.
  27. Riztyan, T. Nishida, R. Worawut, T. Shimogiri, A. A. Maw, K. Kawabe, Y. Kawamoto, and S. Okamoto. 2012. Genetic variation and phylogeographic analysis of native chicken populations in Myanmar and Thailand. J. Poult. Sci. 49:68-73.
  28. Rosenberg, N. A. 2004. DISTRUCT: a program for the graphical display of population structure. Mol. Ecol. Notes 4:137-138.
  29. Sawai, H., H. L. Kim, K. Kuno, S. Suzuki, H. Gotoh, M. Takada, N. Takahata, Y. Satta, and F. Akishinonomiya. 2010. The origin and genetic variation of domestic chickens with special reference to jungle fowls Gallus g. gallus and G. varius. PLoS One. 5:e10639.