Genetic diversity analysis of Thai indigenous chickens based on complete sequences of mitochondrial DNA D-loop region

  • Teinlek, Piyanat ;
  • Siripattarapravat, Kannika ;
  • Tirawattanawanich, Chanin
  • Received : 2017.08.17
  • Accepted : 2018.01.09
  • Published : 2018.06.01


Objective: Complete mtDNA D-loop sequences of four Thai indigenous chicken varieties, including Pra-dhu-hang-dam (PD), Leung-hang-khao (LK), Chee (CH), and Dang (DA) were explored for genetic diversity and relationships with their potential ancestor and possible associates to address chicken domestication in Thailand. Methods: A total of 220 complete mtDNA D-loop sequences of the four Thai indigenous chicken varieties were obtained by Sanger direct sequencing of polymerase chain reaction amplicons of 1,231 to 1,232 base pair in size. A neighbor-joining dendrogram was constructed with reference complete mtDNA D-loop sequences of Red Junglefowl (RJF) and those different chicken breeds available on National Center for Biotechnology Information database. Genetic diversity indices and neutrality test by Tajima's D test were performed. Genetic differences both within and among populations were estimated using analysis of molecular variance (AMOVA). Pairwise fixation index ($F_{ST}$) was conducted to evaluated genetic relationships between these varieties. Results: Twenty-three identified haplotypes were classified in six haplogroups (A-E and H) with the majority clustered in haplogroup A and B. Each variety was in multiple haplogroups with haplogroups A, B, D, and E being shared by all studied varieties. The averaged haplotype and nucleotide diversities were, respectively 0.8607 and 0.00579 with non-significant Tajima's D values being observed in all populations. Haplogroup distribution was closely related to that of RJF particularly Gallus gallus gallus (G. g. gallus) and G. g. spadiceus. As denoted by AMOVA, the mean diversity was mostly due to within-population variation (90.53%) while between-population variation (9.47%) accounted for much less. By pairwise $F_{ST}$, LK was most closely related to DA ($F_{ST}=0.00879$) while DA was farthest from CH ($F_{ST}=0.24882$). Conclusion: All 4 Thai indigenous chickens are in close relationship with their potential ancestor, the RJF. A contribution of shared, multiple maternal lineages was in the nature of these varieties, which have been domesticated under neutral selection.


Thai Indigenous Chicken;Mitochondrial DNA D-loop;Genetic Diversity;Domestication


  1. Darwin C. The variation of animals and plants under domestication. 1st ed. London, UK: John Murray; 1868.
  2. Fumihito A, Miyake T, Sumi S, et al. One subspecies of the red junglefowl (Gallus gallus gallus) suffices as the matriarchic ancestor of all domestic breeds. Proc Natl Acad Sci USA 1994; 91:12505-9.
  3. Fumihito A, Miyake T, Takada M, et al. Monophyletic origin and unique dispersal patterns of domestic fowls. Proc Natl Acad Sci USA 1996;93:6792-5.
  4. Liu ZG, Lei CZ, Luo J, et al. Genetic variability of mtDNA sequences in Chinese native chicken breeds. Asian-Australas J Anim Sci 2004;17:903-9.
  5. Oka T, Ino Y, Nomura K, et al. Analysis of mtDNA sequences shows Japanese native chickens have multiple origins. Anim Genet 2007;38:287-93.
  6. Liu YP, Wu GS, Yao YG, et al. Multiple maternal origins of chickens: out of the Asian jungles. Mol Phylogenet Evol 2006; 38:12-9.
  7. Miao YW, Peng MS, Wu GS, et al. Chicken domestication:an updated perspective based on mitochondrial genomes. Heredity 2013;110:277-82.
  8. Hoque MR, Seo DW, Jo C, et al. Reconstruction of phylogenetic relationships of korean chickens using mitochondrial D-loop sequences. J Fac Agr, Kyushu Univ 2013;58:287-93.
  9. Kanginakudru S, Metta M, Jakati RD, Nagaraju J. Genetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken. BMC Evol Biol 2008; 8:174.
  10. Muchadeyi FC, Eding H, Simianer H, et al. Mitochondrial DNA D-loop sequences suggest a Southeast Asian and Indian origin of Zimbabwean village chickens. Anim Genet 2008;39: 615-22.
  11. Sulandari SRI, Zein MSA, Sartika T. Molecular characterization of Indonesian indigenous chickens based on mitochondrial DNA Displacement (D)-loop sequences. HAYATI J Biosci 2008;15:145-54.
  12. Kawabe K, Worawut R, Taura S, et al. Genetic diversity of mtDNA D-loop polymorphisms in laotian native fowl populations. Asian-Australas J Anim Sci 2014;27:19-23.
  13. Cuc NTK, Simianer H, Groeneveld LF, Weigend S. Multiple maternal lineages of vietnamese local chickens inferred by mitochondrial DNA D-loop sequences. Asian-Australas J Anim Sci 2011;24:155-61.
  14. Brown WM, Matthew George J, Wilson AC. Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci USA 1979; 76:1967-71.
  15. Osman SAM, Nishibori M. Phylogenetic analysis of South East Asian countries chickens based on mitochondrial DNA variations. J Poult Sci 2014;51:248-61.
  16. Nishibori M, Hayashi T, Tsudzuki M, Yamamoto Y, Yasue H. Complete sequence of the Japanese quail (Coturnix japonica) mitochondrial genome and its genetic relationship with related species. Anim Genet 2001;32:380-5.
  17. Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009;25: 1451-2.
  18. Excoffier L, Lischer HE. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 2010;10:564-7.
  19. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013;30:2725-9.
  20. Bhuiyan MS, Chen S, Faruque S, Bhuiyan AK, Beja-Pereira A. Genetic diversity and maternal origin of Bangladeshi chicken. Mol Biol Rep 2013;40:4123-8.
  21. Silva P, Guan X, Ho-Shing O, et al. Mitochondrial DNA-based Analysis of genetic variation and relatedness among Sri Lankan indigenous chickens and the Ceylon junglefowl (Gallus lafayetti). Anim Genet 2009;40:1-9.
  22. Liao Y, Mo G, Sun J, Wei F, Liao DJ. Genetic diversity of Guangxi chicken breeds assessed with microsatellites and the mitochondrial DNA D-loop region. Mol Biol Rep 2016;43:415-25.
  23. Kimura M. The neutral theory of molecular evolution. Cambridge, UK: Cambridge University Press; 1983.
  24. Komiyama T, Ikeo K, Gojobori T. Where is the origin of the Japanese gamecocks? Gene 2003;317:195-202.
  25. Komiyama T, Ikeo K, Tateno Y, Gojobori T. Japanese domesticated chickens have been derived from Shamo traditional fighting cocks. Mol Phylogenet Evol 2004;33:16-21.