Open Access Highly Accessed Research article

Population structure of four Thai indigenous chicken breeds

Supamit Mekchay12*, Pantaporn Supakankul3, Anunchai Assawamakin4, Alisa Wilantho5, Wanwisa Chareanchim5 and Sissades Tongsima5

Author Affiliations

1 Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand

2 Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand

3 School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand

4 Department of Pharmacology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand

5 Biostatistics and Informatics Laboratory, Genome Institute, National Center for Genetic Engineering and Biotechnology (BIOTEC), Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand

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BMC Genetics 2014, 15:40  doi:10.1186/1471-2156-15-40

Published: 27 March 2014



In recent years, Thai indigenous chickens have increasingly been bred as an alternative in Thailand poultry market. Due to their popularity, there is a clear need to improve the underlying quality and productivity of these chickens. Studying chicken genetic variation can improve the chicken meat quality as well as conserving rare chicken species. To begin with, a minimal set of molecular markers that can characterize the Thai indigenous chicken breeds is required.


Using AFLP-PCR, 30 single nucleotide polymorphisms (SNPs) from Thai indigenous chickens were obtained by DNA sequencing. From these SNPs, we genotyped 465 chickens from 7 chicken breeds, comprising four Thai indigenous chicken breeds- Pradhuhangdum (PD), Luenghangkhao (LK), Dang (DA) and Chee (CH), one wild chicken - the red jungle fowls (RJF), and two commercial chicken breeds - the brown egg layer (BL) and commercial broiler (CB). The chicken genotypes reveal unique genetic structures of the four Thai indigenous chicken breeds. The average expected heterozygosities of PD= 0.341, LK= 0.357, DA=0.349 and CH= 0.373, while the references RJF= 0.327, CB=0.324 and BL= 0.285. The FST values among Thai indigenous chicken breeds vary from 0.051 to 0.096. The FST values between the pairs of Thai indigenous chickens and RJF vary from 0.083 to 0.105 and the FST values between the Thai indigenous chickens and the two commercial chicken breeds vary from 0.116 to 0.221. A neighbour-joining tree of all individual chickens showed that the Thai indigenous chickens were clustered into four groups which were closely related to the wild RJF but far from the commercial breeds. Such commercial breeds were split into two closely groups. Using genetic admixture analysis, we observed that the Thai indigenous chicken breeds are likely to share common ancestors with the RJF, while both commercial chicken breeds share the same admixture pattern.


These results indicated that the Thai indigenous chicken breeds may descend from the same ancestors. These indigenous chicken breeds were more closely related to red jungle fowls than those of the commercial breeds. These findings showed that the proposed SNP panel can effectively be used to characterize the four Thai indigenous chickens.

Thai indigenous chicken; Population structure; Genetic variation; SNP; AFLP