Population genetic structure of Betong chicken breed collected from different locations revealed by InDel markers
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Abstract
This research aims to study the genetic diversity and population structure of the Betong chicken breed collected from different locations: Betong Pikunthong chickens from Pikun Thong Royal Development Study Centre, Narathiwat Province (A), Betong chickens from model farm, Yala Province (B), Betong chickens from Bo Namron farm, Yala Province (C) and Betong chickens from Animal Production Innovation and Management Division, Faculty of Natural resources, Prince of Songkla University, Songkhla Province (PSU). A total of 60 chickens were selected from Betong chicken breed populations. The samples were analyzed by using 10 insertion-deletion (InDel) markers. This result reveals polymorphism in 7 indels and it was found that the average of polymorphic loci (Ppoly) was 0.750±0.068. According to the average expected heterozygosity (He) was 0.299±0.038. Analysis of Molecular Variance (AMOVA) indicated that most of the variation was within the population (91%). The genetic differences from the F-coefficient, we found that a slight reduction in heterozygosity was observed in all populations (FIT=0.016±0.035), while in the subpopulation was no inbreeding (FIS=-0.094±0.041), and moderate genetic differences were found between populations (FST=0.098±0.030). The analysis of genetic relationships using a phylogenetic tree constructed with Neighbor-joining (NJ) revealed that Betong chicken population from farms A, B, and C were genetically close. The Principal Component Analysis (PcoA) and Structure analysis depicted that the studied samples can be divided into two groups (∆K=2). In conclusion, InDel markers could be used to indicate the genetic structure of Betong chicken populations collected from different areas and may be applied to study the future genetic analyses of other local chicken breeds.
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References
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