Genetic Variation and Phylogeographic Analysis of Native Chicken Populations in Myanmar and Thailand

Abstract

Native chickens in Myanmar and Thailand have been being domesticated for generations and yielded a wide variety of chickens. The objective of the research is to analyze the genetic variation and relationships of native chicken populations in Myanmar and Thailand. A total number of 249 genomic DNA samples from a total nine populations including the commercial lines, were genotyped using 98 autosomal SNP markers. The average heterozygosity of each population was in the range of 0.181-0.262. The neighbor-joining trees constructed by pair-wise F ST estimates corresponded that the native chickens in Myanmar and Thailand were at a distance from the commercial chickens. The STRUCTURE analysis revealed that the nine chicken populations used in this study might be derived from six genetic populations (K＝6). The AMOVA showed significant value of F ST with 79-90% of the total genetic variation found within populations. The F CT value was significant but accounted for only 4.45% of the total variability among countries. Finally, the mantel test for Isolation by Distance result (r＝0.5964; P＜0.01) suggested the contribution of geographic distance to the genetic structure of native chicken populations in Myanmar and Thailand.

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

“…Additionally, their study stated that 81 (86.2%) and 76 (80.9%) out of 94 indels markers could be validated as polymorphic loci in dogs (n = 7) and wolves (n = 18), respectively ( Väli et al, 2008 ). The H E values of chickens native to Myanmar in the present study were similar to those obtained by SNPs in an earlier report by Riztyan et al (2012) . However, for Thai and Laotian native chicken populations, the H E values in the present study were higher than those obtained by SNPs and blood protein polymorphisms in earlier studies ( Okamoto et al, 1999 ; Riztyan et al, 2012 ).…”

“…The H E values of chickens native to Myanmar in the present study were similar to those obtained by SNPs in an earlier report by Riztyan et al (2012) . However, for Thai and Laotian native chicken populations, the H E values in the present study were higher than those obtained by SNPs and blood protein polymorphisms in earlier studies ( Okamoto et al, 1999 ; Riztyan et al, 2012 ). The H E values of Myanmar native chickens were lower than those of the Thai and Laotian populations.…”

“…The genetic characterization of Thai indigenous chickens and commercial chickens has been assessed by 20 microsatellite loci ( Dorji et al, 2011 ). In addition, the genetic variation and phylogeographic analysis of native chicken populations from Myanmar and Thailand have been studied using 98 autosomal single nucleotide polymorphism (SNP) markers ( Riztyan et al, 2012 ).…”

Genetic Diversity and Ancestral Relationships of Red Junglefowls and Domestic Chickens in Southeast Asia

“…The genotype data from these samples was combined with our previous subset of data from domestic chickens (Riztyan et al, 2011(Riztyan et al, , 2012, which was composed of two groups, native chickens and commercial breeds of chickens. Genomic DNA was purified from these samples using the proteinase K and phenol-chloroform method (Sambrook et al, 1989).…”

“…The SNP markers have been successfully used to perform the STRUCTURE analysis for the native chicken populations in Indonesia. Recently, we have demonstrated that the contribution of a certain number of assumed ancestral populations could be explained through the membership coefficients in the STRUCTURE analysis (Riztyan et al, 2012). Therefore, we expected that the SNP markers could reveal distinct ancestral relationships between RJF and domestic chickens.…”