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 FST 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 FST with 79-90% of the total genetic variation found within populations. The FCT 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.

Keywords

• genetic variation
• genetic relationship
• heterozygosity
• native chicken phylogeography