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

In the present study, we have explored the genetic relationships between red junglefowls and domestic chickens in Southeast Asia by using single nucleotide polymorphism (SNP) markers. We genotyped 475 individuals from 17 populations of red junglefowls (4 subspecies, n＝39), native chickens (10 populations, n＝346) and commercial breeds (3 breeds, n＝90) using PCR-RFLP for the 98 autosomal SNP markers. The genotyping results showed that average heterozygosity was 0.225±0.077 for red junglefowl, 0.272±0.009 for native chickens, and 0.211±0.037 for commercial breeds of chickens. The resultant neighbor-joining (NJ) tree with three distinct clusters corresponds to red junglefowls, native chickens and commercial breeds. The subspecies of red junglefowl was clustered into one clade and more closely related to native chickens than the commercial lines. Furthermore, the results of the population structure analysis suggested that the 17 populations appear to be derived from 11 genetic populations (K＝11). Among the domestic chickens, the NJ tree and genetic structure analysis revealed that Thailand native chickens was the most ancestral group of all chickens. These findings provide molecular evidence supporting the theory that the original domestication event occurred in Thailand. They also provide additional clustering information to classify red junglefowls and domestic chickens.