Genetic Diversity of Native Chicken Populations and Red Jungle Fowl in Southern Thailand Based on Mitochondrial a DNA D-loop Region

ABSTRACT The mtDNA D-loops of four chicken breeds (Betong, Khao Chang, Srivijaya Naked-Neck, and Dang) from the native chicken populations of Narathiwat province and Red jungle fowl from the southern region of Thailand were analyzed to assess their genetic diversity and genetic relationships. The 558 fragments of the mtDNA D-loop were genotyped using PCR, and 20 variation sites and 23 haplotypes were detected in 326 mtDNA D-loop sequences. The haplotype diversity and nucleotide diversity of the Red jungle fowl were 0.936 ± 0.034 and 0.00806 ± 0.00087, respectively. Thai native chicken populations had a haplotype diversity of 0.000 to 0.9050, and a nucleotide diversity of 0.00000 to 0.00856, thus revealing the high genetic diversity of the native Thai chicken breeds. Analysis of molecular variance indicated that most of the variation was within the population (78.20%). The results of the median-joining network and phylogenetic tree were consistent and revealed that Thai local chicken breeds and Red jungle fowl were divided into eight main haplogroups (A-F, H, and V). The greatest number of haplotypes was classified into haplogroup B (6 haplotypes), followed by haplogroup V (5 haplotypes). Moreover, there was no breed-specific haplogroup. These results suggest that the breeds likely originated from multiple matrilineal lines, and the mtDNA D-loops assessed in this study appear to lack breed specificity.