Mitochondrial DNA-based analysis of genetic variation and relatedness among Sri Lankan indigenous chickens and the Ceylon junglefowl (Gallus lafayetti)

Indigenous chickens (IC) in developing countries provide a useful resource to detect novel genes in mitochondrial and nuclear genomes. Here, we investigated the nature and level of genetic diversity in IC from five distinct regions of Sri Lanka using a PCR-based resequencing method. Additionally, we investigated the relatedness of IC to different species of junglefowls including Ceylon (CJF; Gallus lafayetti), a subspecies that is endemic to Sri Lanka, green (Gallus varius), grey (Gallus sonneratii), and red (Gallus gallus) junglefowl. A total of 140 birds including eight CJF were used to screen 613 bp of IC and 675 bp of CJF control region of the mitochondrial DNA sequence for single nucleotide polymorphisms (SNPs) and other variants. We detected and validated 44 SNPs, which formed 42 haplotypes and six haplogroups in IC. The SNPs observed in the CJF were distinct and the D-loop appeared to be missing a 62 bp found in IC and the red junglefowl (RJF). Among the six haplogroups of IC, only one was region-specific. Estimates of haplotype and nucleotide diversities ranged from 0.901 to 0.965 and from 0.011 to 0.013, respectively. Estimates of genetic divergence were inconsistent but generally low in all the regions. Further, variation among individuals within regions accounted for 92% of the total molecular variation among birds. The Sri Lankan indigenous chickens were more closely related to red and grey junglefowls than to CJF, suggesting a multiple origin. The molecular information on genetic diversity revealed in our study may be useful in developing genetic improvement and conservation strategies to better utilize indigenous Sri Lankan chicken resources.