Genetic relationship and population structure of three Indian local chicken populations as revealed by mtDNA D-loop

The genetic information obtained from the mitochondrial DNA D-loop region has paramount importance in understanding the evolution of closely related individuals, and designing proper breeding or conservation plans. The present study was conducted using partial D-loop sequences of three local poultry populations from Odisha, India. The partial D-loop sequences were found to be highly polymorphic having 164 polymorphic sites with 89 singletons and 75 parsimony informative sites. Furthermore, 25 insertion and deletion sites were observed. High genetic diversity was observed within three local chicken populations. Highest genetic difference was observed between Gujuri and Kalua population (0.2230) followed by Gujuri and Hansli (0.199) and Kalua with Hansli (0.166). The pairwise mismatch distribution showed that all populations are of constant size over time. Phylogenetic tree analysis indicated that the said three populations were close to the referred population of China, Sri Lanka, Indonesia and Japan than Aseel and Kadaknath (Indian native breeds).