Molecular Characterization of Mitochondrial D Loop of Indian Red Jungle Fowl

Abstract

Mitochondrial DNA has the characteristic of quick evolution, matrilineal inheritance, and simple molecular structure, and it serves as the most used marker for molecular study. As an important role of genomics, studying it can help understand the origins, history, and adaptation of domestication. A 1325 bp fragment of the mtDNA D-loop region was amplified, sequenced and phylogenetic study was done. Out of 400 sites about 12 % were polymorphic between the Gallus gallus (G.g.) subspecies and most of them (60%) were transitions. Indian RJF showed very low genetic distances (0.008-0.013) with G.g. gallus birds from Thailand as compared to those from Japan and Indonesia. The G.g. murghi showed comparatively high genetic distance i.e. 031-0.034 with G.g. spadiceus and from 0.061-0.066 with G. gallus bankiva. The phylogenetic tree showed that G.g. banikva is well separated from the other three subspecies as it made a separate cluster. G.g. gallus makes two separate clusters i.e. one those from Thailand and other those from Japan and Indonesia. Within each chicken breed, there is an excess of homozygosity, but there is no significant reduction in the nucleotide diversity. Phenotypic modifications of chicken breeds as a result of artificial selection appear to stem from ancestral polymorphisms at a limited number of genetic loci.