Genetic diversity in mitochondrial DNA D-loop region of indigenous pig breeds of India

Abstract

India is home for at least 18 indigenous pig breeds; however, the genetic diversity of Indian pig, Sus scrofa domesticus, population is poorly known. Here, the hypervariable region (HVR) of mitochondrial DNA D-loop (~487 bp) of 214 pigs representing five indigenous and three exotic breeds was sequenced and analysed with reference sequences from other countries. A total of 54 segregating sites among the sequences revealed 56 different haplotypes. Two, 11, eight, seven and six haplotypes were identified with some haplotype sharing in indigenous breeds: Doom, Ghungroo, Mali, Niang-Megha and Tenyi-Vo, respectively. Population pairwise differences (PhiST) (0.409) were found significant (P<0.001), and variance within breeds (59.1%) was more than that of among breeds (40.9%). Similar topology was noted in phylogeny and median-joining network. Indian domestic pigs from this study were found to possess unique and highly differentiated haplotypes on network analysis. The diverse haplotypes and phylogenetic lineages identified here is the first report on Indian pig breeds that need to be further explored by complete mitochondrial DNA sequencing and analysis. These findings provide indicative insights for conservation and optimum utilization of the porcine genetic resources.