Abstract
In India, goats are considered to be one of the important livestock species that reinforce the rural economy. Even though India has 23 well-recognized goat breeds, the knowledge about their genetic diversity and domestication history is limited. In this study, we have analyzed the genetic diversity of 104 goats representing five different south Indian breeds using mtDNA D-loop region. The haplotype diversity of the breeds ranged from 0.9524 ± 0.0403 (Malabari) to 0.9921 ± 0.0154 (Kanni aadu). Analysis of molecular variance showed only 1.05% variation among breeds. On other hand, the variation within breed was remarkably high (98.95%) which suggested the weak phylogeographic structure of south Indian goats. The phylogenetic analysis revealed three haplogroups representing maternal lineages namely A, B and D. The analysis of 466 Indian goat sequences showed an additional lineage C. As reported in the previous studies, a major fraction of analyzed goats fell into haplogroup A. Our study confirms the presence of three maternal lineages for south Indian domestic goats.