Indigenous cattle of India belong to the species, Bos indicus and they possess various adaptability and production traits. However, little is known about the genetic diversity and origin of these breeds. To investigate the status, we sequenced and analyzed the whole mitochondrial DNA (mtDNA) of seven Indian cattle breeds. In total, 49 single-nucleotide variants (SNVs) were identified among the seven breeds analyzed. We observed a common synonymous SNV in the COII gene (m.7583G > A) of all the breeds studied. The phylogenetic analysis and genetic distance estimation showed the close genetic relationship among the Indian cattle breeds, whereas distinct genetic differences were observed between Bos indicus and Bos taurus cattle. Our results indicate a common ancestor for European Zwergzebu breed and South Indian cattle. The estimated divergence time demonstrated that the Bos indicus and Bos taurus cattle lineages diverged 0.92 million years ago. Our study also demonstrates that ancestors of present zebu breeds originated in South and North India separately ∼30,000 to 20,000 years ago. In conclusion, the identified genetic variants and results of the phylogenetic analysis may provide baseline information to develop appropriate strategies for management and conservation of Indian cattle breeds.

India has 40 distinct zebuine cattle breeds with different adaptability and production traits. In the present study, we report the complete mitochondrial genome sequence of Indian cattle for the first time. The mitogenome contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a control region (D-loop region). The phylogenetic analysis showed close genetic relationship among the Indian cattle breeds studied, where as, distinct genetic differences were observed between Bos indicus and Bos taurus cattle. Our results will expand genomic information for further studies on evolution, domestication and conservation of indigenous cattle breeds in India.

No abstract