Sequence analysis of four caprine mitochondria DNA lineages

Genetic diversity analysis among Indian goat breeds based on mitochondrial DNA

India ranks second in goat population with 34 genetically recognized and registered breeds. Information on their diversity and origin and ancestry is little known. Hence, the mtDNA based genetic diversity analysis of Indian goats; targeting mitochondrial HVR1 region from 21 Indian breeds belonging to different geographical regions was undertaken. A total of 124 haplotypes were identified and haplotype diversity estimate ranged from 0.67 to 1.0 with an average value of 0.99. The average nucleotide diversity was minimum (0.02) in Kanniadu and maximum in Surti breeds. Analysis of molecular variance revealed 5.16% variation among the breeds and 94.84% within breeds indicating weak phylogeographic structure. Neighbor-joining tree analysis revealed that the maximum number of individuals of Indian goats fall under A and few in B and C lineages. Principal component analyses of the Indian goat breeds revealed that Kanniadu goats clustered distantly from rest of the breeds of the country. Mantel test revealed a significant correlation between FST and geographical distance (r=0.29) among the goat breeds. The mismatch distribution analysis of the Indian goat breeds revealed bimodal distribution patterns. The analysis revealed that Kanniadu is highly distinct from the rest of the breeds.

Complete mitogenome reveals genetic divergence and phylogenetic relationships among Indian cattle (Bos indicus) breeds

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.