Twenty-seven microsatellite loci were used to define genetic variation and relationships among eight Indian riverine buffalo breeds. The total number of alleles ranged from 166 in the Toda breed to 194 each in the Mehsana and the Murrah. Significant departures from the Hardy-Weinberg equilibrium were observed for 26 locus-breed combinations due to heterozygote deficiency. Breed differentiation was analysed by estimation of F(ST) index (values ranging from 0.75% to 6.00%) for various breed combinations. The neighbour-joining tree constructed from chord distances, multidimensional scaling (MDS) display of F(ST) values and Bayesian clustering approach consistently identified the Toda, Jaffarabadi, and Pandharpuri breeds as one lineage each, and the Bhadawari, Nagpuri, Surati, Mehsana and Murrah breeds as admixture. Analysis of molecular variance refuted the earlier classification of these breeds proposed on the basis of morphological and geographical parameters. The Toda buffaloes, reared by a tribe of the same name, represent an endangered breed from the Nilgiri hills in South India. Divergence time of the Toda buffaloes from the other main breeds, calculated from Nei's standard genetic distances based on genotyping data on seven breeds and 20 microsatellite loci, suggested separation of this breed approximately 1800-2700 years ago. The results of the present study will be useful for development of rational breeding and conservation strategies for Indian buffaloes.

Water buffalo (Bubalus bubalis) is broadly classified into river and swamp categories, but it remains disputed whether these two types were independently domesticated, or if they are the result of a single domestication event. In this study, we sequenced the mitochondrial D-loop region and cytochrome b gene of 217 and 80 buffalo respectively from eight breeds/locations in northern, north-western, central and southern India and compared our results with published Mediterranean and swamp buffalo sequences. Using these data, river and swamp buffalo were distinguished into two distinct clades. Based upon the existing knowledge of cytogenetic, ecological and phenotypic parameters, molecular data and present-day distribution of the river and swamp buffalo, we suggest that these two types were domesticated independently, and that classification of the river and swamp buffalo as two related subspecies is more appropriate.

BackgroundThe water buffalo- Bubalus bubalis holds tremendous potential in livestock sector in many Asian countries, particularly India. The origin, domestication and genetic structure of the Indian river buffalo are poorly understood. Therefore, to understand the relationship among the maternal lineages of Indian river buffalo breeds and their domestication process, we analysed mitochondrial D-loop region of 217 animals representing eight breeds from eight different locations in India along with published sequences of Mediterranean buffalo.ResultsThe maximum parsimony tree showed one major clade with six internal branches. Reduced median network revealed expansion from more than one set of haplotypes indicating complex domestication events for this species. In addition, we found several singleton haplotypes. Using rho statistics, we obtained a time estimate of 6300 years BP for the expansion of one set of hapltoypes of the Indian domestic buffalo. A few breed specific branches in the network indicated an ancient time depth of differentiation of some of the maternal lineages of river buffalo breeds. The multidimensional display of breed pairwise FST values showed significant breed differentiation.ConclusionPresent day river buffalo is the result of complex domestication processes involving more than one maternal lineage and a significant maternal gene flow from the wild populations after the initial domestication events. Our data are consistent with the available archaeological information in supporting the proposition that the river buffalo was likely to be domesticated in the Western region of the Indian subcontinent, specifically the present day breeding tracts of the Mehsana, Surati and Pandharpuri breeds.

Length variation in the human mtDNA intergenic region between the cytochrome oxidase II (COII) and tRNA lysine (tRNA(lys)) genes has been widely studied in world populations. Specifically, Austronesian populations of the Pacific and Austro-Asiatic populations of southeast Asia most frequently carry the 9-bp deletion in that region implying their shared common ancestry in haplogroup B. Furthermore, multiple independent origins of the 9-bp deletion at the background of other mtDNA haplogroups has been shown in populations of Africa, Europe, Australia, and India. We have analyzed 3293 Indian individuals belonging to 58 populations, representing different caste, tribal, and religious groups, for the length variation in the 9-bp motif. The 9-bp deletion (one copy) and insertion (three copies) alleles were observed in 2.51% (2.15% deletion and 0.36% insertion) of the individuals. The maximum frequency of the deletion (45.8%) was observed in the Nicobarese in association with the haplogroup B5a D-loop motif that is common throughout southeast Asia. The low polymorphism in the D-loop sequence of the Nicobarese B5a samples suggests their recent origin and a founder effect, probably involving migration from southeast Asia. Interestingly, none of the 302 (except one Munda sample, which has 9-bp insertion) from Mundari-speaking Austro-Asiatic populations from the Indian mainland showed the length polymorphism of the 9-bp motif, pointing either to their independent origin from the Mon-Khmeric-speaking Nicobarese or to an extensive admixture with neighboring Indo-European-speaking populations. Consistent with previous reports, the Indo-European and Dravidic populations of India showed low frequency of the 9-bp deletion/insertion. More than 18 independent origins of the deletion or insertion mutation could be inferred in the phylogenetic analysis of the D-loop sequences.

Genetic diversity in the Indian population of the tiger shrimp Penaeus monodon was determined by using partial sequence data of the mitochondrial DNA (mtDNA) control region (D‐loop) and the 16S rRNA gene. Eight populations from different geographical locations (Mumbai, Kochi, Mangalore, Kakinada, Gopalpur, Chilika, Paradeep and Andaman) were collected and analysed. The amplified polymerase chain reaction products of size 577 bp for the control region and 472 bp for 16S rRNA were sequenced in both directions and data were analysed through clustal, arlequin, mega and phylip. A significant genetic structure was found among the Indian populations. The mtDNA control region proved to be a powerful marker in comparison with 16S rRNA for population studies of this species. The east coast population was more genetically diverse than the west coast. The Andaman population was found to be the most diverse among all the populations. The populations on the west coast were found to be genetically more structured and differentiated than the populations on the east coast. The results revealed a high level of genetic diversity and also distinct population structuring of P. monodon, suggesting great possibilities of genetic improvement for growth and other economic traits.