Genetic variation and relationships among eight Indian riverine buffalo breeds

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Abstract
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 FST 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 FST 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.