ORIGINAL PAPER Evaluation of genetic variability and mutation drift equilibrium of Banni buffalo using multi locus microsatellite markers B. P. Mishra & R. S. Kataria & P. Kathiravan & S. S. Bulandi & K. P. Singh & D. K. Sadana Accepted: 9 December 2008 / Published online: 9 January 2009 # Springer Science + Business Media B.V. 2009 Abstract The present study was conducted to evaluate genetic diversity of Banni buffalo and its relationship/ differentiation with Murrah using genotypic data on 24 heterologus bovine specific microsatellite marker loci. A total of 138 alleles were observed with a mean of 5.75 alleles/locus across two populations. The mean ob- served and expected heterozygosities were found to be 0.441 and 0.572 respectively in Banni buffaloes while it was 0.464 and 0.610 respectively in Murrah buffaloes. The average heterozygosity deficit was significantly positive with substantially higher values observed in Banni (22.3%) and Murrah (24%) buffalo populations. Banni buffalo population, when evaluated for mutation drift equilibrium revealed significant heterozygosity excess under IAM while no such excess was observed under SMM and TPM. The qualitative graphical test revealed a normal L-shaped distribution of allele frequencies indicating the absence of genetic bottleneck in Banni buffaloes. The mean estimates of F-statistics over all the loci were 0.376 for F IT , 0.187 for F ST and 0.232 for F IS respectively. Analysis of molecular variance (AMOVA) revealed 18.95% of the total variation being explained by between breed differences while 14.36% of the variation explained differences between individuals within each breed. Genotype assignment test revealed distinct clustering of Banni and Murrah buffaloes. Genetic distance was estimated using three different methods, the results of which revealed considerable genetic differentiation between these two buffalo populations. The divergence time between Banni and Murrah buffaloes was estimated to be around 7286 years. The results of the present study may be helpful in decision making for conservation programs as Banni buffalo population is on decline. Keywords Banni buffalo . Microsatellite markers . Genetic distance . AMOVA . Genotype assignment Introduction Buffaloes in the Indian sub-continent are an integral part of traditional agriculture and hold the greatest promise and potential for food production (Cockrill 1994). They were first domesticated by the ancient Indus valley people around 2500 to 5000 B.C (Nanda and Nakao 2003). Of the total 158 million buffalo population in the world, India alone accounts for about 59.5% of them (FAOSTAT 2003). Indian buffaloes contribute 48 million tonnes of milk, which is about 55.6% of total milk produced in the country. Trop Anim Health Prod (2009) 41:1203–1211 DOI 10.1007/s11250-008-9301-8 B. P. Mishra (*) : R. S. Kataria : P. Kathiravan : S. S. Bulandi : D. K. Sadana National Bureau of Animal Genetic Resources, Karnal – 132001 Haryana, India e-mail: bpmishra_1@hotmail.com K. P. Singh Department of Animal Genetics and Breeding, College of Veterinary and Animal Husbandry, SDAU, Sardar Krushinagar, Gujarat, India