The present study aimed at assessing the status of the Chilika buffalo population of eastern India employing cytogenetic and molecular markers. The Chilika buffaloes investigated cytogenetically possess a somatic chromosome count of 50, identical to that of typical riverine buffaloes. Various diversity estimates, viz. observed number of alleles (4.68), effective number of alleles (2.79), and observed (0.487) and expected (0.602) heterozygosity across 25 heterologous microsatellite markers indicated the presence of a moderate level of genetic diversity in Chilika buffaloes, comparable with three other prominent Indian riverine buffalo breeds (Murrah, Nagpuri and Toda) included in this study. Across the four buffalo populations, mean estimates of F-statistics from Jackknifing over loci were significantly different from zero (p < 0.05), with F(IT) (total inbreeding estimate) = 0.315 +/- 0.038, F(IS) (within-population inbreeding estimate) = 0.178 +/- 0.038, and F(ST) (population differentiation) = 0.166 +/- 0.025. Inter-breed analysis reflected Chilika buffaloes to be genetically close to Nagpuri followed by Murrah and Toda buffaloes. Factorial correspondence analysis (FCA) revealed low breed-specific clustering of Chilika and Nagpuri buffaloes. Additionally, the neighbour-joining tree structure of mitochondrial DNA D-loop haplotypes indicated clear grouping of the Chilika haplotypes with the riverine buffalo. Thus the cytogenetic, microsatellite and mitochondrial data analysed in the present study classify Chilika buffalo of eastern India to be of the riverine type and not swamp-type buffalo.

The present study was undertaken to evaluate different Indian riverine buffalo breeds (Bubalus bubalis) for mutation drift equilibrium and occurrence of any recent genetic bottleneck. A total of 330 animals from seven different breeds were analyzed with a set of 24 heterologous microsatellite markers. Three different tests revealed significant heterozygosity excess in all the seven buffalo breeds studied when assumed under infinite alleles model of microsatellite evolution, while it was the reverse with no significant heterozygosity excess when assumed under conservative stepwise mutation model. Under the two-phase model, all the buffalo breeds except Mehsana were found to be in mutation drift equilibrium when evaluated by all the three statistical methods. Standardized differences test and Wilcoxon signed-rank test revealed significant heterozygosity excess suggesting possible cryptic demographic bottleneck in Mehsana buffaloes of Western India.

The Toda buffalo of South India was evaluated for its genetic variability and mutation drift equilibrium using a set of 25 bovine specific heterologous microsatellite markers. A total of 105 alleles were detected across 25 loci with mean effective number of alleles being 2.661. The mean observed and expected heterozygosity were 0.570 and 0.598, respectively. The test for Hardy-Weinberg equilibrium (HWE) revealed significant deviations in many of the investigated loci. There were highly significant deviations from mutation drift equilibrium while the qualitative test of mode shift did not reveal any genetic bottleneck in the recent past. The mitochondrial DNA D-loop sequence analysis of 165 bp region in three buffalo breeds viz. Toda, Assamese and Murrah revealed a total of 12 haplotypes, of which five were unique and remaining seven were found to be shared among different breeds. The phylogenetic analysis indicated clustering of all the riverine buffalo haplotypes together in a single clade including Toda and Assamese while the swamp buffaloes formed a separate cluster.

Mishra, B.P., Kataria, R.S., Bulandi, S.S., Kumar, V. and Mukesh, M. 2008

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 observed 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.