Genetic characterization and diversity assessment in ‘Bhangor’ indigenous swamp buffalo population using heterologous microsatellite markers

Background: The present study was aimed at genetic characterization and diversity analysis of indigenous swamp buffalo population ‘Bhangor’ from Tripura, India using the Food and Agriculture Organization (FAO) recommended bovine microsatellite markers. So far buffaloes of the north-eastern states of India have been studied except for Tripura. Results Buffalo blood samples were collected from Tripura. Of the 24 microsatellite markers studied only 15 markers (CSSM33, BM1818, CSRM60, HEL13, ILSTS019, ILSTS025, ILSTS028, ILSTS029, ILSTS030, ILSTS033, ILSTS036, ILSTS056, ILSTS058, ILSTS061, ILSTS089 and ETH003) were found to be highly polymorphic in the population. A total of 114 alleles were secured, with an overall average of 7.60 alleles per locus. The number of alleles ranged from 3 (CSRM60 and ILSTS025) to 12 (ILSTS056 and ILSTS061). The mean effective number of alleles across all polymorphic loci was found to be 3.76. The overall mean expected heterozygosity and unbiased expected heterozygosity values were 0.67 and 0.68, ranging from 0.067 (ILSTS025) to 0.85 (ILSTS058) and 0.068 (ILSTS025) to 0.86 (ILSTS058), respectively. Within-population inbreeding estimates (FIS) for bhangor buffalo ranged between − 0.4352 and 0.804 with an average FIS of 0.114 ± 0.033. Conclusions The outcome for IAM, TPM and test for mode shift revealed the absence of any recent bottleneck in Bhangor buffalo population. The population was found to be in optimum diversity based on polymorphic microsatellite markers. This is the newly characterized buffalo population from north-east India.