The present study is the first attempt toward the genetic characterization of Bhangor buffaloes using microsatellite markers. Sufficiently high allelic diversity was observed with a total number of 114 distinct microsatellite alleles across 15 loci. Tripura is landlocked state and its physiography is characterised by hills and valleys. Buffaloes are distributed in the hills as well as valley/plain regions of different parts of the state. The state has nine major rivers, over 400 wetlands, and swamps, providing a natural habitat for swamp buffaloes to wallow [24]. The total buffalo population of Tripura is estimated around 7000 (20th Livestock Census, 2019), 50% of which is found in Unakoti district alone. Livestock in the state is mainly livelihood oriented and generally owned by small and marginal farmers. Population of the animal is decreasing over the years due to mechanisation of agriculture work and change in crop cultivation pattern. Destruction of natural grazing lands is one of the major concerns. The world famous indigenous Murrah buffalo has been brought in Tripura in the year 2013 for research and developmental purposes, to be explored for boosting milk production [25].
The observed number of alleles (Na) and mean number of alleles are indicators of genetic variation in a population. The observed numbers of alleles (Na) were higher than the effective numbers of alleles (Ne) for all the loci studied. The mean observed and effective numbers of alleles were found to be a little higher in the present study than that reported in Toda, Jaffrabadi (4.76), Bhadawari (4.7), Tarai (4.7), Chilika (4.68), Marathwada (4.48), Nagpuri, Pandharpuri and Banni buffaloes [4, 6, 7, 10, 26–29] but is lower than the swamp population of Manipur and Nagaland [22]. The higher number of allele secured implies increased allelic diversity present in the population. However 11 to 26 alleles per locus are also reported in Indian water buffalo [5]. These allelic differences may be attributed to the population under study, microsatellite markers studied, and the genetic polymorphism existing within the population itself.
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The average number of alleles obtained in the present study (7.60) was in line with FAO recommendation that suggests an analysis of at least 5 alleles per locus for genetic diversity based studies in livestock. Under the present study locus CSRM60 and ILSTS025 (3 alleles) all the markers demonstrated a good amount of polymorphism. Sukla et al. 2006 reported an average estimate of 5.5 alleles per locus for six Indian buffalo breeds based on 10 polymorphic microsatellite loci [30]. Similarly, an average of 5.15 alleles per locus was reported by Ozkan et al. in buffalo breed of Turkey [31]. The effective number of alleles across all loci was lower than the observed values. The alleles with lower/rare frequency were considered as novel ones and these alleles may be assigned to population.
The average heterozygosity estimate of 0.670 was observed across all polymorphic loci for the population. The expected heterozygosity estimate was highest for ILSTS058 locus (0.85) and lowest for ILSTS025 (0.06). All the loci, except ILSTS025, exhibited high expected gene diversity, which are good measures to assess genetic diversity in a population. A similar average for Ho and He was observed in Colombian buffalo [32]. Substantially high average heterozygosity values pointed toward the existence of considerable genetic variability in the Bhangor buffalo population and suitability of the markers as well.
PIC value indicates an estimate associated with a particular marker for detecting polymorphism and it ranges from 0 to 1. Markers with PIC value greater than 0.5 are considered important for genetic diversity based analysis [25]. Microsatellite loci ILSTS025 showed PIC estimate less than the threshold of 0.5 (Table 2). The other markers were informative and important for genetic diversity and paternity based analysis in Bhangor population. Given the estimates of the observed and effective number of alleles, heterozygosity and PIC parameters, these marker loci may be used for carrying out the genetic studies on Bhangor population. Thus, the result suggests that there is substantial genetic variation and heterozygosity across the studied loci in Bhangor buffalo as assessed on the basis of 15 polymorphic microsatellite markers.