Genetic diversity and population structure of the threatened chocolate mahseer (Neolissochilus hexagonolepis McClelland 1839) based on SSR markers: implications for conservation management in Northeast India.

Neolissochilus hexagonolepis (MacClend 1839), commonly known as chocolate mahseer, is an ecologically threatened fish species. The species is reported from Southeast Asia and in India, it is distributed across the Northeast region. The present study was carried out to develop species-specific novel microsatellite markers using next-generation sequencing and to assess the genetic diversity of wild chocolate mahseer populations distributed through Northeastern India. A total of 25 polymorphic loci (mean PIC = 0.933) were amplified in 194 individuals belonging to seven different populations. We observed high genetic diversity across the loci with mean observed (Ho) and expected heterozygosity (He) of 0.557 and 0.939 respectively. The studied loci didn't show significant deviation from Hardy-Weinberg equilibrium. Genetic analyses indicate substantial pairwise Nei's genetic distance and moderate to high levels of genetic differentiation among populations (mean FST = 0.23). The structure, factor and cluster analysis identified five major clusters that can be considered as different conservation units while formulating any management measures. Furthermore, the migration analysis inferred that there is no active migration among the studied populations. Results suggested that two populations i.e. Dikrong river (Arunanchal Pradesh) and Umiam river have high genetic diversity. These populations can be utilized for the breeding programme to achieve substantial genetic variations in the descendant populations. The Nongbareh populations showed very less genetic vigor and need an immediate attention for conservation. The SSR markers developed in the present study will provide a valuable resource for future population genetic assessment and implementation of effective conservation strategies for wild chocolate mahseer.