Development of novel microsatellite markers for population differentiation and detection of natural selection in wild populations of Butter catfish, Ompok bimaculatus (Bloch, 1794)

Abstract Background: Butter catfish (Ompok bimaculatus) is a preferred species in South East Asia, with huge aquaculture potential. However, there is limited information about genetic stock composition due to insufficient markers. The goal of this study was to develop de novo microsatellite markers. Methods and Results: For sequencing, genomic SMRT bell libraries (1.5 Kbp size) were prepared for O. bimaculatus. A total of 114 SSR containing sequences were used for primer designing and tested. Polymorphic loci were validated by genotyping 83 individuals from four distant riverine populations, viz., Brahmaputra, Bichiya, Gomti and Kaveri. A total of 30 microsatellite loci were polymorphic, of which, five were found to be associated with functional genes and eight (four positive and four negatives) loci were found to be under selection pressure. A total of 115 alleles were detected in all loci and PIC ranged from 0.539 to 0.927 and pair-wise FST values from 0.1267 to 0.26002 (p<0.001), with overall FST value of 0.17047, indicating presence of population sub-structure. Cross-species transferability of 29 loci (96.67%) was successful in congener species, O. pabda. Conclusion: The novel SSR markers developed in this study will facilitate stock characterization of natural populations, to be used in future selection breeding programs and planning conservation strategies in these species. Identified non-neutral markers will give insights into the effect of local adaptation on genetic differentiation in the natural population of this species.