Genetic Diversity Assessment of Bagrid Catfish ( Rita rita ) Using SSR Markers: Implications for Riverine Conservation

Understanding genetic diversity is essential for conserving and sustainably managing fish populations in riverine ecosystems. However, overexploitation, habitat degradation, pollution, and ineffective fisheries management threaten the genetic integrity of many species, including the bagrid catfish ( Rita rita ). This study used simple sequence repeat (SSR) markers to assess the genetic diversity and population structure of R. rita across five sites along the Indus River. Genomic DNA was extracted from dorsal muscle tissues, and cross‐species microsatellite primers from Bagarius yarrelli were used for polymerase chain reaction (PCR) amplification. Genetic diversity was evaluated using allelic richness (Ar), heterozygosity, inbreeding coefficients ( F IS ) and genetic differentiation ( F ST ). The results revealed moderate genetic diversity, with allelic richness ranging from 2.400 to 5.800 and expected heterozygosity (He) between 0.617 and 0.699. Lower observed heterozygosity (Ho) across most populations suggests potential inbreeding effects. Significant genetic differentiation ( F ST ) indicated moderate population structuring, with a strong correlation between geographic distance and genetic variation. Analysis of molecular variance (AMOVA) showed that 85.72% of genetic variation occurred within individuals, while restricted gene flow (Nm) across certain loci suggested geographical barriers affect genetic diversity. UPGMA clustering and STRUCTURE analysis identified two major genetic clusters, suggesting the presence of distinct evolutionary lineages. These findings highlight the need for targeted conservation strategies to maintain genetic integrity and reduce further genetic loss. This study establishes a molecular framework for future marker‐assisted conservation and aquaculture programs to sustain R. rita populations in their natural habitats.