Nile tilapia (Oreochromis niloticus), native to Africa and the Levant, is an important species for both aquaculture and capture fisheries. Despite these attributes, Nile tilapia has been negatively impacted by anthropogenic activities ranging from overfishing, and habitat destruction to translocations. These human-mediated activities have threatened the genetic evolutionary integrity of Nile tilapia and its congeneric species through admixture, demographic bottleneck, and introgressive hybridization. In this context, the genetic contrast between farmed/bred strains and or natural Nile tilapia populations in the L. Victoria basin remains confounding. Therefore, understanding the genetic structure reference maps of Nile tilapia populations in the basin is key as may lessen the risks that result from aquaculture maladaptation, unfold ideal strains for selective breeding, help in the conservation & management of stocks, and enhance fish productivity in the region. We sampled 756 Nile tilapia individuals in the major water bodies of Uganda (Lake Victoria basin), and genotyped them using a panel of 34 microsatellite loci based on the Microsatellite Genotyping-By-Sequencing (SSR-GBS) technique. The samples were sequenced using Next Generation Sequencing (NGS) platform. The results indicate three discrete genetic clusters of, the Edward-George system; Albert, Kyoga, Kyoga-Nile; and Kyoga-Nakuwa. We also report that Nile tilapia in Lakes Victoria, Kyoga-Kwania, and the fish farm at ARDCK lie intermediary between other populations which may be an indicator of admixture. Evidence of the historical fish translocations was noted through a number of migration rates as a proxy to gene flow. Importantly, we observed some genetically distant populations coupled with high genetic diversity which can be ideal sources for future selective breeding programmes aimed at elevating aquaculture production in the region.
Keywords: Nile tilapia, Genetic structure, Introgressive hybridization, Admixture