Fisheries and aquaculture are vital for regional food security and economic development. Tilapiine species, especially those from the Oreochromis genus, play a central role in fisheries and aquaculture due to their adaptability to diverse aquatic ecosystem. This study responds to the growing need for molecular tools to monitor genetic diversity in tilapiines, as climate change and aquaculture intensification increasingly threaten both wild and farmed populations by exacerbating disease outbreaks and accelerating genetic diversity loss. By developing Exon-Primed Intron Crossing (EPIC) markers that cross-amplify species, we provide a resource to support biodiversity assessment and conservation efforts in East Africa. Using EPIC markers targeting immune genes, this study examined genetic diversity, population structure, and differentiation of tilapiine species and populations in East African water bodies and aquaculture farms. Fifty (50) EPIC markers were designed, and 45 successfully amplified target regions across four species: Oreochromis niloticus, O. esculentus, O. leucostictus, and O. jipe.
Genetic diversity varied among the wild O. niloticus populations, with higher heterozygosity observed in Lake Turkana (He = 0.467) and lower in Lake Jipe (He = 0.294). Similarly, Lake Victoria showed higher diversity (He = 0.362) and Lake George (He = 0.349), compared in Lake Albert (He = 0.329). Populations from Lake Hashenge (He = 0.147) showed reduced diversity relative to those from Lake Chamo (He = 0.237) and Lake Tana (He = 0.151). Between the farmed populations, diversity was higher in Kyanamira population (He = 0.393) and reduced in Kajjansi (He = 0.372). Populations from Lake Albert and Lake Kyoga exhibited higher gene flow (FST = 0.016) in comparison to Lake Tana and Lake Hashenge (FST= 0.819). Similarly, between farmed populations, high gene flow was observed between Kyanamira and Kajjansi (FST = 0.033). O. esculentus from lakes Kanyaboli and Bisina show a lower genetic differentiation (FST = 0.076). Analysis of Molecular Variance (AMOVA) results indicated 51% of the total genetic variation was found among populations, while 42% occurred within populations, highlighting a moderate differentiation within populations. Based on STRUCTURE analysis, Uganda populations (Albert, George, Kajjansi, Kyanamira, Kyoga and Victoria) formed a distinct cluster, while those from Lake Chamo, Hashenge and Tana formed a distinct cluster. Multivariate analyses based on Principal Coordinate Analysis (PCoA) and Neighbour-Joining revealed distinct clusters by species and geographical location. O. niloticus, Tana populations show distinct cluster compared to Uganda populations that are clustered together; Kyoga, Victoria, Kyanamira, George, Kajjansi and Albert. The observed genetic diversity, gene flow, and population differentiation confirm the applicability of EPIC markers as molecular tools for monitoring biodiversity and guiding the conservation of tilapiine species under increasing anthropogenic and environmental pressures.
Keywords: Tilapia. EPIC markers. Genetic diversity. Population structure. Conservation