Nile tilapia is one of the most important aquaculture species globally, providing high-quality animal protein for human nutrition and representing a source of income to sustain the livelihoods of many people in low and middle-income countries. This species is native to Africa, but the genetic makeup of its wild and farmed populations remains poorly characterized. Additionally, there has been important introgression and movement of farmed (and wild) strains connected to tilapia aquaculture, but the relationship between wild and farmed populations is also unknown in most of the continent. Genetic characterization of African populations has the potential to support the conservation of the species and selective breeding to improve the indigenous strains for profitable aquaculture production.
In the current study, a total of 382 fish genotyped for 60,785 genome-wide single nucleotide polymorphism loci were utilized to investigate the genetic structure, ancestry, diversity, and inbreeding levels within and between farmed and wild Nile tilapia populations in Uganda. The presence of putative signatures of selection was also investigated in the genomes of the studied tilapia populations. The wild fish in the current study were sourced from Lake Albert, Lake Kyoga, and Lake Victoria , while the farmed fish were sourced from 10 hatchery farms located mostly in the catchment regions of the three lakes (Figure 1) .
We observed a clear genetic structure of the fish sourced from the lakes, with L. Kyoga and L. Albert populations showing higher genetic similarity . However, L. Victoria’s population was genetically distinct from fish of both L. Albert and L. Kyoga. Among the farmed populations, we also observed noticeable genetic structure among farmed populations, with most of them being genetically similar to L. Albert and L. Kyoga fish. Indeed, our a dmixture results showed a higher (4 – 53.2%) contribution of L. Albert / L. Kyoga strains to Uganda’s farmed fish than the strain from L. Victoria (0.8 – 31.7%). We observed relatively high genetic diversity and low inbreeding rates across both wild and farmed populations, but some farms had sizable numbers of highly inbred fish, raising concerns about management practices. Finally, w e identified a genomic region on chromosome 5, harbouring a key innate immune gene BPI and the key growth gene GHRH, putatively under selection in the Ugandan Nile tilapia population. In addition, this region overlaps with the genomic region previously identified to be associated with growth rate in farmed Nile tilapia.