Tilapia aquaculture systems in the East Africa Community (EAC) region are based on a handful of species, notably O. niloticus. However, there are other wild tilapia species and strains that could be potential candidate species for fish farming with or without genetic improvement. The additional tilapia species may contain genes contributing to disease resistance, accelerated growth, or tolerance to adverse environmental factors such as temperature or salinity. However, the uncontrolled movement and introduction of genetic materials between populations of these groups of species could result in a loss of biodiversity. At the same time, aquaculture operations can potentially benefit from selective breeding campaigns where this does not negative impact sustainability. While aquaculture production has increased remarkably in the EAC region, it is likely that the increase might have occurred at the expense of aquatic biodiversity. In EAC, there is currently paucity of information on the status of the wild tilapia strains, the level of distribution and stocking of alien strains, and their potential impact on biodiversity in the Lake Victoria basin.
We sequenced 389 tilapia samples from the Lake Victoria basin (Uganda, Kenya and United Republic of Tanzania) using an Illumina HiSeq 4000 to identify informative 32,125,84 Single nucleotide polymorphisms (SNPs). Our results show that 33 individuals were classified as hybrids, all involving O. niloticus. 19 of these are crosses with O. esculentus (from seven sites), 11 with O. variabilis (from six sites) and 3 with O. leucostictus (from one site). No site had more than one type of hybrid. Result revealed that, Orieochromis niloticus from Lake Albert had one ancestry group, while those from Lakes Kakyera and Kijanibarola were from another, fish from Lake Victoria had a mix of the two groups. It was evident that there is weak population structure within O. niloticus, with a small amount of differentiation segregating, which can be described as ongoing. These results will facilitate making informed decisions on how best management could preserve the diversity of these resources with a view of using them sustainably for selective breeding programs and consequently promoting their use in improving commercial aquaculture in EAC.