Nile tilapia (Oreochromis niloticus) is the most important aquaculture species in Uganda and Africa at large, providing high-quality animal protein for human nutritional security, and a major source of income that sustains the livelihoods of many people involved in the value chain. Although the species is native to Africa, the genetic background of key traits in the indigenous farmed populations on the continent is largely unknown which constrains genetic improvement of these populations for increased production efficiency.
Our study evaluated ~600 juvenile tilapia produced from a commercial hatchery broodstock population (originally sourced from Lakes Albert, Kyoga, and Victoria in Uganda) were evaluated for growth. Fish were tagged at ~3 months of age, and body weight and morphometric traits were measured biweekly. Fin clip tissues were collected from 500 fish, and subsequently used for genotyping the fish for 27 M variants (SNP and INDELs) via low-coverage sequencing and imputation. Genotype data was cleaned of variants with low minor allele frequency (maf < 0.05) and those that significantly deviated from Hardy-Weinberg Equilibrium (HWE, P < E-7), resulting in 497 fish that had good-quality genotype data (5.4M SNP and INDELs). This data was then used for principal component analysis (PCA) and genome-wide association study (GWAS) analyses for average daily gain (ADG), and sex.
Fish from the three stocks did not significantly (P > 0.05) differ in growth, but L. Albert stock grew slightly faster (0.58g/day) than the stocks from L. Victoria (0.57g/day) and L. Kyoga (0.54g/day). In all three sub-populations, male fish grew significantly (P < 0.05) faster than the females. Despite the minimal physical separation of the three subpopulations at the hatchery, PCA results showed substantial genetic differentiation between the three sub-populations kept by the hatchery (Figure 1A). The GWAS identified a polygenic architecture for growth rate (Figure 1B). We identified three major quantitative loci (QTLs, 2 on Chromosome 23 and 1 on Chromosome 6) underlying sex determination in the studied Nile tilapia populations (Figure 1C). Our results contribute genomic resources towards sustainably improving tilapia aquaculture production.