Nile tilapia is the most important aquaculture species on the African continent, providing high-quality nutrients, and a major source of income to sustain the livelihoods of many people involved in the supply chain on the continent. This species is native to Africa, however, the genetic background of key traits in the indigenous strains on the continent is largely unknown which limits the genetic improvement of these strains for better production.
In the current study, ~600 juvenile fish produced from a commercial Nile tilapia hatchery broodstock population (originally sourced from Lake Albert, Lake Kyoga, and Lake Victoria) were evaluated for growth. Fish were tagged at ~3 months of age and body weight and morphological traits were measured biweekly. Fin clip tissues were collected for 500 fish and subsequently genotyped 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), clean genotype data was subsequently used to perform principal component analysis (PCA) and genome-wide association study (GWAS) analyses for average daily gain, body weights, and sex.
In the current study, a total of 499 fish had good-quality genotype data (5.4M SNP and INDELs). Fish from the three stocks did not significantly (P > 0.05) differ in growth, but L. Albert stock grew 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 being kept together in the same pond without tagging, PCA results showed substantial genetic differentiation between the three sub-populations kept by the hatchery (Figure 1A). GWAS results showed generally polygenic architecture for growth rate (Figure 1B) and body weight, however, we identified three major quantitative loci (QTLs, 2 on Chromosome 6 and 1 on Chromosome 23) underlying sex determination in the studied Nile tilapia populations (Figure 1C). Our results are a resource contributing towards improving tilapia production.