A major quantitative trait locus affecting resistance to Tilapia lake virus in farmed Nile tilapia (Oreochromis niloticus)

Abstract

Enhancing host resistance to infectious disease has received increasing attention in recent years as a major goal of farm animal breeding programs. Combining field data with genomic tools can provide opportunities to understand the genetic architecture of disease resistance, leading to new opportunities for disease control. In the current study, a genome-wide association study was performed to assess resistance to the Tilapia lake virus (TiLV), one of the biggest threats affecting Nile tilapia (Oreochromis niloticus); a key aquaculture species globally. A pond outbreak of TiLV in a pedigreed population of the GIFT strain was observed, with 950 fish classified as either survivor or mortality, and genotyped using a 65 K SNP array. A significant QTL of large effect was identified on chromosome Oni22. The average mortality rate of tilapia homozygous for the resistance allele at the most significant SNP (P value = 4.51E-10) was 11%, compared to 43% for tilapia homozygous for the susceptibility allele. Several candidate genes related to host response to viral infection were identified within this QTL, including lgals17, vps52, and trim29. These results provide a rare example of a major QTL affecting a trait of major importance to a farmed animal. Genetic markers from the QTL region have potential in marker-assisted selection to improve host resistance, providing a genetic solution to an infectious disease where few other control or mitigation options currently exist.

Fig. 1. Manhattan plot for resistance to Tilapia lake virus (TiLV) in a Nile tilapia (Oreochromis niloticus) breeding population.

Manhattan plot of GWAS for host resistance, as binary survival, to TiLV. On the y axis is the –log10(P-value). The horizontal dashed red line shows the genome-wide significance threshold. Oni24 represent SNPs with unknown chromosome location.

Fig. 2. Predicted mortality values for host resistance to Tilapia lake virus in a Nile tilapia breeding population.

Host resistance as binary survival predictive values for each genotype of the SNPs with the stronger genome-wide association. The bars on yellow, light blue, and green show the predicted values for the top three SNPs located on Oni22. The bars show the standard error. Numbers above the bars indicate the number of fish with the specific genotype.