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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.

Tilapia are among the most important farmed fish species worldwide, and are fundamental for the food security of many developing countries. Several genetically improved Nile tilapia (Oreochromis niloticus) strains exist, such as the iconic Genetically Improved Farmed Tilapia (GIFT), and breeding programs typically follow classical pedigree-based selection. The use of genome-wide single-nucleotide polymorphism (SNP) data can enable an understanding of the genetic architecture of economically important traits and the acceleration of genetic gain via genomic selection. Due to the global importance and diversity of Nile tilapia, an open access SNP array would be beneficial for aquaculture research and production. In the current study, a ∼65K SNP array was designed based on SNPs discovered from whole-genome sequence data from a GIFT breeding nucleus population and the overlap with SNP datasets from wild fish populations and several other farmed Nile tilapia strains. The SNP array was applied to clearly distinguish between different tilapia populations across Asia and Africa, with at least ∼30,000 SNPs segregating in each of the diverse population samples tested. It is anticipated that this SNP array will be an enabling tool for population genetics and tilapia breeding research, facilitating consistency and comparison of results across studies.

Tilapia Lake Virus (TiLV) is one of the primary disease concerns for tilapia farming, with mass mortality events and biosecurity restrictions threating aquaculture in several continents. Selective breeding for improved host resistance to TiLV may help to mitigate this problematic disease, but the extent of genetic variation in resistance is not yet known. The objective of the current study was to estimate genetic parameters for host resistance to TiLV in a Nile tilapia breeding population of the Genetically Improved Farmed Tilapia (GIFT) strain. Using data from 1821 pedigreed fish (from 124 full-sibling families) collected during and after a pond ‘field’ outbreak, resistance was defined using both binary survival (BS) and days to death (TD) traits. Animal and sire-dam linear mixed models were fitted for BS and TD, and BS was also evaluated with using two sire-dam threshold models with either probit (Pro-SD) or logit-link (Log-SD) functions. Cumulative mortality was 39.6% at the end of the outbreak, with family survival rates ranging from 0 to 100%. Moderate to high heritability values were estimated for resistance to TiLV using all models. Significant heritabilities were estimated on the binary scale (0.40 for both animal and sire-dam models) which equates to 0.63 on the underlying liability scale. Using threshold models, heritabilities of 0.56 and 0.48 were estimated for Pro-SD and Log-SD, respectively. Correlation among the full-sib families EBVs predicted by the different models ranged from 0.912 to 0.999, suggesting a low re-ranking of the families and a high consistency of the results obtained using the different models. In addition, significant and moderate heritability of 0.41 (0.06) was estimated for harvest weight (HW), and the genetic correlation between this trait and resistance to TILV was not statistically different from zero. These results demonstrate that host resistance to TiLV is highly heritable in a Nile tilapia breeding population with GIFT origin. Therefore, selective breeding to increase resistance and reduce mortalities due to TiLV is a feasible and promising approach.