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.
Highlights
Aquaculture is the fastest-growing food production sector worldwide, with an average growth in production of 5.3% per annum during the period 2001–2018 (FAO 2020)
Field outbreak Throughout the Tilapia lake virus (TiLV) outbreak, clinical signs related to this viral infection were observed, including damage at the base of fins, hemorrhage, and skin erosion
Data collection and genomic information Experimental challenges are commonly used as a means to collect measurements of host disease resistance for the purposes of genetic improvement in aquaculture (Ødegård et al 2011; Yañez et al 2014; Houston et al 2020)
Summary
Aquaculture is the fastest-growing food production sector worldwide, with an average growth in production of 5.3% per annum during the period 2001–2018 (FAO 2020). The recent emergence of Tilapia lake virus (TiLV) has presented major threats to the sustainability of tilapia production, affecting both Nile tilapia and interspecific hybrids (Eyngor et al 2014; Ferguson et al 2014; Dong et al 2017), with mass mortalities up to 90% possible at several stages of the production cycle (Dong et al 2017; Fathi et al 2017). This disease is produced by an RNA virus which has recently been classified as a member of the Tilapinevirus genus, Amnoonviridae family (ICTV 2018). There are currently only a few treatments and options for prevention, and with outbreaks possible in very young juvenile fish, the potential of vaccination is limited (Thammatorn et al 2019)
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