Discovery and functional annotation of quantitative trait loci affecting resistance to sea lice in Atlantic salmon

Abstract

Word count: 323Sea lice (Caligus rogercresseyi) are ectoparasitic copepods which have a large negative economic and welfare impact in Atlantic salmon (Salmo salar) aquaculture, particularly in Chile. A multi-faceted prevention and control strategy is required to tackle lice, and selective breeding contributes via cumulative improvement of host resistance to the parasite. While host resistance has been shown to be heritable, little is yet known about the individual loci that contribute to this resistance, the potential underlying genes, and their mechanisms of action. In this study we took a multifaceted approach to identify and characterise quantitative trait loci (QTL) affecting hose resistance in a population of 2,688 Caligus-challenged Atlantic salmon post-smolts from a commercial breeding programme. We used low and medium density genotyping to collect genome-wide SNP marker data for all animals.Moderate heritablility estimates of 0.28 and 0.24 were obtained for lice density (as a measure of host resistance) and growth during infestation respectively. Three QTL explaining between 7 and 13 % of the genetic variation in resistance to sea lice (as represented by the traits of lice density) were detected on chromosomes 3, 18 and 21. Characterisation of these QTL regions was undertaken using RNA sequencing and pooled whole genome sequencing data. This resulted in the identification of a shortlist of potential underlying causative genes, and candidate functional mutations for further study. For example, candidates within the chromosome 3 QTL include a putative premature stop mutation in TOB1 (an anti-proliferative transcription factor involved in T cell regulation) and an uncharacterized protein which showed significant differential allelic expression (implying the existence of a cis-acting regulatory mutation). While host resistance to sea lice is polygenic in nature, the results of this study highlight significant QTL regions together explaining a moderate proportion of the heritability of the trait. Future investigation of these QTL may enable improved knowledge of the functional mechanisms of host resistance to sea lice, and incorporation of functional variants to improve genomic selection accuracy.

Genome-scale comparative analysis for host resistance against sea lice between Atlantic salmon and rainbow trout

“…These results agree with previous studies on sea lice resistance, where a similar genetic architecture was suggested by Tsai et al (2016), Rochus et al (2018) and Correa et al (2017) 7,10,30 for Lepeophtheirus salmonis and C. royercresseyi resistance. Recently Robledo et al (2018) 31 described three QTL in Atlantic salmon related to sea lice resistance, using RNA-seq and WGS data. Since sea lice resistance is polygenic, the genetic improvement of sea lice resistance would most likely be best accomplished by means of genomic selection instead of marker assisted selection.…”

Prevention not cure: a review of methods to avoid sea lice infestations in salmon aquaculture

“…2018; Robledo et al . 2019). Salmon families with greater resistance to sea lice show upregulation of several immune pathway and pattern recognition genes compared to more susceptible families (Robledo et al .…”

Characterising the mechanisms underlying genetic resistance to amoebic gill disease in Atlantic salmon using RNA sequencing

“…The potential benefits of the identification of causative variation impacting on complex traits are substantial, ranging from fundamental knowledge of the biology underlying the traits of interest to their application for enhancing these traits in farmed populations. However, even with the addition of various layers of information such as RNA sequencing, determining the causative gene underlying a QTL is not straightforward, especially because the QTL regions tend to be large and contain a large number of genes, as previously described for sea lice resistance QTL [42].…”