Mapping quantitative trait loci for infectious salmon anaemia resistance in a North American strain of Atlantic salmon

Abstract

Infectious salmon anaemia (ISA) is a highly virulent viral disease of Atlantic salmon that causes massive economic losses to infected aquaculture operations. Our goal was to detect and map quantitative trait loci (QTL) that confer resistance to ISA in an admixed commercial strain of Atlantic salmon that was largely founded from the Saint John River (SJR) in North America. Full‐sibling families were challenged with a virulent strain of ISA virus. Mortality was tracked during two annual trials with individual fish that survived to the end of the trial being classified as ‘resistant’, and those that died were classified as ‘susceptible’. Ten families with intermediate levels of mortality and an average size of 54.2 individuals were chosen for genotyping with a 50K SNP array designed for the SJR strain. Single nucleotide polymorphisms that were segregating within families were first used to make a composite 11K female linkage map that was then used to find the positions of QTL for ISA resistance using a half‐sib model. The dam‐based HS model detected a total of three QTL for ISA resistance including an experiment‐wide significant QTL on Ssa25 that accounted for 8.3% of the phenotypic variance and chromosome‐wide significant QTL on Ssa03 and on Ssa04 that accounted for 6.0% and 6.6% respectively. We conclude that classic linkage mapping within families continues to be an important method of detecting QTL for oligogenic traits in strains founded from multiple populations. Single nucleotide polymorphisms with moderate trait effects are being used to select within families for more ISA‐resistant strains of Atlantic salmon.

Exploring genetic resistance to Infectious Salmon Anaemia Virus in Atlantic salmon by genome-wide association and RNA sequencing

“…Yet, four genomic regions explaining > 2.5% of the genetic variation in resistance to ISAV were detected. Two previous studies found resistance QTL for ISAV on chromosomes Ssa03, Ssa04, Ssa15 and Ssa25 [28,29], however, in our study, no signal of resistance was detected in these chromosomes; this is not surprising considering the different origins of the populations and the polygenic nature of resistance to ISAV (and the different nature of the challenge, through intraperitoneal injection, in [29]).…”

“…Several studies have shown that host resistance to ISAV has a significant additive genetic component in Atlantic salmon, with heritability estimates ranging from 0.13 to 0.40 [23][24][25][26][27]. Furthermore, studies using molecular markers to investigate the genetic architecture underlying this heritability have revealed putative QTL on chromosomes 3, 4, 15 and 21 [28,29], and a comparative genomic analysis highlighted potential underlying genes [30]. Several studies have also examined the host response to ISAV by profiling gene expression in tissues and cell lines [31][32][33][34][35][36].…”

Exploring genetic resistance to infectious salmon anaemia virus in Atlantic salmon by genome-wide association and RNA sequencing

“…Furthermore, previous studies using co-habitation have used a higher proportion of ‘Trojan’ fish, which may result in a higher infection pressure and differences in host response [ 37 ]. Finally, the genetic correlation between resistance to ISAV in freshwater (this study, [ 28 ]) and seawater [ 29 ] should be addressed in future studies; the life stage of the fish can have an important impact on resistance to ISAV and could also explain some of the differences between studies.…”

Applying genetic technologies to combat infectious diseases in aquaculture

“…Infectious salmon anaemia 178,179 Pancreas disease 180,181 Piscine myocarditis virus [182][183][184] Amoebic gill disease [185][186][187] Sea lice 65,188,189 Infectious pancreatic necrosis 81,154,190,191 Piscirickettsia salmonis 192…”