Genome-wide association analysis of salmon lice (Lepeophtheirus salmonis) resistance in a North American Atlantic salmon population

Abstract

Our objective was to detect single nucleotide polymorphisms (SNPs) associated with resistance to the salmon louse in the Saint John River aquacultural population of North American Atlantic salmon using estimated breeding values (EBVs) and 6K genotypes from the parent-generation and lice count phenotypes from the challenged, but ungenotyped, offspring-generation. In 2011 and 2012, we challenged recent smolts with approximately 100 copepodids each. Fish were euthanized once the lice reached the chalimus stages and lice count, sex, tank and salt water weight were recorded. We used a multiple trait model to estimate breeding values for the parent-generation using their own fresh water weights and the salt water weights and lice counts of the offspring-generation. Salmon lice count heritability for untransformed and transformed data was 0.17 and 0.29 respectively. Two different genome-wide association study methods were compared: (i) forward multiple linear regression and (ii) a mixed linear model using principal components to correct for population stratification as implemented in the egscore function of GenABEL. The two methods detected different SNPs located on different chromosomes. The multiple regression method incorporated 70 SNPs found on chromosomes 2, 7, 9, 12, 14, 15, 21, 22, 1p/23, 24. Many SNPs entered into the forward multiple regression are likely to be false positives from not correcting for the observed population stratification and cryptic relatedness. In contrast, the mixed linear model identified only two SNPs, one on chromosome 1p/23 (6.9%) and one on chromosome 1q (6.1%) consistent with louse-resistance being a quantitative trait.

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

“…many genes with small effect are involved in the trait). 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.…”

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

“…Quantitative trait loci explaining between 6% and 13% of the genetic variation in sea louse resistance (louse density on fish) have been detected in North American and Chilean populations of Atlantic salmon (Rochus et al . 2018; Robledo et al . 2019).…”

Identification of Growth-Associated Genes by Genome-Wide Association Study and Their Potential Application in the Breeding of Pacific White Shrimp (Litopenaeus vannamei)

“…It utilizes high-density SNPs distributed along the genome to determine the QTLs by statistical associations between SNP genotypes and particular phenotypes. GWAS has been successfully carried out in fish, referring to many traits, such as filet texture, fat content ( Sodeland et al, 2013 ), growth ( Gonzalez-Pena et al, 2016 ; Li et al, 2017 ), sexual maturation ( Gutierrez et al, 2015 ), disease resistance ( Liu et al, 2015 ; Zhou et al, 2017 ; Rochus et al, 2018 ; Tan et al, 2018 ), low oxygen tolerance ( Zhong et al, 2017 ), and fatty acid composition ( Horn et al, 2020 ). As for crustaceans, reports to use GWAS to discover SNPs or genes related to interesting traits are relatively less.…”