Disease & heat resistance

Selection for resistance to cardiomyopathy syndrome (CMS) in Atlantic salmon: experiences from four generations of selective breeding

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Abstract

Cardiomyopathy syndrome (CMS) is a viral disease that affects Atlantic salmon, characterized by inflammation and necrosis of the heart. The etiologic agent is the piscine myocarditis virus (PMCV). A genome-scan (GWAS) for resistance to CMS was conducted on fish sampled at harvest, coming from a cohort (year class 2008) which had been through a CMS outbreak at sea. The phenotype was virus levels in the heart, measured using RT-qPCR. Genotypes came from a 6k SNP-chip. The GWAS was conducted using GCTA (MLMA-LOCO) without additional covariates. Two quantitative trait loci (QTL) were identified, located on chromosomes 27 and 12. The two QTL were used in marker-assisted selection from 2012 to 2018. Jointly they explained 20% of the genetic variance in the original GWAS. From 2018, genomic selection (GS) was implemented, with training data coming from challenge tests performed at VESO Vikan (Namsos, Norway) on the year classes 2018, 2021, 2022, 2024, and 2025. GS was conducted using GCTB with a Bayes B model, with year classes as fixed effects. The GS model was re-trained following each new challenge test (N = 5027 fish in total). The phenotype was virus levels in the heart, measured using RT-qPCR. Genotypes came from a 70k SNP-chip. Heritabilities were 0.41 on average (range 0.25 to 0.50). Genetic correlations between year-classes were 0.91 on average (range 0.73 to 1.00). Using 10x cross-validation, selection accuracies were found to increase over time, from 0.83 (yc 2018) to 1.00 (yc 2024). GWASes performed on the challenge test data (following the GWAS model above but with year class as fixed effect) validated the QTL on chromosomes 12 and 27, but also revealed a large QTL on chromosome 23. That QTL originally had low frequency of the beneficial allele. Genomic selection has, since 2018, led to a steady increase in the frequency of the resistance allele at chromosome 23. Concomitantly, the fraction of genetic variance explained by the QTL has increased, to a current 75%. With increasing frequency of the resistance allele, we have seen that an increasing number of fish have non-detectable virus levels at the end of the challenge test. In a test group where the frequency of the resistance allele was 100%, 75% of fish were virus negative.

Keywords: 2026

How to Cite:

Moen, T., Grammes, F., Kjøglum, S. & Korsvoll, S., (2026) “Selection for resistance to cardiomyopathy syndrome (CMS) in Atlantic salmon: experiences from four generations of selective breeding”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2287051. doi: https://doi.org/10.31274/wcgalp.24201

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