Meta-analysis of GWAS for sea lice load in Atlantic salmon

Sea lice (Caligus rogercresseyi) is an ectoparasite that causes major production losses in the salmon aquaculture industry of the southern hemisphere. Atlantic salmon (Salmo salar) is an important salmonid for the aquaculture industry and a species which is highly susceptible to sea lice infestation. Genetic variation for resistance to sea lice, defined as parasite load, has been found in Atlantic salmon. In addition, sea lice load has been shown to be a polygenic trait, controlled by several quantitative trait loci (QTL) which have small to medium effect, making them difficult to map with sufficient statistical power when sample sizes are limited. The use of medium density single nucleotide polymorphisms (SNP) can also adversely affect the success of identifying genetic variants significantly associated to sea lice load. In order to improve the ability to detect QTL significantly associated to sea lice load, we combined genotype imputation from medium- to high SNP-density and performed genome-wide association studies (GWAS) across different populations of Atlantic salmon. The imputation of genotypes of 6,144 fish challenged against sea lice from four year-classes was performed to increase density from 70K SNPs to 600K SNPs. A meta-GWAS was then carried out for three different traits: lice count, lice density and log-lice density. Using this approach, we detected a genomic region highly associated to sea lice load on Atlantic salmon chromosomes (ssa) 3 and 12 pronounced peaks and several other regions surpassing the significance threshold across almost all other chromosomes. We also identified important genes within the QTL regions, many of these genes are involved in tissue reparation, such as Mucin-16-like isoform X2 and Filamentous growth regulator 23-like isoform X1. The QTL region on ssa03 also contained cytoskeletal-modifying and immune response related genes such as Coronin 1A and Claudin. Our results confirm the highly polygenic architecture of sea lice load, but they also show that high experimental power can lead to the identification of candidate genes and thus to increased insight into the biology of sea lice resistance in Altantic salmon.