GWAS meta-analysis of resistance against Piscirickettsia salmonis in Atlantic salmon

ABSTRACT Salmonid rickettsial syndrome (SRS) remains as one of the most important pathogens for salmon farming. Genetic improvement has proven to be a viable alternative to reduce mortality in breeding stock. Understanding the genetic architecture of resistance has been a matter of ongoing research aimed at establishing the most appropriate method by which genomic information can be incorporated into breeding programs. However, the genetic architecture of complex traits such as SRS resistance may vary due to genetic and environmental background. In this work, we used the genotypes of a total of 5839 Atlantic salmon from 4 different experimental challenges against Piscirickttsia salmonis , which were imputed high density (∼930K SNP) to perform within-population genomic-association analyses, followed by a meta-analysis of resistance to SRS defined as binary survival and day of death. The objectives of this study were to i) uncover the genomic regions associated with resistance to SRS among multiple populations; and ii) identify candidate genes associated with each trait definition. SNP-based meta-analysis revealed a clear QTL on Ssa02 for both traits while gene-based meta-analysis revealed 16 genes in common for both traits. Our results suggest a polygenic genetic architecture and provide novel insights into the candidate genes underpinning resistance to P. salmonis in Salmo salar .