Genome-wide SNP Association Analysis of Body Weight in Atlantic Salmon (salmo salar)

Atlantic salmon body weight is an economically important trait controlled by numerous genes. Given the complexity of this trait, the identification of genes and chromosomal regions associated with growth has been difficult. We performed an association study based on the Atlantic salmon 6.5K SNP panel in a population from the Mainstream Canada broodstock program. Over 400 individuals (comprising 5 full-sib families and 202 parents) were genotyped and according to their phenotypic values classified as fast or slow growing fish. The 30 individuals showing the highest and lowest values were selected for the association analysis using over 4000 SNPs distributed on the 29 Atlantic salmon chromosomes. Single marker allele association within the 202 parents representing the population showed numerous SNPs significantly associated with growth (p < 1E-4) and located in different chromosomes. Analyses performed by comparing the five sampled families showed highly significant (p < 1E-10) SNPs associated with growth. Specific genotypes associated with fast growth were determined for significant SNPs, showed a family effect. Markers with a significant association with growth were searched against Atlantic salmon sequences available at Asalbase (www.asalbase.org). Identified genes were GO annotated giving numerous associations to metabolic and cellular processes. Overall, our findings provide useful evidence for SNPs associated with body weight. These SNPs should be valuable candidates for use in marker-assisted selection breeding programs. Moreover, it is an important step towards the identification of genes and the understanding of the genetic components underlying growth in Atlantic salmon.