Genomic analysis of fillet quality traits in North American Atlantic salmon (Salmo salar)

The downgrading of Atlantic salmon due to fillet quality traits, such as textural and compositional traits, cause high economic loss for the aquaculture industry. However, very few studies have investigated the heritability and genomic architecture of textural and compositional traits in fish. Therefore, the aims of this study were: 1) to provide insight into the heritability of sixteen quality metrics, such as gumminess, moisture, and glucidic traits, 2) to determine the correlation between these traits, and 3) to identify any genomic regions associated with variation of the phenotypes using 50K SNP array data. A total of 196 Saint John River strain North American Atlantic salmon from the 2011 year-class were harvested and the phenotypes recorded. Moderate genomic heritabilities (>0.2) were estimated in eight of the sixteen fillet quality traits, including moisture and fat. There were generally moderate to high correlations (0.16 to 0.98) between many of the quality traits implying that a change in one trait would likely impact some of the others. In particular, fat and glucose both had moderate heritability and moderate to high correlations to many other traits, implying they could possibly be used for selection to represent most traits evaluated in this study. Maturity and bled weight effects were significant for 13 traits, implying some of these quality traits may already be benefiting from selection pressures on growth and age traits that are currently in the breeding program. No significant loci were found to be associated with any of the traits. However, purge loss had a distinct peak that approached the significance threshold and passed the suggestive threshold. These results provide important baseline data on the genomic architecture of fillet quality traits in Atlantic salmon.