Bridging the gap between breeding programs and commercial populations: Investigating the genetic basis of post-handling resilience in Atlantic Salmon (Salmo salar) using DNA pooling

Some traits relevant to commercial performance of Atlantic salmon, such as post-handling resilience, are not expressed or routinely measured in breeding nucleus populations, making it difficult to investigate genetic associations with other traits. In this study, we used a DNA pooling approach to bridge the gap between breeding nucleus and commercial Atlantic salmon populations, enabling genetic analysis of traits not directly expressed in the breeding program. Our aim was to investigate whether post-handling resilience is genetically associated with cardiac morphology and to explore potential unintended consequences and opportunities to improve resilience within current breeding objectives. Tissue samples were collected from 1000 fish across 10 commercial cohorts that experienced mortality following stressful management events such as amoebic gill disease (AGD) treatments, transfers, or handling. Cohorts were tracked through to harvest, and matched samples were collected from surviving fish. Samples were pooled by phenotype (survivor or mortality), genotyped using a custom 50 k SNP array, and genomic estimated breeding values (GEBVs) were generated for cardiac, survival, thermal tolerance, AGD resistance, and production traits using prediction equations developed from breeding nucleus data. Survivor pools had significantly lower heart weight, HOG weight, and condition factor GEBVs, suggesting a genetic link between larger body size and increased susceptibility to handling stress. Survivor pools also had higher summer and post-summer survival GEBVs and higher thermal tolerance GEBVs. These results demonstrate the value of DNA pooling for linking breeding nucleus-derived genomic predictions with commercial phenotypes and identifies strategies to improve post-handling resilience in the Tasmanian Atlantic salmon industry. • DNA pooling linked breeding nucleus traits to post-handling resilience on farms. • Larger body size genetically associated with post-handling mortality. • No strong genetic associations between cardiac traits and post-handling resilience. • Surviving fish showed higher genetic merit for survival and heat tolerance.