Uncovering Allele-Specific Expression Patterns Associated with Sea Lice (<em>Caligus rogercresseyi</em>) Resistance in Atlantic Salmon

Sea lice (Caligus rogercresseyi), represents a major constraint to Atlantic salmon (Salmo salar) aquaculture, affecting both fish health and production efficiency. Genetic variation for sea lice load has been previously documented in Atlantic salmon. To investigate the basis of the variation in sea lice burden at a transcriptomic level, two consecutive challenge trials were conducted. Infestation success rates of 47.5% and 43.5% were achieved, indicating high parasite attachment efficiency. For transcriptomic analysis, a total of 85 fish were selected based on their phenotypic values of parasite load, comprising 42 individuals with low lice burden and 43 with high lice burden. To elucidate the regulatory mechanisms underlying sea lice load variation, allele-specific expression (ASE) analysis was integrated with differential gene expression profiling. A total of 60 genes (33 overexpressed, 27 underexpressed) exhibited significant ASE (p &lt; 0.05), indicating the presence of cis-regulatory variants influencing key host response pathways. Notably, overexpressed ASE genes included structural and immune-related components such as Keratin 15, Collagen types IV and V, TRIM16, and Angiopoietin-1-like, which are associated with epithelial integrity, inflammation, and tissue remodeling. In contrast, underexpressed ASE genes such as SOCS3, CSF3R, and Neutrophil cytosolic factor suggest genotype-dependent modulation of cytokine signaling and oxidative stress responses. Several ASE genes co-localized with previously reported QTLs for sea lice burden variation, supporting a model in which cis-regulatory variation contributes to phenotypic variation in host response against the parasite. These findings underscore the utility of ASE analysis for the identification of functionally relevant genomic regions and provide promising candidates for genetic improvement and precision breeding.