# Uncovering Allele-Specific Expression Patterns Associated with Sea Lice (Caligus rogercresseyi) Burden in Atlantic Salmon

## TL;DR

This study identifies gene expression patterns in Atlantic salmon linked to sea lice infestation, offering insights into genetic resistance for aquaculture improvement.

## Contribution

The novel integration of differential gene expression and allele-specific expression analysis reveals cis-regulatory variation affecting sea lice resistance in salmon.

## Key findings

- Sixty genes showed significant allele-specific expression, with 33 overexpressed and 27 underexpressed.
- Overexpressed genes are linked to epithelial integrity and immune response, while underexpressed genes relate to cytokine signaling and oxidative stress.
- Several ASE genes overlap with QTLs for sea lice resistance, suggesting cis-regulatory variants influence parasite susceptibility.

## Abstract

Background/Objetives: Sea lice (Caligus rogercresseyi) pose a major threat to Atlantic salmon (Salmo salar) aquaculture by compromising fish health and reducing production efficiency. While genetic variation in parasite load has been reported, the molecular mechanisms underlying this variation remain unclear. Methods: two sea lice challenge trials were conducted, achieving high infestation rates (47.5% and 43.5%). A total of 85 fish, selected based on extreme phenotypes for lice burden (42 low, 43 high), were subjected to transcriptomic analysis. Differential gene expression was integrated with allele-specific expression (ASE) analysis to uncover cis-regulatory variation influencing host response. Results: Sixty genes showed significant ASE (p < 0.05), including 33 overexpressed and 27 underexpressed. Overexpressed ASE genes included Keratin 15, Collagen IV/V, TRIM16, and Angiopoietin-1-like, which are associated with epithelial integrity, immune response, and tissue remodeling. Underexpressed ASE genes such as SOCS3, CSF3R, and Neutrophil cytosolic factor suggest individual variation in cytokine signaling and oxidative stress pathways. Conclusions: several ASE genes co-localized with previously identified QTLs for sea lice resistance, indicating that cis-regulatory variants contribute to phenotypic differences in parasite susceptibility. These results highlight ASE analysis as a powerful tool to identify functional regulatory elements and provide valuable candidates for selective breeding and genomic improvement strategies in aquaculture.