The sea louse Caligus rogercresseyi is a major ectoparasite affecting Atlantic salmon (Salmo salar) aquaculture, causing significant economic losses due to reduced fish health, growth performance, and increased treatment costs. Selective breeding programs that enhance salmon resistance to sea lice have emerged as a sustainable alternative to chemical control methods.
This study explores how genetically resistant salmon influence both the transcriptomic response and bacterial community composition of C. rogercresseyi. Sea lice were collected from three salmon families categorized as susceptible (S), acquired lice resistant (ALR)-which developed resistance during the trial-, and resistant (R) after three successive experimental infestations. RNA-seq (Illumina) and 16S rRNA gene sequencing (Oxford Nanopore) were used to characterize gene expression and bacterial profiles in lice.
Differential expression analysis revealed distinct transcriptomic patterns across lice from different host phenotypes. Lice from resistant families (ALR and R) exhibited a predominance of downregulated transcripts (Figure 1.A), particularly in genes linked to metabolism, signaling, and digestion, whereas lice from the S group showed upregulation of genes related to cuticle formation and development. KEGG analysis further confirmed functional modulation in pathways associated with immune, excretory, and digestive systems in lice from host resistant families. Microbiota profiling revealed higher microbial diversity in lice from the susceptible group (Figure 1.B), dominated by Proteobacteria and Bacteroidetes, while lice from ALR and R groups harbored over 88% Proteobacteria. Core microbiome and functional prediction analyses supported the existence of group-specific microbial signatures.
These findings provide new insights into host–parasite–microbiome interactions and support the implementation of genetically resistant salmon as a practical and environmentally friendly strategy for sea lice control in aquaculture.
Funding: ANID-Chile FONDECYT #11220307; FONDECYT #1210852; y FONDAP #1523A0007