Abstract

Salmon aquaculture is constantly threatened by pathogens that impact fish health, welfare, and productivity. Thus, the breeding programs allow the selection of individuals with characteristics that improve productive performance. Understanding the mechanism associated with better behavior in salmons requires holistic studies. Thus, this study uses a model of controlled repeated infestations to explore the genomics and microbiome changes in fifteen Atlantic salmon families with contrasting phenotypes after three successive infestations with the sea louse Caligus rogercresseyi. Transcriptional information of skin tissue from three phenotypes, resistant (R), susceptible (S), and one salmon family that showed a putative acquired resistance to sea lice (ALR), was obtained by RNA sequencing by Illumina. In addition, 16S RNA Nanopore sequencing determined each phenotype's skin microbiota. Transcriptome data was assembled into the Atlantic salmon genome, and the chromosome genome expression (CGE) index was applied, showing differences in chromosome modulation among the phenotypes. The R and ALR families showed up-modulation of immune genes compared with the S family. Notably, the skin microbiota of the R and the ALR exhibited the highest diversity. Moreover, among bacteria identified in the R and ALR highlining, Pseudomonadaceae produces metabolites with antiparasitic functions. This is the first study performed in Atlantic salmon families associated with sea lice resistance and susceptibility under successive infestations. Moreover, our finding suggests a putative sea lice resistance acquire in one salmon phenotype after the successive infections.