Rearing system type affects baseline and post-vaccination immune gene expression in Atlantic salmon gills during smoltification

Atlantic salmon undergo critical development before sea transfer, and vaccination during this stage isroutine tobuild protective immunity. This study compared immune responses tovaccination insmolt-stage salmon reared inflow-through (FT) versus recirculating (REC) aquaculture systems. Ten clinically healthy fish per facility were collected one week before and two weeks after intraperitoneal vaccination with commercial multivalent vaccines. Using qPCR, wecompared immune gene expression inthe fish gills. Before the vaccination, REC fish exhibited higher relative expression ofgenes coding cathelicidin-1 (cath-1), interleukin-1β (il-1β), and tumour necrosis factor-α (tnf-α) than FT fish. Fourteen days after vaccination, REC fish showed increased expression ofgene coding defensin (def) and decreased expression ofgene for transforming growth factorβ (tgf-β), while inFTfish, vaccination was associated with increased relative gene expression oftnf-α, tgf-β, and il-10. Within REC, cath-1 expression declined postvaccination, concurrent with anincrease inil-10, suggesting apossible counter-regulatory response; inFT, the coordinated rise ofpro-inflammatory (tnf-α) and anti-inflammatory (tgf-β, il-10) transcripts is consistent with an activation followed by regulatory signalling. These transcriptomic patterns imply that baseline immune gene expression and post-vaccination gill transcriptomic responses differ between rearing water systems used during smoltification in Atlantic salmon.