The bacterial pathogens Renibacterium salmoninarum, Moritella viscosa, and Piscirickettsia salmonis cause infectious diseases [Bacterial Kidney Disease (BKD), Winter Ulcer Disease (WUD), and Salmonid Rickettsial Septicemia (SRS), respectively] that are serious threats to global Atlantic salmon aquaculture. Genomics approaches [i.e. 44K microarrays, RNA sequencing, and real-time quantitative PCR (qPCR)] were used to identify and validate head kidney transcripts that respond to R. salmoninarum and P. salmonis, and skin transcripts that respond to M. viscosa. Thousands of genes were identified as significantly responsive to each pathogen, and qPCR assays were developed for over 100 of these immune-relevant biomarker genes. Gene ontology (GO) term and pathway enrichment analyses of transcriptomic data (i.e. pathogen-responsive genes) provided insights into molecular mechanisms involved in the infections. For example, GO terms enriched in M. viscosa-induced skin transcripts included several related to phagocyte function (e.g. macrophage migration, regulation of macrophage activation, phagosome maturation, respiratory burst, Fc-gamma receptor involved in phagocytosis). These transcriptomic studies identified and validated molecular biomarker genes that can be used at the transcript expression level (e.g. qPCR) for aquaculture Research and Development (e.g. diagnostics, vaccine efficacy testing, and studies of the influence of dietary components and feeding regimens on Atlantic salmon responses to these pathogens). In addition, our studies provide comprehensive trait-relevant gene lists (e.g. genes up-regulated and down-regulated by BKD, WUD, or SRS) that can be mined to identify candidate genes for SNP discovery and association analyses, potentially accelerating the development of tools for marker assisted selection of disease resistant Atlantic salmon broodstock.
Eslamloo K, Caballero-Solares A, Inkpen SM, Emam M, Kumar S, Bouniot C, Avendaño-Herrera R, Jakob E, and Rise ML. (2020). Transcriptomic profiling of the adaptive and innate immune responses of Atlantic salmon to Renibacterium salmoninarum infection. Frontiers in Immunology 11: 567838.
Eslamloo K, Kumar S, Xue X, Parrish KS, Purcell SL, Fast MD and Rise ML. 2022. Global gene expression responses of Atlantic salmon skin to Moritella viscosa. Scientific Reports 12(1): 4622.
Xue X, Caballero-Solares A, Hall JR, Umasuthan N, Kumar S, Jakob E, Skugor S, Hawes C, Santander J, Taylor RG, and Rise ML. (2021). Transcriptome profiling of Atlantic salmon (Salmo salar) parr with higher and lower pathogen loads following Piscirickettsia salmonis infection. Frontiers in Immunology 12: 789465.