Gene Expression Response to Sea Lice in Atlantic Salmon Skin: RNA Sequencing Comparison Between Resistant and Susceptible Animals

Abstract

Sea lice are parasitic copepods that cause large economic losses to salmon aquaculture worldwide. Frequent chemotherapeutic treatments are typically required to control this parasite, and alternative measures such as breeding for improved host resistance are desirable. Insight into the host–parasite interaction and mechanisms of host resistance can lead to improvements in selective breeding, and potentially novel treatment targets. In this study, RNA sequencing was used to study the skin transcriptome of Atlantic salmon (Salmo salar) parasitized with sea lice (Caligus rogercresseyi). The overall aims were to compare the transcriptomic profile of skin at louse attachment sites and “healthy” skin, and to assess differences in gene expression response between animals with varying levels of resistance to the parasite. Atlantic salmon pre-smolts were challenged with C. rogercresseyi, growth and lice count measurements were taken for each fish. 21 animals were selected and RNA-Seq was performed on skin from a louse attachment site, and skin distal to attachment sites for each animal. These animals were classified into family-balanced groups according to the traits of resistance (high vs. low lice count), and growth during infestation. Overall comparison of skin from louse attachment sites vs. healthy skin showed that 4,355 genes were differentially expressed, indicating local up-regulation of several immune pathways and activation of tissue repair mechanisms. Comparison between resistant and susceptible animals highlighted expression differences in several immune response and pattern recognition genes, and also myogenic and iron availability factors. Components of the pathways involved in differential response to sea lice may be targets for studies aimed at improved or novel treatment strategies, or to prioritize candidate functional polymorphisms to enhance genomic selection for host resistance in commercial salmon breeding programs.

Genome-scale comparative analysis for host resistance against sea lice between Atlantic salmon and rainbow trout

“…Meanwhile in trout on Omy21, serine/threonine-protein phosphatase 2A 56 kDa was identified, which is described as having participated in cell growth and signaling 40 . Robledo et al (2018) 26 recently found that in Atlantic salmon, this protein showed the most significant change in the expression ratio between healthy skin and skin where sea lice were found 26 . In Atlantic salmon, we identified Tripartite motif-containing protein 45 (TRIM) on Ssa25 which belongs to a large family of proteins present in diverse organisms that can function as a ligase, and can modify ubiquitins and proteins stimulated by interferon of 15 kDa (ISG15) 41 .…”

“…The number of parasites counted in each species after the challenge is below the range determined in previous studies. For instance, Ødegård et al (2014) 9 obtained an average of 20.96 ± 19.68, while Robledo et al (2018) 26 reported an average of 38 ± 16.…”

“…Studies have described T-bet expression in NK cells (natural killer), dendritic cells and T CD8+ cells 37,38 . A recent study 26 on gene expression with C. rogercresseyi infestation in susceptible and resistant Atlantic salmon indicated that several components of the immune system (inflammatory response, cytokine production, TNF and NF-kappa B signaling and complement activation) and tissue repair are upregulated during infection.…”

“…This gene is part of a superfamily of receptors with tyrosine kinase activity that have been described in a variety of organs with growth promoter functions, cellular differentiation 46 and could participate in tissue repair by promoting cell growth 36 . In rainbow trout, fibroblast growth factors ( fgf11 - Omy10, fgf13 - Omy29 ) have similar functions (angiogenesis and pro-inflammatory response), and were identified as important genes involved in sea lice resistance by Skugor et al (2009) and Robledo et al (2018) in Atlantic salmon 26,43…”

Advances in genetic improvement for salmon and trout aquaculture: the Chilean situation and prospects

“…Combining different sources of information, including GWAs, transcriptomic [e.g. Robledo et al (2018)] and re-sequencing of whole genomes, will improve the identification of QTN for polygenic traits, which is key for the international initiative called Functional Annotation of All Salmonid Genomes, which is aimed at generating a deeper understanding of the underlying biology and identification of QTN for different economically important traits in salmonids (Macqueen et al 2017).…”