Characterising the mechanisms underlying genetic resistance to amoebic gill disease in Atlantic salmon using RNA sequencing

• Published in: BMC Genomics
• Main Authors: Robledo, Diego, Hamilton, Alastair, Gutiérrez, Alejandro P, Bron, James E, Houston, Ross D
• Other Authors: Scottish Aquaculture Innovation Centre, Biotechnology and Biological Sciences Research Council, Royal Society, H2020 European Research Council, University of Edinburgh, Institute of Aquaculture, orcid:0000-0002-9616-5912, orcid:0000-0003-3544-0519
• Format: Article in Journal/Newspaper
• Language: English
• Published: Springer Science and Business Media LLC 2020
• Subjects: AGD; Genomics; Amoeba; Gene expression; RNA-seq; Transcriptome; Salmo salar; Disease resistance; Allelic specific expression; Atlantic salmon
• Online Access: http://hdl.handle.net/1893/30957; https://doi.org/10.1186/s12864-020-6694-x; http://dspace.stir.ac.uk/bitstream/1893/30957/1/s12864-020-6694-x.pdf

Background Gill health is one of the main concerns for Atlantic salmon aquaculture, and Amoebic Gill Disease (AGD), attributable to infection by the amoeba Neoparamoeba perurans, is a frequent cause of morbidity. In the absence of preventive measures, increasing genetic resistance of salmon to AGD via selective breeding can reduce the incidence of the disease and mitigate gill damage. Understanding the mechanisms leading to AGD resistance and the underlying causative genomic features can aid in this effort, while also providing critical information for the development of other control strategies. AGD resistance is considered to be moderately heritable, and several putative QTL have been identified. The aim of the current study was to improve understanding of the mechanisms underlying AGD resistance, and to identify putative causative genomic factors underlying the QTL. To achieve this, RNA was extracted from the gill and head kidney of AGD resistant and susceptible animals following a challenge with N. perurans, and sequenced. Results Comparison between resistant and susceptible animals primarily highlighted differences mainly in the local immune response in the gill, involving red blood cell genes and genes related to immune function and cell adhesion. Differentially expressed immune genes pointed to a contrast in Th2 and Th17 responses, which is consistent with the increased heritability observed after successive challenges with the amoeba. Five QTL-region candidate genes showed differential expression, including a gene connected to interferon responses (GVINP1), a gene involved in systemic inflammation (MAP4K4), and a positive regulator of apoptosis (TRIM39). Analyses of allele-specific expression highlighted a gene in the QTL region on chromosome 17, cellular repressor of E1A-stimulated genes 1 (CREG1), showing allelic differential expression suggestive of a cis-acting regulatory variant. Conclusions In summary, this study provides new insights into the mechanisms of resistance to AGD in Atlantic salmon, and ...