Gill and liver transcript expression changes associated with gill damage in Atlantic salmon (Salmo salar)

Gills of teleost fish represent a vital multifunctional organ; however, they are subjected to environmental stressors, causing gill damage. Gill damage is associated with significant losses in the Atlantic salmon aquaculture industry. Gill disorders due to environmental stressors are exacerbated by global environmental changes, especially with open-net pen aquaculture (as farmed fish lack the ability to escape those events). The local and systemic response to gill damage, concurrent with several environmental insults, are not well investigated. We performed field sampling to collect gill and liver tissue after several environmental insults. Using a 44K salmonid microarray platform, we aimed to compare the transcriptomes of pristine and moderately damaged gill tissue. The gill damage-associated biomarker genes and associated qPCR assays arising from this study will be valuable in future research aimed at developing therapeutic diets to improve farmed salmon gill health. Using a 44K salmonid microarray platform, we aimed to compare the transcriptomes of pristine and moderately damaged gill tissue. The fish were sampled on the 13th and 14th of November 2017. The average weights for all of the collected fish was 1348 grams. The gill samples were collected from the net pen-grown Atlantic salmon located in BC. Fish were randomly netted then euthanized using 400 mg L−1 tricaine-methane sulfonate bath (TMS; Syndel Laboratories, Nanaimo, BC, Canada) after 24 h of fasting. The sampled fish were weighed, fork length-measured, and their gills were scored following the farm’s protocol. Gills with no lesions visible and with single necrotic filament or spot were scored as G0 (i.e., pristine). Gills showing affected area up to 10% of the total gill filament were scored as G1, while G2 was defined as gills having damage affecting ~10% to 25% of the total gill filament. Gills with affected area > 25% of the total fill filament surface are scored as G3. Fish with more than 50% of the total gill filament surface area covered with necrotic tissue were routinely observed but generally in mortalities or very moribund fish and not in healthy fish (B. Milligan, personal communication). Gills were collected for gene expression analyses. Samples around 50-100 mg of each tissue were preserved in 1 mL of RNAlater® solution (Ambion, Inc., Austin, TX, USA) and kept at 4°C overnight, then moved to -20°C until the shipping date to the Ocean Sciences Centre, Memorial University. All the collected samples were subjected for preliminary qPCR study, for sample choice and we aimed to target gills with moderate gill damage. Using a 44K salmonid microarray platform, we aimed to compare the transcriptomes of pristine and moderately damaged gill tissue.