From gross morphology to gill transcriptome in farmed Atlantic salmon (Salmo salar): Lessons from multi-site sampling

E. Krol, A. Douglas, P. Noguera, V. Valdenegro, K. Gajardo, R. Bickerdike, S. A. M. Martin* (Corresponding Author)

*Corresponding author for this work

Research output: Contribution to journalAbstractpeer-review


The gill is a multifunctional organ involved in many physiological processes such as gas exchange, osmotic and ionic regulation, acid-base balance and excretion of nitrogenous waste. Due to its interface with the environment, the gill plays a key role as primary mucosal defence tissue against pathogens and is equipped with the gill-associated lymphoid tissue (GIALT). In recent years, the prevalence of gill damage and gill diseases has increased significantly, leading to the substantial losses in Atlantic salmon aquaculture worldwide. Both the transition from healthy to unhealthy gill phenotypes as well the progression of various gill pathologies such as proliferative gill disease (PGD), amoebic gill disease (AGD) and complex gill disease (CGD) are commonly characterised by inflammation and epithelial cell hyperplasia. Routine monitoring for PGD relies on gross (macroscopic) evaluation of gill health, coupled with histological examination of gill sections. To explore underlying molecular events that are associated with progression of PGD, we examined Atlantic salmon from geographically diverse aquaculture sites in Scotland. Total RNA was extracted from 43 fish presenting low or medium gill PGD scores and analysed by whole transcriptome analysis using RNA-seq to determine the molecular signature of the advanced PGD. For each fish, 20M reads were generated and mapped to the Atlantic salmon genome. Importantly, we showed that the sampling site had greater effect on the gill transcriptome than the actual PGD score, providing support for a complex and multifactorial aetiology of PGD, with minimal common molecular responses between different sites. Similar pattern was found for histology, agreeing with the outcome of the RNA-seq analysis. In general, both RNA-seq and histology data clustered together based on the origin of samples, suggesting that the PGD scores may inform about the overall progression of gill damage, but not about the underlying pathology.
Original languageEnglish
Pages (from-to)467
Number of pages1
JournalFish & Shellfish Immunology
Early online date17 Jun 2019
Publication statusPublished - Aug 2019


  • Proliferative gill disease
  • gill histopathology
  • gill transcriptome
  • PGD scores
  • RNA-seq


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