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  EASTBIO: Genomics and Gill Health in Atlantic salmon

   School of Biological Sciences

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  Prof S Martin, Dr Elżbieta Król  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

This fully funded, 4-year PhD project is part of a competition funded by the BBSRC EASTBIO Doctoral Training Partnership.

 The Atlantic salmon aquaculture industry is worth over £1 billion to the Scottish economy. However, with progressively warming waters and the novel pathogens emerging under climate change, improving fish health is of high importance. The current focus of sustainable aquaculture is to improve gill health. The gills are not only the main gas exchange site, but also a key immune organ and a site for pathogen entry. Recent research has revealed that gill health and gill function is particularly compromised during the marine stage of salmon production, the phenomenon driven by many different environmental and pathogen factors. We have been using state-of-the-art genomics approaches to understand the gill immune system by investigating how different pathogens and environmental factors can lead to different gene expression outcomes. The PhD student will be based in the Scottish Fish Immunology Research Centre (University of Aberdeen), which has an internationally recognised vibrant research activity. The project will be linked to the ongoing funded projects on gill health and there will be a strong interaction with salmon producers and other industrial partners. This is an exciting time for research into salmon genomics with new tools for epigenetics and gene editing being used to answer industrially relevant question. The project will be linked with the International Program for “Functional Annotation of All Salmonid Genomes (FAASG)”. The PhD student will benefit from extensive molecular, statistical and bioinformatics training, provided by several research laboratories and the Aberdeen Centre for Genome Enabled Biology and Medicine.



Applicants should hold a minimum of a 2:1 UK Honours degree (or international equivalent) in a relevant subject. Those with a 2:2 UK Honours degree (or international equivalent) may be considered, provided they have (or are expected to achieve) a Distinction or Commendation at master’s level.

All students must meet the eligibility criteria as outlined in the UKRI guidance on funding for postgraduate training and development. This guidance should be read in conjunction with the UKRI Training Grant Terms and Conditions.



  • Please visit this page for full application information: How to apply | eastbio (
  • Please send your completed EASTBIO application form, along with academic transcripts to Alison Innes at [Email Address Removed]
  • Two references should be provided by the deadline using the EASTBIO reference form. References should be sent to [Email Address Removed]
  • Unfortunately, due to workload constraints, we cannot consider incomplete applications.
  • CV's submitted directly through a FindAPhD enquiry WILL NOT be considered.
  • If you require any additional assistance in submitting your application or have any queries about the application process, please don't hesitate to contact us at [Email Address Removed]
Biological Sciences (4)

Funding Notes

This fully funded, 4-year PhD project is part of a competition funded by the EASTBIO BBSRC Doctoral Training Partnership.
This opportunity is open to UK and International students (The proportion of international students appointed through the EASTBIO DTP is capped at 30% by UKRI BBSRC).
EASTBIO studentships includes a UKRI doctoral stipend (estimated at £18,622 for the 2023/2024 academic year – rate not yet set for 2024/2025), plus a training grant of £5,000 per annum (year 1-3; £1,500 year 4) and a travel/conference grant of £230 per annum.
EASTBIO does not provide funding to cover visa and associated healthcare surcharges for international students.


• Clark, T C. Naseer, S. Gundappa, M. K. Laurent, A. Perquis, A. Collet, B. Macqueen, D.J. Martin, SAM, Boudinot, P. 2023. Conserved and divergent arms of the antiviral response in the duplicated genomes of salmonid fishes. Genomics. 115. 4: 110663.
• Taylor RS, Ruiz Daniels R, Dobie R, Naseer S, Clark TC, Henderson NC, Boudinot P, Martin SAM, Macqueen DJ. 2022 Single cell transcriptomics of Atlantic salmon (Salmo salar L.) liver reveals cellular heterogeneity and immunological responses to challenge by Aeromonas salmonicida. Front Immunol. 13:984799.
• Król, E., Noguera, P., Shaw, S., Costelloe, E., Gajardo, K., Valdenegro, V., Bickerdike, R., Douglas, A., Martin, S.A.M. 2020. Integration of Transcriptome, Gross Morphology and Histopathology in the Gill of Sea Farmed Atlantic Salmon (Salmo salar): Lessons from Multi-Site Sampling. Frontiers in Genetics. 11: 610
• Houston, R.D., Bean, T.P., Macqueen, D.J., Gundappa, M.K., Jin, Y.H., Jenkins, T.L., Selly, S.L.C., Martin, S.A.M., Stevens, J.R., Santos, E.M., Davie, A., Robledo, D. 2020. Harnessing genomics to fast-track genetic improvement in aquaculture. Nature Reviews Genetics. 21: 389-409.

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