PhD: Multiomics investigations – salmon

PhD on multiomics investigations of the role played by embryonic temperature in programming long-term immune function in Atlantic salmon.

PhD project title: Multiomics investigations of the role played by embryonic temperature in programming long-term immune function in Atlantic salmon

Closing Date: 10 September 2021

Supervisors: Professor Dan Macqueen, (the Roslin Institute, University of Edinburgh, UK) and Dr Erik Burgerhout (Nofima, Tromsø, Norway)


Finfish aquaculture plays an important role in global food and economic security, and the scale of production is growing year on year. In the UK and Norway, Atlantic salmon aquaculture is a leading national food production sector that contributes to major economic and societal benefits. To ensure a fast production cycle, farmed Atlantic salmon have been bred to promote fast growth and are reared at temperatures during early life that exceed what is experienced in nature. However, many fish fail to reach the end of the production line, largely due to infectious diseases, and there thus exists a demand to produce robust animals that show fast growth without compromising their resilience to disease.

‘Metabolic programming’ is a potentially adaptive process where an environmental stimulus during a critical temporal window permanently alters an organism’s physiological development, potentially mediated through changes in the epigenome. Temperature has a pervasive influence on the biology of ectothermic fishes, influencing many biochemical, metabolic and physiological processes. It has been previously shown that changing temperature for a short period of embryogenesis alters the development of many phenotypes later in life, such as growth rate, muscle development, and swimming performance. It is also well established that immune function and growth are highly interlinked in fishes due to trade-offs in energetic allocation. We hypothesise that selection for fast growth and the use of higher than natural embryonic rearing temperatures in salmon aquaculture leads to metabolic programming that impacts development of the immune system and may negatively affect the robustness of adult fish.

Coolfish project

This PhD is funded within a four-year Norwegian project called ‘Coolfish’ due to start in late 2021, which aims to define the role and mechanistic basis for metabolic programming (by embryonic temperature) on the development of Atlantic salmon immune function throughout the aquaculture production cycle. The primary supervisor Macqueen is a WP leader, and the secondary supervisor Burgerhout is the overall project coordinator. A major objective is to elucidate the ‘multi-omic’ (specifically, epigenetic, transcriptomic, proteomic and metabolomic) mechanisms of metabolic programming by embryonic temperature on immune function. This studentship will contribute broadly to this objective, with the student responsible for performing single cell transcriptomics and proteomics analyses of immune tissues. The work will be done collaboratively with researchers at Nofima and other collaborators in Norway, and the student will get the chance to develop multi-omic analyses that link epigenomic changes to metabolic and immune phenotypes via remodelling of the transcriptome and proteome.

Training and networking opportunities

The student will receive training in state-of-the-art functional genomics, including LC/MS proteomics and single cell transcriptomics, covering both the lab work and downstream bioinformatic analyses. There will be scope to work with methylation, bulk transcriptomic, and metabolomic immune tissue datasets, and receive training in the associated data analyses. There will be opportunities to travel to Nofima to support the generation of samples in Coolfish under the supervision of Burgerhout. The student will have the opportunity to present their findings at international conferences during the project and develop an extensive network of contacts with internationally recognized researchers.

Candidate profile and eligibility

We seek a candidate with interests spanning animal physiology, development, genomics and/or functional genomics, ideally with research experience in at least one of these areas. All candidates must have or expect to receive a minimum upper 2nd class BSc degree in a relevant subject. To qualify for full funding students must be UK or EU citizens that have been resident in the UK for 3 years before the PhD starts. We aim for a start date in March 2022, but other start dates will be considered.

Application procedure and further information

Applications including a statement of interest and full CV with names and addresses (including email addresses) of two academic referees, should be emailed to our PGR student team at When applying for the studentship please state clearly the project title and the supervisors in your covering letter.

For informal enquiries, please contact Professor Dan Macqueen ( For more information on the Macqueen lab see

Source: The University of Edinburgh

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