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Under the US-Ireland Research and Development Partnership, the five-year project, Environmental RNA-based Assessment of Fish Health (eRNA-FISH), brings together researchers from Queen’s University Belfast, Dublin City University (DCU) and the University of Maine (UMaine).

The team aims to create an early warning system capable of detecting stress and disease in farmed Atlantic salmon using simple water samples.

Atlantic salmon are the most productive marine finfish in global aquaculture. However, disease and environmental stress can cause substantial economic losses, with costs running into hundreds of millions annually. Current diagnostic approaches often require invasive or lethal sampling or only detect problems once they have already progressed.

Professor Paulo Prodöhl, Professor of Population and Evolutionary Genetics from the School of Biological Sciences will lead the research team at Queen’s, he said:

“This new research will test whether environmental RNA (eRNA), genetic material shed by fish into surrounding water, can provide early insight into fish physiology, including responses to heat stress and infection.

“Environmental RNA technology is still at an early stage of development, but its potential is significant. At Queen’s, we will apply advanced genomics and bioinformatics approaches to identify the molecular signatures of stress and disease in salmon. By working closely with colleagues at DCU and UMaine, we aim to ensure that this technology moves from proof-of-concept to practical application for the aquaculture industry.”

Unlike environmental DNA (eDNA), which primarily identifies which species are present, eRNA is dynamic and reflects how organisms are responding to their environment in near real time. By analysing RNA signals in water, researchers hope to detect physiological stress before visible symptoms appear.

Professor Anne Parle-McDermott from Dublin City University’s Life Sciences Institute and Water Institute said: “This funding is a testament to the power of interdisciplinary research. By combining our molecular expertise with the knowledge and expertise at UMaine and QUB, we are uniquely positioned to tackle one of aquaculture’s biggest challenges. 

“While traditional eDNA tells us which organisms are present, our focus on environmental RNA (eRNA) allows us to capture the physiological 'signals' fish release into their surroundings. Leveraging CRISPR-Cas technology will enable us to transform a simple water sample into a high-tech diagnostic tool, moving the industry away from invasive testing toward a more sustainable, proactive model of animal welfare."

Michael Kinnison, Professor of Evolutionary Applications and Director of the Maine Center for Genetics in the Environment at UMaine said: “This eRNA technology is really at the developmental stage, but we believe in its potential as a tool for monitoring Atlantic salmon as well as other organisms. The range of expertise this project brings together is essential to realizing this potential and developing tools that improve the aquaculture industry.”

Erin Grey, Associate Professor of Ecological Informatics at UMaine said:  “We are going to start simple with a controlled system and a pilot study. As this technology is established, we plan to work with stakeholders to understand their needs and test this technology in more open systems.”

The total tripartite award of €1.2 million is supported by funders in all three jurisdictions, including the Department of Agriculture, Food and the Marine (DAFM) in Ireland, the U.S. Department of Agriculture’s National Institute of Food and Agriculture (NIFA), and the Department of Agriculture, Environment and Rural Affairs (DAERA) in Northern Ireland.

Professor Paulo Prodöhl

Professor of Population and Evolutionary Genetics, School of Biological Sciences

Media

For media enquiries please contact Grace White at Queen’s Communications Office: g.white@qub.ac.uk