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Development of genomic tools to improve cleaner fish performance, welfare and efficiency at delousing salmon

   Institute of Aquaculture

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  Dr A Gutierrez, Prof H Migaud, Prof R Houston, Dr Michael Bekaert  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

Stirling United Kingdom Bioinformatics Ecology Genetics Marine Biology Molecular Biology

About the Project

This is a great opportunity to take part in an exciting project focused on the development and analysis of genomic resources for cleaner fish. We are looking for an enthusiast and motivated student interested in aquaculture genomics to be part of a multidisciplinary team and collaborate with commercial partners, to tackle one the main issues affecting salmon aquaculture.


The greatest disease threat challenging salmon aquaculture is the infection by caligid sea lice (salmon louse Lepeophtheirus salmonis and the sea louse Caligus elongatus). These parasites feed on the skin, mucous, and blood, leading to skin erosion and immunosuppression. Sea lice is thought to cost the Scottish salmon sector around £50m and £700m globally. To mitigate the effect of these parasites, the use of cleaner fish (that forage on lice) has become a promising biological control solution to manage sea lice infections. Particularly the use of two cleaner fish species, ballan wrasse (Labrus bergylta) and lumpfish (Cyclopterus lumpus) have gained importance. Recently, the life cycle of both species has been closed in captivity offering great opportunities for domestication and improvement programs to make this unique pest management strategy more effective and sustainable.

Genomic resources remain limited for both cleaner fish species although recent efforts have been made with the recent publication of the first genome assembly for both cleaner fish species. Next-generation sequencing and high-throughput genotyping technologies are called to play a fundamental role in the development of genomic resources. The availability of genomic markers such as SNPs will facilitate the improvement of commercially important traits but also provide a better understanding of the genetic structure and diversity of the captive and farmed populations. In addition, the strong physiological differences between both species in performances (lumpsucker growing too fast as opposed to ballan wrasse growing too slow), behaviour, disease susceptibility, environmental tolerance provide an interesting comparative approach.


This project aims to develop genomic resources for both ballan wrasse and lumpfish and utilize these for the understanding of the genomic architecture behind important economic traits such as growth, disease resistance, robustness and possibly delousing behaviour and the study of population genetics for both captive farmed and wild populations. The prospective student will join a team of leading academics in the field based at the Institute of Aquaculture, University of Stirling and The Roslin Institute, University of Edinburgh and will acquire expertise in breeding, health, genomics and bioinformatics. The project will take advantage of commercial scale experiments as part of current BBSRC/NERC funded AQUALEAP project and KTP project, looking at lumpsucker and wrasse population genetics, growth and disease resistance.

The student will be in charge of performing sampling of cleaner fish populations across the UK at commercial partners facilities including phenotyping and genotyping. RAD-seq libraries will be prepared for the identification of SNP markers which will later be used for genome-wide association study (GWAS) analysis of selected traits. Genomic regions and genes will be identified and new markers identified will be used for the improvement of cleaner fish selective breeding programs.

Funding Notes

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership  This opportunity is open to UK and International students and provides funding to cover stipend and UK level tuition (Please state if your institution will provide funding to cover the difference in fees). Please refer to UKRI website and Annex B of the UKRI Training Grant Terms and Conditions for full eligibility criteria.