Genomic research to improve cleaner fish performance, welfare and efficiency at delousing salmon

Aquaculture contributes more than £1.8bn to the UK economy every year and supports over 8,800 livelihoods - many in remote communities. Farmed Scottish salmon is the most valuable farmed food export in the UK. Industry and Government have strong aspirations for growth (from 162,817t in 2016 to >300,000t by 2030, Marine Scotland Science and Aquaculture growth to 2030, Scotland Food and Drink) to meet increasing market demands. However, considerable pressures are being experienced by the farming sector because of emergency harvests due to disease outbreaks and losses and concerns over the sustainability of the sector. 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, physical damage, osmoregulatory failure, increased disease incidence, stress, and immunosuppression. Sea lice is thought to cost the Scottish salmon sector in excess of £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 in commercial Atlantic salmon farming. Particularly the use of two cleaner fish species, ballan wrasse (Labrus bergylta) and lumpfish (Cyclopterus lumpus) have gained importance, but the use of wild caught fish has raised significant concerns over the sustainability of this practice. 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. Having that in consideration, next-generation sequencing and high-throughput genotyping technologies are called to play a fundamental role in the development of genomic resources such as the identification of thousands of single nucleotide polymorphism (SNP) in relation to important traits. The availability of genomic markers such as SNPs will facilitate the domestication of cleaner fish species and improvement of commercially important traits (e.g. growth, feed efficiency, disease resistance, survival, delousing) 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. The project intends to identify quantitative trait loci and genetic markers associated to growth, disease resistance, delousing behaviour and robustness and the study of population genetics. 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 already planned in 2021-2022 as part of current BBSRC/NERC funded AQUALEAP project (BB/S004416/1 and BB/S004343/1) awarded to UoS and UoE, respectively) and KTP project awarded to UoS 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 li