AquaLeap: Innovation in Genetics and Breeding to Advance UK Aquaculture Production

Lead Research Organisation: University of Exeter
Department Name: Biosciences

Abstract

Sustainable and profitable aquaculture in the UK relies on high quality stock. In contrast to terrestrial agriculture, the sources of stock for aquaculture species range from use of wild stock for several species, to pedigree-based breeding programmes incorporating genomic tools in salmon. Well managed programmes of domestication and breeding have huge potential for cumulative gains in production, including by preventing infectious disease outbreaks. Barriers to applying such approaches in commercial aquaculture include knowledge gaps in the genetic basis of economically important traits, and a lack of genetic tools and expertise applied to aquaculture. 'AquaLeap' establishes a leading interdisciplinary hub focused on innovation in aquaculture genetics to enable each sector to take a 'step' or 'leap' forward in stock enhancement.

We will target advances for four species of economic importance or potential for UK aquaculture; European lobster (Homarus gammarus), European flat oyster (Ostrea edulis), lumpfish (Cyclopterus lumpus) and Atlantic salmon (Salmo salar). For each of these species, we will develop genomic tools and methods which will then be used to tackle industry-defined barriers to progress in stock enhancement.

The genomic tools include high quality reference genome sequences using cutting-edge sequencing technology for the species for which they are currently lacking (lobster, oyster, lumpfish). These genome sequences will be used to exploit standard (e.g. single nucleotide polymorphism, SNP) and novel [e.g. copy number variation (CNV) and epigenetic modifications] sources of variation. Gene editing techniques will be developed, as this technology is likely to lead to breakthroughs in addressing aquaculture problems in the near future.

Lobsters are a high value species with potential for diversifying UK aquaculture. Building on previous studies into the on-growing of hatchery-reared lobsters in aquaculture systems, and using the aforementioned genomic tools, we will assess the contribution of genetic and epigenetic variation to growth and survival traits. These results will inform selective breeding, hatchery conditions and choice of juveniles for on-growing, and has potential to improve the performance of lobsters at sea.

Native oysters have declined dramatically in recent years, and there is significant interest in restocking from both an aquaculture and ecological perspective. A major barrier to hatchery-based restocking and production is the parasitic disease Bonamia. We will build on previous genomic tool development to identify SNP markers that can be used to predict breeding animals with innate resistance to Bonamia, informing selection of native oysters for stocking and tackling a major production issue.

Lumpfish are used extensively as cleaner fish for biological control of sea lice in salmon farming. Hatchery reproduction is now possible, and the next step is selective breeding for traits to enhance their robustness and performance. To help facilitate this, we will assess wild stock diversity to inform base populations for breeding, to estimate genetic parameters for production traits, and develop SNP marker panels for stock management.

Breeding of salmon is advanced, and uses genomic tools to enhance trait improvement and inbreeding control via genomic selection (GS). We will apply innovative approaches to improve the cost-efficiency of GS, and test these approaches for the emerging aquaculture species. We will assess the role of potential novel sources of genetic variation (CNVs) in gill health traits. Finally, we will use gene editing to modify a specific gene causing resistance to a viral disease in salmon, with a view to future editing of salmon genes to improve resistance to infectious diseases.

The scientific programme is complemented by a series of training, dissemination and public engagement activities, including addressing skills gaps identified by the ARCH-UK network.

Technical Summary

The primary goal of AquaLeap is to tackle industry-defined barriers to advances in selective breeding and domestication of aquaculture species. To achieve this goal across diverse aquaculture sectors, we will develop appropriate underpinning genomic tools and techniques, and then apply those to specific end-user-defined problems in three 'emerging' species (European lobster, European flat oyster, Lumpfish) and one 'established' species (Atlantic salmon.)

The reference genome assemblies for the emerging species will be created using 10X genomics and PacBio sequencing approaches. These will underpin several downstream tasks, including choice of SNP marker panels for stock management and breeding value calculations, genotype imputation and study of epigenetic marks using bisulphite sequencing.

In lobster, we will estimate heritability for growth and survival traits using mixed model approaches, and will assess the relative contribution of genetics and epigenetics to these traits. In oyster, we will use a recently developed SNP array to study resistance to Bonamia, harnessing data from a large-scale laboratory disease challenge. In lumpfish, we will assess stock diversity using RAD-Sequencing to inform choice of animals for base populations, and will assess heritability of production traits. In salmon, we will assess the contribution of copy number variants to genetic variation in disease resistance, with a focus on gill health traits.

Across all species, we will develop SNP marker panels for parentage and stock management, and also use the genomic resources to test imputation approaches to improve the affordability of genomic selection via combined parentage - imputation panels.

Gene editing has transformative potential for aquaculture and we will improve CRISPR-Cas9 editing techniques in salmon, and use editing to target putative causative variants underlying a major disease resistance QTL in salmon cell lines and embryos.

Planned Impact

AquaLeap is based on close cooperation and interdependency between the academic and non-academic partners, providing clear routes for immediate translation of research results. This is augmented by exchange of personnel and skills between partners, across sectors, including industrial placements for PDRAs. The broader impacts will arise from the creation of a hub of expertise in breeding and genetics, including animal and plant breeding experts, with associated training and capacity building. The following groups can expect positive impact from the proposal:

(i) UK and global aquaculture production: The immediate impacts will be via project partners. For the National Lobster Hatchery, the outputs include tools and knowledge to inform selection of lobsters for breeding to improve performance and robustness at sea. For Tethys oysters, the outputs will include methods to inform selection of stock with increased resistance to Bonamia in the field, with downstream benefits for survival and robustness of stocks. For Otterferry Sea Farms, the outputs will include validated tools to inform lumpfish selective breeding for improved stock to tackle sea lice in the salmon industry. For Hendrix Genetics, the primary output will be improvement of gene editing methods and methods for use of new breeding technologies to improve disease resistance in salmon. The longer term impacts include improved performance and reliability of stock in UK aquaculture, making step advances in the various sectors. In turn, this offers potential for cumulative gains in production, including disease resistance. This will help tackle existing and emerging disease threats in an environmentally friendly and sustainable manner, helping to address animal welfare concerns. The focus on several emerging species will also assist with UK aquaculture diversification, which is an important component of maximising sustainable production and minimising risk.

(ii) Genetic services industry: There are several companies in the UK and globally whose core business is to support aquaculture breeding and production by offering genetic services, including management of breeding programmes. For project partner Xelect, the outputs will include potential new products which can be offered to new and existing customers, all of which may be useful to other partners in the project (e.g. marker panels for parentage and cost-effective estimation of breeding values, CNV assays for marker-assisted selection).

(iii) UK economy: This project has potential for long term impact for the UK economy via improved sustainable production of various high quality food products with reduced environmental impact. There will be direct contribution to the UK treasury via improved competitiveness and market share for project partners, and also downstream positive impacts on fish farming companies, and the communities that depend on these industries.

(iv) UK science capacity. This project will enable capacity and expertise for use of genetic and genomic tools to answer fundamental biological questions via research programs in academia and industry. This includes the development of universal genomic resources such as reference genome assemblies and SNP panels. This should help cement the position of the UK as a leading country in aquaculture bioscience.

(v) Political and regulatory bodies. Aquaculture is assuming increasing political importance, and solutions to production and environmental issues are key to its expansion. The outputs of this project may influence ethical and regulatory frameworks to encourage exploitation of new breeding technologies such as gene editing.

(vi) General public and society. This project has potential to influence societal attitudes to aquaculture, including use of selective breeding and gene editing. In the longer term, there will be direct benefits to society via improved economic stability and reduced environmental impact of the aquaculture industry.

Publications

10 25 50
 
Description The project is only running for just over one year and all work described below is in progress:

1 - Development of genomic resources for the European Lobster, an emerging species for aquaculture. We have used PacBio sequencing to sequence the lobster genome. Genome assembly and annotation are currently in progress, but preliminary results suggest this will be a high quality genome, with over 90% of all genes represented.
2 - Identification of genetic determinants of growth for the European Lobster. Samples were obtained from a previous research project, in collaboration with the National Lobster Hatchery and prepared for sequencing using RAD-Seq. This will identify genetic variants associated with faster growth in a population of farmed lobsters.
3 - Identification of the epigenetic determinants of growth for the European Lobster. This part of the project is in the planning phase. Samples have been collected and the final selection of samples and design of the methylation experiments will depend on the results obtained for part 1 and 2 above.
Exploitation Route The outcomes of the work will be used directly by the industrial partners (National Lobster Hatchery) who will utilise the information generated to inform on their hatchery practices. Further, the genome sequence and SNPs will be of high utility to the scientific and end user community working on European lobsters or other related crustacean species who will be able to utilise our sequence data for their own experiments. These include our partners in the project, Cefas, who are collaborating in the bioinformatics data analysis and who will directly use the genomic resources generated in their research activity.
Sectors Agriculture, Food and Drink,Environment

 
Title Genomic resources for the European Lobster 
Description We have obtained PacBio long read sequence data for the European Lobster and the genome of this species is currently being assembled and annotated. This genomic resource will be of significant utility to the research and end-user community working on this or related species. A research paper will be published in due course and the data will be made available in public databases. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? No  
Impact This resource is still being developed and so it is currently not available to the community. 
 
Description Epigenetics approaches for disease prevention 
Organisation Centre For Environment, Fisheries And Aquaculture Science
Country United Kingdom 
Sector Public 
PI Contribution The links developed during the project with the Cefas partners have led to the agreement of a shared PhD studentship to start in October 2020. To date, we have conceptualised the project and organised a training plan for the studentship which will be advertised this spring.
Collaborator Contribution The Cefas partners have contributed to the development of a PhD studentship which will be partially funded by Cefas and by the University of Exeter. This studentship will continue to address issues related to disease in aquaculture and specifically to study whether epigenetics theory can be utilised to increase host resistance to disease.
Impact The partnership has just been initiated.
Start Year 2020
 
Description Exeter Marine Dessimination videos 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Speaker in dissemination videos promoting the research being undertaken in the topics of Marine Biology and Aquaculture at Exeter. The use of genomics in marine research and to address the key challenges of aquaculture were highlighted. These videos have been disseminated via various social media platforms (Twitter, Facebook, YouTube, etc) and it is envisaged that they have reached general public audiences, students and industries both nationally and internationally.
Year(s) Of Engagement Activity 2020
URL https://www.youtube.com/watch?v=_ZY3-MQzxl8
 
Description Workshop with end users - Aquaculture 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact I was invited to participate in the workshop 'Sustainable Aquaculture through the One Health Lens' at the Department for Environment, Food and Rural Affairs (Defra) London, on 1st July 2019 where I led one of the discussion groups on sustainable aquaculture. The workshop included participants from research organisations, governmental agencies (Cefas, DEFRA) end-user communities and international research organisations and agencies. The concept of One Health applied to aquaculture was discussed and adopted as a framework in which to base future research and practice. The discussions generated during and after the workshop resulted in a publication which has been submitted to 'Nature Food' (revised version invited).
Year(s) Of Engagement Activity 2019