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

Lead Research Organisation: University of Edinburgh
Department Name: The Roslin Institute

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 Using genome sequencing and a mature bioinformatic pipeline, we have identified ~3,000 new structural variants (SVs) and confirmed ~3,000 already known SVs in 20 Atlantic salmon individuals, 10 resistant and 10 susceptible to to ameobic gill disease. We have identified SVs that represent candidate functional variants for disease resistance. The work is ongoing, and only partly fulfils the objectives of the original grant.
Exploitation Route In ongoing research, we will use the outcomes of this funding to improve our understanding of the genetic basis for disease resistance in Atlantic salmon, in addition to the role of SVs in influencing variation in gene expression.
Sectors Agriculture, Food and Drink

 
Title Genome re-sequencing of salmon with different resistance to gill disease 
Description 20 genomes (10 susceptible, 10 resistant to ameobic gill disease according to gEBVs) were sequenced at 15-20x coverage and used to characterize structural variation 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? No  
Impact Identification of candidate functional variants for disease resistance 
 
Title Structural Variation Analysis in Salmonids 
Description New bioinformatic workflow developed for reliable detection of structural variation in salmonid genome. Used to characterize SVs in 493 Atlantic salmon 
Type Of Material Data analysis technique 
Year Produced 2018 
Provided To Others? No  
Impact Data and bioinformatic workflow being used in ongoing projects and collaboration with industry partners 
 
Description AquaLeap consortium 
Organisation Centre For Environment, Fisheries And Aquaculture Science
Country United Kingdom 
Sector Public 
PI Contribution Co-principal investigator on grant supporting collaboration. Leading on research to assemble genomes and investigate structural variation.
Collaborator Contribution Prof. Ross Houston (Roslin) leading consortium. SAIC provided cash funding to support collaboration. Hendrix providing key samples to investigate structural variation. Exeter and Stirling collaborating on genome assembly of aquaculture species.
Impact In process
Start Year 2019
 
Description AquaLeap consortium 
Organisation Hendrix Genetics
Country Netherlands 
Sector Private 
PI Contribution Co-principal investigator on grant supporting collaboration. Leading on research to assemble genomes and investigate structural variation.
Collaborator Contribution Prof. Ross Houston (Roslin) leading consortium. SAIC provided cash funding to support collaboration. Hendrix providing key samples to investigate structural variation. Exeter and Stirling collaborating on genome assembly of aquaculture species.
Impact In process
Start Year 2019
 
Description AquaLeap consortium 
Organisation Scottish Aquaculture Innovation Centre
Country United Kingdom 
Sector Multiple 
PI Contribution Co-principal investigator on grant supporting collaboration. Leading on research to assemble genomes and investigate structural variation.
Collaborator Contribution Prof. Ross Houston (Roslin) leading consortium. SAIC provided cash funding to support collaboration. Hendrix providing key samples to investigate structural variation. Exeter and Stirling collaborating on genome assembly of aquaculture species.
Impact In process
Start Year 2019
 
Description AquaLeap consortium 
Organisation University of Aberdeen
Department Institute of Biological and Environmental Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution Co-principal investigator on grant supporting collaboration. Leading on research to assemble genomes and investigate structural variation.
Collaborator Contribution Prof. Ross Houston (Roslin) leading consortium. SAIC provided cash funding to support collaboration. Hendrix providing key samples to investigate structural variation. Exeter and Stirling collaborating on genome assembly of aquaculture species.
Impact In process
Start Year 2019
 
Description AquaLeap consortium 
Organisation University of Edinburgh
Department The Roslin Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution Co-principal investigator on grant supporting collaboration. Leading on research to assemble genomes and investigate structural variation.
Collaborator Contribution Prof. Ross Houston (Roslin) leading consortium. SAIC provided cash funding to support collaboration. Hendrix providing key samples to investigate structural variation. Exeter and Stirling collaborating on genome assembly of aquaculture species.
Impact In process
Start Year 2019
 
Description AquaLeap consortium 
Organisation University of Exeter
Department College of Life and Environmental Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution Co-principal investigator on grant supporting collaboration. Leading on research to assemble genomes and investigate structural variation.
Collaborator Contribution Prof. Ross Houston (Roslin) leading consortium. SAIC provided cash funding to support collaboration. Hendrix providing key samples to investigate structural variation. Exeter and Stirling collaborating on genome assembly of aquaculture species.
Impact In process
Start Year 2019
 
Description AquaLeap consortium 
Organisation University of Stirling
Country United Kingdom 
Sector Academic/University 
PI Contribution Co-principal investigator on grant supporting collaboration. Leading on research to assemble genomes and investigate structural variation.
Collaborator Contribution Prof. Ross Houston (Roslin) leading consortium. SAIC provided cash funding to support collaboration. Hendrix providing key samples to investigate structural variation. Exeter and Stirling collaborating on genome assembly of aquaculture species.
Impact In process
Start Year 2019
 
Description AquaLeap consortium 
Organisation Xelect Ltd
Country United Kingdom 
Sector Private 
PI Contribution Co-principal investigator on grant supporting collaboration. Leading on research to assemble genomes and investigate structural variation.
Collaborator Contribution Prof. Ross Houston (Roslin) leading consortium. SAIC provided cash funding to support collaboration. Hendrix providing key samples to investigate structural variation. Exeter and Stirling collaborating on genome assembly of aquaculture species.
Impact In process
Start Year 2019
 
Description Coordinated meeting of the international 'Functional Annotation of All Salmonid Genomes' initiative 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact This meeting was attended by 30 salmonid biologists linked to the international FAASG initiative (https://www.faasg.org/). Key discussions were held on the future of the initiative, its links to UK infrastructure (EMBL-EBI) and future funding priorities, influencing funders in attendence (Norwegian Research Council and Genome Canada)
Year(s) Of Engagement Activity 2019
URL https://icisb.org/faasg-meeting/
 
Description Fish Farming Expert Magazine Piece "Full exploitation of genetics in aquaculture requires a better understanding of how the genome 'blueprint' functions" 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Published the non-scientific piece "Full exploitation of genetics in aquaculture requires a better understanding of how the genome 'blueprint' functions" in Fish Farming Expert Magazine. Pg. 46-47 (April 19), an example of knowledge exchange via lay communication of the objectives of our work relevant to the BBSRC Roslin ISP1 goals
Year(s) Of Engagement Activity 2019
 
Description Invited talk at International workshop Functional annotation of the Atlantic salmon genome, translation to improved health and performance in aquaculture. 'Advancing aquaculture by genome functional annotation: Memorial University, Canada. Aug 26-27th 2019. 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Gave an invited talk at International workshop Functional annotation of the Atlantic salmon genome, translation to improved health and performance in aquaculture. 'Advancing aquaculture by genome functional annotation: Memorial University, Canada. Aug 26-27th 2019. The outcomes were an increased mutual understanding of research and collaborative activity with international collaborating scientists.
Year(s) Of Engagement Activity 2019
 
Description Lead coordinator of the fourth International Conference on the Integrative Biology of Salmonids (https://icisb.org/). 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact The fourth International Conference on Integrative Salmonid Biology (ICISB 2019), followed on from previous meetings in 2012 (Oslo, Norway), 2014 (Vancouver, Canada) and 2016 (Puerto Varas, Chile). The ICISB meetings have been core funded and organized by the International Cooperation to Sequence the Atlantic Salmon Genome (ICSASG), a trilateral effort between Canada, Chile and Norway. The theme of ICISB 2019 was'Beyond the genome: taking leaps forward in salmonid biology' to reflect the recent staggering progress in genomic resource development and exploitation since the Atlantic salmon reference genome was published in 2016.

There was an audience of ~200, which represented a mixture of researchers from Professors leading in the field, to undergraduate students. Many international collaborations and opportunities for further research, funding and meetings were explored with a range of stakeholders, including funders, media and industry.
Year(s) Of Engagement Activity 2019
URL https://icisb.org/