AquaLeap: Innovation in Genetics and Breeding to Advance UK Aquaculture Production
Lead Research Organisation:
University of Edinburgh
Department Name: The Roslin Institute
Abstract
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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.
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.
(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.
Organisations
- University of Edinburgh (Lead Research Organisation)
- Natural Environment Research Council (Co-funder)
- Scottish Aquaculture Innovation Centre (Collaboration)
- UNIVERSITY OF ABERDEEN (Collaboration)
- CENTRE FOR ENVIRONMENT, FISHERIES AND AQUACULTURE SCIENCE (Collaboration)
- Hendrix Genetics (Collaboration)
- University of Stirling (Collaboration)
- Xelect Ltd (Collaboration)
- UNIVERSITY OF EDINBURGH (Collaboration)
- UNIVERSITY OF EXETER (Collaboration)
Publications
Houston RD
(2019)
Atlantic salmon (Salmo salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding.
in Animal genetics
Gundappa MK
(2022)
Chromosome-level reference genome for European flat oyster (Ostrea edulis L.).
in Evolutionary applications
Bean T
(2022)
Two parallel chromosome-level reference genomes to support restoration and aquaculture of European flat oyster Ostrea edulis
in Evolutionary Applications
Sambade IM
(2022)
A single genomic region involving a putative chromosome rearrangement in flat oyster (Ostrea edulis) is associated with differential host resilience to the parasite Bonamia ostreae.
in Evolutionary applications
Peñaloza C
(2022)
Genome-Wide Association and Genomic Prediction of Growth Traits in the European Flat Oyster (Ostrea edulis)
in Frontiers in Genetics
Bertolotti AC
(2020)
The structural variation landscape in 492 Atlantic salmon genomes.
in Nature communications
Houston RD
(2020)
Harnessing genomics to fast-track genetic improvement in aquaculture.
in Nature reviews. Genetics
| Description | The AquaLeap project focussed on advancing the uptake and exploitation of genomic technologies in four species of relevance or significant potential for UK aquaculture and the seafood market (Atlantic salmon, European flat oyster, European lobster, and lumpfish). The key idea was that the different species of interest are at very different stages in the process of up-taking genomics and the project should advance the current state of the art for each species, taking lessons from the more advanced species. The award in question funded work on two of these species, Atlantic salmon and European flat oyster. Discoveries and achievements in Atlantic salmon: 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 ameobic gill disease. We have identified SVs that represent candidate functional variants for disease resistance. This data adds to a much larger dataset of 15,483 SVs we have generated for 492 Atlantic salmon, in BBSRC funded work, which were published in Nature Communications (https://doi.org/10.1038/s41467-020-18972-x). SVs are a major source of genetic and phenotypic variation, but have remained challenging to accurately type and thus remain poorly characterized in most species. Our analyses have been overcoming these barriers and have provided insights into the role of SVs in genome evolution and the genetic architecture of farmed salmon traits. We have also generated new resources supporting reliable SV discovery in non-model species. A key objective for Atlantic salmon was to be able to study SVs in large scale population genetics studies. This is a big challenge, because of the cost and time it takes to generate high-confidence SV genotypes in a large number of individuals. We have achieved this key objective by developing a novel approach to genotype SVs accurately across the genome using low-coverage (cost-effective) whole genome sequencing followed by imputation against a reference panel of variants. In short, this work enables SVs and SNPs (commonly used genetic markers) to be captured in future studies, which should enhance our ability to predict traits based on genetic information. This work is currently under review for publication and has been made available as a pre-print (Gundappa et al. bioRxiv, 2023; https://www.biorxiv.org/content/10.1101/2023.03.05.531147v1). Related to the above, we have also sequenced 500 Atlantic salmon genomes at low coverage, from a commercial population with extensive existing data on AGD resistance. We plan to use this data to genotype SVs and SNPs genome-wide, estimate the heritability explained by SVs, before performing a genome wide association study aimed at understand the value of SV information for enhancing genomic prediction accuracy for AGD resistance. Such approaches will allow future studies to capture SVs as genetic markers at a much reduced cost, which may advance their exploitation in aquaculture and other areas such as salmon conservation genetics. The results of the work done on sequencing these 500 Atlantic salmon genomes will be delayed, and cannot be achieved in the bounds of the AquaLeap project. Nonetheless, the original objective has been largely met for Atlantic salmon. Discoveries and achievements in European flat oyster: In a separate task within the AquaLeap project, we have generated a new chromosome level reference genome for the European flat oyster. Despite a growing interest in genetic applications to support population management and aquaculture in this species, a reference genome assembly has been lacking. Our chromosome-level genome assembly and annotation was generated by combining several technologies: Oxford Nanopore, Illumina, and Dovetail OmniCTM proximity ligation sequencing. A contig assembly (N50: 2.38Mb) was scaffolded into the expected karyotype of 10 pseudo-chromosomes. The finished assembly has a total length of 935.13 Mb, scaffold-N50 of 95.56 Mb and is comprised of 57.3% repeats, dominated by unclassified elements specific to O. edulis. The assembly was verified for quality and accuracy using multiple metrics, including a novel linkage map built with ddRAD-Seq technology, comprising 4,016 SNPs from four full-sib families (8 parents and 163 F1 offspring). Annotation of the genome integrating multi-tissue RNA-Seq, comparative protein evidence and ab-initio gene prediction identified 35,699 protein-coding genes. Chromosome level synteny was demonstrated against several high-quality bivalve genome assemblies, including an O. edulis genome generated independently for a French O. edulis individual. Comparative genomics was used to characterize gene family expansions during Ostrea evolution, in a phylogenetic framework capturing diverse bivalve lineages, revealing potential functions and genes that may have facilitated recent flat oyster adaptation. This new reference genome for European flat oyster opens the door to high-resolution genomics in support of conservation and aquaculture initiatives, and improves our understanding of bivalve genome evolution. The genome and all underlying data has been submitted to NCBI under BioProject PRJNA772111. The new genome assembly has been published (Gundappa et al. 2022), alongside a commentary discussing the value of collaborating on genome sequencing projects by competing groups (Bean et al. 2022). In this latter respect, during the course of our work, it became evident that a group in France had a project with the same objective to sequence the Flat oyster genome. We met with this group and agreed on the value of collaboration rather than competition, ultimately co-publishing the two genome assemblies in the same Journal at the same time. The collaboration also allowed us to share knowledge and information that ultimately enhanced the scientific quality of each separate genome assembly study (see Bean et al. 2022). We also took advantage of the genome assembly in an AquaLeap study that validated the potential of genomic prediction in European flat oyster (Peñaloza et al. 2022). Finally, the flat oyster genome we produced is already being used by researchers around Europe in efforts to advance flat oyster conservation, aquaculture and genetic management. During the course of the AquaLeap project, we collaborated with a group in Spain to help them understand the genetic basis for resistance to Bonamia - a devastating parasite of flat oyster. Leveraging our reference genome, this work identified a promising genomic variant that may impart resistance to Bonamia, and has potential to be applied in selective breeding in the future (Sambade et al. 2022). The original objectives for the Flat oyster have been more than achieved, with several additional achievements beyond the original aims. In total, this award has produced 8 peer reviewed publications to date, with at least two more anticipated. |
| Exploitation Route | The structural variation data and analysis pipelines generated in this project will be widely used in ongoing studies of salmon genetic variation and has potential applications supporting genome-enabled selective breeding in aquaculture and understanding genotype to phenotype relationships in both farmed and wild salmon. The flat oyster genome will be widely used in future genetics studies supporting the genetic management and improvement of aquaculture populations, and restoration of threatened wild populations. |
| Sectors | Agriculture, Food and Drink |
| Description | Competitive international PhD studentship on Structural Variation in Farmed Animal Genomes |
| Amount | £146,000 (GBP) |
| Organisation | University of Edinburgh |
| Department | Royal School of Veterinary Studies |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 09/2021 |
| End | 03/2025 |
| Title | Structural and single nucleotide variation imputation in Atlantic salmon |
| Description | We developed an efficient bioinformatic pipeline to jointly impute structural and single nucleotide variation in the Atlantic salmon genome using low-coverage WGS data against a reference panel of variants, including a high-confidence set of structural variants previously published by our group. The method provides novel opportunities to enhance the resolution of genome-wide association studies by capturing structural variation, in addition to more commonly used single nucleotide variation. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | Too early to say, as preprint just released. Next year I expect the current preprint to be published in a peer reviewed article (currently under review), and we will see if it makes an impact, for example by being uptaken by others, or in industry. |
| URL | https://doi.org/10.1101/2023.03.05.531147 |
| Title | A single genomic region involving a putative chromosome rearrangement in flat oyster (Ostrea edulis) is associated with differential host resilience to the parasite Bonamia ostreae |
| Description | European flat oyster (Ostrea edulis) is an ecologically and economically important marine bivalve, that has been severely affected by the intracellular parasite Bonamia ostreae. In this study, a flat oyster SNP array (~14,000 SNPs) was used to validate previously reported outlier loci for divergent selection associated with B. ostreae exposure in the Northeast Atlantic Area. A total of 134 wild and hatchery individuals from the North Sea, collected in naïve (NV) and long-term affected (LTA) areas, were analysed. Genetic diversity and differentiation were related to the sampling origin (wild vs hatchery) when using neutral markers, and to bonamiosis status (NV vs LTA) when using outlier loci for divergent selection. Two genetic clusters appeared intermingled in all sampling locations when using outlier loci and their frequency was associated with their bonamiosis status. When both clusters were compared, outlier datasets showed high genetic divergence (FST > 0.25) unlike neutral loci (FST not ? 0). Moreover, the cluster associated with LTA samples showed much higher genetic diversity and significant heterozygote excess with outlier loci, but not with neutral data. Most outliers mapped on chromosome 8 (OE-C8) of the flat oyster genome, supporting a main genomic region underlying resilience to bonamiosis. Furthermore, differentially expressed genes previously reported between NV and LTA strains showed higher mapping density on OE-C8. A range of relevant immune functions were specifically enriched among genes annotated on OE-C8, providing hypotheses for resilience mechanisms to an intracellular parasite. The results suggest that marker-assisted selection could be applied to breed resilient strains of O. edulis to bonamiosis, if lower parasite load and/or higher viability of the LTA genetic cluster following B. ostreae infection is demonstrated. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | http://datadryad.org/stash/dataset/doi:10.5061/dryad.s1rn8pkbp |
| Title | Chromosome level reference genome for European flat oyster (Ostrea edulis L.) |
| Description | Data associated with the manuscript - Chromosome level reference genome for European flat oyster (Ostrea edulis L.) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | Multiple new collaborations with Flat Oyster research community outside UK. Genome is further being used by several research groups in applications in support of flat oyster population restoration and aquaculture. |
| URL | https://figshare.com/articles/dataset/Chromosome_level_reference_genome_for_European_flat_oyster_Ost... |
| Title | Chromosome level reference genome for European flat oyster (Ostrea edulis L.) |
| Description | Data associated with the manuscript - Chromosome level reference genome for European flat oyster (Ostrea edulis L.) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/Chromosome_level_reference_genome_for_European_flat_oyster_Ost... |
| 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 | Reference genome for European flat oyster |
| Description | A reference genome assembly for the European flat oyster (Ostrea edulis) has been generated by the AquaLeap project. The genome assembly is based on 120x coverage by Nanopore long-read sequencing with at least 15x coverage of reads >15,000bp length. The contig-level assembly (N50: 2.38 Mb; 2,759 contigs) was generated by merging assemblies from two different approaches (Flye and Redbean) after purging of haplotigs. The final chromosome-level assembly was generated by sequencing a library generated by "Omni-C", a chromosome conformation capture method unique to Dovetail Genomics, which was used to scaffold the contigs into ten 'super-scaffolds' matching the expected species karyotype. The final assembly had a scaffold N50 of 94.05 Mb, and a BUSCO completeness score of >95% compared to the BUSCO Mollusca:odb10 reference (5295 genes). The genome is being annotated currently to predict genes, including using empirical RNA-Seq data from multiple tissues. The genome resource should be published in summer 2021. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | No |
| Impact | The reference genome is being used for ongoing research within the AquaLeap consortium, specifically as a reference for genomic analyses seeking to identify regions in the genome associated with disease resistance, with applications for restoration and aquaculture. We have initiated several new collaborations and ongoing agreements with groups in Spain and France based around the usage and publication of the flat oyster reference genome. |
| URL | https://onlinelibrary.wiley.com/doi/10.1111/eva.13460 |
| Title | Structural Variation in the Atlantic salmon genome |
| Description | Novel bioinformatic workflow developed for reliable detection of structural variation in salmonid genome. Used to characterize SVs in 492 Atlantic salmon reported in Bertolotti et al. 2020 |
| Type Of Material | Data analysis technique |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | Data and bioinformatic workflow being used in ongoing projects and collaboration with industry partners |
| URL | https://www.nature.com/articles/s41467-020-18972-x |
| 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. Took over as overall consortium coordinator in Spring 2022, when Prof. Ross Houston moved into industry. Leading on research to assemble the flat oyster genome and investigating novel methods for capturing structural variation in Atlantic salmon genetics investigations. |
| Collaborator Contribution | Prof. Ross Houston (Roslin) leading consortium until Spring 2022. 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 | The AquaLeap consortium has published 18 peer reviewed articles to date, 8 of which are assigned to this award. We have developed novel genetic resources and tools for four species of great importance of potential for UK aquaculture. |
| Start Year | 2019 |
| Description | AquaLeap consortium |
| Organisation | Hendrix Genetics |
| Country | Netherlands |
| Sector | Private |
| PI Contribution | Co-principal investigator on grant supporting collaboration. Took over as overall consortium coordinator in Spring 2022, when Prof. Ross Houston moved into industry. Leading on research to assemble the flat oyster genome and investigating novel methods for capturing structural variation in Atlantic salmon genetics investigations. |
| Collaborator Contribution | Prof. Ross Houston (Roslin) leading consortium until Spring 2022. 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 | The AquaLeap consortium has published 18 peer reviewed articles to date, 8 of which are assigned to this award. We have developed novel genetic resources and tools for four species of great importance of potential for UK aquaculture. |
| 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. Took over as overall consortium coordinator in Spring 2022, when Prof. Ross Houston moved into industry. Leading on research to assemble the flat oyster genome and investigating novel methods for capturing structural variation in Atlantic salmon genetics investigations. |
| Collaborator Contribution | Prof. Ross Houston (Roslin) leading consortium until Spring 2022. 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 | The AquaLeap consortium has published 18 peer reviewed articles to date, 8 of which are assigned to this award. We have developed novel genetic resources and tools for four species of great importance of potential for UK aquaculture. |
| 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. Took over as overall consortium coordinator in Spring 2022, when Prof. Ross Houston moved into industry. Leading on research to assemble the flat oyster genome and investigating novel methods for capturing structural variation in Atlantic salmon genetics investigations. |
| Collaborator Contribution | Prof. Ross Houston (Roslin) leading consortium until Spring 2022. 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 | The AquaLeap consortium has published 18 peer reviewed articles to date, 8 of which are assigned to this award. We have developed novel genetic resources and tools for four species of great importance of potential for UK aquaculture. |
| 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. Took over as overall consortium coordinator in Spring 2022, when Prof. Ross Houston moved into industry. Leading on research to assemble the flat oyster genome and investigating novel methods for capturing structural variation in Atlantic salmon genetics investigations. |
| Collaborator Contribution | Prof. Ross Houston (Roslin) leading consortium until Spring 2022. 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 | The AquaLeap consortium has published 18 peer reviewed articles to date, 8 of which are assigned to this award. We have developed novel genetic resources and tools for four species of great importance of potential for UK aquaculture. |
| 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. Took over as overall consortium coordinator in Spring 2022, when Prof. Ross Houston moved into industry. Leading on research to assemble the flat oyster genome and investigating novel methods for capturing structural variation in Atlantic salmon genetics investigations. |
| Collaborator Contribution | Prof. Ross Houston (Roslin) leading consortium until Spring 2022. 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 | The AquaLeap consortium has published 18 peer reviewed articles to date, 8 of which are assigned to this award. We have developed novel genetic resources and tools for four species of great importance of potential for UK aquaculture. |
| 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. Took over as overall consortium coordinator in Spring 2022, when Prof. Ross Houston moved into industry. Leading on research to assemble the flat oyster genome and investigating novel methods for capturing structural variation in Atlantic salmon genetics investigations. |
| Collaborator Contribution | Prof. Ross Houston (Roslin) leading consortium until Spring 2022. 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 | The AquaLeap consortium has published 18 peer reviewed articles to date, 8 of which are assigned to this award. We have developed novel genetic resources and tools for four species of great importance of potential for UK aquaculture. |
| Start Year | 2019 |
| Description | AquaLeap consortium |
| Organisation | Xelect Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Co-principal investigator on grant supporting collaboration. Took over as overall consortium coordinator in Spring 2022, when Prof. Ross Houston moved into industry. Leading on research to assemble the flat oyster genome and investigating novel methods for capturing structural variation in Atlantic salmon genetics investigations. |
| Collaborator Contribution | Prof. Ross Houston (Roslin) leading consortium until Spring 2022. 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 | The AquaLeap consortium has published 18 peer reviewed articles to date, 8 of which are assigned to this award. We have developed novel genetic resources and tools for four species of great importance of potential for UK aquaculture. |
| Start Year | 2019 |
| Description | ARCH-UK webinar series - 13th July 2020 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk by Manu Kumar Gundappa and Daniel Macqueen: Sequencing and assembly of the European flat oyster genome assembly. Aim was to disseminate key outcome from AquaLeap project to stakeholders. |
| Year(s) Of Engagement Activity | 2020 |
| Description | AquaLeap Webinar and in person workshop |
| 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 | Webinar disseminating the key outcomes of the AquaLeap BBSRC project coordinated by the Roslin Institute and University of Stirling - 85 individuals registered, 60 in attendance. Explored ways in which genomics can tackle challenges in aquaculture sustainability. Included two external speakers, Prof. Bruce Whitelaw (Director of Roslin Institute) and Dr Anna Wargelius, who contributed also to a panel discussion about genome editing applications in aquaculture, comparing the regulatory situation in the UK to Norway. Attendees included researchers from all career stages, industry, companies, funders and third party organizations. Also, session included an in-person workshop held at the University of Stirling, with a breakout discussion on challenges faced in UK aquaculture, opportunities, and how genomics can address these issues. Groups explored these themes and prioritized research areas for next 5 years. Results of group work expected to influence future research directions, and to contribute to an upcoming policy brief led by Roslin Institute and Innogen Institute. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.eventbrite.co.uk/e/aqualeap-final-meeting-webinar-tickets-547333638647 |
| 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 | Genomics of fishes from aquaculture to evolution - Presentation at Launch Event for "Genomics at Edinburgh" network |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Invited talk at University of Edinburgh launch event for 'Genomics at Edinburgh'. This was an online event, with ~200 individuals in attendance representing the broad base of genomics researchers within the University. There were several follow up questions, and the talk achieved knowledge exchange on aquaculture genomics research at the Roslin Institute, and there were several follow up questions and additional off-line discussions. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Harnessing functional annotation to improve disease resistance in farmed fish - 72nd Annual Meeting. of the European Federation of Animal Science |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | This was a presentation focussed at animal breeding companies, given jointly online by myself and Prof. Ross Houston. The main outcome was knowledge exchange about the impacts of putting into practise research on genome functional annotation in aquaculture species, which is an important activity at the Roslin Institute under the FAANG initiative effort. The talk is available on Youtube. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.youtube.com/watch?v=jw5e2c5Q6p0 |
| Description | HiLIFE Webinar - Fishing into fish genomes: from evolution to applications - Life Sciences Departmental seminar - University of Helsinki |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | This was a departmental seminar held online, attended by academics, post-docs, post-graduate and undergraduate students. There were a range of follow up questions and discussions surrounding my research, with various faculty members and their teams. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www2.helsinki.fi/en/conferences/hilife-life-science-seminars/hilife-webinars-fall-2021#secti... |
| 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/ |
| Description | Native Oyster Restoration Alliance - genetics workshop - 25th Feb, 2021 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk by Manu Kumar Gundappa, Tim Bean, Ross Houston and Daniel Macqueen: A chromosome level Ostrea edulis genome assembly and assessing genetics of resistance to Bonamia ostreae Disseminated a major deliverable from AquaLeap project to diverse stakeholders interested in flat oyster restoration and aquaculture. Led to new collaborations and agreements to harmonize research with several attendee academics at NORA workshop, with the view to maximise the future scientific and applied impact of the genome resource. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Presentation at Aquaculture Europe 2019 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation titled "THE STRUCTURAL VARIATION LANDSCAPE IN ATLANTIC SALMON AND IT'S POTENTIAL CONTRIBUTION TO DISEASE RESISTANCE" was given at Aquaculture Europe 2019 (October 2019, Berlin). The purpose was to disseminate findings from AquaLeap and other research projects focused on structural variation. The talk sparked several scientific questions. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.aquaeas.eu/images/stories/Meetings/AE2019/AE19_Blue_9-30_003.pdf |
| Description | Roslin aquaculture seminar series - 11th Dec, 2020 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk by Manu Kumar Gundappa and Daniel Macqueen: Genome assembly for the European flat oyster. Aim to disseminate key outcome from AquaLeap project to stakeholders. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Seminar given to AquaGen Dumfries Hatchery about collaborative research on salmon genomics - 8th Dec 2022 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | I gave a talk to the staff at the AquaGen Hatchery in Scotland, which produces selectively bred salmon ova for production. My talk gave an outline of results from my group's collaborative research with AquaGen. The purpose was to strengthen ties with the company. The impacts were a closer ongoing working relationship with this company, with ideas explored for collaborative projects. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Seminar given to Xelect Ltd (aquaculture genetic company) about my research on aquaculture genomics - 30th June 2022 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | I gave an 30 minute seminar to the entire Xelect Team, describing my groups research, focussing on themes most relevant to the companies business. The purpose was to strengthen ties with the company. The impacts were a closer ongoing working relationship with this company, with ideas explored for collaborative projects. |
| Year(s) Of Engagement Activity | 2022 |