Periodic Reporting for period 3 - AQUA-FAANG (Advancing European Aquaculture by Genome Functional Annotation)
Periodo di rendicontazione: 2022-05-01 al 2023-10-31
The AQUA-FAANG project aimed to promote sustainable European aquaculture by creating a major up-step in the use of genomic information to predict biological traits in the six most commercially important farmed fish in Europe (Atlantic salmon, rainbow trout, common carp, turbot, European seabass, and Gilthead seabream). A core focus was to address the major problem of infectious disease in aquaculture.
To fully exploit genetic variation shaping traits in aquaculture, we must first understand how the DNA sequence (genome) shapes phenotypes. This requires knowledge of mechanisms controlling gene expression in different biological conditions. The AQUA-FAANG project addressed this challenge by generating ‘maps’ spanning the entire genome of each species, revealing DNA regions with important functions, including elements that regulate gene expression. This approach is called genome functional annotation.
AQUA-FAANG had five objectives:
1) Standardize functional annotation protocols and share the resulting data and expertise, to ensure the results are robust, comparable, and freely available to maximize scientific and commercial impact.
2) Generate and interpret functional annotation maps for healthy and immune active states, to identify functional regions in farmed fish genomes across different tissues, life-stages, sexes, and after viral and bacterial immune challenges.
3) Predict disease resistance and other commercial traits using genome functional annotation, identify genetic variants responsible for resistance to problematic aquaculture pathogens
4) Enhance genome functional annotation by comparing fish species split by millions of years of evolution, revealing functional regions conserved or specific to particular lineages, making the results transferable to other species.
5) Engage stakeholders and ensure the results are translated into novel practices in the aquaculture commercial sector
These objectives were achieved, creating an up-step in the research community’s ability to generate, analyze, interpret and share functional annotation datasets to better understand the genomic basis of complex traits, and exploit functional annotation to improve selective breeding approaches in the major European farmed fish species.
To fully exploit genetic variation shaping traits in aquaculture, we must first understand how the DNA sequence (genome) shapes phenotypes. This requires knowledge of mechanisms controlling gene expression in different biological conditions. The AQUA-FAANG project addressed this challenge by generating ‘maps’ spanning the entire genome of each species, revealing DNA regions with important functions, including elements that regulate gene expression. This approach is called genome functional annotation.
AQUA-FAANG had five objectives:
1) Standardize functional annotation protocols and share the resulting data and expertise, to ensure the results are robust, comparable, and freely available to maximize scientific and commercial impact.
2) Generate and interpret functional annotation maps for healthy and immune active states, to identify functional regions in farmed fish genomes across different tissues, life-stages, sexes, and after viral and bacterial immune challenges.
3) Predict disease resistance and other commercial traits using genome functional annotation, identify genetic variants responsible for resistance to problematic aquaculture pathogens
4) Enhance genome functional annotation by comparing fish species split by millions of years of evolution, revealing functional regions conserved or specific to particular lineages, making the results transferable to other species.
5) Engage stakeholders and ensure the results are translated into novel practices in the aquaculture commercial sector
These objectives were achieved, creating an up-step in the research community’s ability to generate, analyze, interpret and share functional annotation datasets to better understand the genomic basis of complex traits, and exploit functional annotation to improve selective breeding approaches in the major European farmed fish species.
All project deliverables were completed, generating many exploitable results:
• We developed robust frameworks for functional annotation in six fish species, from sampling to data generation, analysis and sharing.
• We generated 4,639 sequencing datasets (1,485, 716 and 2,438 for RNA-Seq, ATAC-Seq and ChIP-Seq respectively) representing more than one thousand unique biological samples. This is a unique resource for fish biology, with all raw data shared openly.
• High-quality genomes for all target species were integrated into the Ensembl genome browser as open data resources. The project sequencing data was used to predict genes, open chromatin regions and regulatory elements, creating new opportunities to understand gene regulation and identify genetic variants impacting gene expression. We are also predicting microRNAs across all project species, which will be openly shared through the FishmiRNA database.
• Functional annotation datasets were used to understand genome activity across embryonic development and in adult tissues at different stages of sexual maturity for both sexes in the target fish species. These efforts provide fundamental information on the genomic basis of many traits of importance to aquaculture.
• We developed protocols for functional annotation after bacterial and viral immune stimulation, which were applied across the target species to reveal changes in gene expression, regulatory elements, and chromatin accessibility driven by pathogens.
• We applied single-cell sequencing to reveal novel immune cell heterogeneity and its potential link to disease resistance in fish and identified novel marker genes for diverse immune cells - an important resource for ongoing exploitation by immunologists.
• We generated gene edited fish cell lines as a tool for understanding viral disease resistance, which can be exploited in vaccine development and immunology studies.
• We identified a major QTL for resistance to viral nervous necrosis (VNN) in European sea bass and used functional annotation to reveal the potential causative mutations.
• We tested the value of functional annotation in genomic selection for VNN resistance in European seabass and early sexual maturation in Atlantic salmon, with promising results suggesting higher prediction accuracy using functionally prioritized variants.
• We used functional genomics to improve understanding of disease resistance to Vibrio anguillarum in gilthead seabream, Scuticociliatosis in turbot and Koi Herpes Virus in common carp.
• We produced low-density SNP marker panels incorporating SNPs targeting resistance to VNN in European seabass and photobacteriosis in gilthead seabream, ready to deploy in aquaculture breeding programmes.
• We developed comparative genomics methods and visualization tools to compare functional annotation data across species and to understand how whole genome duplication events shape gene expression and epigenetic regulation in different biological conditions
• We used comparative genomics to transfer understanding gained from functional annotation in turbot to other key flatfish species used in aquaculture, revealing conserved regulatory elements involved in development, growth and immunity.
• We established lasting collaborative partnerships with the BovReg and Gene-SWitCH projects, and co-developed the EuroFAANG initiative, which has grown substantially in recent years and was recently funded as a Horizon Europe Infrastructure.
• A vast programme of communication, dissemination and knowledge exchange was delivered, ensuring the project and its results impacted stakeholders in the aquaculture industry, research community, general public, and influenced policy makers. We published 22 peer-reviewed articles, with an additional 24 planned in the next six months. We created many dissemination resources and promotional materials, including a project website, results brochures, newsletters, a policy brief, flyers, and numerous videos shared on our YouTube channel, including training resources and recorded talks from our eLearning webinars and final conference. Project results were presented 60 times at scientific meetings and conferences around the world.
• A whitepaper was published in a peer reviewed journal, providing a roadmap for the ongoing and future use of AQUA-FAANG data to improve aquaculture breeding.
• We developed robust frameworks for functional annotation in six fish species, from sampling to data generation, analysis and sharing.
• We generated 4,639 sequencing datasets (1,485, 716 and 2,438 for RNA-Seq, ATAC-Seq and ChIP-Seq respectively) representing more than one thousand unique biological samples. This is a unique resource for fish biology, with all raw data shared openly.
• High-quality genomes for all target species were integrated into the Ensembl genome browser as open data resources. The project sequencing data was used to predict genes, open chromatin regions and regulatory elements, creating new opportunities to understand gene regulation and identify genetic variants impacting gene expression. We are also predicting microRNAs across all project species, which will be openly shared through the FishmiRNA database.
• Functional annotation datasets were used to understand genome activity across embryonic development and in adult tissues at different stages of sexual maturity for both sexes in the target fish species. These efforts provide fundamental information on the genomic basis of many traits of importance to aquaculture.
• We developed protocols for functional annotation after bacterial and viral immune stimulation, which were applied across the target species to reveal changes in gene expression, regulatory elements, and chromatin accessibility driven by pathogens.
• We applied single-cell sequencing to reveal novel immune cell heterogeneity and its potential link to disease resistance in fish and identified novel marker genes for diverse immune cells - an important resource for ongoing exploitation by immunologists.
• We generated gene edited fish cell lines as a tool for understanding viral disease resistance, which can be exploited in vaccine development and immunology studies.
• We identified a major QTL for resistance to viral nervous necrosis (VNN) in European sea bass and used functional annotation to reveal the potential causative mutations.
• We tested the value of functional annotation in genomic selection for VNN resistance in European seabass and early sexual maturation in Atlantic salmon, with promising results suggesting higher prediction accuracy using functionally prioritized variants.
• We used functional genomics to improve understanding of disease resistance to Vibrio anguillarum in gilthead seabream, Scuticociliatosis in turbot and Koi Herpes Virus in common carp.
• We produced low-density SNP marker panels incorporating SNPs targeting resistance to VNN in European seabass and photobacteriosis in gilthead seabream, ready to deploy in aquaculture breeding programmes.
• We developed comparative genomics methods and visualization tools to compare functional annotation data across species and to understand how whole genome duplication events shape gene expression and epigenetic regulation in different biological conditions
• We used comparative genomics to transfer understanding gained from functional annotation in turbot to other key flatfish species used in aquaculture, revealing conserved regulatory elements involved in development, growth and immunity.
• We established lasting collaborative partnerships with the BovReg and Gene-SWitCH projects, and co-developed the EuroFAANG initiative, which has grown substantially in recent years and was recently funded as a Horizon Europe Infrastructure.
• A vast programme of communication, dissemination and knowledge exchange was delivered, ensuring the project and its results impacted stakeholders in the aquaculture industry, research community, general public, and influenced policy makers. We published 22 peer-reviewed articles, with an additional 24 planned in the next six months. We created many dissemination resources and promotional materials, including a project website, results brochures, newsletters, a policy brief, flyers, and numerous videos shared on our YouTube channel, including training resources and recorded talks from our eLearning webinars and final conference. Project results were presented 60 times at scientific meetings and conferences around the world.
• A whitepaper was published in a peer reviewed journal, providing a roadmap for the ongoing and future use of AQUA-FAANG data to improve aquaculture breeding.
AQUA-FAANG is the first coordinated functional annotation effort for multiple aquaculture species, creating a world-leading knowledge hub moving past the state-of-the-art in understanding the functional regulation of farmed fish genomes. We produced and openly shared comprehensive functional annotation maps in highly usable formats via the Ensembl genome browser, creating substantial scope for novel scientific and commercial exploitations. Through a close relationship with industry, the project enhanced scope for the uptake of functional genomics in aquaculture practice. Improved precision breeding methods delivered using project results are being tested by industry to support the continued profitability and sustainability of European aquaculture.