AQUA-FAANG is a 4-year EU funded project that will generate genome-wide functional annotation maps for the six commercially most important fish species within European aquaculture and exploit their contribution to variation in traits of commercial relevance, focusing on improved resistance to disease.


One of the main threats in sustainable farmed fish production is the occurrence of infectious diseases, in Europe alone accumulating to a yearly economic loss of 1800 million Euros. The occurrence of infectious diseases is expected to increase even more because of climate change, pressing the need for more resilient fish species. Advanced understanding on the regulation of genes in fish will help us to find genetic solutions to improve important traits such as disease resistance.


Recent developments in genomics have advanced innovation in European aquaculture. However, despite the creation of reference quality genome sequences for the main species, our understanding of genome functions remains limited.

• AQUA-FAANG will deliver a step improvement in the understanding of genome function and exploitation of genotype-to-phenotype prediction in the six most important European farmed fish species.

• The project brings together world-leading interdisciplinary expertise and industry partners providing direct pathways to commercial exploitation. AQUA-FAANG will functionally annotate the genomes of all six species, employing standardized experimental assays and analysis pipelines defined by the FAANG initiative.

• AQUA-FAANG datasets will be shared and coordinated with other FAANG initiatives via the FAANG data coordination centre, and made available through the Ensembl genome browser.

• As infectious disease is of paramount concern for sustainable aquaculture, the project focuses on understanding functional genomic regions in both healthy and immune-challenged fish. This will improve knowledge of the genomic basis for disease resistance and is complemented by novel approaches to increase understanding of immune cell heterogeneity.

• Standardized comparative analyses will provide essential insights into genome functions that cannot be gained from study of single species.

• Functional assays will be used to study intermediate phenotypes and prioritise causative genetic variants in trait-associated genomic regions to accelerate selection of disease-resistant stocks. Functionally-enriched marker panels will be developed to improve accuracy of genomic selection.

• An active programme of stakeholder engagement and dissemination will ensure uptake of project outputs by industry, academia, the public and in policy.

• The outputs will enhance precision breeding, drive competitiveness within the aquaculture sector, and enhance food and nutrition security in Europe.


To achieve its objectives, AQUA-FAANG is organised within nine work packages. The research driven WPs are integrated across all included fish species, ensuring knowledge advances will be rapidly transferred from species to species and partner to partner. All research-driven WPs will provide input to WP7, which focuses on dissemination, exploitation and communication. Finally, one WP is dedicated to project management, to enable communication within the consortium and ensure that the project is progressing according to plan. Wageningen University is involved mainly in WP3 and partly in WP6.

WP3 - Genomic basis of immune phenotypes (WUR)

The overarching aim of WP3 is to enhance our fundamental understanding of the genomic basis for innate immune function in farmed fishes by generating standardized ImmunoMaps in the six selected AQUA-FAANG species. Read more.

WP6 - Comparative analyses (UEDIN)

The overarching objective of WP6 is to exploit comparative approaches to enhance the quality, description and impact of functional annotation maps generated during the AQUA-FAANG project, beyond what is possible by analysis of single species. Read more.