AQUAFAANG White Paper
Advancing fish breeding in aquaculture through genome
functional annotation

​By Ian A. Johnston, Matthew P. Kent, Pierre Boudinot, Mark Looseley, Luca Bargelloni, Sara Faggion, Gabriela A. Merino, Garth R. Ilsley, Julien Bobe, Costas S. Tsigenopoulos, Joseph Robertson, Peter W. Harrison, Paulino Martinez, Diego Robledo,
Daniel J. Macqueen, Sigbjørn Lien
Genomics is increasingly applied in breeding programmes for farmed fish and shellfish species around the world. However, current applications do not include information on genome functional activity, which can enhance opportunities to predict relationships between genotypes and phenotypes and hence increase the accuracy of selection. Here, we review prospects for improving aquaculture breeding practises through the uptake of functional genomics data in light of the EU Horizon 2020 project AQUA-FAANG: ‘Advancing European Aquaculture by Genome Functional Annotation’. This consortium targeted the six major farmed fish species in European aquaculture, producing thousands of functional genomic datasets from samples representing embryos to mature adults of both sexes, and following immunological stimulation. This data was used to catalogue functional activity across the genome of each species, revealing transcribed regions, distinct chromatin states and regulatory elements impacting gene expression. These functional annotations were shared as open data through the Ensembl genome browser using the latest reference genomes for each species. AQUA-FAANG data offers novel opportunities to identify and prioritize causative genetic variants responsible for diverse traits including disease resistance, which can be exploited to enhance selective breeding. Such knowledge and associated resources have the potential to improve sustainability and boost production in aquaculture by accelerating genetic gain for health and robustness to infection, whilst reducing the requirement for animal testing. We further outline directions to advance and leverage genome functional annotation beyond the AQUA-FAANG project. Given the diversity of aquaculture sectors and businesses, the incorporation of functional genomic information into breeding decisions will depend on technological readiness level and scale of operation, with cost-benefit analysis necessary to determine the most profitable approach for each species and production system.
AQUAFAANG White Paper - Advancing fish breeding in aquaculture through genome functional annotation
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Moving towards Precision Breeding in European aquaculture:
​AQUA-FAANG results and their impact

​By Professor Dan Macqueen and Professor Sigbjørn Lien
The H2020 AQUA-FAANG project has generated extensive new functional genomics datasets in the six main finfish species farmed in European aquaculture. This article introduces these datasets, how they are shared with the research and innovation community, and how AQUA-FAANG results provide valuable opportunities to develop precision breeding strategies to increase aquaculture sustainability and profitability.
Moving towards Precision Breeding in European aquaculture: ​AQUA-FAANG results and their impact
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Genomic revolution in aquaculture: AQUA-FAANG's breakthrough for disease resistant seabass

​By Sara Faggion and Luca Bargelloni
The rapid growth of the aquaculture sector has intensified concerns over sustainability and environmental impact. Disease resistance, a pivotal trait, is crucial for both hatchery and on-growing phases. To enhance disease resistance through selective breeding, genomic selection is key. 
Genomic revolution in aquaculture: AQUA-FAANG's breakthrough for disease resistant seabass
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Advancing fish breeding in aquaculture through   genome functional annotation: The AQUA-FAANG White Paper 

Lead Authors Ian Johnston (Xelect Ltd.) & Dan Macqueen (UEDIN) ​
Classical genetic selection techniques using pedigree relationships have resulted in transformative gains in aquaculture production and sustainability over the last 40-50 years.
​More recently, advances in genomics have seen improved methods of aquaculture breeding, including marker-assisted selection and genomic selection, resulting in accelerated rates of genetic progress. However, incomplete assemblies of genomes at the chromosome level and an almost complete lack of understanding of how the millions of letters of the genetic code relate to characteristics of importance to aquaculture remain a barrier to further progress.  
The AQUA-FAANG White Paper.pdf
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