AQUA-FAANG unveils the power of genomics for a sustainable future in aquaculture

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By Milthon Lujan

A channel to exploit AQUA-FAANG data sets in new breeding applications. Source: Johnston et al., (2024); Aquaculture.
A channel to exploit AQUA-FAANG data sets in new breeding applications. Source: Johnston et al., (2024); Aquaculture.

Aquaculture, the fastest-growing sector in the food industry, assumes a crucial responsibility in the significant challenge of feeding a growing population. But, like any high-performance engine, aquaculture needs adjustments to achieve optimal efficiency and sustainability. This is where AQUA-FAANG comes in, an innovative EU-funded project harnessing the power of genomics to revolutionize aquaculture breeding.

The AQUA-FAANG project focused on the six most important species in European aquaculture: Atlantic Salmon (Salmo salar), Rainbow Trout (Oncorhynchus mykiss), Common Carp (Cyprinus carpio), Gilthead Seabream (Sparus aurata), European Seabass (Dicentrarchus labrax), and Turbot (Scophthalmus maximus).

The challenge: overcoming diseases and boosting production

While fast-growing, disease-resistant fish may seem like a utopia, they represent the ultimate prize in aquaculture. Picture fish farms teeming with robust fish that produce healthy food while protecting animal welfare and minimizing environmental impact. This is not a utopian dream—it is within reach thanks to cutting-edge advances in understanding fish DNA.

Traditionally, improvement in disease resistance and other desirable traits relied on measuring physical characteristics in controlled trials. This involved expensive and time-consuming experiments, often subjecting animals to pathogens. But what if we could predict these traits directly from the fish’s genetic model?

The solution: functional genomics takes center stage

Understanding what different parts of DNA do, and their “function,” is equally crucial. This is where functional annotation comes into play, revealing the hidden language of the genome.

Think of DNA as a comprehensive instruction manual for building a fish. Functional annotation helps decipher which sections encode proteins, regulate gene activity, and influence traits such as disease resistance and growth.

AQUA-FAANG (“Advancing European Aquaculture by Genome Functional Annotation”) is a project taking a novel approach by delving into the intricate dance of genes and their regulatory elements. This “functional annotation” reveals the true activity of DNA, going beyond protein-coding genes to identify regulatory regions that control gene expression. Understanding how these regions influence disease resistance is highly promising for breeding fish with enhanced immunity.

The AQUA-FAANG project, an innovative initiative under the EU’s Horizon 2020 program, spearheaded this quest in aquaculture. Focusing on six key fish species, they meticulously mapped the functional landscape of their genomes using sophisticated techniques.

The project employed a sophisticated arsenal of tools to unravel the complexities of fish genomes:

  • RNA-Seq: This technology captures the expression of both coding and non-coding genes, providing a snapshot of cell transcriptional activity.
  • ATAC-Seq: This technique reveals “open” chromatin regions, indicating active DNA areas, including potential regulatory elements.
  • ChIP-Seq: This powerful method identifies specific DNA sequences bound by proteins involved in genetic regulation.

By applying these tools across various tissues, developmental stages, and disease challenges, AQUA-FAANG generated a treasure trove of data shedding light on the intricate workings of the immune system in different fish species.

Beyond the lab: Transforming aquaculture breeding

The wealth of information is not locked away. AQUA-FAANG made it freely available through the Ensembl genome browser, a digital oasis where researchers and breeders can explore the inner workings of these fish genomes.

This new knowledge changes the game. By identifying genetic variants responsible for desirable traits, such as disease resistance, breeders can prioritize individuals with these “superpowers” for breeding, resulting in offspring with a natural advantage against pathogens.

AQUA-FAANG’s findings paved the way for a paradigm shift in aquaculture breeding:

  • Identification of “functional variants”: By pinpointing crucial regulatory elements for disease resistance, breeders can prioritize these variants in selection programs, leading to faster and more accurate genetic gains.
  • Reduced reliance on costly disease exposure experiments: Functional genomic information can be used to predict disease resistance in fish without the need for expensive and time-consuming trials.
  • Adaptation of breeding programs for specific diseases: By understanding the unique genetic pathways involved in different diseases, breeders can develop specific strategies for each threat.

How can this new knowledge transform aquaculture?

Imagine selecting breeding candidates based not only on their size or appearance but also by predicting their disease resistance or growth potential directly from their DNA. This kind of precision breeding, based on functional annotations, changes the rules of the game.

Here are just a few glimpses of the future:

  • Accelerated breeding programs: Instead of waiting generations to see which fish possess desirable traits, breeders can identify them from the start, drastically speeding up the selection process.
  • Enhanced disease resistance: By identifying genes related to immunity, we can develop specific breeding strategies to raise fish that are naturally resistant to common diseases, reducing reliance on antibiotics and improving welfare.
  • Optimized growth and quality: Unraveling the genetic basis of growth rate and meat quality allows breeders to tailor fish to specific markets, maximizing profitability and resource efficiency.

The road ahead: building a sustainable future

AQUA-FAANG marks a significant leap forward, but the journey is far from over. Future research and development priorities include:

  • Refining functional annotation methods: Expanding the range of tissues and conditions studied will further perfect our understanding of genetic regulation.
  • Developing user-friendly tools for fish farmers: Making genomic data accessible and interpretable for fish farmers will be crucial for the widespread adoption of these technologies.
  • Quantifying economic benefits: Demonstrating the financial benefits of genomic improvement will foster industry acceptance and ensure sustainable implementation.

AQUA-FAANG’s legacy extends beyond the realm of aquaculture. Its insights and innovative approaches hold promise for improving the health and welfare of all livestock species, contributing to a more sustainable and food-secure future for our planet.

The road ahead: challenges and opportunities

As with any innovative technology, challenges remain. Translating genomic insights into practical breeding programs requires collaboration between scientists, fish farmers, and industry stakeholders. We need standardized platforms for data sharing, user-friendly tools for breeders, and a deeper understanding of the economics of implementing these new approaches.

But the potential rewards are simply too vast to ignore. A future where aquaculture thrives, feeding the world with healthy and sustainable fish, all thanks to the power of understanding fish DNA—that is a future worth fighting for.

Ian A. Johnston
Xelect Ltd, Horizon House, St Andrews, Scotland KY16 9LB, UK
Email: ian.johnston@xelect.co.uk

Daniel J. Macqueen
The Roslin Institute and Royal (Dick) School of Veterinary Studies
University of Edinburgh, UK
Email: daniel.macqueen@roslin.ed.ac.uk

Reference (open access)
Johnston, I. A., Kent, M. P., Boudinot, P., Looseley, M., Bargelloni, L., Faggion, S., … & Lien, S. (2024). Advancing fish breeding in aquaculture through genome functional annotation. Aquaculture, 740589.