Unravelling the epigenetic mechanisms underlying nutritional programming for sustainable aquaculture

Project Information

EPIAQUA

Grant agreement ID: 101076685

DOI

10.3030/101076685

EC signature date 29 August 2023

Start date 1 January 2024

End date 31 December 2028

Funded under

• European Research Council (ERC)

Total cost

€ 1 500 067,19

EU contribution

€ 1 500 000,00

Coordinated by

UNIVERSIDAD DE LA LAGUNA
Spain

Periodic Reporting for period 1 - EPIAQUA (Unravelling the epigenetic mechanisms underlying nutritional programming for sustainable aquaculture)

Reporting period: 2024-01-01 to 2026-06-30

Summary of the context and overall objectives of the project

Aquaculture is the fastest-growing food production sector worldwide and already provides more than half of the fish consumed by humans. As global demand for healthy and affordable protein continues to rise, aquaculture must expand in a way that is both environmentally sustainable and economically viable. One of the main challenges facing the sector is its continued reliance on fish-derived ingredients, such as fish meal and fish oil, which are limited resources and place increasing pressure on wild fish stocks. This highlights the urgent need for more sustainable feeding strategies.
Replacing fish-based ingredients with plant alternatives is essential, but many farmed species do not efficiently use plant nutrients, leading to reduced growth, poorer health, and lower nutritional value. Overcoming this limitation is key to ensuring sustainable feeds maintain productivity, welfare, and product quality.
Nutritional programming offers a promising solution: early-life diets can “program” metabolism, improving the use of carbohydrates and plant-derived fats later in life. Evidence shows these effects are mediated by epigenetic mechanisms, which regulate gene activity without changing DNA. Epigenetic changes can persist throughout life and, in some cases, be transmitted to future generations. Despite their potential, these mechanisms remain poorly understood in fish. Despite this potential, the epigenetic basis of nutritional programming in fish remains poorly understood.
The EPIAQUA project aims to investigate how early nutrition shapes fish metabolism through epigenetic mechanisms and how these effects persist across life stages and generations. Using Nile tilapia, the project studies how early diets based on sustainable ingredients affect growth, health, and nutrient use, and how these effects are controlled at the molecular level.
By generating a comprehensive understanding of the links between early nutrition, epigenetic regulation, and long-term performance, EPIAQUA seeks to provide the scientific foundation needed to design more efficient and sustainable aquafeeds. The expected impact of the project includes reduced dependence on fish-derived feed ingredients, improved resource efficiency, and enhanced nutritional quality of farmed fish. In the longer term, these advances will contribute to a more resilient and sustainable aquaculture sector, supporting food security, environmental protection, and economic growth in line with European and global sustainability goals.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

During the reporting period, the project has focused on building the scientific and technical foundations required to understand how early-life nutrition can shape fish metabolism through epigenetic mechanisms. Epigenetics refers to molecular processes that regulate how genes are used without changing the DNA sequence itself and can explain long-lasting biological effects of early environmental conditions, such as diet.
The main activities carried out so far have concentrated on developing and validating advanced experimental and analytical methods that are essential for studying these mechanisms in aquaculture species. In particular, the project established robust genome-wide approaches to analyse gene expression and epigenetic regulation, with special emphasis on long non-coding RNAs, a class of molecules increasingly recognised as key regulators of metabolism and biological memory.
A major technical achievement has been the development of reliable methods to isolate and analyse RNA molecules carried by extracellular vesicles circulating in fish blood. These vesicles act as biological messengers between tissues and may play an important role in transmitting nutritional information within the organism and potentially across generations. The project demonstrated, for the first time in a farmed fish species, that long RNA molecules, including long non-coding RNAs, can be consistently detected and characterised from these vesicles using advanced long-read sequencing technologies.
In parallel, the project has implemented state-of-the-art long-read sequencing and targeted RNA capture approaches to improve the detection and structural characterisation of low-abundance regulatory RNAs. These methods allow the identification of previously unknown regulatory RNA molecules in fish liver, a key metabolic organ. Together, these advances provide a solid and reliable analytical framework for the forthcoming experimental phases of the project.
In addition, all experimental diets required for the nutritional trials have been formulated and and pilot experimental activities are initiated to validate protocols and analytical pipelines ahead of large-scale experimentation. Although some experimental work has been delayed due to infrastructure and logistical constraints, the work completed to date has significantly reduced scientific and technical risks and ensures that the project is well positioned to deliver its objectives in the next phases.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

At this interim stage, the project has primarily contributed to the state of the art by establishing and adapting advanced methodological approaches that are necessary to investigate how nutrition may influence long-term biological outcomes in aquaculture species. Existing studies in this field have often focused on short-term responses or on individual molecular pathways. In contrast, the work carried out so far has laid the groundwork for an integrated, genome-wide analysis that will allow multiple layers of epigenetic regulation to be studied in parallel in future experimental phases.
A key methodological development has been the establishment of approaches to analyse circulating long RNA molecules, including long non-coding RNAs, in fish. While the biological role of these molecules in nutritional programming remains to be experimentally tested within the project, the availability of reliable analytical tools now makes it possible to address questions related to tissue-to-tissue communication and the persistence of nutritional signals over time in a way that was previously not feasible in aquaculture species.
The potential longer-term impact of the project lies in the knowledge that is expected to emerge from the planned nutritional and multigenerational experiments. By improving understanding of how early-life nutrition may influence metabolic regulation, the project aims to provide a scientific basis for the future development of more efficient and sustainable feeding strategies in aquaculture. In the longer term, such knowledge could support improved use of plant-based feed ingredients, reduced reliance on marine resources, and the maintenance of high-quality farmed fish products.
To ensure further uptake and success, the next steps of the project will focus on completing the planned experimental work, generating and validating biological data on candidate epigenetic mechanisms, and assessing their consistency across life stages and generations. Subsequent collaboration with aquaculture stakeholders, including feed producers and practitioners, will be important to evaluate how the scientific results could eventually be translated into practical applications and guidelines.