Aquaculture, the process of controlled fish and shellfish cultivation, is a sustainable alternative to fisheries. The sector has seen tremendous growth and Nile tilapia is one of the most important commercially farmed species worldwide. To date, the optimization of production yields is limited to traditional selective breeding programs, that exclusively focus on genetic markers. As a result, unknown variability in growth selection remains, which may be diminished through epigenetic selection. Prof. Jorge Fernandes’ group has found evidence for the direct involvement of multiple categories of epigenetic markers in growth rate and size of Nile tilapia. During the ERC Consolidator project EPIFISH (#683210), Fernandes’ group observed important differences in expression levels of non-coding RNAs (ncRNAs): full-sibling groups of Nile tilapia with distinct growth rates expressed different sets of ncRNAs in muscle, despite being reared under the same environmental conditions. EPISELECT will explore the technical and commercial feasibility of a multi-panel for the assessment of epigenetic markers for fish growth optimization. This multi-panel will assess the newly discovered ncRNAs in combination with the previously identified DNA modification markers. As a result, EPISELECT may improve selective breeding programs, leading to higher profitability and increased sustainability of the aquaculture sector. To reach the proof-of-concept stage, we will: 1) Explore ncRNA markers for growth prediction and validate the multi-panel of epimarkers; 2) Define an IPR position and strategy; 3a) Assess the market size, added value, cost analysis, and commercialisation route of the novel multi-panel of epigenetic markers; 3b) Establish connections with aquaculture industry and embed the project for commercialisation.

Due to increasing environmental and economic pressures, there is a need to develop more efficient and sustainable food, feed and fuel production systems. Microalgae have substantial potential as single-cell molecular factories for producing high quality lipids, proteins and carbohydrates. They are capable of faster growth rates than crop plants and synthesize valuable metabolites that do not occur naturally in other primary producers. However, a major bottleneck that currently limits widespread microalgae production are the low yields achieved by commercial strains in cold climates. This project will develop new varieties of microalgae isolated from Arctic and Antarctic environments for applied bioprocesses. The work will include studying the metabolism of novel microalgae in low temperature bioreactors using functional genomics. The researcher will spend the outgoing phase at an established microalgae metabolism laboratory in the USA, where complete and very high quality training will be given in cutting-edge Next Generation Sequencing (NGS) technology. Genomic and transcriptomic work will be paired with metabolomics to give new insights into the regulation of metabolism in non-model microalgae species. The research will also include integrating data together into metabolic flux model frameworks. The major research outcomes will be (1) Genome-scale characterization of brand-new varieties of microalgae (2) Development of novel microalgae bioprocesses for high yields of lipids, proteins and carbohydrates in cold climates (3) Predictive metabolic models for maximizing yields of products of interest in non-model varieties of microalgae. In addition, comprehensive work and dissemination plans are presented that will target scientists, industry and the public.

Domestication and selective breeding of the major commercial fish species are essential to enable sustainability of the rapidly expanding aquaculture sector. The existing improvement programmes are based exclusively on genetic markers, overlooking the fact that selection for complex traits is strongly affected by environmental conditions and that epigenetics likely account for a large proportion of the observed phenotypic variation. Non-coding RNAs (e.g., miRNAs) and cytosine methylation (5mC) and hydroxymethylation (5hmC) of DNA are key mechanisms underlying epigenetic regulation of gene expression. We have recently identified a panel of 5mCs, 5hmCs and miRNAs that are potential epigenetic markers (epimarkers) of improved growth in Nile tilapia (Oreochromis niloticus). EPIMARK will evaluate the commercial feasibility of our novel kit of growth epimarkers, so that they can be applied in selective breeding programmes. This will be achieved by (i) validating the miRNA, 5mC and 5hmC epimarkers, (ii) developing an assay for their quantification, (iii) investigating the commercial and financial feasibility and (iv) developing the optimal business strategy, consolidated in a business plan. The EPIMARK kit will lead to a more efficient selection of fish in breeding programs based on growth potential, thereby increasing the profitability and sustainability of the aquaculture industry. The technology developed in EPIMARK will also open important avenues of innovation, including the use of epimarkers for selection of other superior production traits and disease resistance in Nile tilapia and in other species of commercial importance.

Diatoms, unicellular algae, grow on a wide range of submerged surfaces. However, some diatom species and even entire genera (Chelonicola, Poulinea, Tursiocola) are highly specialised and thrive exclusively on the surface of glabrous aquatic animals (sea turtles, sea snakes, cetaceans, manatees). These taxa tolerate frequent environmental changes related to the biology and lifestyle of their hosts but, in nature, cannot survive without them. We will use sea turtle biofilm samples to investigate whether this unique association makes epizoic diatoms suitable indicators of their host’s health. This proposition is based on our preliminary observations that in sea turtles, the relative abundance of epizoic diatoms is high (>35 %) on generally healthy individuals, but rarely exceeds 10 % in visibly debilitated animals. First, skin and carapace biofilm samples will be collected from 350 presumably healthy and 175 visibly debilitated sea turtles from three distant geographic regions (WP1). Second, the collected material will be used to determine diatom species composition based on molecular (metabarcoding) and morphological approaches (WP2). We will develop an automated diatom identification and counting method using deep learning technology to further simplify the morphology-based assessment of diatom community composition. Third, the relative abundance of specialist sea turtle diatoms will be assessed and tested for correlation with standard sea turtle health indices collected for every sampled animal (WP3). Diatom indices of sea turtle health will be designed should such correlation be found. Finally, we will test the newly developed tools in a zoo setting, where they will be used to gain insights into the overall health and wellbeing of captive sea turtles and other aquatic vertebrates (WP4). The proposed studies will develop novel, non-invasive, cost-efficient and straightforward diatom-based tools for sea turtle monitoring and the assessment of marine ecosystem health.

Aquaculture is the fastest growing food production sector in the world, since there is an increasing demand for fish protein to feed a growing global population, which cannot be met by fisheries. In order to ensure the sustainability of this sector it is critical to domesticate and selectively improve the major commercial fish species. To date, the genetic markers used in selective breeding of fish account only for a fraction of the observed phenotypic variation. EPIFISH is a scientifically innovative and timely project that will address fish domestication and selection from a new perspective using a multidisciplinary approach. The rapid pace of substantial phenotypic changes during adaptation to new environmental conditions in fish undergoing domestication raises the original hypothesis that epigenetic mechanisms are involved in this process. Thus, the overarching aim of EPIFISH is to ascertain the importance of epigenetics in fish domestication using the Nile tilapia (Oreochromis niloticus) as model species. Specific objectives are i) to determine how selection affects the miRNA transcriptome and the epigenetic landscape during domestication, ii) to perform a functional characterization of miRNA variants and epigenetic alleles associated with growth, and iii) to validate them as potential epigenetic markers for future selective breeding programmes. The identification of epigenetic markers will be a ground-breaking element of EPIFISH with major impact on aquaculture biotechnology, since they will enable the development and application of epigenomic selection as a new feature in future selective breeding programmes. Moreover, the project outcomes will provide novel mechanistic insights into the role of epigenetics in fish domestication, which will surely open new horizons for future frontier research in epigenetics, namely transgenerational inheritance and nutritional epigenetics.