Innovative Epigenetic Markers For Fish Domestication

Informations

Funding country

Norway

Acronym

-

URL

-

Start date

1/1/2016

End date

12/31/2022

Budget

344,400 EUR

Fundings

Abstract

Domestication of animals as a reliable food source was a critical point in human history and it is still shaping our society nowadays. Fish farming is one of the fastest growing food production sectors worldwide, since fisheries are unable to meet the increasing demand for fish protein. In order to ensure sustainability of the aquaculture sector it is critical to selectively improve the major commercial fish species. The EPIFISH project INNOVATIVE EPIGENETIC MARKERS FOR FISH DOMESTICATION adopts a multidisciplinary approach to address fish domestication at the research frontier, based on the innovative hypothesis that epigenetic mechanisms (e.g., DNA modifications and non-coding RNAs) are involved in selection and adaptation of fish to farming conditions. The overarching aim of EPIFISH is to ascertain the importance of epigenetics in fish domestication using the Nile tilapia (Oreochromis niloticus) as model species, since tilapias are the second most important group of farmed fish. The project started with a field trip to Alexandria and Luxor in Egypt. The team spent 7 weeks with local fisherman capturing live Nile tilapia using traditional methods, such as traps. Fertilised eggs collected from the mouth of several females were transported to the research station at Nord University in Bodø (Norway), where they were reared in a state-of-the-art recirculating aquaculture system. At 5 months old, the fish were separated in two groups according to their weight: a control line comprising individuals of average weight and a selected line of fish that were at least 10% larger than average. We have completed the third generation of selection, which was the goal of our selective breeding program. All the required samples have been humanely collected and we are now determining how the muscle fibres changed. Using next-generation sequencing to compare gene expression levels in muscle, we found several thousand protein-coding genes that were differentially expressed between wild tilapia females and their progeny reared in captivity. In general, domestication was associated with reduced expression of genes involved in the immune response, which is likely explained by the lower number of pathogens in the research station compared to wild conditions. There was a concomitant up-regulation of genes related to metabolic processes and muscle development, which may account for the improved growth of domesticated fish and the observed changes in muscle cellularity. We have identified several miRNAs and isomiRs that are known to target genes involved in metabolic pathways and muscle development. Several of these miRNAs were expressed at different levels in muscle and blood serum between slow- and fast-growing Nile tilapia. They are promising candidates for epigenetic markers (epimarkers) of growth, since their expression is strongly correlated to fish weight. We have also expanded our research to circular RNAs (circRNAs), which are a novel type of non-coding RNAs. To this aim, we have developed a bioinformatic pipeline for circRNA host gene prediction and discovered several circRNAs that are related to growth. After optimising a protocol to cover a larger proportion of methylated cytosines in the genome, we have obtained a high-resolution, genome-wide methylation map in fast muscle of Nile tilapia. We have found many cytosines that were differentially methylated between small and large fish of the same age and that were associated with muscle growth. Another study comparing wild and domesticated fish revealed that differentially methylated genes were mainly associated with muscle growth, epigenetic regulation, immunity and diet. In parallel, we have obtained the first mitochondrial methylome map in a non-model fish species. We have also investigated a DNA modification termed hydroxymethylation, since there is increasing evidence that it is a stable epigenetic mark. Our genome-wide profiling revealed that hydroxymethylation is a ubiquitous DNA modification throughout the nuclear and mitochondrial genomes both in muscle and liver. Nile tilapia domestication was associated with a decrease in muscle hydroxymethylation, especially in genes related to growth and immunity. Several genes involved in metabolism and growth were differentially hydroxymethylated between pituitary, liver and muscle. Functional characterization of the key miRNAs, circRNAs and DNA methylation/ hydroxymethylation marks that we identified can be performed using the microinjection and in vitro fertilization protocols that we developed. These data will provide ground-breaking mechanistic insights into the role of epigenetics in fish domestication, which will surely open new horizons for research in transgenerational inheritance and nutritional epigenetics. Moreover, the novel epimarkers will provide an innovative basis for a more effective selection and increased sustainability of the aquaculture industry.