EpiFish: Innovative Epigenetic Markers for Fish Domestication

Click here for the EPIFISH website at Nord Universitet

About the project

Domestication of plants and animals has been critical to expansion of the human population and emergence of modern society as we know it.  Remarkably, the number of domesticated fish species of commercial relevance is very limited, even if aquaculture is the fastest growing food production sector in the world, accounting for almost 50% of the fish for human consumption worldwide.  In order to ensure the sustainability of the acquaculture industry it is critical to domesticate and selectively improve the major commercial fish species.

To date, the molecular basis of domestication is poorly understood and 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.

The identification of epigenetic markers (DNA methylation marks and miRNA variants) will be a ground-breaking element of EPIFISH with major inpact 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

Objectives

1. To investigate changes in the miRNA transcriptome in fish undergoing domestication.

2. To determine how selection affects the epigenetic landscape (DNA methylation) during domestication

3. To perform a functional characterisation of MiRNA variants (isomiRs) and methylated epialleles associated with growth.

4. To identify isomiRs and epialleles associated with the growth phenotype and to validate them as potential epigenetic markers for future selective breeding programmes.

 

Background

The EPIFISH project will use a multidisciplinary approach involving transcriptomics, epigenomics, aquaculture and evolutionary biology to study domestication at its research frontier and to generate results that will have a broad and significant impact on various fields of life sciences.  The cutting-edge next-generation sequencing  technologies applied in the project will substantially deepen our understanding of domestication with an unprecedented level of detail at the whole epigenome level.

The project is organised in 5 interconnected work packages, which address the following research question: What is the contribution of epigenetic mechanisms (DNA methylation and miRNAs) to the observed growth improvement during fish domestication?

Financing

This Project is funded by the Research Council of Norway (RCN) FRIMEDBIO funding through Nord Univeristet

RCN Project Number: 250548 (Project data bank at RCN)

UiO Project Number: 190772

Period

01.01.2016 - 30.06.2021

Publications

  • Podgorniak, Tomasz; Dhanasiri, Anusha; Chen, Xianquan; Ren, Xu; Kuan, Pei-Fen & Fernandes, Jorge Manuel de Oliveira (2022). Early fish domestication affects methylation of key genes involved in the rapid onset of the farmed phenotype. Epigenetics. ISSN 1559-2294. doi: 10.1080/15592294.2021.2017554.
  • Geraerts, Mare; Vangestel, Carl; Artois, Tom; Fernandes, Jorge Manuel de Oliveira; Jorissen, Michiel & Manda, Auguste [Show all 16 contributors for this article] (2022). Population genomics of introduced Nile tilapia (Oreochromis niloticus (Linnaeus, 1758)) in the Democratic Republic of the Congo: repeated introductions since colonial times with multiple sources. Molecular Ecology. ISSN 0962-1083. doi: 10.1111/mec.16479.
  • Toledo-Solís, F.J.; Fernandes, Jorge Manuel de Oliveira; Sarropoulou, Elena & Fernandez, Ignacio (2022). Non-coding RNAs in fish physiology and development: miRNAs as a cornerstone in gene networks. In Fernandez, Ignacio & Fernandes, Jorge Manuel de Oliveira (Ed.), Cellular and Molecular Approaches in Fish Biology. Academic Press. ISSN 978-0-12-822273-7. p. 105–146.
  • Jafari, Omid; Ebrahimi, M.; Hedayati, Ali-Akbar; Zeinalabedini, Mehrshad; Poorbagher, Hadi & Nasrolahpourmoghadam, Maryam [Show all 7 contributors for this article] (2022). Integration of morphometrics and machine learning enables accurate distinction between wild and farmed common carp. Life. ISSN 2075-1729. 12. doi: 10.3390/life12070957.
  • Nedoluzhko, Artem; Mjelle, Robin; Renström, Maria; Skjærven, Kaja H.; Piferrer, Francesc & Fernandes, Jorge Manuel de Oliveira (2021). The first mitochondrial 5-methylcytosine map in a non-model teleost (Oreochromis niloticus) reveals extensive strand-specific and non-CpG methylation. Genomics. ISSN 0888-7543. 113(5), p. 3050–3057. doi: 10.1016/j.ygeno.2021.07.007. Full text in Research Archive
  • Konstantinidis, Ioannis; Anastasiadi, Dafni; Sætrom, Pål; Nedoluzhko, Artem; Mjelle, Robin & Podgorniak, Tomasz [Show all 8 contributors for this article] (2021). Epigenetic mapping of the somatotropic axis in Nile tilapia reveals differential DNA hydroxymethylation marks associated with growth. Genomics. ISSN 0888-7543. 113(5), p. 2953–2964. doi: 10.1016/j.ygeno.2021.06.037. Full text in Research Archive
  • Abdelhafiz, Yousri Abdelmutalab Ahmed; Fernandes, Jorge Manuel de Oliveira; Stefani, Erika; Albanese, Davide; Donati, Claudio & Kiron , Viswanath (2021). Power Play of Commensal Bacteria in the Buccal Cavity of Female Nile Tilapia. Frontiers in Microbiology. ISSN 1664-302X. 12. doi: 10.3389/fmicb.2021.773351. Full text in Research Archive
  • Abdelhafiz, Yousri Abdelmutalab Ahmed; Fernandes, Jorge Manuel de Oliveira; Larger, Simone; Albanese, Davide; Donati, Claudio & Jafari, Omid [Show all 8 contributors for this article] (2021). Breeding Strategy Shapes the Composition of Bacterial Communities in Female Nile Tilapia Reared in a Recirculating Aquaculture System. Frontiers in Microbiology. ISSN 1664-302X. 12, p. 1–16. doi: 10.3389/fmicb.2021.709611. Full text in Research Archive
  • Rbbani, Md Golam; Nedoluzhko, Artem; Galindo-Villegas, Jorge & Fernandes, Jorge Manuel de Oliveira (2021). Function of Circular RNAs in Fish and Their Potential Application as Biomarkers. International Journal of Molecular Sciences. ISSN 1661-6596. 22(13), p. 1–19. doi: 10.3390/ijms22137119. Full text in Research Archive
  • Lopez-Canovas, Amanda; Cabas, Isabel; Chaves-Pozo, Elena; Ros-Chumillas, Maria; Navarro-Segura, Laura & Lopez-Gomez, Antonio [Show all 9 contributors for this article] (2020). Nanoencapsulated Clove Oil Applied as an Anesthetic at Slaughtering Decreases Stress, Extends the Freshness and Lengthens Shelf Life of Cultured Fish. Foods. ISSN 2304-8158. 9(12), p. 2–20. doi: 10.3390/foods9121750. Full text in Research Archive
  • Konstantinidis, Ioannis; Sætrom, Pål; Mjelle, Robin; Nedoluzhko, Artem; Robledo, Diego & Fernandes, Jorge Manuel de Oliveira (2020). Major gene expression changes and epigenetic remodelling in Nile tilapia muscle after just one generation of domestication. Epigenetics. ISSN 1559-2294. 15(10), p. 1052–1067. doi: 10.1080/15592294.2020.1748914. Full text in Research Archive
  • Nedoluzhko, Artem; Slobodova, Natalia; Sharko, Fedor S.; Shalgimbayeva, Gulmira; Tsygankova, Svetlana V. & Boulygina, Eugenia S. [Show all 13 contributors for this article] (2020). A new strain group of common carp: The genetic differences and admixture events between Cyprinus carpio breeds. Ecology and Evolution. ISSN 2045-7758. 10(12), p. 5431–5439. doi: 10.1002/ece3.6286. Full text in Research Archive
  • Nedoluzhko, Artem; Sharko, Fedor S.; Rbbani, Md Golam; Teslyuk, Anton; Konstantinidis, Ioannis & Fernandes, Jorge Manuel de Oliveira (2020). CircParser: a novel streamlined pipeline for circular RNA structure and host gene prediction in non-model organisms. PeerJ. ISSN 2167-8359. 8. doi: 10.7717/peerj.8757. Full text in Research Archive
  • Podgorniak, Tomasz Krzysztof; Brockmann, Sven; Konstantinidis, Ioannis & Fernandes, Jorge Manuel de Oliveira (2019). Differences in the fast muscle methylome provide insight into sex-specific epigenetic regulation of growth in Nile tilapia during early stages of domestication. Epigenetics. ISSN 1559-2294. 14(8), p. 818–836. doi: 10.1080/15592294.2019.1618164. Full text in Research Archive

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  • Fernandez, Ignacio & Fernandes, Jorge Manuel de Oliveira (2022). Cellular and Molecular Approaches in Fish Biology. Academic Press. ISBN 978-0-12-822273-7. 438 p.
  • Fernandes, Jorge Manuel de Oliveira; Sarropoulou, Elena; Kiron , Viswanath; Power, Deborah M. & Liu, John (2018). GIA2018: 5th International Symposium on Genomics in Aquaculture : Book of Abstracts. CCWP Events Lda. ISBN 978-989-99099-3-9. 62 p.

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  • Fernandes, Jorge Manuel de Oliveira (2021). Unveiling the massive epigenome changes that occur during Nile tilapia domestication.
  • Fernandes, Jorge Manuel de Oliveira (2021). Trends and limitations of epigenetic biomarkers.
  • Rbbani, Md Golam; Nedoluzhko, Artem; Siriyappagouder, Prabhugouda; Raeymaekers, Joost A. M.; Galindo-Villegas, Jorge & Fernandes, Jorge Manuel de Oliveira (2021). Exploration of circRNA , miRNA and mRNA expression to identify their role in growth regulation in Nile tilapia.
  • Nedoluzhko, Artem; Sharko, Fedor; Rbbani, Md Golam; Teslyuk, Anton; Konstantinidis, Ioannis & Fernandes, Jorge Manuel de Oliveira (2021). Circular RNA host gene prediction in Nile tilapia using the novel circParser pipeline.
  • Rbbani, Md Golam; Nedoluzhko, Artem; Siriyappagouder, Prabhugouda; Raeymaekers, Joost A. M.; Galindo-Villegas, Jorge & Fernandes, Jorge Manuel de Oliveira (2021). circRNA, miRNA and mRNA muscle transcriptomes indicate their role in growth regulation in Nile tilapia.
  • Nedoluzhko, Artem; Mjelle, Robin; Renström, Maria; Skjærven, Kaja Helvik; Piferrer, Francesc & Fernandes, Jorge Manuel de Oliveira (2021). The mitochondrial 5-methylcytosine profile in Nile tilapia (Oreochromis niloticus).
  • Nedoluzhko, Artem; Rbbani, Md Golam; Sharko, Fedor; Siriyappagouder, Prabhugouda; Galindo-Villegas, Jorge & Fernandes, Jorge Manuel de Oliveira (2021). Circular RNA workflow analysis and its application in aquaculture.
  • Konstantinidis, Ioannis; Sætrom, Pål; Liedtke, Hannes; Pohlmann, Caroline; Tsoulia, Thomais & Fernandes, Jorge Manuel de Oliveira (2021). Differences in liver DNA hydroxymethylation reflect the growth phenotype.
  • Konstantinidis, Ioannis; Sætrom, Pål; Brieuc, Marine Servane Ono; Jakobsen, Kjetill Sigurd; Liedtke, Hannes & Pohlmann, Caroline [Show all 8 contributors for this article] (2021). DNA hydroxymethylation is linked to higher growth rate in Nile tilapia.
  • Rbbani, Md Golam; Nedoluzhko, Artem; Sharko, Fedor; Konstantinidis, Ioannis & Fernandes, Jorge Manuel de Oliveira (2021). Differences in the circular RNA transcriptome between wild and captive-bred Nile tilapia.
  • Fernandes, Jorge Manuel de Oliveira (2020). Epigenetics in aquaculture.
  • Fernandes, Jorge Manuel de Oliveira & Renström, Maria (2020). Mitochondrial DNA methylation in Nile tilapia Oreochromis niloticus.
  • Nedoluzhko, Artem; Dandara Da Silva Berrutti, Paula; Guimarães, Igo Gomes; Konstantinidis, Ioannis; Babiak, Igor & Fernandes, Jorge Manuel de Oliveira (2020). Hydroxymethylation changes during early embryonic development in zebrafish.
  • Nedoluzhko, Artem; Sharko, Fedor S.; Rabbani, Md Golam; Teslyuk, Anton; Konstantinidis, Ioannis & Fernandes, Jorge Manuel de Oliveira (2020). Circular RNA host gene and orthologue prediction using the self-designed CircParser pipeline.
  • Konstantinidis, Ioannis; Sætrom, Pål & Fernandes, Jorge Manuel de Oliveira (2019). Tissue-specific hydroxymethylome profiles of Nile tilapia Oreochromis niloticus at single nucleotide resolution.
  • Fernandes, Jorge Manuel de Oliveira (2019). Hooking the bigger fish through epigenetics. EU Research.
  • Fernandes, Jorge Manuel de Oliveira; Konstantinidis, Ioannis; Nedoluzhko, Artem & Mjelle, Robin (2019). Muscle transcriptome changes within one generation of Nile tilapia domestication.
  • Fernandes, Jorge Manuel de Oliveira (2019). Developmental plasticity of growth in teleosts.
  • Fernandes, Jorge Manuel de Oliveira; Konstantinidis, Ioannis; Pohlmann, Caroline; Tsoulia, Thomais & Liedtke, Hannes (2019). Differences in liver hydroxymethylomes of Nile tilapia with distinct growth rates.
  • Fernandes, Jorge Manuel de Oliveira; Wardale, Alex; Podgorniak, Tomasz Krzysztof & Babiak, Igor (2018). Growth-associated circulating miRNAs in Nile tilapia Oreochromis niloticus.
  • Konstantinidis, Ioannis; Sætrom, Pål & Fernandes, Jorge Manuel de Oliveira (2018). Fast muscle hydroxymethylation patterns in wild and captive Nile tilapia (Oreochromis niloticus) provide insights into fish domestication.
  • Podgorniak, Tomasz Krzysztof; Brockmann, Sven & Fernandes, Jorge Manuel de Oliveira (2018). Growth-related epigenetic crossroads in fast muscle of Nile tilapia sharing a similar genetic background.
  • Ekvall, Hans; Konstantinidis, Ioannis; Podgorniak, Tomasz Krzysztof & Fernandes, Jorge Manuel de Oliveira (2018). DNA hydroxy- and methylation profiles of the Nile tilapia pituitary link hypermethylation and hyperhydroxymethylation to faster growth.
  • Wardale, Alex; Podgorniak, Tomasz Krzysztof; Renström, Maria; Babiak, Igor & Fernandes, Jorge Manuel de Oliveira (2018). Circulating micrornas as potential biomarkers of growth in Nile tilapia (Oreochromis niloticus).
  • Fernandes, Jorge Manuel de Oliveira; Konstantinidis, Ioannis & Podgorniak, Tomasz Krzysztof (2018). Growth-associated DNA methylation and hydroxymethylation marks in Nile tilapia muscle.
  • Fernandes, Jorge Manuel de Oliveria (2017). The emerging field of epigenetics in aquaculture.
  • Fernandes, Jorge Manuel de Oliveria; Podgorniak, Tomasz Krzysztof & Brockmann, Sven (2017). A reduced representation of the DNA methylome in fast muscle of Nile tilapia Oreochromis niloticus.
  • Podgorniak, Tomasz Krzysztof; Brockmann, Sven & Fernandes, Jorge Manuel de Oliveria (2017). Growth and the DNA methylation landscape in pituitary and fast muscle of Nile tilapia (Oreochromis niloticus).
  • Konstantinidis, Ioannis; Fernandes, Jorge Manuel de Oliveria & Sætrom, Pål (2017). The first hydroxymethylation map of fast muscle in Nile tilapia (Oreochromis niloticus).
  • Fernandes, Jorge Manuel de Oliveria; Podgorniak, Tomasz Krzysztof & El-Zaeem, Samy (2016). Expression changes of miRNAs involved in epigenetic regulation are associated with domestication in Nile tilapia (Oreochromis niloticus).
  • Fernandes, Jorge Manuel de Oliveira (2016). EPIFISH: Innovative Epigenetic Markers for Fish Domestication.
  • Fernandes, Jorge Manuel de Oliveira & Konstantinidis, Ioannis (2020). DNA hydroxymethylation and improved growth of Nile tilapia (Oreochromis niloticus) during domestication. Nord Universitet. Full text in Research Archive
  • Fernandes, Jorge Manuel de Oliveira & Wardale, Alex (2019). Circulating miRNAs as potential non-invasive biomarkers of growth in Nile tilapia (Oreochromis niloticus). Nord University.

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Published Mar. 5, 2021 10:55 AM - Last modified Mar. 9, 2021 10:01 AM