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

  • Artem Nedoluzhko; Fedor S. Sharko; Md Golam Rbbani; Anton Teslyuk; Ioannis Konstantinidis & Jorge Manuel de Oliveira Fernandes (2020). CircParser: a novel streamlined pipeline for circular RNA structure and host gene prediction in non-model organisms. PeerJ.  ISSN 2167-8359.  8
  • Ioannis Konstantinidis; Pål Sætrom; Robin Mjelle; Artem Nedoluzhko; Diego Robledo & Jorge Manuel de Oliveira Fernandes (2020). Major gene expression changes and epigenetic remodelling in Nile tilapia muscle after just one generation of domestication. Epigenetics.  ISSN 1559-2294.  15, s 1052- 1067
  • Artem Nedoluzhko; Natalia Slobodova; Fedor S. Sharko; Gulmira Shalgimbayeva; Svetlana V. Tsygankova; Eugenia S. Boulygina; Zsigmond Jeney; Van Q. Nguyen; Thế T. Pham; Đức T. Nguyen; Alexander Volkov; Jorge Manuel de Oliveira Fernandes & Sergey M Rastorguev (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, s 5431- 5439
  • Tomasz Krzysztof Podgorniak; Sven Brockmann; Ioannis Konstantinidis & Jorge Manuel de Oliveira Fernandes (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, s 818- 836

View all works in Cristin

  • John Liu; Elena Sarropoulou; Jorge Manuel de Oliveira Fernandes; Deborah M. Power & Viswanath Kiron (ed.) (2018). GIA2018: 5th International Symposium on Genomics in Aquaculture : Book of Abstracts. CCWP Events Lda.  ISBN 978-989-99099-3-9.  62 s.

View all works in Cristin

  • Artem Nedoluzhko; Paula Dandara Da Silva Berrutti; Igo Gomes Guimarães; Ioannis Konstantinidis; Igor Babiak & Jorge Manuel de Oliveira Fernandes (2020). Hydroxymethylation changes during early embryonic development in zebrafish.
  • Artem Nedoluzhko; Fedor S. Sharko; Md Golam Rabbani; Anton Teslyuk; Ioannis Konstantinidis & Jorge Manuel de Oliveira Fernandes (2020). Circular RNA host gene and orthologue prediction using the self-designed CircParser pipeline.
  • Jorge Manuel de Oliveira Fernandes (2020). Epigenetics in aquaculture.
  • Jorge Manuel de Oliveira Fernandes & Maria Renström (2020). Mitochondrial DNA methylation in Nile tilapia Oreochromis niloticus.
  • Ioannis Konstantinidis (2020). DNA hydroxymethylation and improved growth of Nile tilapia (Oreochromis niloticus) during domestication.
  • Jorge Manuel de Oliveira Fernandes; Ioannis Konstantinidis; Caroline Pohlmann; Thomais Tsoulia & Hannes Liedtke (2019). Differences in liver hydroxymethylomes of Nile tilapia with distinct growth rates.
  • Ioannis Konstantinidis; Pål Sætrom & Jorge Manuel de Oliveira Fernandes (2019). Tissue-specific hydroxymethylome profiles of Nile tilapia Oreochromis niloticus at single nucleotide resolution.
  • Jorge Manuel de Oliveira Fernandes (2019). Developmental plasticity of growth in teleosts.
  • Jorge Manuel de Oliveira Fernandes; Ioannis Konstantinidis; Artem Nedoluzhko & Robin Mjelle (2019). Muscle transcriptome changes within one generation of Nile tilapia domestication.
  • Alex Wardale (2019). Circulating miRNAs as potential non-invasive biomarkers of growth in Nile tilapia (Oreochromis niloticus).
  • Jorge Manuel de Oliveira Fernandes (2019). Hooking the bigger fish through epigenetics. EU Research.
  • Ioannis Konstantinidis; Pål Sætrom & Jorge Manuel de Oliveira Fernandes (2018). Fast muscle hydroxymethylation patterns in wild and captive Nile tilapia (Oreochromis niloticus) provide insights into fish domestication.
  • Tomasz Krzysztof Podgorniak; Sven Brockmann & Jorge Manuel de Oliveira Fernandes (2018). Growth-related epigenetic crossroads in fast muscle of Nile tilapia sharing a similar genetic background.
  • Hans Ekvall; Ioannis Konstantinidis; Tomasz Krzysztof Podgorniak & Jorge Manuel de Oliveira Fernandes (2018). DNA hydroxy- and methylation profiles of the Nile tilapia pituitary link hypermethylation and hyperhydroxymethylation to faster growth.
  • Alex Wardale; Tomasz Krzysztof Podgorniak; Maria Renström; Igor Babiak & Jorge Manuel de Oliveira Fernandes (2018). Circulating micrornas as potential biomarkers of growth in Nile tilapia (Oreochromis niloticus).
  • Jorge Manuel de Oliveira Fernandes; Ioannis Konstantinidis & Tomasz Krzysztof Podgorniak (2018). Growth-associated DNA methylation and hydroxymethylation marks in Nile tilapia muscle.
  • Jorge Manuel de Oliveira Fernandes; Alex Wardale; Tomasz Krzysztof Podgorniak & Igor Babiak (2018). Growth-associated circulating miRNAs in Nile tilapia Oreochromis niloticus.
  • Jorge Manuel de Oliveria Fernandes (2017). The emerging field of epigenetics in aquaculture.
  • Tomasz Krzysztof Podgorniak; Sven Brockmann & Jorge Manuel de Oliveria Fernandes (2017). Growth and the DNA methylation landscape in pituitary and fast muscle of Nile tilapia (Oreochromis niloticus).
  • Ioannis Konstantinidis; Jorge Manuel de Oliveria Fernandes & Pål Sætrom (2017). The first hydroxymethylation map of fast muscle in Nile tilapia (Oreochromis niloticus).
  • Jorge Manuel de Oliveria Fernandes; Tomasz Krzysztof Podgorniak & Sven Brockmann (2017). A reduced representation of the DNA methylome in fast muscle of Nile tilapia Oreochromis niloticus.
  • Jorge Manuel de Oliveria Fernandes; Tomasz Krzysztof Podgorniak & Samy El-Zaeem (2016). Expression changes of miRNAs involved in epigenetic regulation are associated with domestication in Nile tilapia (Oreochromis niloticus).
  •  (2016). EPIFISH: Innovative Epigenetic Markers for Fish Domestication.

View all works in Cristin

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