Epidiverse

European Traning Network
Epidiverse group photo

EpiDiverse was a Marie Skłodowska-Curie Innovative Training Network from 1 September 2017 - 28 February 2022. EpiDiverse aimed at the study of epigenetic variation in wild plant species. The network joined research groups from ecology, molecular (epi)genetics and bioinformatics to explore the genomic basis, molecular mechanisms and ecological significance of epigenetic variation in natural plant populations.

The cross-disciplinary research program applied epigenomic research tools to a selection of different wild plants (annual plants, asexually reproducing perennial plants, and long-lived trees) to investigate how epigenetic mechanisms contribute to natural variation, stress responses and long-term adaptation of plants. Understanding the epigenetic contribution to adaptive capacity will help to better understand species responses to global environmental change, and can open new directions for sustainable agriculture and crop breeding.

The EpiDiverse consortium trained 15 Early Stage Researchers to become expert plant epigeneticists, and equipped them with the interdisciplinary skills to successfully tackle this new research area. EpiDiverse training emphasized fluency in both empirical and informatics skills to become creative in working with big ‘omics data in natural contexts.

EpiDiverse is funded by the EU Horizon 2020 programme and involves 12 partners from academia, non-profit organizations and industry located in the Netherlands, Germany, France, Spain, Czech Republic, Italy and Austria.  

Output

Project Output

About

About The EpiDiverse network

EpiDiverse is a Marie Skłodowska-Curie Innovative Training Network aimed at the study of epigenetic variation in wild plant species. The network joins research groups from ecology, molecular (epi)genetics and bioinformatics to explore the genomic basis, molecular mechanisms and ecological significance of epigenetic variation in natural plant populations.

The cross-disciplinary research program applies epigenomic research tools to a selection of different wild plants: annual plants, asexually reproducing perennial plants, and long-lived trees. Understanding the epigenetic contribution to adaptive capacity will help to better understand species responses to global environmental change, and can open new directions for sustainable agriculture and crop breeding. 

Research

EpiDiverse research aims

The capacity of plants to adapt to their environments is key to their success in a world that is constantly changing. Individual plants can adjust to environmental change by being flexible in the traits that they express in different environments (phenotypic plasticity). Over longer time scales populations can adapt to specific environments by selection on heritable traits, resulting for instance in populations with modified flowering time, drought tolerance, or different capacity for phenotypic plasticity. Epigenetic mechanisms play an important role in these processes. Epigenetic mechanisms are reversible chemical modifications of the DNA code that determine if the underlying DNA code is active or silenced. These mechanisms can play a role in the adjustment of gene expression in response to specific environments. Moreover, epigenetic variants exist in plants that are stable between generations, which can lead to differences in heritable traits even between genetically uniform plants.

Thus, to understand the adaptive capacity of plants, we need to look not only at the information within the DNA code, but also at the epigenetic information on top of the DNA code. Much of our current knowledge of DNA methylation in plants comes from research on the molecular model plant species Arabidopsis thaliana. But it is unclear how important epigenetic variation is in the wild for the adaptive capacity of natural plant populations in various ecological contexts. To what extent do epigenetic responses control ecologically relevant stress responses and heritable traits? Do patterns of epigenetic variation in natural populations reflect an important epigenetic role in adaptive capacity? And is the role of epigenetics different for species that differ in important life history traits, such as sexual versus clonal reproduction or in annual versus long-lived species? These are the research questions that EpiDiverse takes on.

The EpiDiverse research applies high-resolution epigenomic research tools and ecological experimental designs to an ecologically diverse set of natural plant species, with the ultimate aim to expose the contribution of epigenetic variation to the adaptive capacity of plants.

Specific research objectives of the network are to:

  1. Optimize genomic and bioinformatic tools to enable high-resolution DNA methylation analysis in non-model plant species
  2. Identify natural patterns of DNA methylaiton variation and its associations with phenotype, local environment, climate and geographic location
  3. Unravel the underlying molecular mechanisms of epigenetic responses to ecologically relevant stress environments. 

Project structure

In EpiDiverse, research projects are clustered around a few study species (Populus nigra, Fragaria vesca and Thlaspi arvense) with very different life histories and ecological characteristics. For each species, research groups from different backgrounds collaborate to generate genomic resources and epigenomic analysis pipelines (the “bioinformaticians”, work package 1) and to use these tools for exploring patterns of epigenetic variation in natural populations (the “ecologists”, work package 2) and to understand the epigenetic mechanisms of plant responses to environmental stress (the “molecular biologists”, work package 3).

Projects

We have 15 PhD projects in 3 work packages. PhD students from the fields of plant sciences, ecology, (epi)genetics, (epi)genomics, computational biology or bioinformatics work on these projects. The EpiDiverse network facilitates close collaboration between individual PhD projects. These projects provide an excellent opportunity to receive cross-disciplinary doctoral training and to do cutting-edge research in plant epigenetics.

The EpiDiverse research focuses on three wild plant species. For each of these species, research groups from computational biology, molecular genetics and ecology team up to address the genomic basis, the molecular mechanisms and the ecological significance of epigenetic variation.

EpiDiverse provides a comprehensive training program that includes summer schools, workshops and exchange visits to different groups in the network. We will offer training in molecular, genomic, computational, and ecological aspects of studying epigenetic variation, as well as in transferable skills. Students will be part of a group of 15 PhD students from across Europe that will all work on similar questions, and that will regularly meet and interact.

Training

EpiDiverse training aims

Interdisciplinary scientific training

The research program of EpiDiverse was characterized by integration of bioinformatics, molecular genetics and ecology expertise. A key aim of the academic training provided to EpiDiverse students was to develop the interdisciplinary skills for combining these fields. The ability to link genetic/epigenetic information with experimental proficiency, bioinformatics skills, and creativity in distilling knowledge from big data. This training prepared for academic careers in modern biology where technological ‘omics’ advancements are revolutionizing genetic, ecological, and medical research agendas.

Experience in non-academic work environments

The EpiDiverse consortium includes academic and non/academic participants. The non-academic participants carried out an integral part of the research program and host several of the EpiDiverse research projects. Furthermore, they provided training opportunities (secondments) for those students that were hosted at academic research groups in the network. Non-academic participants were:

  • Roche Diagnostics, Mannheim, Deutschland GmbH.  At Roche the students can experience the industrial work environment. Here the bioinformatics students will be trained in new technology for DNA methylation screening.
  • EcSeq contributes with knowledge of pipeline maintenance, hands-on bioinformatics training. This company supported the students with their data analysis.
  • IGA-TS, IGA Technology Services SRL, contributed with expertise of (Epi)genomic sequencing data and facilities for library preparation and Illumina sequencing.
  • All three mentioned companies, ECSEQ, IGA-TS and ROCHE, represent large and growing life sciences and -omics data industries.
  • WiD (Wissenschaft im Dialog), Berlin, Germany trained the students in public outreach of information and science communication. 

Transferable skills

EpiDiverse organized platforms for scientific presentations and interaction, training in research ethics, data management, scientific writing and project design to ensure that all ESRs received training in these essential research skills. Because the research topic of EpiDiverse is of fundamental scientific interest, it was important for the ESRs to develop skills in science communication in order to explain the research and its relevance to a general audience. ESR received training in science communication and helped develop an online portal for learning on epigenetics, which was integrated with the outreach goals of the network

Contact

Contact

EpiDiverse Coordinator

Dr. Koen Verhoeven
Department of Terrestrial Ecology
Netherlands Institute of Ecology (NIOO-KNAW)

EpiDiverse Project manager

Margreet Bruins
Department Terrestrial Ecology
Netherlands Institute of Ecology (NIOO-KNAW)

Visiting address

Droevendaalsesteeg 10
6708 PB Wageningen
T 0317 47 34 00 
nioo.knaw.nl

Postal address

Postbus 50 
6700 AB Wageningen

For members

For members

For consortium member access to archived project documents, please contact Koen Verhoeven