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I coordinate the H2020 Marie Skłodowska-Curie Innovative Training Network EPIDIVERSE. This network includes 15 PhD student projects in 12 research groups from ecology, molecular genetics and bioinformatics in seven countries. Together, these projects address epigenetic variation in three plant species (wild strawberry, black poplar and field pennycress). The aim of EPIDIVERSE is to investigate how epigenetic mechanisms contribute to natural variation, stress responses and adaptation of plants with different life history characteristics. The network is a joint effort to apply high-resolution epigenetic analysis approaches to natural plant systems in ecological contexts. In our group, 2 EPIDIVERSE projects are carried out:
Heritable epigenetic variation in asexual plant lineages. Asexually reproducing lineages are excellent models for studying the causes and consequences of heritable epigenetic variation, also in natural ecological contexts, that builds up within genetically uniform backgrounds. This research line was established via an NWO-funded VIDI personal research grant (2011-2016). Focus is on analysis of DNA methylation in clonal duckweed (the world’s fastest-growing angiosperm) and apomictic dandelion. Output from this research includes a reduced-representation method for highly multiplexed, reference-free screening of DNA methylation (epiGBS) and a draft dandelion reference genome (with Wageningen University collaborators).
Plants engage in biotic interactions with pathogenic as well as to beneficial soil organisms. For instance, through association with beneficial soil microbes plants can express increased growth via improved nutrient uptake, disease resistance, and abiotic stress tolerance. Such microbe-mediated plant traits could be important for ecological adaptation and for crop improvement, but natural or artificial selection can only shape these traits if genetic variation exists for the ability to engage with specific beneficial microbes. In this research we explore genetic variation for, and ecological consequences of, plant interactions with specific soil biota.
Prof. Dr. Lauren McIntyre (Department of Molecular Genetics & Microbiology, University of Florida, Gainesville): design and analysis of -omics experiments
Prof. Dr. Nele Horemans (Biosphere Impact Studies, CSK-CEN, Mol, Belgium): epigenetic inheritance in duckweed and epigenetic effects of radiation in dandelion
Prof. Dr. Frank Johannes (Technical University Munich): quantitative epigenetics in Arabidopsis
Prof. Dr. Eric Schranz (Biosystematics, Wageningen University): Dandelion reference genome
Prof. Dr. Kees van Oers (NIOO-KNAW, Animal Ecology): Epigenetic variation in Great Tit
Prof. Dr. Christina Richards (University of South Florida, Tampa): epiGBS and DNA methylation in natural populations