Report
Teaser, summary, work performed and final results
Periodic Reporting for period 1 - EPIDIVERSE (Epigenetic Diversity in Ecology)
Teaser
Plants are the foundation of all ecosystems and they provide humans with essential services. Unprecedented rates of global environmental change are now putting plants under increased risk, and it is important to understand the capacity of plants to adapt to rapid change...
Summary
Plants are the foundation of all ecosystems and they provide humans with essential services. Unprecedented rates of global environmental change are now putting plants under increased risk, and it is important to understand the capacity of plants to adapt to rapid change. EpiDiverse takes a cross-disciplinary approach to investigate the role that epigenetic mechanisms, specifically DNA methylation, play in plant adaptation. Understanding the epigenetic contribution to adaptation will help to predict species responses to global warming and can open new directions for sustainable agriculture and crop breeding. EpiDiverse joins a consortium of academic and entrepreneurial groups to train 15 early-stage researchers (ESRs) to become a first generation of expert eco-epigeneticists, equipping them with the interdisciplinary skills - molecular, (epi)genomic, ecological and bioinformatics - to successfully tackle this new research area. Training emphasizes empirical and informatics skills to become fluent and creative in extracting knowledge from big ‘omics’ data in natural contexts.
To explain the real-life relevance of epigenetic variation in natural plant systems and ecological contexts, objectives of EpiDiverse are to: (1) Optimize genomic and bioinformatic tools to enable high-resolution DNA methylation analysis in non-model plant species; (2) determine natural epigenetic diversity, and its relationship with environmental factors, climate, and phenotypes, in three common wild plant species across Europe; and (3) characterize the molecular basis and functional consequences of epigenetic responses to specific environmental factors. This approach is innovative and timely because it integrates several so far disconnected areas of research, and it will transfer analytical methods from laboratory research to the real world.
Work performed
During the first two years of the EpiDiverse project, activities in three inter-connected research work packages have laid the foundation for epigenomic analysis in three focus plant species: Black poplar, Wild strawberry and Field pennycress. These species were chosen to represent plants with very different ecological and life history characteristics. Five ESRs were recruited in the ‘Genomes and Bioinformatics’ work package. This work package produced reference genomes for the two study species for which no reference genome was yet available, Black poplar and Field pennycress, and annotation of these genomes is underway. Bioinformatic analysis pipelines were developed for the analysis of Whole-Genome Bisulfite Sequencing data (WGBS and DMR pipelines) and for analysis of DNA methylation in reduced genomic fractions (RRBS) in the three plant species. Ongoing work is producing a pipeline for linking (epi)genomic data to ecological, climatic and phenotypic data. A central computing facility was set up for the ESRs to store and analyze their data using these pipelines. In the ‘Natural patterns’ work package, five ESRs were recruited who are using the genomic and bioinformatics tools to analyze patterns of DNA methylation variation in natural populations of the three plant species across a European scale, and to address specific hypothesis on the role of DNA methylation in plant herbivory defenses and phenotypic plasticity in species with different life histories. Sampling trips were done to collect seeds (Field pennycress), ramets (Wild strawberry) or cuttings (Black poplar) across Europe, resulting in live collections of 400-500 plants per species. These live collections are maintained as common gardens at the research facilities of three institutes in the network. Experimental protocols for plant cultivation, phenotypic analysis and specific environmental treatments (e.g. herbivory) have been worked out. Based on collected material, DNA samples have been isolated, processed into bisulfite sequencing libraries and subsequently sequenced for two of the three species; these data are ready for analysis using the bioinformatics pipelines. For one species (Wild strawberry) isolation of high-quality DNA was challenging and took longer; DNA samples are currently prepared for processing into bisulfite sequencing libraries. Targeted herbivory experiments were performed in the three species and a four-generation experiment is underway using multiple plant species; for these experiments the RRBS DNA methylation pipeline was tested and first RRBS bisulfite-sequencing libraries have been generated. In the ‘Molecular mechanisms’ work package, five ESRs were recruited who are using the collected plant samples and the genomic and bioinformatics tools to analyze DNA methylation and associated mechanisms (small RNAs, transposable element activity and gene expression) in controlled experiments in response to drought stress and various other environmental factors. Experiments focused on within-generation stress memory in long-lived Black poplar and on both within- and between-generation stress memory in the short-lived other species. The first DNA methylation and phenotypic results suggest epigenetic stress memory in Black poplar and Field pennycress. Experiments in this work package were extended to different plant species for easier development of methodologies (small RNA and transposable element analysis in Arabidosis and rice), which are subsequently applied to the target species of EpiDiverse.
Supporting its research and training programmes, the network organized two summer schools (on plant ecological epigenetics in Wageningen and on bioinformatics training in Leipzig), two annual network meetings with contributions from invited experts, all ESRs were enrolled in local PhD programmes or graduate schools, and a total of 20 sectoral and cross-sectoral secondments have been carried out by the ESRs. A data management plan was develope
Final results
EpiDiverse will deliver a systematic analysis of the involvement of epigenetic mechanisms in ecological adaptation of different plant species. The scientific impact of this is that high-resolution epigenomic analysis approaches are translated from model species in the lab and applied to natural populations and ecological contexts in a range of different wild species. This is a novel but necessary step for revealing the role of epigenetic mechanisms in adaptation. Insight in these underlying mechanisms of ecological adaptation is important for better understanding, and possibly managing, plant adaptability to current environmental challenges, imposed by climate change and other anthropogenic effects, both for natural species and for agricultural crops.
Website & more info
More info: http://epidiverse.eu.