An epigenome-wide association studys in plants

The creation, or selection, of plant cultivars with more sophisticated traits and improved adaptability to extreme environmental perturbations will require detailed knowledge of the many factors controlling the plant phenotype. Heritable variation was traditionally thought to occur exclusively as a result of DNA sequence polymorphisms, but it is now clear that a significant portion of heritable variation occurs by other means, among which epigenetic processes appear to play a major role (Madlung and Comai, 2004; Richards, 2006; Richards, 2008; Bossdorf et al., 2008). Understanding the degree of epigenetic diversity and its influence on the relationship between environment, genotype and phenotype should improve our ability to predict the effect of environmental changes on performance and potential of plants and their progeny. To reach this goal this project aims to: 1. quantify the amount of epigenetic variation that occurs as a result of DNA sequence polymorphisms, and identify which epigenetic marks are involved, 2. quantify the amount of epigenetic variation that occurs as a result of environmental variation, and detect which environmental changes and which marks are involved, 3. investigate the interplay of genetic, epigenetic and environmental variation on phenotype. To date, a major stumbling block in the field has been the sheer complexity of, and the interplay between, the many factors that control the phenotype. We propose to overcome this by integrating methodologies from the fields of both population genetics and classical epigenetics. Specifically, we will extend genome-wide association studies by using whole genome approaches such as sequencing after chromatin immunoprecipitation (ChIP-seq) and after bisulfite conversion (BS-seq) to map the epigenome, and RNA-sequencing (RNA-seq) to investigate the transcriptome. In this approach, a set of Arabidopsis accessions, selected to be both genetically and potentially epigenetically most divergent, will be subject to epigenomic profiling for DNA methylation, histone modifications and nucleosome occupancy. The differences in distribution of chromatin marks between the accessions will then be used as "epi-phenotypes" for genome-wide association mapping. They will also be used as "epi-polymorphisms" for epigenome-wide association studies (EWAS). These experiments will be repeated on plants that have been grown for multiple generations under a variety of conditions favoring slow or fast growth, in extreme habitats or under different climatic conditions, nutrition or light regimes. This will enable us to understand the relationship between genetic, environmental and chromatin variation, to address which biotic and abiotic factors induce epigenetic variation, and to explore the link between genetic and epigenetic variation, phenotypic plasticity and environmental adaption. The inheritance of chromatin marks over multiple generations and their effect on phenotype will be used to examine the role of epigenetics in transgenerational memory and environmental adaption.