Grant: Discovery Grants Program - Individual

Plants are sedentary organisms that cannot avoid or escape stress. Our previous research suggests that the progeny of plants exposed to various abiotic and biotic stresses exhibit changes in their biomass, leaf size and number, flowering time, seed size and metabolite levels. This project aims to understand the role of epigenetic factors in transgenerational responses to stress in plants and to decipher genetic and epigenetic changes that occur in plants after a multigenerational exposure to stress. We want to answer the following questions: How specific are epigenetic hallmarks of stress adaptation? How long does the transgenerational memory last? How stable are epigenetic changes? Do genetic changes occur at a higher rate in the progeny of stressed plants, and if they do, are they random? We will analyze 25 consecutive generations of wild-type and mutant Arabidopsis thaliana plants propagated in the presence of one of the stresses: heat, cold, salt or UVC. Mutant plants include dcl2, dcl3 and dcl4 used to examine the role of Dicers; and rad51, rad54, ku70 and atm1 plants to investigate their role in the maintenance of genome stability across generations. In addition, to identify the role of RNA-dependent DNA methylation (RdDM), we have initiated a similar exposure of met1, cmt3, drm2, rdr2 and rdr6 mutants. First, we will profile plant phenotypes under normal conditions and in response to stress. We will then profile genome and epigenome by sequencing of the genome - to identify a genetic diversity in plants propagated with and without stress and by bisulfite sequencing - to identify the diversity in methylation patterns; sequencing of ncRNAs and ChIP-seq - for identifying the distribution of major permissive and repressive marks. We hypothesize that we will find a larger genotypic diversity in the population of plants exposed to stress than in the population propagated without stress. It will be important to identify genomic regions that are more prone to genetic and epigenetic instability as well as to find out whether any epigenetic markers persist across many generations, and whether they are associated with specific traits of stress tolerance (epiQTLs). Since our previous work demonstrated a potential role of DNA methylation and ncRNAs in transgenerational responses, we will analyze what potential targets of RdDM in the genome are and establish correlative links between ncRNA expression, RdDM, chromatin structure and gene expression patterns. This work is critical for the understanding of the mechanisms of stress adaptation, and it will help find out what genetic and epigenetic mechanisms are involved in plant adaptation to a stressful environment. We believe that this knowledge can be applied to identify specific QTLs and epiQTLs associated with stress tolerance and can be used to produce stress tolerant crops.