Grant: Discovery Grants Program - Individual

Heritable variation in plant phenotypes originates, in principle, from DNA variation. It may also originate from an epigenetic variation, which adds new elements to heritable phenotypic variation and, thus, to the diversity and genetic differentiation of natural populations. There are two main types of epigenetic modifications: DNA methylation and histone modifications. For example, DNA methylation, the principal type of epigenetic modification, modulates gene expression and plays a major role in repressing the transcription and movement of transposable elements (TEs), which are the primary source of genomic mutations. Several plant species have reported variations in epigenetic marks (and phenotypic variations) in response to environmental cues (biotic and abiotic). The possible heritability and stability of epigenetic modifications make its potential contribution to phenotypic plasticity and the adaptive capacity of trees to climate change a central question. However, limited work has been done regarding the potential role of TEs and epigenetics phenomena in rapid environmental adaptation for most boreal tree species. This research program has innovative potential because we will address many research questions in the context of evolution that relates to selection acting on adaptive traits. Based on the availability of whole-genome sequence data of a large number of natural accessions of Populus trichocarpa (c.900), we will investigate transposable elements (TEs) as a source of adaptation and build a genome-wide atlas of TEs. Because P. tremuloides is closely related to the model species P. trichocarpa, we will assess the contribution of epigenetic variation to drought adaptation and its stability over generations. We will significantly improve our understanding of tree adaptation to changing environment by using the most promising markers and combining them with the single nucleotide polymorphism (SNPs) that have already been analysed. Building a genome-wide atlas of TEs and epigenetic marks will also allow for the identification of functional genes associated with interesting traits through, for example, the construction of transposon-based mutation libraries and the development of TEs as molecular markers to be used in tree breeding. We will examine the transcriptome and methylome in adaptation to water stress. These will allow us to evaluate the potential contribution of the short epigenetic memory to plant response to repetitive water stress and recovery capacity. Through this work, we will gain a better understanding of the molecular mechanisms underlying the formation of new epialleles and their effects on gene expression and regulation. We also aim to integrate TEs tree epigenetics as a possible new source of beneficial functional traits for tree breeding and forest management under climate change. This proposal will train 2 PhDs, 2 MS, and 5 BSc students.