Evolutionary and functional impact of epigenetic variations in forest trees. – EPITREE

Forest trees are sessile, long-lived organisms with a major role in the ecology of the Earth. They have developed sensitivity to environmental variation and the potential to adapt, through their high level of standing genetic variations and remarkable phenotypic plasticity. However, forest die-off has been observed in recent years following episodes of drought and high temperatures, which are predicted to become more frequent in the future, due to climate change. Studies of the genetic basis of tree adaptation have focused principally on the contribution of standing structural variation to local adaptation. Surprisingly, epigenetic mechanisms have remained largely unstudied, despite their known importance in long-lived organisms, in which they facilitate rapid phenotypic modifications in response to environmental changes. In this context, DNA methylation has been extensively studied in the model plant Arabidopsis thaliana and several crop species, and shown to have effects extending from gene expression to integrated phenotypes. A few studies involving EPITREE partners have already shown that epigenomic approaches are useful for improving our understanding of the development and response to environmental constraints of forest trees. However, no epigenomic study of forest tree populations has ever been published, despite the demonstrated value of this emerging approach in Arabidopsis. Epigenomic variation is particularly relevant for studies of tree meristems, the morphogenetic centre for specific tree traits, such as the regulation of vegetative bud dormancy and secondary xylogenesis. We will study two complementary model species with large genomic resources and of economic interest: poplar and oak. The general objective of EPITREE is to study the impact of epigenetic mark (DNA methylation) together with gene expression, and allelic variation on forest tree adaptation to local environments and phenotypic plasticity. In particular, we will explore the benefits of considering epigenetic marks in addition to genetic polymorphisms and phenotypes in plant breeding and the characterisation of genetic resources, to provide proof-of-concept in two major forest tree species, with a view to establishing ambitious objectives for tree breeders and the managers of genetic resources. To this end, EPITREE brings together experts in tree epigenetics, genomics, statistics, mathematical modelling, breeding and ecophysiology. EPITREE will achieve its objectives through five workpackages (WPs): (WP1) Comprehensive identification of candidate regions for epigenomic analysis by whole-genome bisulphite sequencing; (WP2) Characterisation of the extent of epigenomic variation in natural populations and its functional consequences, using previously identified candidate regions and a sequence capture-based approach followed by bisulphite sequencing; (WP3) Characterisation of the extent of epigenomic plasticity in response to environmental constraints and its functional consequences; (WP4) Modelling the multiscale relationships between quantitative traits and their molecular determinants; and (WP5) Coordination and dissemination of the project results to the international scientific community, scientific clusters, professionals, students, and the general public.