Integration and Visualization of Epigenome and Mobilome Data in Crops

National audienceIn the coming years, the study of the interaction between the epigenome and the mobilome is likely to give insights on the role of TEs on genome stability and evolution. In the present project we have created tools to collect epigenetic datasets from different laboratories and databases and translate them to a standard format to be integrated, analyzed and finally visualized

Epigenetic regulation of adaptive responses of forest tree species to the environment

Epigenetic variation is likely to contribute to the phenotypic plasticity and adaptative capacity of plant species, and may be especially important for long-lived organisms with complex life cycles, including forest trees. Diverse environmental stresses and hybridization/polyploidization events can create reversible heritable epigenetic marks that can be transmitted to subsequent generations as a form of molecular “memory”. Epigenetic changes might also contribute to the ability of plants to colonize or persist in variable environments. In this review, we provide an overview of recent data on epigenetic mechanisms involved in developmental processes and responses to environmental cues in plant, with a focus on forest tree species. We consider the possible role of forest tree epigenetics as a new source of adaptive traits in plant breeding, biotechnology, and ecosystem conservation under rapid climate change.This is the publisher’s final pdf. The published article is copyrighted by the authors and published by Blackwell Publishing Ltd. and can be found at: http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%292045-7758.Keywords: forest trees, phenotypic plasticity, epigenetic memory of stressful conditions, adaptive response, epigenetics, environmental stres

Recherche de gènes impliqués dans la tolérance au zinc chez l'espèce modèle hyperaccumulatrice de zinc Arabidopsis halleri : un nouveau rôle possible pour les défensines de plantes

Le zinc est un métal essentiel pour les êtres vivants, mais sa présence en excès dans la cellule peut s'avérer toxique. Or certaines plantes dites hyperaccumulatrices ont la capacité surprenante d'accumuler de fortes quantités de zinc dans leurs parties aériennes (jusqu'à 1% de leur matière sèche), sans présenter de symptômes de toxicité. La plante tolérante et hyperaccumulatrice de zinc Arabidopsis halleri représente, par sa proximité phylogénétique avec la plante modèle Arabidopsis thaliana, un matériel biologique parfaitement adapté pour aborder les mécanismes moléculaires de l'homéostasie du zinc chez les plantes, qui sont encore mal connus. L'expression hétérologue d'une banque d'ADNc de feuilles d'A. halleri dans la levure Saccharomyces cerevisiae en conditions de toxicité en zinc nous a permis d'isoler 5 clones indépendants présentant un phénotype de tolérance au zinc. Les ADNc correspondants codent tous des protéines fortement homologues à des protéines appelées défensines de plantes (PDF) chez Arabidopsis thaliana. Ces protéines sont ubiquitaires chez les plantes mais également chez les mammifères où elles sont connues pour participer aux mécanismes de défense immunitaire innée. Cependant, à notre connaissance, aucun rôle des défensines dans la physiologie des métaux n'a été établi à ce jour. Les résultats du travail de thèse qui seront présentés proposent un nouveau rôle des défensines de plantes dans l'homéostasie des métaux

DNA Methylation in Rice and Relevance for Breeding

The challenge of sustaining food security in the context of global changes is at the heart of plant research. Environmental stresses, in particular, are known to impact genome stability and epigenetic mechanisms. Epigenetic pathways are well characterized in plants, particularly in the dicotyledon model plant Arabidopsis thaliana, but an increasing number of epigenetic and epigenomic studies are also performed on rice (Oryza sativa). Rice represents a major food crop of worldwide importance and is also a good model for monocotyledons owing to its relatively small genome size and fully sequenced well-annotated genome. Today, the main regulators of DNA methylation are identified in rice. Moreover, compared to Arabidopsis, rice has an important evolutionary history due to human selection since its domestication. DNA methylation may be involved in both adaptation and agronomic performances and thus, a better understanding of epigenetic regulations in rice should contribute to improving the adaptation of crops to a changing environment. In this review, we expose the current knowledge on DNA methylation in rice and future perspectives to be considered

Transposable elements, a treasure trove to decipher epigenetic variation : insights from Arabidopsis and crop epigenomes

In the past decade, plant biologists and breeders have developed a growing interest in the field of epigenetics, which is defined as the study of heritable changes in gene expression that cannot be explained by changes in the DNA sequence. Epigenetic marks can be responsive to the environment, and evolve faster than genetic changes. Therefore, epigenetic diversity may represent an unexplored resource of natural variation that could be used in plant breeding programmes. On the other hand, crop genomes are largely populated with transposable elements (TEs) that are efficiently targeted by epigenetic marks, and part of the epigenetic diversity observed might be explained by TE polymorphisms. Characterizing the degree to which TEs influence epigenetic variation in crops is therefore a major goal to better use epigenetic variation. To date, epigenetic analyses have been mainly focused on the model plant Arabidopsis thaliana, and have provided clues on epigenome features, components that silence pathways, and effects of silencing impairment. But to what extent can Arabidopsis be used as a model for the epigenomics of crops? In this review, we discuss the similarities and differences between the epigenomes of Arabidopsis and crops. We explore the relationship between TEs and epigenomes, focusing on TE silencing control and escape, and the impact of TE mobility on epigenomic variation. Finally, we provide insights into challenges to tackle, and future directions to take in the route towards using epigenetic diversity in plant breeding programmes

Transposable elements: all mobile, all different, some stress responsive, some adaptive?

International audienc

Epigenetic contribution to stress adaptation in plants

Plant epigenetics has recently gained unprecedented interest, not only as a subject of basic research but also as a possible new source of beneficial traits for plant breeding. We discuss here mechanisms of epigenetic regulation that should be considered when undertaking the latter. Since these mechanisms are responsible for the formation of heritable epigenetic gene variants (epialleles) and also regulate transposons mobility, both aspects could be exploited to broaden plant phenotypic and genetic variation, which could improve long-term plant adaptation to environmental challenges and, thus, increase productivity

Recherche de gènes impliqués dans la tolérance au zinc chez l'espèce modèle hyperaccumulatrice de zinc Arabidopsis halleri (un nouveau rôle possible pour les défensines de plantes)

Le zinc est un métal essentiel pour les êtres vivants, mais sa présence en excès dans la cellule peut s'avérer toxique. Or certaines plantes dites hyperaccumulatrices ont la capacité surprenante d accumuler de fortes quantités de zinc dans leurs parties aériennes (jusqu à 1% de leur matière sèche), sans présenter de symptômes de toxicité. La plante tolérante et hyperaccumulatrice de zinc Arabidopsis halleri représente, par sa proximité phylogénétique avec la plante modèle Arabidopsis thaliana, un matériel biologique parfaitement adapté pour aborder les mécanismes moléculaires, encore mal connus, de l homéostasie du zinc chez les plantes. L expression hétérologue d une banque d ADNc de feuilles d A. halleri dans la levure Saccharomyces cerevisiae en conditions de toxicité en zinc nous a permis d isoler 5 clones indépendants présentant un phénotype de tolérance au zinc. Les ADNc correspondants codent tous des protéines fortement homologues à des protéines appelées défensines de plantes (PDF) chez Arabidopsis thaliana. Ces protéines sont ubiquitaires chez les plantes mais également chez les mammifères où elles sont connues pour participer aux mécanismes de défense immunitaire innée. Cependant, à notre connaissance, aucun rôle des défensines dans la physiologie des métaux n a été établi à ce jour. Une des défensines d A. halleri, une fois exprimée chez A. thaliana, confère aux plantes transgéniques une tolérance accrue à des concentrations toxiques de zinc. De plus, chez A. halleri, l expression des défensines semble être induite par un traitement des plantes par le zinc, que ce soit au niveau des transcrits ou des protéines. Ces résultats originaux proposent un nouveau rôle des défensines de plantes dans l homéostasie des métauxZinc (Zn) is an essential metal that can become highly toxic when present in excess amount in the cell, indicating that Zn homeostasis has to be tightly regulated. Interestingly, Arabidopsis halleri, a close Arabidopsis thaliana relative, is able to accumulate more than 1% DW of Zn in its shoots without showing any toxicity symptom suggesting the existence of dedicated detoxification mechanisms. We exploit this natural Zn tolerant and hyperaccumulator plant species to characterize the molecular basis of Zn tolerance in plants. To identify A. halleri genes involved in Zn tolerance, we carried out a functional screening by expressing an A. halleri cDNA library in the yeast Saccharomyces cerevisiae. Selecting A. halleri cDNAs conferring Zn tolerance in yeast grown on Zn contaminated medium, we isolated five cDNAs encoding for A. halleri defensins (AhPDFs). Overexpression of one of them (AhPDF1.1) in A. thaliana Col-0 gave rise to a Zn tolerance phenotype. Thus, at least one of the AhPDF members is able to confer Zn tolerance both in yeast and in planta. In A. halleri, AhPDFs are constitutively accumulated at a higher level in shoots compared to A. thaliana. Furthermore, both AhPDF1.1 mRNA and AhPDFs steady state levels were shown to be increased upon Zn treatment. Therefore, we assume that AhPDFs could be involved in A. halleri Zn tolerance. Finally, this work highlights that plant defensins, well-known for their antifungal actvity, could also be implicated in metal physiologyMONTPELLIER-BU Sciences (341722106) / SudocSudocFranceF