The RICE team (Rice, Interspecies Comparison & Evolution) works on different rice species.
Asian cultivated rice, Oryza sativa, is a staple food for a large part of the world population and yield increase, for instance through better resistance to stress, is one of the major challenges of coming years to deal with the population increase. RICE team's activities aim to explore genetic diversity in O. sativa (including its sub-species indica and japonica), and its related species, including African cultivated species, O. glaberrima, and wild, O. barthii, to identify new genes or alleles of interest for the improvement of Asian rice. We particularly focus on original sources of putative diversity associated to the pangenome concept or to the epigenic control of genome stability. We have also set up genetic (collections, populations) and genomic resources, as well as bioinformatics tools targeted at high-throughput genomic analysis and data integration.
The main interests of the «Epigenetic Regulations and Seed Development» team are the establishment and functional roles of chromatin states during plant sexual reproduction. We are also interested in the alterations required for the transition from sexuality to apomixis, an asexual path leading to maternal embryos within seeds. The knowledge produced should contribute to key innovations in plant breeding and biotechnologies, a critical step for adapting agricultural productions to climate uncertainties and a growing food demands, particularly in tropical regions. We work on two main biological models, Arabidopsis and maize, and as well, through our collaborators, on natural apomicts (Paspalum) and basal plants (Marchantia polymorpha). Using genetic approaches combined with (epi)genomics and state-of-the-art microscopy, we aim at understanding:
What are the dynamics of epigenetic marks during plant reproduction?
Our goal is to determine the dynamics of DNA methylation, and its functional role during sporogenesis, gametogenesis and early embryogenesis in Arabidopsis and maize. Defining and monitoring epigenetic reprogramming in cell types deeply embedded in sporophytic tissues is a difficult task. We have thus designed a set of transgenic reporters, termed "DYNAMETS", for live imaging of DNA methylation and hemimethylation. Using epigenomics approaches, we also study DNA methylation dynamics in maize reproductive tissues, during meiosis and embryogenesis.
Chromatin dynamics within young ovules of Arabidopsis. (Picture: M. Ingouff)
What are the mechanisms of female germ cells specification within plant ovules?
Over recent years, we have identified mutations in several genes that phenocopy partially apomictic ovule development. They encode members of RNA-dependent DNA Methylation (RdDM) and histone modifications pathways. Notably, in maize, these pathways are acting specifically in reproductive tissues. We are currently pursuing their characterization by (i) analyzing novel mutants either affected in chromatin condensation or obtained after piling up mutations of interest, (ii) exploring the effects of restoring RdDM function in reproductive tissues of apomictic forms, and (iii) studying the functional role of these pathways during sexual reproduction, comparing their phenotypic impact in Arabidopsis, maize and basal plants such as Marchantia. Additional candidate genes identified from natural apomicts, such as Paspalum notatum, are under characterization. In a complementary approach, we also explore the functional link between early ovule architecture and germ cell fate, using quantitative and live imaging combined to computational modeling.
Picture legend : A-B. Maize : Sterility phenotype of ago104 mutant. C. Maize : Expression pattern of Dmt102 DNA methyltransferase. D. Arabidopsis : histone marker in early ovule. E. Arabidopsis: histone methylation mark during gametogenesis. F. Arabidopsis : histone turn over in mature gametophyte.
What are the mechanisms involved in establishing paramutations in maize?
Paramutation is a well-known transgenerational epigenetic phenomenon, yet its controlling molecular and developmental mechanisms remain mysterious. Using a transversal approach, we aim at defining the core elements required for paramutation by comparing the classical maize model to divergent situations such as in Marchantia (in collaboration with Mario Arteaga-Vazquez in Mexico) and Drosophila.
To which extent epigenetic mechanisms are involved in dosage effects in maize?
Our goal is to identify and characterize the molecular, yet elusive bases underlying dosage effects in the endosperm. These effects that arise typically in genomically imbalanced endosperms after interploidy crosses trigger developmental failure and thus consist in a strong biological barrier for the use of exotic germplasm and apomixis in agriculture. Using RNA-seq we identified the transcriptional modifications resulting from interploidy crosses and we are currently exploring chromatin states to unravel both the nature and the regulatory mechanisms mediating developmental alterations.
The team collaborates on international projects with overseas partners from Mexico, (JEAI EpiMaize U. of Veracruz ; LANGEBIO/CINVESTAV, Irapuato), Argentina (U. Nacional de Rosario, Rosario ; U. Nacional del Sur, Bahia Blanca; IBONE, Corrientes), USA (Cold Spring Harbor Laboratory), and Europe (U. Hamburg, U. Zürich, U. Milano, et U. Perugia). Recently, this network was consolidated by two European Marie Skłodowska-Curie actions, two Agropolis Foundation grants for international mobility, and an ANR-SNF international collaborative research project. We are also involved in initiatives and projects with national laboratories (IBMP, IBP, ENS Lyon, CNRS-Paris 7, AGAP).
We participate in education by training Master and PhD students, participating in plant sciences Master programs at the University of Montpellier and other institutions (University of Orsay XI, ENS Paris), and coordinating the Plant Epigenetics course as part of the Plant Functional Biology Master program at the University of Montpellier.
ANR CHOMOBREED - Elucidating the role and regulation of heterochromatin during maize reproduction, and exploring its potential for developing novel plant breeding strategies.
Agropolis Foundation APOMOVIE - Live Imaging of Reproductive Development in Sexual and Apomictic Grasses
Agropolis Fondation EPIMAIZE - Innovative Tools to Study Trans-generational Epigenetic Inheritance in maize
Agropolis Foundation RNAPO - RNA methylation and reproductive modes in plants: characterization of molecular factors involved in the transition between sexual reproduction and apomixis
ANR REMET - Dynamics of Eukaryotic DNA Remethylation
H2020 MSCA-RISE PROCROP - Harnessing Plant Reproduction for Crop Improvement
ANR-SNF IMAGO - Imaging and Modelling Growth of Plant Ovules
Unraveling processes that underlie plant adaptive divergence and phenotypic plasticity is a crucial step towards identifying breeding strategies for maintenance of crop yield and quality under environmental constraint or predicting the adaptive potential of wild plant populations in the context of global change.