Epigenetic Regulation & Seed development

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Research focuses

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The main research interests of the «Epigenetic Regulations and Seed Development» team are the establishment, and the functional roles, of chromatin states during plant sexual reproduction and apomixis, an asexual path leading to maternal embryos within seeds. The knowledge produced should contribute to key innovations in plant breeding and biotechnolgies, a critical step for adapting agricultural productions to increased climate uncertainties and growing food demands, particularly in tropical regions (IPCC, Summary for policymakers, 2014). Among these are (i) the design of alternate strategies to sexual reproduction (haploid induction, clonal reproduction), (ii) the extension of crop allelic reservoirs (epialleles).

Using genetic approaches combined with (epi)genomics and state-of-the-art microscopy in two biological models, Arabidopsis thaliana and maize, we aim at understanding :  

How female germ cells are specified within plant ovules ?

Over recent years, we have identified mutations in several genes that phenocopy partially apomictic  early ovule development. They all encode members of a RNA-dependent DNA Methylation (RdDM) pathway acting specifically in reproductive tissues. We are currently pursuing its 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 the RdDM function in reproductive tissues of apomictic forms, and (iii) studying the functional role of the RdDM pathway during plant reproduction. 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 ovule architecture and germ cell fate, using quantitative and live imaging combined to computational modeling.  

A thaliana

What is the dynamics of chromatin marks during plant reproduction ?

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Picture legend : Chromatin dynamics within young ovules of Arabidopsis. The arrows indicate the variations (white + / red -) observed in the nucleus of the female germline. (Picture: M. Ingouff)



Our goal is to determine the dynamics of DNA methylation, a key chromatin mark in gene expression regulation and genome stability, and its functional role during sporogenesis, gametogenesis and early embryogenesis in Arabidopsis. Defining and monitoring chromatin remodeling in cell types deeply embedded in sporophytic tissues is a difficult task. To achieve this, we are currently designing DYNAMETS, a new tool for live imaging of DNA methylation at all three contexts (CG, CHG, CHH, H=A , T, C). 

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.


Picture legend : RNA-seq analysis revealing transcriptional modifications between normal endosperms (3x) and maternally (5x; left) and paternally (4x; right) imbalanced endosperms (Picture : O Leblanc).


Partnerships & Education

The team collaborates on international projects with overseas partners from Mexico, (JEAI EpiMaize; LANGEBIO, Irapuato; U. of Veracruz), Argentina (U. Nacional de Rosario,  Rosario; U. Nacional del Sur, Bahia Blanca; IBONE, Corrientes), USA (Cold Spring Harbor Laboratory), and Europe (U. Zürich, U. de Milan, et U. de 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, INRIA Montpellier, ENS Lyon, CNRS-Paris 7).

Finally, 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

Recent projects

  • Agropolis Foundation, International mobility (visiting scientist Mario Arteaga, U.Veracruz).
  • French National Research Agency - Swiss National Fund (international bilateral call), IMAGO, coordination, 2017-2020.
  • Agropolis Foundation, International Mobility, RNAPO, 2016-2017
  • French National Research Agency, EPIMETH, partner, 2016-2019.
  • European Marie Skłodowska-Curie Global Fellowship, Daniel Grimanelli, Cold Spring Harbor Laboratory, 2015-2017.
  • European Marie Skłodowska-Curie Action RISE, PROCROP, Italy/France/Mexico/Argentina, 2015-2019.
  • French National Research Agency, SEXYchrom, coordination, 2012-2017.
  • French National Research Agency, AdaptInWild, participant, 2012-2015.
  • Joint IRD Research Team, EpiMaize, U. of Veracruz, Mexico, 2011-2015.

Team members

  • Daphné Autran, IRD
  • Daniel Grimanelli, IRD
  • Mathieu Ingouff, University of Montpellier
  • Olivier Leblanc, IRD, team leader
  • Caroline Michaud, IRD
  • Benjamin Selles,  Post Doc, IRD (2013-2017)
  • Pauline E. Jullien, Post Doc, IRD (2016-2017)
  • Lorena Siena, CONICET/IICAR (University of Rosario, Argentina), Visiting Scientist (2015-2016-2017). 

People welcomed

  • Mario Arteaga, Prof. U. of Veracruz (Mexico), one year starting 06/2017
  • Juan Pablo Ortiz, Prof. CONICET/IICAR (U. of Rosario, Argentina), 09/2016
  • Omar Oltehua, PhD, U. Veracruz (Mexico), 03-12/2015
  • Andrea Sabbio, PhD, Cinvestav (Mexico), 04-06/2015
  • John Silva Andia, Master 2, U. Montpellier, 01-06/2015
  • Goeffrey Jacquemin, Master 1, U. Montpellier, 03-06/2015
  • Bastien Masse, Licence 3, U. Montpellier, 04-06/2015

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