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Laboratory of Plant-Microbe Interactions - LIPM

Laboratory of Plant-Microbe Interactions

Research themes - Ecological genomics of adaptation in plant communities

Ecological genomics of adaptation in Arabidopsis thaliana at different geographical scales

bandeau theme de recherche Fabrice Roux


Despite the increasing number of genomic tools, identifying the genetics underlying adaptive complex traits remains challenging in the model species A. thaliana. This is due, at least in part, to the lack of data on the geographical scale of adaptive phenotypic variation. Based on (i) a new set of French populations, (ii) phenotyping in ecologically realistic conditions, (iii) reciprocal transplantations and resurrection studies, and (iv) NGS technologies, the aims of this theme are:

- to tease apart the historical roles of adaptive and nonselective processes in shaping phenotypic variation at different geographical scales (from a worldwide scale to a within-population scale).

- to gain insights into the spatial scale of adaptive variation by identifying the putative selective agents responsible for this selection.

- to integrate genetic variation of reaction norms in the study of adaptive potential.

- to identify the genomic regions and to functionally  validate the candidate genes involved in local adaptation and/or adaptive phenotypic plasticity.

 Identifying the genetic bases of coevolution inthe natural pathosystem A.thaliana–Xanthomonas campestris

Manhattan plot

Black rot of crucifers caused by the bacterial pathogen Xc is possibly the most important disease of crucifers worldwide. The disease has a wide geographical distribution, causing reduction in yield and quality and is expected to increase in incidence and geographical range under climate change. Xc is also one of a few known natural pathogens of A. thaliana, and is highly prevalent in natural populations of A. thaliana. In collaboration with Dominique Roby (LIPM, Toulouse) and Joy Bergelson (University of Chicago), we aimed at (i) finely map by GWA mapping genomic regions associated with natural variation of quantitative resistance to Xc, (ii) functionally validate candidate genes, and (iii) elucidate the ecological and evolutionary forces shaping the natural genetic diversity observed at those quantitative resistance genes.

 Identifying the genetic bases of coevolution in natural plant-plant interacting systems

A. Thaliana in its local plant community

Biotic specialization between neighbouring genotypes of two plant species has been suggested from more than 25 years ago. Still, the genetic bases associated with natural variation of plant-plant interactions remain to be elucidated. Based on a local polymorphic French population of A. thaliana, we found extensive genetic variation for the response to interspecific competition (four plant species associated with A. thaliana in the native plant community). We currently adopt a GWA mapping approach to test whether genomic regions associated with natural variation of the response to interspecific competition differ among competitive species.


  • Local collaboration : group of Dominique Roby and Yves Marco (INRA, Toulouse) 
  • National collaborations: Valérie Le Corre (INRA, Dijon) ;  Valérie Schurdi-Levraud (INRA, Bordeaux) ; Françoise Budar and Christine Camilleri (INRA, Versailles) ; Laurent Amsellem, Hélène Frérot, Nina Hautekéete, Maxime Pauwels and Yves Piquot (Université de Lille 1). 
  • International collaborations: Joy Bergelson (University of Chicago, USA), Angela Hancock (University of Vienna, Austria), Paul Neve (University of Warwick, UK).

 Current fundings

  • 2015 - 2019: ANR RIPOSTE (Exploitation of pathogen quantitative resistance diversity to improve disease resistance tolerance in crops). PI: Dominique Roby (LIPM, Toulouse). 248k€.
  • 2014 - 2017: Région Midi-Pyrénées, programme « Accueil de nouvelles équipes d’excellence ». Etudier le potentiel des populations naturelles végétales face au changement climatique en identifiant les gènes associés à la résistance aux pathogènes (CLIMARES). PI : Fabrice Roux. 236k€.
  • 2014 - 2015: Projet du département INRA – SPE. Une étude de résurrection pour étudier l’évolution phénotypique et génomique d’une population naturelle d’Arabidopsis thaliana face à la compétition interspécifique d’une graminée adventice. PI : Fabrice Roux. 30k€.
  • 2012 - 2016 : ANR BIOADAPT, CYTOPHENO (Cyto-nuclear co-adaptation and plant adaptive phenotypes). PI : Françoise Budar (INRA IJPB, Versailles). 25 k€. 
  • 2013 - 2018 : Starting grant Labex TULIP. PI : Fabrice Roux. 250k€.