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ECOGEN

ECOLOGICAL GENOMICS OF ADAPTATION IN PLANT COMMUNITIES

In the context of global environmental change, one of the main challenges in evolutionary ecology is to determine the type and structure of genetic and epigenetic variation underlying phenotypic natural variation to assess the potential and dynamics of an adaptive response to natural selection and / or changes resulting from anthropogenic environment.

A potential lack of response from species to selection due to global changes (like global warming) would cause an erosion of biodiversity, disrupting ecosystems sustainably. This is especially important for plants species whose dispersion is on average limited in comparison to pathogens and animals.
 

We have to keep in mind that the adaptive potential response from a species to global change will not only depend on its direct interactions with the abiotic environment, but also on the environmental effects on its biotic interactions (pathogenic interactions, intra- and inter-specific competition…). However, our knowledge on adaptive dynamics of organism – organism interacting systems, and more precisely of co-evolution between two interacting species, remains surprisingly very limited.

This is particularly relevant when studying the recruitment of the mutations in both biotic partners conferring the phenotypic variant likely to be retained by the natural selection. Because the molecular landscape of organism-organisms interactions (host-pathogen interactions, plant-plant interactions) can only be achieved by accounting for their genetic specificities, characterizing the molecular basis underlying host-pathogen specificity and plant-plant specificity will considerably increase our understanding of disease emergence and evolution of plant communities, respectively.
 

 The main objective of our group is to establish a link between molecular biology and evolutionary ecology in order to predict the evolutionary trajectories of plant and pathogen communities face to global change, by identifying the genetic basis underlying coevolution in plant-pathogen and plant-plant interacting systems. The ever-decreasing cost of sequencing provides an exciting time to map the genetic bases of complex traits in any species and put them in the context of ecology and adaptation.

 

RESEARCH THEMES

Ecological genomics of adaptation in Arabidopsis thaliana at different geographical scales

 

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
 

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
 

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.

 

Collaborations
 

  • 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€.

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PUBLICATIONS

  • Fulgione, A., M. Koornneef, F. Roux, J. Hermisson and A. Hancock. 2018. Evolutionary dynamics of island colonization: Arabidopsis thaliana from the island of Madeira. Molecular Biology and Evolution 35(3): 564-574.

  • Brachi, B., N. Faure, J. Bergelson, J. Cuguen and F. Roux. Genome-wide association mapping of flowering time in Arabidopsis thaliana in nature: genetics for underlying components and reaction norms across two successive years. Acta Botanica Gallica – Botany Letters 160: 205-218. Special Issue ‘Quantitative genetics in natural populations’