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Laboratory of Plant-Microbe Interactions - LIPM

Laboratory of Plant-Microbe Interactions

Research themes - Sunflower Genetics and Genomics

Plateforme de phénotypage Heliaphen

Tolerance to abiotic stresses (Coordinated by Nicolas Langlade)

  • Identification of molecular and functional polymorphism, within cultivated and wild genetic resources, in candidate genes involved in tolerance to abiotic stresses and development.  Gene selection was based on our results in sunflower but mainly on model species genetic data, i.e. Arabidopsis thaliana.
  • Genetic analysis of (1) oil yield under limited water availability, and (2) physiological and developmental responses to moderate and severe drought stress in field and controlled conditions using  LD and linkage mapping. This work aims at integrating genetic modeling into the agronomic model Sunflo (Casadebaig et al. 2011)
  • Systems biology of gene regulation in responses to hormones and abiotic stresses.  Using either a range of hormone and time course applications, or genetic variability of hormone application responses, we aim at inferring gene networks related to limited factors identified in agronomy such as ABA mediated regulation of transpiration, leaf senescence or flowering time.  This models are then confronted to abiotic stress responses and genetic variation to identify how the environment interplays with gene networks at short and long time scales.

Resistance to O. cumana, the sunflower broomrape (coordinated by Stéphane Muños)

  • Mapping and cloning of major genes and quantitative resistance for the more virulent races of O. cumana.
  • Physiological characterization of the interaction between sunflower and O. cumana
  • Genes expression during the first steps of the interaction

New strategies in statistical analysis for Genome Wide Association mapping and Genomic Selection (coordinated by Brigitte Mangin)

  • Development of statistical models for GWAs and confidence intervals for detected QTLs
  • Improvement of the accuracy to predict complex traits in plants of agronomic interest

Resources development and maintenance:

  • Publicly available
    • Sunflower Core collections:
    • Genetic populations developed by Felicity Vear (INRA Clermont-Ferrand) and Hervé Serieys (INRA Montpellier)
    • Bioinformatic resources (with the strong support of the LIPM bioinfo  team):
      • HELIAGENE Portal (Carrere et al., 2008): a sunflower annotated gene atlas based on publically available data on September 2007 assembled by Mike Barker (U. British Columbia, Vancouver) ,
      • « H+P » Portal : Annotated EST from sunflower plantlets infected by Plasmopara halstedii :
  • Available under research agreement or scientific collaboration:
    •  TILLING population
    •  Bioinformatic resources (with the strong support of the LIPM bioinfo  team):
      • Genome resequencing of INRA sunflower lines (including the INRA reference line XRQ)
      • Gene atlas (transcriptome mRNA and sRNA) of the INRA reference line XRQ
      • Sunflower SNP and indel polymorphism database developed on candidate genes and identified in cultivated and wild material
      • Transcriptome of P.halstedii (four races)


  •  Sunflower genome sequencing project: University of British Columbia (Canada, L.Rieseberg): (Kane et al., 2010, 2011)
  • INRA : F. Delmotte (Bordeaux), P.Mestre (Colmar)

Current fundings

  • SUNRISE: Projet retenu dans le cadre d'"Investissements d'Avenir" (vague 2011), rassemblant 10 équipes de recherche publique, le CETIOM et 6 partenaires industriels impliqués dans l'amélioration génétique du tournesol. Coordination du projet par l'équipe du LIPM. Financement global: 7 M€, dont 2.6M€ pour le LIPM. Durée: 7.4 ans (2012-2019)
  • OLEOSOL (labeled by the French Competitiveness Cluster AGRIMIP Innovation Funded by Midi-Pyrénées Region, FEDER and governmental support to Competitiveness Clusters (FUI). Partnership with BIOGEMMA, SYNGENTA Seeds, SOLTIS, R2N: Tools and resources towards sunflower genetic improvement for oil yield production.1296 K€
  • AIP INRA Bioressources 2009 and 2010, INRA Plant Breeding Department Call for Proposals 2010: Contribution to sunflower genome sequencing. 248K€
  • [2009-2001] : PROMOSOL: Genetic analysis of tolerance to Phoma macdonaldii, 30K€ 
  • [2013-2014] : Helianthus annuus * Orobanche cumana interaction
  • [2013-2015] : HELIADIV : Analysis of sequence polymorphism for a least 200 candidate genes involved in abiotic or biotic sunflower responses, within a large inbred lines collection (1000 accessions) and diverse genetic pools, all of them being currently maintained as sunflower genetic resources in the lab.
  • CETIOM: Phenotypic assessment of quantitative resistance to Downy Mildew Plasmopara halstedii.17K€