Etiology and diagnosis of plant diseases associated with emerging pathogens

Thanks to our expertise in the four main groups of phytopathogenic microorganisms (bacteria, fungi, oomycetes and viruses), as well as in insect vectors of viruses, our unit is particularly involved in the etiology of diseases of vegetable, fruit and ornamental crops. Our objectives are to identify and characterize emerging, re-emerging, atypical and/or damaging crop pathogens and pests.
These etiology studies are an essential step before tackling other scientific issues, especially those linked to understanding epidemics and the evolutionary dynamics of pathogen and pest populations, for optimum disease management.

This area contributes to maintain: :

• our responsiveness to requests and feedback from horticultural professionals
• a plant health monitoring that enables us to identify and develop action drivers to control plant diseases more rapidly (e.g. diagnostic tools, prophylaxis, identification of sources of plant resistance and biocontrol agents).

The 3 main objectives of this area are to:

Identify and characterize pathogens

Etiology work has focused on damaging diseases of various crops, in particular:

• tomato: bacterial canker (Clavibacter michiganensis), tomato rot (Botrytis cinerea), tomato brown rugose fruit virus (ToBRFV),
• cucurbits : tomato leaf curl New-Delhi virus (ToLCNDV),
• garlic: fusariosis,
• pepper: variants of cucumber mosaic virus ) in the Espelette protected designation of origin area (Southwest France)...

Improve diagnosis by developing detection tools for better risk anticipation and monitoring, and in particular:

• Molecular amplification (RT-PCR, qPCR, LAMP, digital PCR, etc.) targeting a variety of matrices (plants, insect vectors, inert supports), some of which can be applied in the field
• High-throughput sequencing (Illumina, MinION technologies) to:
  • Explore the virome of cultivated and reservoir plants,
  • Study intra-host viral polymorphism at different scales (plant, plot, production basin),
  • Understand the intra-plant dynamics of microorganisms in order to assess their evolutionary parameters (selection, genetic drift),
  • Analyze the diversity and structure of microorganism populations in various substrates (e.g. twigs, buds, soil) and dissemination media (e.g. river water).

Maintain strong links with professional and academic partners to offer them our expertise: :

• support samples to investigate the cause of diseases,
• dissemination of information via the INRAE ephytia portal,
• technical training (e.g. electron and photonic microscopy).