Camille RABEAU's s thesis defense

The jury was composed of :

Abstract: Leptosphaeria maculans is a phytopathogenic fungus responsible for one of the most damaging diseases in Brassica napus: phoma stem canker. L. maculans' infectious cycle is long and complex, and goes through an ‘early’ phase of leaf infection and a ‘late’ phase of colonization and infection of the stem. Resistant B. napus cultivars are targeting a limited set of ‘early’ fungal effectors overexpressed during leaf infection and encoded by genes located in dynamic repeat-rich regions. Thus, these resistances can be rapidly bypassed by the pathogen. To find new sources of resistance, previous studies suggested that quantitative resistance partly relies on gene-for-gene interactions with ‘late’ effector genes expressed during stem colonization. Using an innovative phenotyping method consisting of expressing ‘late’ effectors at the early stage of infection, they identified LmSTEE98 and LmSTEE6826, inducing a resistance phenotype on B. napus semi-winter genotypes. LmSTEE98 followed a gene-for-gene interaction with RlmSTEE98, mapped on the A09 chromosome, and led to a quantitative resistance phenotype in the stem. These preliminary results opened up perspectives on the uncovering of new and more durable resistance sources. However, they needed to be further validated from an agronomic point of view. Thus, the aim of this thesis is to build on previous findings to identify, introgress, and validate the agronomic value of major resistance genes involved in the quantitative resistance of rapeseed to L. maculans. To achieve this goal, the project was divided into four main objectives: (i) the study of late effector genes characteristics and conservation in L. maculans populations, (ii) the identification of a larger number of diverse genotypes interacting with late effectors, including new effectors selected based on optimized criteria, (iii) the genetic characterization, marker development, and molecular characterization of the corresponding resistances in B. napus, and (iv) field validation of the effectiveness of this new type of resistance through their introduction into modern cultivars adapted to European cultural conditions. I demonstrated that the genomic characteristics and conservation of late effector genes suggest that the resistance they trigger would be more durable in the field than resistance to classical AvrLm genes. I also demonstrated that the semi-winter genetic pool is the most interesting to uncover new sources of resistance to late effector genes, and that the focus should be on Asian cultivars. Studying genetic and molecular characterization of resistances to late effector genes in B. napus, I identified a strong candidate gene for RlmSTEE98 encoding a phytosulfokine receptor. However, I could not find a similar genetic determinism for AvrLmSTEE6826 resistance, as the results were not sufficient to clearly validate a gene-for-gene interaction. Finally, I demonstrated that introgressing an RlmSTEE QTL region in a winter cultivar was possible and resulted in resistance when tested on cotyledons in controlled conditions. However, the effect of this introgression could not be validated in the field, as the genetic background coming from the semi-winter cultivar was sufficient to affect the resistance phenotype. This project raised questions on a common gene-for-gene genetic determinism for late effector-induced resistances, on the validation of their durability in the field, and on the better use of this new type of resistance in breeding programs.