Leptosphaeria maculans (anamorph Phoma lingam) causes "Phoma stem canker" (also termed Blackleg), a devastating disease of oilseed rape (Brassica napus) and other crucifers. The disease is present in all regions of the world growing oilseed rape (or canola), except China.
The L. maculans-oilseed rape interaction is an important model for INRA because of the agro-economic incidence of the disease. INRA thus develops multiple approaches aiming to sustainable and environment-friendly control of the disease (identification of resistance sources, genetic mapping of genes and QTLs for disease resistance, design of cropping strategies, modeling of resistance deployment to increase durability of resistance). Breeding for efficient and durable resistance is thus an important objective for seed companies, whilst more generic approches towards understandig the fungus, its populations, and its interactions with the host are important objectives for public research. In addition to its economic incidence, L. maculans is also a model of choice to decipher fungal biology and pathogenicity due to the complexity of the developmental and phytopathological programmes it sets up during its life and parasitic cycle.
L. maculans has a saprophytic life followed by a lengthy pathogenic life where it behaves as an hemibiotroph. In Europe, the fungus lives as a saprobe on stem residues for many years, and this si the place where sexual reproduction takes place. In Autumn, shortly after the sowing of oilseed rape, pseudothecia differentiate and produce ascospores which are the primary and main infectious organs. Pseudothecia are disseminated by wind and land on cotyledons or leaves on which they germinate. Infectious hyphae penetrate the plant organs via natural apertures (stomata, wounds) and colonise the leaf mesophyl, eventually causing the typical greyish-green primary leaf symptom. This symptom supports production of asexual multiplication spores, of low relevance in the disease cycle, while mycelia undertake a systemic and symptomless colonisation of leaf, petiole, stem and eventually crown tissues. Mycelia remain within the tissues as an endophyte for months and the fungus shifts to a necrotrophic behaviour at the end of the growing season in spring/summer. It then causes a stem basis necrosis that may result in lodging of the plant before harvest. Alternating lifestyles suggest the existence of a sophisticated molecular dialogue between the fungus and its host plant, and the ability for the fungus to set up complex and finely tuned biological programmes.
Fungicides are uneasy to use efficiently in this system, and control of the disease mainly relies on genetic resistance of oilseed rape. In the agronomical practice major genes for resistance (Rlm genes) operating at the leaf stage are largely used but they are increasingly combined with high level of general resistance in order to maximise the durability of the Rlm genes.
On this model interaction, our group undertakes an integrated research "from the field to the gene" and vice-versa. Our main objectives are to decipher mechanisms involved in fungal pathogenicity and adaptation of the fungus to its host plant to design and propose durable strategies for management of plant resistance. Our strategy encompasses genetic dissection of the plant-pathogen interactions which are the basis for large-scale analysis and survey of races of the fungus occurring in diverse agronomical contexts. This in turn provides us with diversified and world-wide collections of isolates useable for map-baseed cloning of genes involved in specificity of interaction (avirulence genes of the fungus). The cloning of such genes eventually pointed to unusual genome environments whith peculiar relevance in terms of adaptive evolution and regulation of expression. Such approaches both provide novel generic knowledge on genome organisation of fungal phytopathogens and new strategies towards identification and cloning of avirulence/pathogenicity determinants. Recently, comparative genomic approaches within the L. maculans-L. biglobosa species complex were used for a better understanding of evolutionary mechanisms responsible for the birth of new phytopathogens better adapted to their current host plant and emergence/dissemination of novel plant diseases. In parallel, we also produced a large collection of T-DNA mutagenised strains of L. maculans as an alternative strategy to identify pathogenicity determinants of the fungus.
In the past years we thus focused our research on :
(i) analysis of populations of the fungus with two objectives : the characterization of isolates and species making up the L. maculans-L. biglobosa species complex, and the analysis and dynamic survey of races of L. maculans;
(ii) formal genetics of the L. maculans-oilseed rape interactions to genetically identify and map avirulence genes, and their cognate resistance genes in the plant (coll. IGEPP Rennes);
(iii) molecular genetic approaches to clone and characterize avirulence genes and, more globally, fungal effectors;
(iv) generation and analysis of a large collection of T-DNA insertion transformants showing pathogenicity defects;
(v) structural and evolutionary genomic approaches based on whole genome sequencing of L. maculans and other members of the L. maculans-L. biglobosa species complex;
(vi) inclusion of cropping practices to knowledge on fungal biology, fungal genome and fungal populations to understand adaptive dynamics and mechanisms of adaptation of L. maculans populations to resistance genes used in the field.
Our research is (or has been) funded by INRA, ministry of agriculture, technical institutes, EU, ANR, etc...