Biophysical epidemic processes driving the dynamic of polycyclic epidemics have been largely studied in our team during the two past decades. We especially focused on the conditions influencing the early stages of epidemics, the different components of the life cycle during a growing season (epidemic period), and the survival of pathogens between two seasons (interepidemic period). To this end, the comparison of rusts and septoria leaf blotch, for which sexual reproduction plays a different role, was particularly interesting. The biotrophic species Puccinia triticina and P. striiformis can develop and survive during the interepidemic period only on living wheat tissues (plants of the year or volunteers), while Zymoseptoria tritici completes its sexual reproduction cycle and survives as a saprophyte on wheat residues.

Research on the structure of P. striiformis populations, undertaken as part of Sajid Ali's PhD thesis, demonstrated the existence of a high population diversity in the Himalaya area, highlighting the role of sexual reproduction. In parallel, the potential impact of wheat volunteers on the local survival of P. triticina was established during a multi-year survey in South-West France, by comparing the pathotype structure of local populations collected on wheat during the cropping season and on volunteers during the interepidemic period. Furthermore, tests of sexual reproduction began in 2015, on leaf and stripe rusts, which ultimately led to successful crosses in P. triticina achieved on Thalictrum sp.

The early stages of septoria leaf blotch epidemics (quantity, efficacy and origin of primary inoculum) were studied within David Morais' PhD thesis. We established that the quantity of primary inoculum is rarely limiting early in the season. We also showed that adaptation of local pathogen population to the dominant host variety can be phenotypically detected, suggesting that it could be considered to optimize the deployment of host resistance. This work was completed with more fundamental studies of determinants and consequences of sexual reproduction in Z. tritici at different spatio-temporal scales. 

Our research on this issue continues with the Lydie Kerdraon's PhD thesis, in which a whole fungal and bacterial community associated to wheat and oilseed rape residues was characterized by combining classical microbiology, high-throughput metagenomics and interaction networks. We highlighted that crop residues are a pivotal, shifting platform that should be taken into account as a whole microbial ecosystem to manage residues-borne pathogens such as Z. tritici and L. maculans. This work paved the way to future research on the identification of microorganisms exhibiting antagonistic activities on both asexual and sexual stages of Z. tritici.

The efficacy of cultivar mixtures to reduce disease severity during the epidemic period through plant architecture effects has been studied for several years in collaboration with EcoSys, however without considering the adaptation of pathogen populations to the host population (see axis 1). Carolina Orellana-Torrejon’s PhD thesis now aims to understand how a virulence that recently appeared in Z. tritici populations (AvrStb16q) can be transmitted at the pluriannual scale (growing season and interepidemic period) considering the impact of host heterogeneity within canopy through asexual spore dispersal then sexual recombination. The research strategy combines a population experimental approach (assessment of change in frequency of virulence and average aggressiveness in the canopy) and a mechanistic modelling approach (simulation of biophysical processes involved in the development of the disease).

Between two growing seasons, size and composition of the pathogen population change. They are impacted by the ability of the pathogen species to survive locally and then by the intensity of field-to-field inoculum transfers (gene flows). We showed that wheat residues, supporting sexual reproduction, are sources of primary inoculum for Z. tritici, and that wheat volunteers can act as potential local inoculum source of P. triticina. We now address the question of the impact of these local inoculum sources (compared to distant sources) on the ability of these two pathogen populations to adapt to host populations, considering the varietal diversity from field to landscape scales. Our ambition is to make the connection between the "multi-year recurrence of epidemics" and "deployment of varietal resistance" issues, which until now have been addressed separately.