Enhanced DURability Against Crop Enemies – ENDURANCE

Durable use of genetically resistant plant varieties is a major step toward sustainable crop protection. Yet, defining the optimal deployment strategy for plant resistances is still a matter of active debate. We advocate that enhancing resistance durability requires the integration of knowledge on molecular events leading to virulence into relevant evolutionary-epidemiological models. The ENDURANCE project addresses this issue: thanks to population genetics concepts and tools, we will embed genetic determinism(s) of resistance breakdown into pathogen population dynamics.
ENDURANCE involves five partners and gathers 30 persons (researchers, associate professors, engineers and technicians) who are at the forefront of studies on resistance durability, either through evolutionary epidemiology modelling, or through the molecular study of host-pathogen interactions. Our consortium includes mathematicians, modelers, plant pathologists, functional genomicists and population geneticists. Fabien Halkett, who has a strong expertise in population genetics and adaptation of plant pathogens, will lead ENDURANCE.
As a building block for ENDURANCE, all partners joined forces to summarize the current knowledge about plant resistance durability in a recently published opinion note. Molecular studies document a large variability of mechanisms, but little is known about the evolutionary outcomes of such variability. Conversely, most models deal so far with “generic” pathogens (haploid asexual) and need to be adapted to the specificities of life cycles of pathogens in agro-ecosystems. To overcome these limitations, ENDURANCE focuses on three pathogen species (Melampsora larici-populina, Leptosphaeria maculans, Plasmopara viticola) with different ploidies and life cycles to build contextualized evolutionary epidemiology models. Our main working hypothesis is that ecological and biological differences between pathogen species, as well as molecular constraints, translate into various dynamics of emergence and spread of virulence alleles. Each species is mastered by a biological partner. We will broaden the scope of our findings through available data on resistance breakdown dynamics in other pathosystems. Our objectives are:
i) to extend our knowledge on the genetic determinisms of virulence through genome association studies, genomic analyses and functional validations;
ii) to assess the temporal changes in virulence allele frequencies as well as in genetic structure in pathogen populations thanks to time series samples;
iii) to develop new evolutionary epidemiological models that consider the diversity in genetic determinisms of virulence, as well as the characteristics of fungal pathogen life cycles.
These objectives delineate three operational tasks, each task fostering the two others. This will strengthen collaborations among partners. Besides scientific collaboration, ENDURANCE also aims at sharing technical knowledge and ensuring methodological transfers among partners in order to leverage our knowledge.
In ENDURANCE, special interest will be devoted to highlighting complex interactions among loci and to measuring the cost of virulence. We will benefit from large historical collections to highlight transient dynamics in pathogen evolutionary trajectories. We will develop both mathematical models (based on the semi-discrete formalism that matches the seasonality of pathogen life cycles) and simulation models that take all the specificities of the three pathogens into account. Theoretical predictions will be challenged with empirical data and when appropriate, model parameters will be inferred from the time series data acquired from historical surveys and population genetics analyses. Ultimately, the outcome of our project is to determine the best deployment strategies of genetically resistant cultivars by integrating, from gene to population, all relevant and contextual biological knowledge into sound theoretical models.