Crop varieties carrying qualitative resistance to targeted pathogens lead to strong selection pressure on parasites, often resulting in resistance breakdown. It is well known that qualitative resistance breakdowns modify pathogen population structure but few studies have analysed the consequences on their quantitative aggressiveness-related traits. The aim of this study was to characterize the evolution of these traits following a resistance breakdown in the poplar rust fungus, Melampsora larici-populina. We based our experiment on three temporal populations sampled just before the breakdown event, immediately after and four years later. First, we quantified phenotypic differences among populations for a set of aggressiveness traits on a universally susceptible cultivar (infection efficiency, latent period, lesion size, mycelium quantity, and sporulation rate) and one morphological trait (mean spore volume). Then we estimated heritability to establish which traits could be subjected to adaptive evolution, and tested for evidence of selection. Our results revealed significant changes in the morphological trait but no variation in aggressiveness traits. By contrast, recent works have demonstrated that quantitative resistance (initially assumed more durable) could be eroded and lead to increased aggressiveness. Hence, this study is one example suggesting that the use of qualitative resistance may be revealed to be less detrimental to long term sustainable crop production.

We studied 54 strains from a historical collection of M. larici-populina that has been cryopreserved at -80°C at INRAE in Nancy (France). All strains were sampled in northern France and in Belgium among homogenous pathogen populations. All M. larici-populina strains were inoculated on the same cultivar to carry out a common garden experiment. Characterization of quantitative traits was performed on excised leaf disks of Populus deltoides × P. nigra ‘Robusta’ which is known to be susceptible to all tested strains. We used a single-spore inoculation protocol to inoculate leaf disks. Strain replicates were arranged among inoculation plates to minimise confounding experimental effects. All aggressiveness traits classically studied in plant-pathogen systems were measured: infection efficiency, latent period, lesion size, and sporulation rate. Beyond these four classical traits, we also measured the quantity of mycelium in planta developing in an infected leaf disk, through qPCR analysis. We also measured one morphological trait: the volume of spores, which was computed from length and width of spores obtained from image analysis. All details of quantitative traits measurement are described in Maupetit et al. (2020).

Single-spore inoculation protocole lead to high rate of infection failure, hence missing data. Uneven infection efficiency led to large differences in the representation of strains within and among inoculation plates. In order to balance the experimental design and the number of replicates for all strains, 1000 bootstrapped datasets were created by randomly selecting one replicate per strain and per plate. These bootstrapped datasets were used to compute phenotypic differentiation between population, Q_ST, broad-sense heritability (H²) and their confidence intervals. (see Maupetit et al. 2020 for details).