A large European diversity panel reveals complex azole fungicide resistance gains of a major wheat pathogen

Fungicide resistance in crop pathogens poses severe challenges to sustainable agriculture. Demethylation inhibitors (DMIs) are critical for controlling crop diseases but face rapid resistance gains in the field. Even though the main molecular basis of resistance is well established, field surveys have repeatedly revealed alternative resistance mechanisms. The European continent in particular has seen rapid and heterogeneous gains in azole resistance in the past decades. Here, we establish a large genome panel to dissect the genetic architecture of emerging resistance in the major wheat pathogen Zymoseptoria tritici. The European diversity panel spans 15 sampling years and 27 countries for a total of 1394 sequenced and phenotyped strains. Using two complementary assays to quantify resistance levels of each strain, we captured fine-grained shifts in DMI resistance over space and time. We conducted genome-wide association studies based on a comprehensive set of genotyping approaches for six DMIs. We mapped a total of 21,220 genetic variants and 158 genes linked to resistance. The substantial scope in genetic mechanisms underpinning DMI resistance significantly expands our mechanistic understanding how continent-wide resistance arises in fungal pathogens over time. Diversification of the Cyp51 coding sequence was particularly striking with new resistant haplotypes emerging with complex configurations and geographic patterns. This study provides expansive new insights into fungicide resistance gains of crop pathogens relevant for future resistance management strategies.