The complex genetic landscape of fungicide resistance evolution in Zymoseptoria tritici
Over the past three decades, the extensive use of target-site fungicides, such as demethylation inhibitors (DMIs) and succinate dehydrogenases inhibitor (SDHIs), in European agricultural fields has turned the continent into an ideal geographic range for identifying the emergence of specific resistance mutations over time and space. Structural alterations in the target protein are the most common mechanism leading to insensitivity to DMIs as SDHIs. However, there is compelling evidence suggesting that additional genetic loci also contribute to overall resistance. In this study, our objective is to unravel the evolutionary trajectories driving the genetic architecture of fungicide resistance in Zymoseptoria tritici, the major wheat pathogen in Europe. To achieve this, we utilized a panel consisting of 1420 whole-genome sequenced isolates from 27 European countries, spanning a period of 15 years. By employing multiple phenotyping and genotyping techniques, we conducted genome-wide association mapping to identify the genetic factors associated with resistance. As a result, we discovered numerous previously unknown loci that contribute to DMI resistance, in addition to mutations in the gene responsible for encoding the DMI target protein. Remarkably, despite most fungicides are targeting specific proteins, our findings reveals multiple loci linked to resistance adaptation.