Genome-wide association study of DMI fungicide sensitivity detects numerous small-effect variants in the major North American population of Fusarium graminearum

Fusarium head blight (FHB), a major disease of wheat, is primarily managed through applications of demethylation inhibitor (DMI) fungicides during anthesis. However, repeated use of DMIs has led to the emergence of Fusarium graminearum isolates with reduced sensitivity and, in some cases, resistance. In this study, we evaluated the sensitivity of 152 F. graminearum isolates to propiconazole and tebuconazole. While sensitivity varied among isolates, no resistant strains were detected. We also conducted a genome-wide association study (GWAS) to investigate the genetic basis of DMI sensitivity. GWAS identified 48 and 39 quantitative trait nucleotides (QTNs) associated with propiconazole and tebuconazole sensitivity, respectively, with 12 QTNs common to both fungicides--supporting their common mode of action. Candidate gene analysis highlighted genes encoding transporters, secondary metabolite synthesis enzymes, transcription factors, and a heat shock protein as potential candidates for DMI fungicide response. We propose that tolerance to DMIs in F. graminearum is linked to active fungicide efflux out of fungal cells, mediated by transporters, including those associated with secondary metabolite pathways. Data summaryInformation on all strains used in the experiments have been included in a supplemental file. All sequencing data used in this study are publicly available and were described in our previous publication, which has been cited. Additional supporting data (isolate genotype and phenotype files) and code written for the analyses described here are made available on GitHub: https://github.com/Toomajian-laboratory/files_fungicide_manuscript/ Impact statementIsolates from field populations of fungal plant pathogens vary in their sensitivity to DMI fungicides, though in most cases the genetic determinants of this variation are poorly understood. In this study, we measure the sensitivity of isolates from the main US population of Fusarium graminearum to two DMI fungicides. We used GWAS to identify genomic loci and candidate genes that might underlie variation in DMI sensitivity. Our work contributes to the broader effort to understand the evolution of fungicide tolerance and resistance in populations of plant pathogens. The candidate genes identified, most of which are novel, provide good targets for functional studies of the tools fungi use to survive fungicides. The identified variants can also be screened to monitor potential increases in fungicide tolerance. The high-throughput, rapid, and large-scale monitoring of fungicide sensitivity described here advances both fundamental research and resistance management efforts.