Increased FHB pressure due to rotation with corn, no-till farming practices, and conducive weather conditions has increased the threat of FHB epidemics, and coupled with the recent high value of wheat has led to a surge in the use of fungicides. Fusarium graminearum (Fg) isolates collected after 2000, after the beginning of widespread fungicide use on wheat, show significantly lower sensitivity to tebuconazole than isolates collected before. With sufficient exposure to demethylation inhibiting (DMI) fungicides, Fg strains resistant to DMI fungicides will develop, complicating if not crippling current chemical control strategies for FHB. Our aim is to identify genes harboring functional variation that contributes to variation in DMI fungicide sensitivity to inform pathogen management decisions. Specifically, we have performed genome-wide association studies (GWAS) to find the genetic basis of variation in fungicide sensitivity by scanning single nucleotide polymorphisms (SNPs) throughout the Fg genome generated by genotyping-by-sequencing (GBS). We collected fungicide sensitivity data for over 150 Fg isolates, primarily from the NA1 population or carrying an NX-2 TRI locus genotype, using an efficient, high-throughput 96-well microtiter plate in vitro assay. Fungicide sensitivity, as measured by estimates of EC₅₀, varies significantly across isolates within populations, and sensitivity to propiconazole is highly correlated to sensitivity to tebuconazole. Isolates carrying genotypes consistent with the NX-2 trichothecene show a clear trend of greater DMI resistance compared to isolates from the NA1 population, which usually carry 15-ADON genotypes. GWAS scans that screened for statistical associations between SNPs and EC₅₀ estimates for each fungicide implemented various models that could account for potential population structure as well as cryptic relationships between isolates from the same populations. A GWAS scan for tebuconazole sensitivity in a sample that included NA1 and NX-2 isolates identified several associated loci, including the TRI gene cluster. Separate scans for sensitivity to propiconazole and tebuconazole in the NA1 population detect a few candidates, including one SNP common to the two fungicides that is located in the fusarin C gene cluster. 

Acknowledgement and Disclaimer: This material is based upon work supported by the U.S. Department of Agriculture, under Agreement Nos. 59-0206-1-113, 59-0206-6-002, and 59-0206-2-162. This is a cooperative project with the U.S. Wheat & Barley Scab Initiative. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the authors and do not necessarily reflect the view of the U.S. Department of Agriculture.