A winter wheat GWAS identifies a large effect FHB resistance haplotype using diverse lines from U.S. breeding programs

Fusarium head blight (FHB), primarily caused by Fusarium graminearum in North America, is a devastating disease in bread wheat (Triticum aestivum L.). The characteristic mycotoxin production and reduced grain fill cause several million metric tons of annual crop and economic losses. Exome capture-generated single nucleotide polymorphisms (SNPs) from 269 winter wheat breeding lines and cultivars representing most U.S. wheat-growing regions, were associated with FHB resistance using a genome-wide association study (GWAS). The panel was evaluated for FHB symptoms in the Rocky Ford FHB nursery (Manhattan, KS) across three field seasons. Significant variation was observed for FHB incidence (INC, %), area under the disease progress curve (AUDPC), Fusarium-damaged kernels (FDK, %), and deoxynivalenol (DON, ppm). Data analysis revealed significant FHB disease trait correlations (r = 0.32-0.70) across years and moderate broad-sense heritability (H2) estimates (0.65-0.74). We identified 22 significant loci representing priority breeding targets combating FHB damage. Many loci reside within proximity to previously identified native quantitative trait loci (QTL). A 1BL haplotype from the soft winter wheat cultivar 'Jamestown' reduced AUDPC and FDK by 25% and DON by 18%, demonstrating FHB resistance in an environment different from its native environment. We developed KASP assays to identify this resistance haplotype, and five other target SNPs for future incorporation in breeding pipelines increasing FHB resistance. Our findings highlight breeding progress demonstrated by the increased frequency of many resistant alleles in adapted varieties and breeding lines and emphasizes pyramiding native FHB resistance regions as the next step to prevent FHB losses.