Exploration of Genomic Regions Associated with Fusarium Head Blight Resistance in Wheat and Development and Validation of Kompetitive Allele-Specific Polymerase Chain Reaction Markers

<i>Fusarium</i> head blight (FHB), caused by <i>Fusarium graminearum</i>, is a globally significant disease that severely impacts the yield and quality of wheat. Breeding resistant wheat varieties using resistance genes is the most cost-effective strategy for managing FHB, but few markers are available for marker-assisted selection (MAS) of resistance. In this study, we evaluated the resistance of a recombinant inbred line (RIL) population to FHB through single-floret inoculation in four field environments over two years. Combined with quantitative trait loci (QTL) detection through high-density genetic mapping based on wheat 50 K SNP arrays, we identified a total of 21 QTLs influencing FHB resistance. It is worth noting that <i>QFhba-5D.2-1</i> was detected in two field environments as well as in the multi-environment trial (MET) analysis, explaining phenotypic variation ranging from 1.98% to 18.55%. We also pinpointed thirteen resistance genes within the QTL intervals on chromosomes 4A, 5D, 6B, and 7A associated with FHB defense mechanisms. Furthermore, we developed two Kompetitive Allele-Specific PCR (KASP) markers for the <i>QFhba-5D.2-1</i> and <i>QFhba-7A</i> regions to validate their specificity within the RIL population. Subsequently, we validated the polymorphism of these two markers in 305 wheat germplasms and analyzed their effect on thousand kernel weight (TKW) and spike length (SL). These markers will accelerate the development of FHB-resistant wheat varieties through MAS, significantly reducing yield losses and strengthening food security.