Dissecting a novel Fusarium head blight resistance QTL TaFhb-6A in wheat Line R111 using integrated multi-omics strategies

Fusarium head blight (FHB) is a devastating fungal disease that threatens wheat yield and quality worldwide. Breeding FHB-resistant cultivars is the most sustainable solution, whereas the narrow genetic basis of resistance has restricted breeding progress. In this study, we developed a novel wheat line R111 with stable and high FHB resistance through distant hybridization of wheat cultivar MY11 and rye. Cytological analysis confirmed that R111 carries no visible rye chromatin. Using bulked segregant exome sequencing (BSE-seq), we mapped a new major FHB resistance QTL, TaFhb-6 A , to the 0-4.5 Mb interval on chromosome 6 A. Kompetitive Allele-Specific PCR (KASP) markers verified that this locus significantly enhances FHB resistance in multiple populations. By integrating transcriptome profiling, single-nucleotide polymorphism (SNP) variation, and weighted gene co-expression network analysis (WGCNA), we screened two candidate kinase genes from the 56 high-confidence genes in the target interval: TraesCS6A03G0005200 (serine/threonine-protein kinase) and TraesCS6A03G0009000 (receptor-like protein kinase). Both genes carried multiple missense mutations and showed significantly higher expression in R111 than in the susceptible parent MY11 after Fusarium graminearum inoculation. This study provides valuable resistant germplasm, effective molecular markers, and key genetic information for future FHB resistance breeding, marker-assisted selection (MAS), as well as gene cloning and functional dissection of the resistance locus underlying TaFhb-6 A in wheat.