Identification of a stable genetic locus and candidate genes for Fusarium head blight resistance on wheat chromosome 3BL.

Abstract

Fusarium head blight (FHB) is a devastating wheat disease worldwide. Identifying novel quantitative trait loci (QTLs) and resistance-associated genes is critical for breeding resistant cultivars. In this study, we conducted a comprehensive genetic analysis of FHB resistance in a diverse panel of 240 wheat accessions phenotyped over three years. Genome-wide association studies (GWAS) revealed 57 significant SNPs, delineating five stable QTLs on chromosomes 3B, 4A, 7A, and 7D that collectively explained 4.8-7.0% of phenotypic variation. Notably, qFHB3B.1 co-localized with the known Fhb1 locus, the other four QTLs represent novel genomic regions. Allelic stacking analysis demonstrated a strong correlation (R² = 0.96), with accessions carrying four favorable alleles showing a 44.7% reduction in FHB index compared to null allele. Furthermore, we developed and validated a kompetitive allele specific PCR marker for a leading SNP within qFHB3B.2, confirming its stable effects across 132 wheat accessions and two doubled haploid population. Comparative transcriptomic analysis of resistant and susceptible genotypes identified 4,302 consistently differentially expressed genes. Nine high-confidence candidate genes showing both GWAS signals and differential expression were prioritized, including TraesCS3B02G359600 and TraesCS3B02G359800 within qFHB3B.2,which exhibited contrasting expression patterns suggesting opposing roles in FHB resistance. Our findings provide valuable insights into the genetic architecture of FHB resistance and identify promising targets for marker-assisted breeding in wheat.