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Background  Fusarium head blight (FHB) is a major disease of cereal crops, caused by the fungal pathogen  Fusarium graminearum  and related species. Breeding wheat for FHB resistance contributes to increase yields and grain quality and to reduce the use of fungicides. The identification of genes and markers for FHB resistance in different wheat genotypes has nevertheless proven challenging.    Results  In this study, early infection by  F. graminearum  was analyzed in a doubled haploid population derived from the cross of the moderately resistant wheat genotypes Wuhan 1 and Nyubai. Three quantitative trait loci (QTL) were identified: 1AL was associated with lower deoxynivalenol content, and 4BS and 5A were associated with reduced  F. graminearum  infection at 2 days post inoculation. Early resistance alleles were inherited from Wuhan 1 for QTL 1AL and 4BS and inherited from Nyubai for the 5A QTL.  Cis  and  trans  expression QTL (eQTL) were identified using RNA-seq data from infected head samples. Hotspots for  trans  eQTL were identified in the vicinity of the 1AL and 4BS QTL peaks. Among differentially expressed genes with  cis  eQTL within the QTL support intervals, nine genes had higher expression associated with FHB early resistance, and four genes had higher expression associated with FHB early susceptibility.    Conclusions  Our analysis of genotype and gene expression data of wheat infected by  F. graminearum  identified three QTL associated with FHB early resistance, and linked genes with eQTL and differential expression patterns to those QTL. These findings may have applications in breeding wheat for early resistance to FHB.

bmc plant biology

Characterization of QTL and eQTL controlling early Fusarium graminearum infection and deoxynivalenol levels in a Wuhan 1 x Nyubai doubled haploid wheat population