Fusarium head blight (FHB), caused by the fungus Fusarium graminearum, represents one of the major wheat diseases worldwide, determining severe yield losses and reduction of grain quality due to the accumulation of mycotoxins. The molecular response associated with the wheat 2DL FHB resistance QTL was mined through a comprehensive transcriptomic analysis of the early response to F. graminearum infection, at 3 days post-inoculation, in spikelets and rachis. The analyses were conducted on two near isogenic lines (NILs) differing for the presence of the 2DL QTL (2-2618, resistant 2DL+ and 2-2890, susceptible null). The general response to fungal infection in terms of mRNAs accumulation trend was similar in both NILs, even though involving an higher number of DEGs in the susceptible NIL, and included down-regulation of the primary and energy metabolism, up-regulation of enzymes implicated in lignin and phenylpropanoid biosynthesis, activation of hormons biosynthesis and signal transduction pathways and genes involved in redox homeostasis and transcriptional regulation. The search for candidate genes with expression profiles associated with the 2DL QTL for FHB resistance led to the discovery of processes differentially modulated in the R and S NILs related to cell wall metabolism, sugar and JA signaling, signal reception and transduction, regulation of the redox status and transcription factors. Wheat FHB response-related miRNAs differentially regulated were also identified as putatively implicated in the superoxide dismutase activities and affecting genes regulating responses to biotic/abiotic stresses and auxin signaling. Altered gene expression was also observed for fungal non-codingRNAs. The putative targets of two of these were represented by the wheat gene WIR1A, involved in resistance response, and a gene encoding a jacalin-related lectin protein, which participate in biotic and abiotic stress response, supporting the presence of a cross-talk between the plant and the fungus.

Fusarium head blight (FHB) is a problem of great concern in small grain cereals, especially wheat. A quantitative trait locus (QTL) for FHB resistance (FHB_SFI) located on the long arm of chromosome 2D in the spring wheat genotype Wuhan 1 is a resistance locus which has potential to improve the FHB resistance of bread wheat since it confers effective resistance to wheat breeding lines. Recently, differentially expressed genes (DEG) have been identified by comparing near isogenic lines (NIL) carrying the susceptible and resistant alleles for the 2DL QTL, using RNA-Seq. In the present study, we aimed to identify candidate genes located within the genetic interval for the 2DL QTL for FHB resistance, as assessed by single floret inoculation (FHB_SFI), and possibly contributing to it. Combining previous and additional bioinformatics analyses, 26 DEG that were located on chromosome arm 2DL were selected for further characterization of their expression profile by RT-qPCR. Seven of those DEG showed a consistent differential expression profile between either three pairs of near isogenic lines or other genotypes carrying the R and S alleles for the 2DL QTL for FHB resistance. UN25696, which was identified in previous expression work using microarray was also confirmed to have a differential expression pattern. Those eight candidate genes were further characterized in 85 lines of a double haploid mapping population derived from the cross Wuhan 1/Nyubai, the population where the 2DL QTL was originally identified. The expression QTL for gene Traes_2DL_179570792 overlapped completely with the mapping interval for the 2DL QTL for FHB_SFI while the expression QTL for UN25696 mapped near the QTL, but did not overlap with it. None of the other genes had a significant eQTL on chromosome 2DL. Higher expression of Traes_2DL_179570792 and UN25696 was associated with the resistant allele at that locus. Of the 26 DEG from the 2DL chromosome further characterized in this study, only two had an expression QTL located in or near the interval for the 2DL QTL. Traes_2DL_179570792 is the first expression marker identified as associated with the 2DL QTL.

Introduction: Fusarium head blight (FHB), caused primarily by Fusarium graminearum (Fg), poses a significant threat to wheat production. It is necessary to deeply understand the molecular mechanisms underlying FHB resistance in wheat breeding.Methods: In this study, the transcriptomic responses of two Chinese wheat landraces—Wuyangmai (WY, resistant) and Chinese Spring (CS, susceptible)—to F. graminearum infection were examined using RNA sequencing (RNA-seq). Differential expression of mRNAs, long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs) was analyzed at 3 and 5 days post-Fg inoculation (dpi).Results: The results showed that WY exhibited a targeted miRNA response, primarily modulating defense-related pathways such as glutathione metabolism and phenylpropanoid biosynthesis, which are crucial for oxidative stress regulation and pathogen defense response. In contrast, CS displayed a broader transcriptional response, largely linked to general metabolic processes rather than immune activation. Notably, the up-regulation of genes involved in oxidative stress and immune defense in WY confirmed its enhanced resistance to FHB. The integrated analysis of miRNA-mRNA interactions highlighted miRNAs as central regulators of defense mechanisms in WY, particularly at later stages of infection. These miRNAs targeted genes involved in immune responses, while lncRNAs and circRNAs played a more limited role in the regulation of defense responses. The GO and KEGG pathway enrichment analyses further revealed that WY enriched for plant-pathogen interaction and secondary metabolite biosynthesis pathways, which are crucial for pathogen resistance. In contrast, CS prioritized metabolic homeostasis, suggesting a less effective defense strategy.Discussion: Overall, this study underscores the critical role of miRNA-mediated regulation in FHB resistance in WY. These insights into miRNA-mediated regulatory mechanisms provide a molecular basis for breeding FHB-resistant wheat varieties and highlight miRNA-mRNA interactions as promising targets for enhancing disease resilience.

Three genes encoding novel D-hordeins, Ns 1.3, Ns 2.6, and Ns 2.9 were isolated from Psathyrostachys juncea. The Ns 1.3 differed from Ns 2.6 and Ns 2.9 by having a shorter open reading frame (< 1.5 kb versus > 2.5 kb), and was probably not expressed as a normal protein, while the activities for Ns 2.6 and Ns 2.9 were verified by bacterial expression. Though highly similar primary structure to wheat high molecular mass glutenin subunits (HMM-GSs) and barley D-hordeins, Ns 2.6 and Ns 2.9 had more cysteine residues (nine in total) and a larger molecular mass than HMMGSs, and a longer N-terminal length than D-hordeins. Phylogenetic analysis revealed that the Ps. juncea D-hordeins were divided into Ns 1.3 type and Ns 2.6/Ns 2.9 type. Divergence times indicated that Ns 1.3 diverged the earliest from the orthologous Triticeae locus, while Ns 2.6 and Ns 2.9 and the D-hordeins from two Hordeum species diverged nearly at the same time from those loci, and the divergence between the D-hordeins of H. chilense and Ns 2.6/Ns 2.9 was more recent than between the two Hordeum species. The novel Ps. juncea D-hordeins have the potential to be very important for improving the end-use quality of wheat flours because of the presence of extra cysteine residues and longer repetitive domain, in addition they can contribute to the understanding of the evolution of Triticeae prolamins.