Gene and lncRNA expression patterns associated with Qfhs.ndsu-3AS Fusarium head blight resistance QTL in durum wheat

Abstract To identify the transcriptional mechanisms underpinning Fusarium head blight (FHB) resistance in durum wheat, an RNA-seq comparative transcriptome analysis was conducted on spikes 72 h after inoculation of a resistant line Langdon(Dic-3A)10 and a susceptible cultivar ‘Langdon’. Previously, 14 differentially expressed genes (DEGs) were mapped in the region of the quantitative trait locus Qfhs.ndsu-3AS, associated with type II resistance to FHB. Here, we focused on the global response of durum wheat to Fusarium graminearum (Fg) infection, identifying the molecular pathways in which DEGs are involved and lncRNAs with roles in transcriptional and post-transcriptional regulation of gene expression. A set of 921 DEGs was identified using the reference genome of the cultivar ‘Svevo’. Relative to the susceptible cultivar, the resistant line Langdon(Dic-3A)10 showed 452 up-regulated genes and 469 down-regulated genes. Upregulated genes in the resistant line included fungal cell-wall degrading enzymes, transcription factors, and genes involved in kinase signalling, phytohormone pathways, calcium signalling, secondary metabolite biosynthesis and toxin sensitivity. Differentially expressed lncRNAs showed different genome locations: 12 cis intergenic (6 up-regulated in Langdon(Dic-3A)10), 4 trans intergenic (one up-regulated in Langdon(Dic-3A)10), 4 intronic (two up-regulated in Langdon(Dic-3A)10) and 2 putative miRNAs precursors. Possible target genes were predicted for 14 lncRNAs, indicating potential regulative effects on wax and lignin synthesis and ankyrines in the resistant line. In a context where resistance sources against Fg are scarce in durum germplasm, the transcriptomic characterization of a valuable genotype contributes to the understanding of the genetic basis and regulatory network involved in the resistance conferred by Qfhs.ndsu-3AS.