Identification and functional analysis of wheat lincRNAs in response to Fusarium graminearum infection

Intergenic long non-coding RNAs (lincRNAs) have recently been recognized as pivotal regulators in plant-pathogen interactions. However, the specific regulatory mechanisms of lincRNAs responding to Fusarium graminearum (F. graminearum) infection remain largely unexplored. Here, we performed time-series transcriptome profiling (0, 24, 48, and 72 h post-inoculation) and systematic identification of lincRNAs. A total of 1238 expressed lincRNAs were identified, among which 548 were differentially expressed lincRNAs during the time course of F. graminearum infection. We further predicted cis-regulatory lincRNA-mRNA pairs, comprising 347 lincRNAs and potential 1015 target genes, which were found to be mainly involved in amino acid metabolism and biosynthetic pathways. Moreover, 19 lincRNAs were predicted as putative precursors or endogenous target mimics of miRNAs. Subsequently, we verified that two lincRNAs, MSTRG.6494 and MSTRG.32080, showed strong transcriptional responses to F. graminearum infection by quantitative real-time PCR (qPCR) screening. Silencing MSTRG.6494 reduced the expression level of defense-related genes, resulting in reduced resistance to fungal pathogenicity. Meanwhile, the expression level of the potential target gene ATP synthase subunit beta (TaATP2) was significantly decreased in MSTRG.6494-silenced plants infected with F. graminearum. Overall, we performed the genome-wide identification of lincRNAs and their possible regulatory networks during F. graminearum infection-related process, confirming that MSTRG.6494 participates in wheat resistance to F. graminearum, may be via targeting TaATP2 to enhance defense responses. Our findings provide new insights into the regulatory mechanism of lincRNAs for Fusarium head blight (FHB) resistance, suggesting this mechanism as an essential strategy for protecting wheat from F. graminearum.