Genome-Wide Identification and Characterization of Fusarium graminearum-Responsive lncRNAs in Triticum aestivum

Although the war between wheat and Fusarium has been widely investigated for years, long noncoding RNAs (lncRNAs), which have been proven to regulate important processes in the development and stress responses of plants, are still poorly known in wheat against Fusarium. Herein, we systematically reveal the roles of wheat lncRNAs in the process of Fusarium graminearum infection by high-throughput RNA sequencing. Well over 4130 of the total 4276 differentially expressed lncRNAs were already specifically expressed at 12 h postinoculation (hpi), but only 89 of these were specifically expressed at 24 hpi, indicating that the initial stage was the crucial stage for lncRNA-mediated gene regulation of wheat defense against F. graminearum. Target analysis showed the lncRNAs participated in various biological stress processes and had exclusive regulation models at different infection stages. Further H2O2 accumulation and protein ubiquitination assays supported this idea. Moreover, two lncRNAs (XLOC_302848 and XLOC_321638) were identified as Fusarium seedling blight resistance candidates by lncRNA-target expression pattern validation, and two lncRNAs (XLOC_113815, XLOC_123624) were Fusarium head blight resistance potential regulators by cross-validating the RNAseq data with the refined meta-QTL of wheat FHB resistance. These findings extend our knowledge on wheat lncRNAs response to F. graminearum attack and provide new insights for the functional and molecular research of future interactions between wheat and Fusarium.