The RNA interference (RNAi) plays a critical role in gene regulation in a variety of eukaryotic organisms. However, the role of RNAi remains largely unclear in plant pathogenic fungi. In this study, we explored the roles of core components of the RNAi pathway in Fusarium graminearum, the major causal agent of wheat head blight. Our results demonstrated that the hairpin RNA (hpRNA) can efficiently silence the expression level of target gene, and the argonaute protein FgAgo1 and dicer protein FgDicer2 are important in this silencing process. RNAi machinery was not involved in growth, abiotic stress and pathogenesis in F. graminearum under tested conditions. We firstly applied high-throughput sequencing technology to elucidate small RNA (17–40 nucleotides) (sRNA) transcriptome in F. graminearum, and found that a total of forty-nine micro-like-RNA (milRNA) candidates were identified in the wild-type and ∆FgDICER2, and twenty-four of them were FgDicer2-dependent. Fg-milRNA-4 negatively regulated expression of its target gene. Taken together, our results indicated that the hpRNA-induced gene silencing was a valuable genetic tool for exploring gene function in F. graminearum. FgAgo1 and FgDicer2 proteins played a critical role in the hpRNA mediated gene silencing process. In addition, FgDicer2 was involved in sRNA transcription and milRNA generation in this fungus.

To develop an effective biocontrol strategy for management of Fusarium head blight on wheat caused by Fusarium graminearum, the bacterial biocontrol agent Pcho10 was selected from more than 1,476 wheat-head-associated bacterial strains according to its antagonistic activity in vitro. This strain was subsequently characterized as Pseudomonas chlororaphis subsp. aurantiaca based on 16S ribosomal DNA sequence analysis, assays of the BIOLOG microbial identification system, and unique pigment production. The major antifungal metabolite produced by Pcho10 was further identified as phenazine-1-carboxamide (PCN) on the basis of nuclear magnetic resonance data. The core PCN biosynthesis gene cluster in Pcho10 was cloned and sequenced. PCN showed strong inhibitory activity against F. graminearum conidial germination, mycelial growth, and deoxynivalenol production. Tests both under growth chamber conditions and in field trials showed that Pcho10 well colonized on the wheat head and effectively controlled the disease caused by F. graminearum. Results of this study indicate that P. chlororaphis subsp. aurantiaca Pcho10 has high potential to be developed as a biocontrol agent against F. graminearum. To our knowledge, this is the first report of the use of P. chlororaphis for the management of Fusarium head blight.