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Background Fusarium head blight (FHB) caused by  Fusarium graminearum  is a devastating fungal disease of wheat. The mechanism underlying  F. graminearum -wheat interaction remains largely unknown. tRNA-derived fragments (tRFs) are RNase-dependent small RNAs derived from tRNAs, and they have not been reported in wheat yet, and whether tRFs are involved in wheat- F. graminearum  interactions remains unknown. Results Herein, small RNAs from the spikelets inoculated with  F. graminearum  and mock from an FHB-susceptible variety Chinese Spring (CS) and an FHB-resistant variety Sumai3 (SM) were sequenced respectively. A total of 1249 putative tRFs were identified, in which 15 tRFs was CS-specific and 12 SM-specific. Compared with mock inoculation, 39 tRFs were significantly up-regulated across both wheat varieties after  F. graminearum  challenge and only nine tRFs were significantly down-regulated. tRF Glu , tRF Lys  and tRF Thr  were dramatically induced by  F. graminearum  infection, with significantly higher fold changes in CS than those in SM. The expression patterns of the three highly induced tRFs were further validated by stem-loop qRT-PCR. The accumulation of tRFs were closely related to ribonucleases T2 family members, which were induced by  F. graminearum  challenge. The tRFs’ targets in host were predicted and were validated by RNA sequencing. Conclusion Integrative analysis of the differentially expressed tRFs and their candidate targets indicated that tRF Glu , tRF Lys  and tRF Thr  might negatively regulate wheat resistance to FHB. Our results unvealed the potential roles of tRFs in wheat- F. graminearum  interactions.

tRNA-derived fragments from wheat are potentially involved in susceptibility to Fusarium head blight