miR171c and miR172a confer resistance to tomato mottle mosaic virus in tobacco by targeting SCL and AP2 transcription factors

BACKGROUND: Tomato mottle mosaic virus (ToMMV) is an emerging tobamovirus that posing a significant threat to the yield and quality of solanaceous crops globally. To elucidate the regulatory role of small RNAs in the host response to ToMMV, we used Nicotiana tabacum var. Xanthi nc as a model system and performed small RNA sequencing across three distinct disease stages: mosaic symptom onset, linear leaf symptom development, and the recovery phase. By integrating qRT-PCR validation with functional assays, including miRNA overexpression, virus-induced gene silencing, and biological inoculation, several miRNAs specifically associated with ToMMV resistance were identified. RESULTS: Functional characterization revealed that overexpression of miR171c, miR172a, and a novel miRNA (novel-miR363) significantly suppressed ToMMV accumulation and thereby enhancing plant resistance, whereas silencing of miR171c resulted in an approximately threefold increase in viral accumulation. In contrast, overexpression of another novel miRNA, novel-miR1022, promoted viral accumulation and facilitated viral infection. Further analysis through target prediction and experimental validation confirmed that miR171c and miR172a target transcripts encoding Scarecrow-like (SCL) and APETALA2 (AP2) class transcription factors, respectively. Specifically, miR171c appears to confer resistance by repressing NtSCL6 and NtSCL22, whereas miR172a likely mediates this effect through the downregulation of NtRAP2-7. CONCLUSION: These findings elucidate key miRNA-mediated regulatory modules governing ToMMV resistance, advancing the understanding of host defense mechanisms against tobamoviruses.