Expanding the RNAi Toolkit: Host-induced gene silencing of CHITIN SYNTHASE VI via linear double-stranded and paperclip RNA confers plant tolerance to Sclerotinia sclerotiorum

To investigate the molecular basis of this protection, we performed global dual-RNA sequencing directly at the plant–pathogen interface. In addition to CHITIN SYNTHASE VI silencing, we found enrichment of biological processes involved in cell wall turnover in Sclerotinia infecting both ds- and pcRNA transgenic lines, accompanied by a significant reduction in fungal load at the site of infection. This reduction in pathogen pressure translated into improved plant tolerance, as growth- and photosynthesis-associated pathways were concurrently enriched in both transgenic plant lines.

Together, these findings demonstrate that HIGS of chitin synthesis can effectively suppress S. sclerotiorum disease progression and confer plant protection. Finally, the engineering of alternative RNA constructs, such as paperclip RNA, expands the potential of RNAi-based crop protection tools as flexible and sustainable options for disease management against fungal pathogens.