Sclerotinia sclerotiorum is a broad-host-range necrotrophic fungal pathogen that infects hundreds of plant species and causes major crop yield losses worldwide. Fungal pathogens such as Botrytis cinerea can deploy small RNAs (sRNAs) to silence host gene expression via cross-kingdom RNAi (ckRNAi), but whether S. sclerotiorum uses this strategy was unknown.
To test this, we identified fungal sRNAs associated with the host Argonaute AGO1 in infected Arabidopsis thaliana, demonstrating their loading into the host RNA-induced silencing complex. By integrating AGO1 immunoprecipitation, small RNA sequencing, transcriptome, and degradome data from wild-type and ago1 plants, we identified candidate host transcripts undergoing fungal-sRNA-directed, AGO1-mediated cleavage during infection. Many encode proteins with established or putative roles in immune signalling and disease resistance. Using a 5′-RLM-RACE assay, we functionally validated silencing of AtBEH3 by a pathogen-derived sRNA. AtBEH3 is a transcription factor that regulates brassinosteroid (BR) signalling, a pathway integral to mediating the growth-defence trade-off.
These results establish ckRNAi as a potential virulence strategy of S. sclerotiorum and pinpoint host genes that could be edited to improve quantitative disease resistance across the many crops this pathogen attacks.