Cross-kingdom RNA interference (RNAi) is a key virulence mechanism in which pathogens deliver small RNAs (sRNAs) into host plants, hijacking host ARGONAUTE (AGO) proteins to silence immunity-related genes. However, systematic studies on cross-kingdom RNAi in staple crops, such as rice, remain lacking. Moreover, the mechanism by which plants modulate cross-kingdom RNAi to restrict pathogen invasion is unknown. Here, we identify OsAGO proteins potentially hijacked by R. solani and perform comprehensive sRNA sequencing to profile fungal-derived sRNAs targeting rice genes. Our analysis reveals two R. solani-derived sRNAs that specifically bind OsAGO1 to silence two rice defense genes: Cytochrome P450 98A1 (OsCYP98A1) and NIMA-related kinase 6 (OsNEK6). Notably, we find that OsmiR168 fine-tunes cross-kingdom RNAi efficiency by regulating OsAGO1 mRNA levels. More importantly, a long non-coding RNA, LncRNA19164, acts as a competing endogenous RNA (ceRNA) to sequester OsmiR168, thereby stabilizing OsAGO1 transcripts and regulating cross-kingdom RNAi. Our findings not only advance the understanding of cross-kingdom RNAi in plant-pathogen interactions but also provide a foundation for developing RNA-based disease control strategies in crops. Rhizoctonia solani delivers its own small RNAs into rice cells to silence the plant’s defense genes. In response, rice employs a long non-coding RNA to counteract this attack, thereby preventing the fungus from silencing the host’s immune genes.
Ni et al. (2026) studied this question.