A nucleotide-binding leucine-rich repeat gene OsCNL1 contributes to strain-specific resistance to bacterial blight in rice.

Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), remains a major threat to rice production, and continued discovery and functional validation of resistance genes remain important for durable disease management. Here, we functionally characterized OsCNL1 (LOC_Os11g37759), a rice coiled-coil (CC)-type nucleotide-binding leucine-rich repeat (NLR) gene associated with BB resistance in the resistant line B5N494. OsCNL1 encodes a 968-amino-acid CC type NLR protein and showed pathogen-responsive expression after PXO99A inoculation. CRISPR/Cas9-mediated disruption of OsCNL1 in B5N494 reduced resistance, whereas introduction of a genomic OsCNL1 fragment into susceptible backgrounds and overexpression of the full-length coding sequence enhanced resistance to PXO99A. These reciprocal loss- and gain-of-function assays indicate that OsCNL1 is a genetic component that positively regulates BB resistance against specific Xoo strains. Resistance-spectrum assays further showed that the effect associated with OsCNL1 is strain specific and strongly influenced by host genetic background. No major agronomic penalty was observed in the transgenic materials when compared to wild type under the field conditions. Furthermore, heterologous and in planta assays pointed to a potential physical association between the CC-containing region of OsCNL1 and the non-transcription activator-like effector (non-TALE) XopAE, providing a preliminary framework for future mechanistic studies. Overall, our results suggest that the functionally validated CNL-type NLR OsCNL1 participates in strain-specific BB resistance and has potential in resistance pyramiding strategies for rice BB management.