Machine Learning Guided Meta-transcriptomics Reveals OsRPM1 as a Key Regulator of Rice Blast Resistance

Abstract

Rice blast, caused by Magnaporthe oryzae , is the most destructive fungal disease of rice, responsible for annual yield losses of 10–30% and posing a major threat to global food security. The rapid evolution of blast pathotypes and the polygenic nature of resistance complicate breeding efforts for durable resistance. In this study, we integrated multiple RNA-sequencing datasets, revealing a dynamic transcriptional landscape during infection. Compared with susceptible genotypes, resistant genotypes showed early downregulation of immune receptors (e.g., OsPtr , OsSAH2 , OsWRKY64 ), followed by active upregulation of defense effectors (e.g., OsPR10b , chitinases, OsLsi6 , OSMORF8a ) during peak response stages. Key pathways, such as immune signaling, receptor kinases, and secondary metabolism, were enriched in resistance modules, whereas susceptibility was linked mainly to primary metabolism. Machine learning (ML) models, especially XGBoost (XGB), achieved high area under the curve (AUC) of up to 0.98 in predicting resistance, with SHapley Additive exPlanations (SHAP) analysis highlighting known and novel genes, including OsLP2 , NB-ARC domain protein, OsRPM1 , OsATG8d , and several uncharacterized proteins. Importantly, ML identified regulators that conventional methods missed, underscoring the value of integrated computational approaches. Functional validation of OsRPM1 using CRISPR/Cas9 knockout (KO) and overexpression (OX) lines confirmed its positive role in blast resistance, where KO mutants exhibited increased lesion length and higher pathogen accumulation. In contrast, OX lines showed enhanced resistance and improved photosynthetic performance and hydrogen peroxide (H 2 O 2 ) accumulation. These findings provide a comprehensive resource of candidate genes and regulatory modules for functional validation and molecular breeding, offering a robust foundation for developing rice cultivars with broad-spectrum and durable blast resistance.