Tuning Tomato Immunity: Integrating Signaling Networks, Epigenetic Regulation, and Rhizosphere Microbiomes for Durable Resistance

Abstract Tomato (Solanum lycopersicum L.) cultivation faces threats from a wide range of pathogenic microorganisms. Research has shifted from characterizing individual resistance (R) genes toward integrated exploration of immune networks, epigenetic regulation, rhizosphere microbiomes, and sustainable control strategies. This review synthesizes recent advances, focusing on: (1) synergy between effector-triggered immunity (ETI) and pattern-triggered immunity (PTI) with emphasis on lifestyle-specific responses to biotrophs, hemibiotrophs, and necrotrophs; (2) regulatory networks orchestrated by phytohormones and non-coding RNAs; (3) epigenetic reprogramming of defense gene expression, including DNA mehtylation and histone modifications; (4) active recruitment of beneficial microbes via root exudates to establish disease-suppressive microbiomes, and the microbe-microbe interactions that underpin biocontrol; (5) deployment of CRISPR/Cas9 and artificial microRNAs (amiRNAs) for durable resistance, alongside the integration of classical R genes from wild relatives. It also highlights root immune specificity, pathogen strategies to subvert host protein networks, and the challenges of QTL introgression and environment-dependent resistance. This review aims to provide a conceptual framework for dissecting tomato disease resistance and for refining breeding strategies.