Integrated transcriptome analysis identifies disease resistance genes and implicates ROP small GTPases in tomato defense against Phytophthora infestans

Background Late blight caused by Phytophthora infestans poses a serious threat to tomato production. Breeding resistant varieties represents a sustainable management strategy, making the elucidation of resistance mechanisms and mining for key resistance genes crucial. Although ROP (Rho of plants) small GTPases are known to participate in plant-pathogen interactions, existing studies have primarily focused on model crops such as rice. However, how the tomato ROP gene family responds dynamically to P. infestans infection over time, its interactions with pattern recognition receptors (PRRs) and molecular chaperones and their coordination with downstream transcription factors remain poorly understood. Results In this study, we performed transcriptome analysis on tomato leaves inoculated with P. infestans and water-treated controls over a time course of 0–60 hours to identify differentially expressed genes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to mine key pathways and genes, while the expression patterns of ROP genes were validated by qRT‑PCR The results showed that the number of DEGs increased with the duration of infection, with early defense genes being up regulated and later shifting towards metabolic and immune homeostasis regulation. Up regulated genes were enriched in pathways related to chitin response and plant-pathogen interactions, identifying key components such as ROP small G proteins, PRR receptors, HSP70 and transcription factors like MYB and ERF. The qRT‑PCR validation showed that the expression trends of ROP genes correlated well with the RNA-seq profiles. Conclusions This study reveals that ROP proteins may construct a multi-layered defense network by coordinating membrane transport, signal transduction and endoplasmic reticulum protein processing, working in synergy with transcription factors. These findings provide an important theoretical basis for elucidating ROP-mediated resistance mechanisms, mining resistance gene resources and breeding disease-resistant tomatoes.