Quercetin enhances tomato seed germination via phenylpropanoid-dependent regulation of ROS, hormone signaling, and starch hydrolysis

Seed germination is a critical transition in plant development, tightly regulated by metabolic and signaling networks. The phenylpropanoid pathway is central to diverse plant physiological processes, yet its specific role in seed germination remains poorly understood. RNA sequencing analysis (RNA-seq) revealed that key phenylpropanoid pathway genes are upregulated during germination, particularly SlPAL5 and SlF3H act as the main regulators. Exogenous phenylpropane metabolites associated with SlPAL5 and SlF3H genes, including chalcone, dihydroquercetin, and quercetin, could promote seed germination. Overexpression of SlPAL5 and SlF3H in tomato ( SlPAL5-OE and SlF3H-OE ) accelerated germination, increased phenylalanine ammonia-lyase (PAL) activity, elevated quercetin accumulation, increased hydrogen peroxide (H 2 O 2 ) content, and modulated gene expressions linked to reactive oxygen species (ROS) scavenging, phytohormone signaling (ethylene, gibberellins, auxin), and starch hydrolysis. Notably, exogenous quercetin treatment also promoted germination and influenced these transcriptional networks, consistent with the phenotypic outcomes observed in SlPAL5-OE and SlF3H-OE lines. Overall, our results demonstrated quercetin, a central metabolite in phenylpropanoid pathway, enhanced germination by coordinating phenylpropanoid-mediated ROS homeostasis, phytohormone signaling, and starch hydrolysis in tomato. This work provides new insights into phenylpropanoid functions in germination and refines quercetin as proactive regulators for improving tomato seed vigor and agricultural productivity. • SlPAL5 and SlF3H regulates tomato seed germination via quercetin accumulation. • Quercetin affects germination via coordinating ROS, phytohormones, and amylase genes. • Enhanced phenylpropanoid flux accelerates seed germination. • Phenylpropanoid pathway serves as a candidate genetic strategy to enhance seed vigor.