Benzoic acid inhibits peach root growth and lateral root emergence by disrupting auxin homeostasis through salicylic acid accumulation.
We established a non-sterile root transformation system in peach seedlings. Using this system, we demonstrated that BA treatment inhibits plant growth and lateral root emergence by SA-mediated disruption of auxin distribution. Allelopathic autotoxins, particularly benzoic acid (BA), are recognized as primary contributors to peach (Prunus persica) replant disease; however, the molecular mechanisms by which BA disrupts root development remain poorly understood. BA treatment significantly reduced stem and root length and inhibited lateral root emergence without affecting lateral root initiation. To investigate the underlying mechanism at cellular resolution, we established a non-sterile Agrobacterium rhizogenes-based root transformation system achieving 27.11% transformation efficiency. Auxin biosynthesis (PpYUC10), influx transport (PpAUX1), and response (PpARF19) genes were markedly downregulated following BA treatment. Transgenic roots expressing the DR5::GUS auxin reporter exhibited reduced DR5 activity in root tips and suppressed expression in tissues surrounding lateral root primordia, indicating impaired auxin signaling at both developmental sites. Hormone profiling revealed a non-significant trend toward reduced auxin metabolites alongside significant accumulation of salicylic acid (SA), an auxin-antagonistic hormone, and its storage conjugate SA 2-O-β-glucoside. Supporting a causal role for SA, exogenous SA phenocopied BA-induced root growth inhibition, whereas co-treatment with IAA or the SA-biosynthesis inhibitor aminoindan-1-phosphonic acid (AIP) significantly rescued lateral root number and root fresh weight. Multi-treatment RNA-seq identified "response to auxin" and "response to salicylic acid" as the most enriched GO terms in BA-treated roots, and AIP treatment restored the expression of key auxin-related genes while reversing BA-induced SA-pathway changes. Together, these findings suggest that BA-induced SA accumulation suppresses auxin biosynthesis, transport, and signaling, thereby inhibiting peach root growth and lateral root emergence. This study elucidates the molecular basis of BA autotoxicity and establishes a transformation platform for functional genomic studies in Prunus.