Spatial Flavonoid Accumulation in Soybean Pericycle Restricts Phytophthora sojae Invasion

Root immunity relies on coordinated defenses across distinct tissues, yet the underlying cellular mechanisms remain unclear. Here, we integrated single-cell transcriptomics, spatial metabolomics, and genetic manipulation to dissect soybean (Glycine max) interactions with Phytophthora sojae. In resistant Williams82 (Wm82) roots, P. sojae hyphae were excluded from the stele, exhibiting negative tropism toward the pericycle. scRNA-seq revealed that this resistance is mediated by infection-induced pericycle cells expressing high levels of flavonoid biosynthetic genes, including GmCHS7 and GmCHI4A. CRISPR-Cas9 knockout of these genes compromised resistance, whereas overexpression enhanced immunity in susceptible cultivars. Metabolomic and spatial metabolic analyses identified naringenin, a flavonoid phytoalexin, as a key antimicrobial compound that specifically accumulates in pericycle-adjacent tissues of Wm82 during infection. Naringenin directly inhibited hyphal growth in vitro and enhanced resistance when applied exogenously. These findings uncover a spatially targeted immune strategy where pericycle-localized activation of flavonoid synthesis forms a chemical barrier to safeguard vascular integrity, highlighting pericycle-centered metabolic immunity as a target for engineering durable resistance.