Cell-type-resolved transcriptional reprogramming in resistant soybean roots reveals cambial activation and early syncytium initiation upon nematode infection

Soybean cyst nematode (SCN) is the most destructive pathogen of soybean, yet the cellular basis of host resistance remains poorly understood. Here, we present a high-quality, cell-type–resolved atlas of root responses during early SCN infection in the highly resistant genotype PI437654, capturing transcriptional states across all major tissues, including rare syncytial cells. Our analyses reveal that resistance is mediated not by a localized defense but by coordinated, multicell reprogramming spanning invasion layers, vascular tissues, and feeding site–associated cells. We identify the vascular cambium as the primary cellular origin of SCN-induced syncytia, resolving a long-standing question in nematology. Mechanistically, resistance arises from disruption of key processes required for feeding site establishment, secretory stress via imbalanced vesicle trafficking, suppression of endoreduplication to prevent hypertrophic syncytial growth, and activation of autophagy to maintain cellular homeostasis. Spatially organized hormone signaling networks, including jasmonic acid, salicylic acid, and ethylene pathways, further reinforce defense, with GmJAZ1 functioning as a central regulator of JA–SA crosstalk. Collectively, PI437654 enforces resistance by targeting host cell identity, nutrient sink formation, and sustained parasitism, deploying a multilayered, tissue-specific defense strategy. This study provides a mechanistic, systems-level framework for SCN resistance and establishes a single-cell resource capturing rare root cell states, offering actionable targets for engineering durable nematode resistance.