Systems-level understanding of plant immune networks through single-cell and spatial omics

Plants have a layered immune system, comprising PAMP-pattern triggered immunity (PTI), effector-triggered immunity (ETI), and systemic acquired resistance (SAR), which enables them to detect and respond to microbial threats. Several studies on plant immunity have advanced our understanding of how nucleotide-binding leucine-rich repeat receptors (NLRs) function within these defense layers. Sensor NLRs recognize pathogen effectors, while helper NLRs form resistosome complexes that drive downstream signaling, including calcium influx, reactive oxygen species production, and transcriptional activation. Moreover, single-cell and spatial omics have revealed heterogeneity in immune activation, identifying specialized "PRIMER" cells that initiate strong local responses and "bystander" cells that respond to cues from neighboring tissues to maintain broader immunity. Additionally, structural analyses have clarified the assembly of resistosomes, and proteomic and interactome studies highlight how protein networks shape signaling specificity and intensity. Epigenetic and RNA-mediated mechanisms further modulate NLR expression and responsiveness. In this review, we focus on an integrative overview of how receptor activation, gene-regulatory circuits, protein interaction hubs, and chromatin dynamics collectively influence immune outcomes. We also discuss the insights of systems and synthetic biology approaches that may guide rational engineering of more durable and broad-spectrum disease resistance in crops.