Small RNAs as systemic signals in plant defense: mechanisms, challenges, and future directions

Abstract Small RNAs (sRNAs) have emerged as central regulators of gene expression, coordinating development, stress responses, and immunity across plant tissues. Far from acting solely within individual cells, sRNAs move through plasmodesmata and the phloem to mediate systemic silencing, forming a long-distance communication network that parallels classical hormonal signaling. This review synthesizes current evidence for sRNA mobility in plants and its extension across species boundaries during host-pathogen interactions. We describe how sRNAs are stabilized by RNA-binding proteins, Argonaute complexes, and extracellular vesicles (EVs), and how these carriers enable selective trafficking within the plant and into fungal or oomycete pathogens. Cross-kingdom RNA interference (ckRNAi) forms the mechanistic basis of Host-Induced Gene Silencing (HIGS) and Spray-Induced Gene Silencing (SIGS), two emerging RNA-based strategies for crop protection. We also addressed the variability of RNA uptake among pathogens, environmental instability of naked RNAs, and the promise of nanocarriers, synthetic biology, and machine-learning design tools to overcome these barriers. Bioinformatic and regulatory challenges, ranging from the identification of functional mobile RNAs to risk assessment and field validation remain key frontiers. Collectively, these advances position mobile RNAs as both mechanistic signals and deployable tools, redefining plant-microbe communication and opening new paths toward predictive, sustainable RNA-driven agriculture.