The OsRALF5-FLR1 Module Regulates Rice Root Development and Provides a Target for Studying Cell–Cell Communication

Rice root system architecture, particularly primary root length, is a crucial agronomic trait that significantly impacts water absorption, nutrient uptake, and drought tolerance. The identification of plant ligand-receptor pairs provides a foundational dataset for studying cell communication in root. However, current understanding of root-based ligand-receptor regulatory modules in rice remains limited. We identified FERONIA-Like Receptor 1 (FLR1), a member of the FERONIA-like receptor (FLR) family of receptor-like kinases (RLKs), as a vital regulator of rice root development. FLR1 governs primary root length by modulating cell division within the root apical meristem (RAM). Using an interaction screening system, we identified multiple Rapid Alkalinization Factor (RALF) peptides, which are secreted small signaling molecules, that interact with FLR1, with OsRALF5 emerging as a key functional ligand. In FLR1 promoter-edited mutants, the co-abundance of OsRALF5 and FLR1 mRNAs showed a strong positive correlation with root length. In situ hybridization and single-cell transcriptomics revealed a striking co-expression of FLR1 and OsRALF5 in the epidermis, cortex, and stele. By mediating cell-cell communication across root tissues, the OsRALF5-FLR1 module coordinates growth and maintains the stem cell niche and RAM homeostasis processes that are fundamental for root patterning. Collectively, this study strongly implicates the OsRALF5-FLR1 module in the regulation of rice root length and supports its potential as a model for studying root-related cell communication through quantitative analysis of ligand-receptor mRNA expression.