The miPEP156e-miR156-SPL2 module functions in rice salt tolerance by regulating ion and ROS homeostasis

Abstract Salt stress severely constrains crop growth and yield, posing a significant threat to global food security. Although primary transcripts of microRNAs (pri-miRNAs) are known to encode regulatory peptides (miPEPs), their functions in salt tolerance remain poorly understood. Here, we report that miPEP156e, a small peptide encoded by pri-miR156e in rice, acts as a positive regulator of salt tolerance. Application or overexpression of miPEP156e markedly enhances salt tolerance in rice, while loss-of-function mutants exhibit increased sensitivity. Transcriptomic and physiological analyses reveal that miPEP156e modulates genes involved in ion transport, ROS scavenging, and osmotic adjustment. Under salt stress, miPEP156e maintains ion balance by limiting Na⁺ accumulation and preserving K⁺, while concurrently strengthening ROS scavenging capacity. Further analysis demonstrates that miPEP156e exerts these effects by regulating the miR156-SPL2 module. Collectively, our study establishes miPEP156e as a key regulatory peptide in rice salt tolerance, providing new insights into how miPEPs help plants cope with environmental stress.