A Wheat‐Specific miRNA, tae‐miR5048, Fine‐Tunes Plant Architecture and Drought Resilience Through Targeting Multiple Kinase Genes

ABSTRACT MicroRNAs (miRNAs) are key regulators of plant development and stress adaptation. While conserved miRNAs have been extensively characterized, the agronomic roles of lineage‐specific miRNAs in crops remain largely unexplored. Here, we demonstrate that tae‐miR5048, a wheat‐specific miRNA, functions as a master regulator concurrently modulating plant architecture and drought tolerance. Overexpression of tae‐miR5048 enhanced early root growth, accelerated reproductive transition, and optimized plant architecture and grain morphology without compromising grain yield. Conversely, CRISPR/Cas9‐mediated knockout of TaMIR5048 homoeologs impaired root development and delayed flowering, yet promoted vegetative growth and grain yield potential, revealing a bidirectional regulatory role. Cytological analysis showed that tae‐miR5048 optimizes plant height, flag leaf size and grain dimension by fine‐tuning cell proliferation and expansion in a tissue‐specific manner. Moreover, tae‐miR5048 confers drought resilience throughout the growth cycle by elevating osmolyte accumulation to maintain tissue water status and alleviating oxidative damage through suppression of ROS production and membrane lipid peroxidation. Mechanistically, degradome sequencing, RLM‑5′ RACE, and transient co‑expression assays demonstrated that tae‐miR5048 directly targets and downregulates multiple kinase genes, including receptor‐like protein kinases and mitogen‐activated protein kinases, thereby modulating key signalling hubs post‐transcriptionally. Transcriptome profiling further revealed that tae‐miR5048 fine‐tunes architectural traits by regulating cellular growth‐related genes and enhances drought tolerance through activation of stress‐responsive and proline biosynthesis pathways. Collectively, our findings establish tae‐miR5048 as a central integrator that balances plant architecture and drought adaptation, providing the first functional evidence for a lineage‐specific miRNA as a promising target for breeding climate‐resilient wheat varieties.