The transcription factors OsIDD and OsSHR jointly regulate ground tissue patterning and differentiation in rice roots

Rice roots have a distinctive ground tissue architecture with multiple cortical layers and a single endodermal layer concentrically surrounding the stele. This architecture promotes aerenchyma formation and adaptability to waterlogged environments, but the underlying molecular mechanisms remain largely unexplored. Here, we identified the INDETERMINATE DOMAIN (IDD) and SHORTROOT (SHR) families as key regulators of ground tissue development in rice. OsIDD2/3/6/8 govern cortical radial symmetry by coordinating cortical organization and auxin distribution independently of OsSHR1/2/3/4/5. Quadruple knockout of OsIDD2/3/6/8 caused cortical asymmetry without affecting apoplastic barrier integrity or mineral uptake but reduced shoot-directed ion transport. OsIDD8 also controls the number of cortical cell layers and endodermal cells, whereas OsSHR1/2/3/4/5 redundantly promote periclinal divisions of the cortical cells, which require OsIDD8 activity. Moreover, OsIDD and OsSHR members coordinate endodermal differentiation by regulating localization of Casparian strip membrane domain protein OsCASP1 and lignin/suberin deposition. These findings establish a genetic framework underlying the spatial organization and functional differentiation of ground tissue in rice roots.