OsSPL3, an SBP-Domain Protein, Regulates Crown Root Development in Rice.

The major root system of cereals consists of crown roots (or adventitious roots), which are important for anchoring plants in the soil and for water and nutrient uptake. However, the molecular basis of crown root formation is largely unknown. Here, we isolated a rice () mutant with fewer crown roots, named (). Map-based cloning revealed that is caused by a mutation of a putative transcription factor-coding gene, (). We demonstrate that the point mutation in perturbs the microRNA156 (OsmiR156)-directed cleavage of transcripts, resulting in the mutant phenotype. Chromatin immunoprecipitation sequencing assays of OsSPL3 binding sites and RNA sequencing of differentially expressed transcripts in further identified potential direct targets of OsSPL3 in basal nodes, including a MADS-box transcription factor, OsMADS50. overexpressing plants produced fewer crown roots, phenocopying , while knocking out in the background reversed this phenotype. We also show that , another OsmiR156 target gene, regulates and crown root development. Taken together, our findings suggest a novel regulatory pathway in which the OsmiR156- module directly activates in the node to regulate crown root development in rice.