An auxin response factor regulates tiller angle and shoot gravitropism by directly activating related gene expression in rice.

Introduction: The angle of tillers is crucial for shaping plant architecture, which in turn affects grain yield of rice. The formation of tiller angle is associated with the asymmetrical distribution and polar transport of auxin. However, the roles of auxin signaling in regulating the development of tiller angle in rice remain unclear.

Objective: In this study, we discovered that Oryza sativa Auxin Response Factor 5 (OsARF5) acts as a key regulator of tiller angle development in rice.

Methods: The bta3-1 mutant was obtained through using chemical mutagenesis. The BTA3 gene was isolated by using a map-based positional cloning method. The differentially expressed genes were identified and examined through quantitative RT-PCR and high-throughput mRNA sequencing. The protein-DNA interactions were analyzed by chromatin immunoprecipitation and dual-luciferase reporter assays. The protein-protein interactions were assessed using yeast two-hybrid and bimolecular fluorescence complementation methods.

Results: The bta3-1 mutation enlarges the tiller angles, weakens shoot gravitropism, and diminishes the response to auxin in rice. After map-based cloning, we found that the BTA3 gene encodes OsARF5, which belongs to an ARF transcription factor superfamily. OsARF5 binds to the cis-acting elements in the promoters of genes related to tiller angle development, including LA1, OsAGPL1, HASF2d and OsPIN1a, thereby activating their expression. Genome-wide studies identify thousands of differentially expressed genes (DEGs), including auxin response genes, between wild-type and osarf5-1. The number of DEGs in osarf5-1 decreases upon gravistimulation, indicating the involvement of OsARF5 in shoot gravitropism. The OsARF5 physically interacts with three rice Indole Acetic Acid (OsIAA) repressors, forming complexes that facilitate their functions. Mutations in OsIAAs lead to a more compact plant architecture, and the expression of OsARF5-target genes is elevated in the osiaa mutants, suggesting that the OsIAAs counteract OsARF5's effects on the tiller angle formation.

Conclusion: OsARF5 is physically associated with three OsIAAs to bind to the promoter of the target genes, thereby regulating the traget gene expression to manage shoot gravitropism and tiller angle in rice. These findings offer new insights into the principles governing tiller angle development in rice.