*4.1. Plant Materials*

The *Japonica* rice (*Oryza sativa* ssp. *japonica* cv. Nipponbare) was used as the wild-type (WT) rice plant for the current study. The *oscyp96b4* semi-dwarf (M) was a *Ds*insertion mutant, and the *OsCYP96B4* ectopic expression (ECE) lines showing the most severe dwarf phenotype were generated constitutively expressing the *OsCYP96B4* gene in the Nipponbare background. The detailed descriptions about the mutant and ectopic expression lines can be found in our previous report [5]. For each genotype of rice plants (i.e., WT, M, and ECE, Figure S3), 19 seedlings were grown in a Phytatray™ II (Sigma-Aldrich, St. Louis, MO, USA) containing half strength Murashige and Skoog medium [53] (Sigma-Aldrich, St. Louis, MO, USA) in a plant growth room maintained at 28 ◦C with 12 h dark and 12 h light. For metabolites extraction, 10 whole 2-week-old seedling shoots without roots were used for each genotype. While for qRT-PCR, 3 independent biological replicates were used, where each replicate was made up of RNA extracted from 3 seedlings pooled together for better representation. Each plant sample was collected individually into a 2 mL Eppendorf tube, weighed, immediately snap-frozen in liquid nitrogen and stored at −80 ◦C until further analyses.
