Comparative transcriptomic analysis of rice lines expressing OsYABBY2-GFP under constitutive and native promoters

YABBY transcription factors are important regulators of lateral organ development in plants, yet the downstream transcriptional effects of OsYABBY2 (OsYAB2) in rice remain incompletely understood. In this study, we compared the leaf transcriptomes of wild-type Nipponbare and two transgenic rice lines expressing OsYAB2-GFP under either the cauliflower mosaic virus 35 S promoter or the native OsYAB2 promoter. Leaf traits and epidermal morphology were examined using quantitative phenotyping and scanning electron microscopy. Strong 35 S-driven overexpression of OsYAB2 promotes leaf elongation, increases macrohair and microhair density on the adaxial leaf surface, and reduces nodular papillae on the abaxial leaf surface. In contrast, moderate native promoter-driven OsYAB2 expression slightly reduces leaf width, enhances microhair density, and inhibits nodular papilla formation without affecting leaf length. In situ hybridization signals of OsYAB2 in leaf primordia and vasculature confirm its role in leaf development. Leaf transcriptomes were analyzed by RNA sequencing, differential-expression analysis, functional enrichment, soft clustering, and qRT-PCR. Relative to Nipponbare, the pro35S::OsYAB2-GFP line showed more differentially expressed genes than the proOsYAB2::OsYAB2-GFP line. Downregulated genes in the constitutive-expression line were enriched for genes annotated with leaf patterning, shoot apical meristem development, and chromatin-associated regulation. Expression patterns of selected genes, including members of the YABBY, bHLH, and CAF-1-related groups, further supported the view that OsYAB2 influences multiple developmental regulatory pathways. qRT-PCR analysis generally validated the RNA-seq trends for representative genes. This study identifies candidate genes and biological processes associated with OsYAB2 function in rice leaf development and provides a foundation for further investigation of its regulatory mechanisms and direct targets. Rice lines expressing OsYAB2-GFP under constitutive and native promoters displayed distinct leaf epidermal phenotypes and transcriptomic profiles, with the constitutive-expression line showing a broader transcriptomic perturbation.