Independent Validation and Refinement of the LAX1-Regulated Transcriptional Network in Rice Panicle Development

Rice panicle architecture plays a critical role in determining grain yield; however, the regulatory networks influencing axillary meristem formation remain inadequately elucidated. A previous study identified LAX1 as a canonical bHLH transcription factor, detailing its direct targets and global transcriptomic alterations in lax1 mutants. In this study, an independent CRISPR/Cas9 LAX1 knockout mutant was generated, followed by transcriptome profiling of young panicles. The lax1-KO mutant displayed a reduction in secondary branches and grain number. Applying a more stringent threshold (|log2 fold change (log2FC)| ≥ 1), 518 high-confidence differentially expressed genes (DEGs) were identified, 131 of which overlapped with previously reported DEGs (direction concordance: 88.5%), supporting the core LAX1-regulated network. The analysis revealed member-specific PIN regulation (OsPIN1c/1d and OsPIN2 downregulated; OsPIN3t and OsPIN9 upregulated), expression changes in hormone-associated genes (OsPP2C09, OsPP2C49, OsRR3, OsRR9, OsGASR9) and OsTPP genes (OsTPP1, OsTPP4, OsTPP9), and altered expression of panicle regulators (IPA1, OsTB1, DEP1, DEP3, CUC, and MADS-box genes). Motif enrichment analysis further identified bHLH motifs as the most frequently represented, whereas CAMTA and FRS/FRF motifs exhibited the highest statistical significance in DEG promoters, suggesting a possible multi-layered transcriptional architecture. Collectively, these findings validate and refine the LAX1-regulated network, positioning LAX1 as a pivotal coordinator of rice panicle development.