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Panicle type is one of the important factors affecting rice (<i>Oryza sativa</i> L.) yield, and the identification of regulatory genes in panicle development can provide significant insights into the molecular network involved. This study identified a <i>large and dense panicle 1</i> (<i>ldp1</i>) mutant produced from the Wuyunjing 7 (WYJ7) genotype, which displayed significant relative increases in panicle length, number of primary and secondary branches, number of grains per panicle, grain width, and grain yield per plant. Scanning electron microscopy results showed that the shoot apical meristem (SAM) of <i>ldp1</i> was relatively larger at the bract stage (BM), with a significantly increased number of primary (PBM) and secondary branch (SBM) meristematic centers, indicating that the <i>ldp1</i> mutation affects early stages in SAM development Comparative RNA-Seq analysis of meristem tissues from WYJ7 and <i>ldp1</i> at the BM, PBM, and SBM developmental stages indicated that the number of differentially expressed genes (DEGs) were highest (1407) during the BM stage. Weighted gene coexpression network analysis (WGCNA) revealed that genes in one module (turquoise) are associated with the <i>ldp1</i> phenotype and highly expressed during the BM stage, suggesting their roles in the identity transition and branch differentiation stages of rice inflorescences. Hub genes involved in auxin synthesis and transport pathways, such as <i>OsAUX1</i>, <i>OsAUX4</i>, and <i>OsSAUR25</i>, were identified. Moreover, GO and KEGG analysis of the DEGs in the turquoise module and the 1407 DEGs in the BM stage revealed that a majority of genes involved in tryptophan metabolism and auxin signaling pathway were differentially expressed between WYJ and <i>ldp1</i>. The genetic analysis indicated that the <i>ldp1</i> phenotype is controlled by a recessive monogene (<i>LDP1</i>), which was mapped to a region between 16.9 and 18.1 Mb on chromosome seven. This study suggests that the <i>ldp1</i> mutation may affect the expression of key genes in auxin synthesis and signal transduction, enhance the size of SAM, and thus affect panicle development. This study provides insights into the molecular regulatory network underlying rice panicle morphogenesis and lays an important foundation for further understanding the function and molecular mechanism of <i>LDP1</i> during panicle development.