Panicle development is crucial to increase the grain yield of rice (Oryza sativa). The molecular mechanisms of the control of panicle development in rice remain unclear. In this study, we identified a mutant with abnormal panicles, termedbranch one seed 1-1(bos1-1). Thebos1-1mutant showed pleiotropic defects in panicle development, such as the abortion of lateral spikelets and the decreased number of primary panicle branches and secondary panicle branches. A combined map-based cloning and MutMap approach was used to cloneBOS1gene. Thebos1-1mutation was located in chromosome 1. A T-to-A mutation inBOS1was identified, which changed the codon from TAC to AAC, resulting in the amino acid change from tyrosine to asparagine.BOS1gene encoded a grass-specific basic helix–loop–helix transcription factor, which is a novel allele of the previously clonedLAX PANICLE 1(LAX1) gene. Spatial and temporal expression profile analyses showed thatBOS1was expressed in young panicles and was induced by phytohormones. BOS1 protein was mainly localized in the nucleus. The expression of panicle development-related genes, such asOsPIN2,OsPIN3,APO1, andFZP, was changed bybos1-1mutation, suggesting that the genes may be the direct or indirect targets of BOS1 to regulate panicle development. The analysis ofBOS1genomic variation, haplotype, and haplotype network showed thatBOS1gene had several genomic variations and haplotypes. These results laid the foundation for us to further dissect the functions of BOS1.