The silique number is one of the important components of yield per plant in oilseed rape (Brassica napus L.) and the exploitation and utilization of its excellent alleles are essential to increase yield. More than hundreds of silique number QTLs have been mapped in oilseed rape, but they are difficult to be fine-mapped or cloned because of their moderate and unstable effects. A oilseed rape mutant (No.7931) was detected in previous study and it had few siliques at mature stage due to the stop growth after differentiation about 10 flowers on the top of inflorescence. A F2 segregating population consisting of 3400 individuals was constructed using this mutant and another more-silique lines No.73290. Among them, we performed BSA-seq on 30 individuals with extreme more- or less-siliques and detected three associated intervals of 0-1.1 Mb, 4.7-6.2 Mb, and 11.5-12.4 Mb on the C02 chromosome. These genomic intervals contained a total of 522 annotated genes in the reference genome DarmorV8.1, among which 235 genes had functional annotation and SNP/InDel variation. At the early stage of flower bud differentiation, the shoot apical meristems of two parents were subjected to RNA-seq, and a total of 8958 differentially expressed genes (DEGs) were detected. These DEGs were significantly enriched into 20 pathways, including carbohydrate metabolism, translation, and amino acid metabolism (highly associated with flower bud differentiation) and so on, among which 99 were located in the associated intervals. By the integration of gene functional annotation as well as sequence and expression variation analysis, a total of nine candidate genes (BnaC02g00490.1D2, BnaC02g01030.1D2, BnaC02g01120.1D2, BnaC02g00270.1D2, BnaC02g02670.1D2, BnaC02g08680.1D2, BnaC02g08890.1D2, BnaC02g09480.1D2, and BnaC02g10490.1D2) were identified, which were mainly involved in the maintenance of inflorescence meristems and the regulation of flower development. The above results lay the foundation for the following fine-mapping and cloning of the silique number mutant gene in oilseed rape. [ABSTRACT FROM AUTHOR]