Two stable QTLs controlling seed density per silique were detected on chromosomes A09 and C05 in rapeseed via GWAS, and ARF18 was the only causal gene of QTL qSDPS-A09. Seed density per silique (SDPS) is a key agronomic trait that directly or indirectly affects seed yield in rapeseed (Brassica napus L.). Exploring the genetic control of SDPS is beneficial for increasing rapeseed production. In this study, we evaluated the SDPS phenotypes of 413 rapeseed cultivars (lines) across five natural environments and genotyped them by resequencing. A GWAS analysis was performed using 5,277,554 high-quality variants with the MLM_PCA + K and FarmCPU models. A total of 51 loci were identified to be significantly (p <
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