[Objective] This study aimed to develop ACGM markers for the clustering analysis of large grained Brassica napus materials. [Method] A total of 44 pairs of ACGM primers were designed according to 18 genes related to Arabidopsis grain development and their homologous rape EST sequences. After electrophoresis, 18 pairs of ACGM primers were selected for the clustering analysis of 16 larger grained samples and four fine grained samples of rapeseed. [Result] PCR result showed that 2-6 specific bands were respectively amplified by each pair of primes, and all the bands were polymorphic and repeatable, suggesting that the optimized ACGM markers were useful for clustering analysis of B. napus species. Clustering analysis revealed that the 20 rapeseed samples were divided into three clusters A, B, and C at similarity coefficient 0.6. Then, the clusters A and B were further divided into five sub clusters A1, A2, A3, B1 and B2 at similarity coefficient 0.67. [Conclusion] This study will provide theoretical and practical values for rape breeding.
