Abstract Glucosinolates(GS), as one of important plant secondary metabolites containing nitrogen and sulfur, is one major flavor source of cruciferous vegetables. In this study we developed SSRs linked to GS content in Chinese cabbage(Brassica rapa ssp. pekinensis), aiming to exploit the variation in gene specific SSR loci or alleles crossed over Chinese cabbage accessions. According to the genomic sequence information of Arabidopsis thaliana and Chinese Cabbage, gene sequences related to GS biosynthesis were alignment and analysis, finding 102 candidate genes associated with GS content distributed in 10 chromosomes. Compared with Arabidopsis, the homologous genes for GS biosynthensis were detected in Chinese cabbage, with 8 zero copy, 13 single copies, 17 double copies, 14 more than 2 copies. By analyzing sequences of candidate genes and their up/down franking 5 kb nucleotides with software FASTPCR 6.0, 237 SSRs were developed in 102 genes, 16 of them had no SSRs, 72 of them had 1~4 SSRs, 5 of them had 5 SSRs, 4 of them had 6 SSRs, 4 of them had 7 SSRs, and 1 of them had 8 SSRs. Within all detected SSRs, four replicated types were found. Most of types were single nucleotide replication, with number of 122 and 51.4% of total SSRs; forty eight replication types of double nucleotide were found, with 20.3% of total SSRs; the most less types were three nucleotide replications, with only 7 SSRs and with 3.0%; the rest 60 replicated types had no clear replications. Seventy seven SSR specific primers linked to GS synthesis genes could be designed from 86 genes with SSR locus. Forty nine SSR primers could amplify available and clear bands in 75 inbred lines of Chinese cabbage, 16 of them (20.8%) were polymorphic, 18 of them (23.4%) had no polymorphism, 15 of them (19.5%) had more bands, 28 of them (36.4%) had no amplification products. Finally 11 pairs of primer were amplified in all accessions and produced 26 SSR alleles. The results can offer basic materials used for molecular marker assistant in breeding new varieties with high valuable GS compositions, and accelerate the process of breeding in nutritional quality in Chinese cabbage.
