Abstract：Aims of this research were to well identify chromosome and chromosome fragments from cabbage under background of Chinese cabbage, and to analyze the effect of cabbage (Brassica oleracea, CC) chromosome or chromosome fragments on Chinese cabbage (Brassica rapa, AA). A total of 797 expressed sequence tag SSR (EST- SSR) markers were used to screen polymorphism between Chinese cabbage and cabbage, 269 of them were polymorphic, and 12 of them were assigned on linkage group C01, 10 of them were assigned on linkage group C02, 22 of them were assigned on linkage group C03, 10 of them were assigned linkage group on C04, 13 of them were assigned on linkage group C05, 10 of them were assigned on linkage group C06, 16 of them were assigned on linkage group C07, 14 of them were assigned on linkage group C08, 13 of them were assigned on linkage group C09, and 156 of them were NOMATCH, Scaffold or Unknown. The EST sequences corresponding 176 EST-SSRs with clear polymorphism and stable amplification between Chinese cabbage and cabbage were blasted with databases of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). EST sequences annotations were obtained. Annotations about cell components had 124, accounting for 12.29% of the total, and mainly including organelle, membrane-enclosed lumen, cell junction, membrane, cell, macromolecular complex, extracellular region, cell part，membrance part, organelle part ect.. Annotations about molecular function had 184, representing 18.24% of the total, and mainly including catalytic activity, nucleic acid bingding transcription factor activity, protein binding transcription factor activity, structural molecule activity, transporter activity, binding, electron carrier activity etc.. Annotations about biological pathways had 688, representing 68.19% of the total, and mainly including cell metabolic processes, biological regulation and stimulus response systerm morphological structure, signal ransduction and signal transmission system, the immune system ect.. The sequences with unknown function had 13, representing 1.29% of the total. The obtained polymorphic EST-SSRs markers between cabbage and Chinese cabbage will be very useful for identification of exogenous cabbage chromosome and chromosome fragments in alien addition lines and translocation lines of Chinese Cabbage - Cabbage. Function annotation of EST-SSRs markers target gene were analyzed in this research, which will provide a reference for speculating the effect of DNA form cabbage on Chinese cabbage.
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