An EST-SSR linkage map of raphanus sativus and comparative genomics of the brassicaceae

Kenta Shirasawa, Maki Oyama, Hideki Hirakawa, Shusei Sato, Satoshi Tabata, Takashi Fujioka, Chiaki Kimizuka-Takagi, Shigemi Sasamoto, Akiko Watanabe, Midori Kato, Yoshie Kishida, Mitsuyo Kohara, Chika Takahashi, Hisano Tsuruoka, Tsuyuko Wada, Takako Sakai, Sachiko Isobe

Research output: Contribution to journalArticlepeer-review

62 Citations (Scopus)


Raphanus sativus (2n 2x 18) is a widely cultivated member of the family Brassicaceae, for which genomic resources are available only to a limited extent in comparison to many other members of the family. To promote more genetic and genomic studies and to enhance breeding programmes of R. sativus, we have prepared genetic resources such as complementary DNA libraries, expressed sequences tags (ESTs), simple sequence repeat (SSR) markers and a genetic linkage map. A total of 26 606 ESTs have been collected from seedlings, roots, leaves, and flowers, and clustered into 10 381 unigenes. Similarities were observed between the expression patterns of transcripts from R. sativus and those from representative members of the genera Arabidopsis and Brassica, indicating their functional relatedness. The EST sequence data were used to design 3800 SSR markers and consequently 630 polymorphic SSR loci and 213 reported marker loci have been mapped onto nine linkage groups, covering 1129.2 cM with an average distance of 1.3 cM between loci. Comparison of the mapped EST-SSR marker positions in R. sativus with the genome sequence of A. thaliana indicated that the Brassicaceae members have evolved from a common ancestor. It appears that genomic fragments corresponding to those of A. thaliana have been doubled and tripled in R. sativus. The genetic map developed here is expected to provide a standard map for the genetics, genomics, and molecular breeding of R. sativus as well as of related species. The resources are available at

Original languageEnglish
Pages (from-to)221-232
Number of pages12
JournalDNA Research
Issue number4
Publication statusPublished - 2011 Aug
Externally publishedYes


  • Raphanus sativus
  • comparative map
  • expressed sequence tag (EST)
  • genetic linkage map
  • simple sequence repeat (SSR)

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


Dive into the research topics of 'An EST-SSR linkage map of raphanus sativus and comparative genomics of the brassicaceae'. Together they form a unique fingerprint.

Cite this