TY - JOUR
T1 - An EST-SSR linkage map of raphanus sativus and comparative genomics of the brassicaceae
AU - Shirasawa, Kenta
AU - Oyama, Maki
AU - Hirakawa, Hideki
AU - Sato, Shusei
AU - Tabata, Satoshi
AU - Fujioka, Takashi
AU - Kimizuka-Takagi, Chiaki
AU - Sasamoto, Shigemi
AU - Watanabe, Akiko
AU - Kato, Midori
AU - Kishida, Yoshie
AU - Kohara, Mitsuyo
AU - Takahashi, Chika
AU - Tsuruoka, Hisano
AU - Wada, Tsuyuko
AU - Sakai, Takako
AU - Isobe, Sachiko
PY - 2011/8
Y1 - 2011/8
N2 - 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 http://marker.kazusa.or.jp/Daikon.
AB - 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 http://marker.kazusa.or.jp/Daikon.
KW - Raphanus sativus
KW - comparative map
KW - expressed sequence tag (EST)
KW - genetic linkage map
KW - simple sequence repeat (SSR)
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U2 - 10.1093/dnares/dsr013
DO - 10.1093/dnares/dsr013
M3 - Article
C2 - 21669962
AN - SCOPUS:80051963684
SN - 1340-2838
VL - 18
SP - 221
EP - 232
JO - DNA Research
JF - DNA Research
IS - 4
ER -