Radish is also characterized by pungent components, i.e., isothiocyanates. In order to understand genetic mechanisms for those traits, we have conducted construction of infrastructure in molecular genetic studies.
For construction of draft sequences of radish, short reads of genomic sequences of 191.1 Gb obtained by an Illumina HiSeq 2000 and 27,904 high-quality BAC-end sequences were de novo assembled, resulting in 76,592 scaffolds of >300 bp (RSA_r1.0; DF384214-DF396802) which span 402 Mb of total size, covering 75.9% of the estimated genome size of radish.
The draft sequences of 76,592 scaffolds are published on this web site. In addition, we have constructed a high density genetic map with ca. 2,550 DNA markers by integration of two published genetic maps (Li et al. 2011, Shirasawa et al. 2011) and addition of new DNA markers (Kitashiba et al. in preparation).
A part of the scaffolds, ca. 1,300 scaffolds, have been assigned to this genetic map. Since we have detected SNPs among eight inbred lines by next generation sequencing of bulked PCR products amplified by 2,880 primer pairs (Zou et al. 2013), the information is also opened on this web site.
This study was supported by the Program for Promotion of Basic and Applied Researches for Innovations in Bio-oriented Industry (BRAIN), Japan.
Draft sequences of the radish (Raphanus sativus L.) genome
Kitashiba H, Li F, Hirakawa H, Kawanabe T, Zou Z, Hasegawa Y, Tonosaki K, Zhang Z, Shirasawa S, Fukushima A, Yokoi S, Takahata Y, Kakizaki T, Ishida M, Okamoto S, Sakamoto K, Shirasawa K, Tabata S, Nishio T (2014)
DNA Res. 21: 481–490, DOI: 10.1093/dnares/dsu014
QTL analysis using SNP markers developed by next-generation sequencing for identification of candidate genes controlling 4-methylthio-3-butenyl glucosinolate contents in roots of radish, Raphanus sativus L.
Zou Z, Ishida M, Li F, Kakizaki T, Suzuki S, Kitashiba H, Nishio T (2013)
PLos One 8: e53541.
Extensive chromosome homoeology among Brassiceae species were revealed by comparative genetic mapping with high-density EST-based SNP markers in radish (Raphanus sativus L.).
Li F, Hasegawa Y, Saito M, Shirasawa S, Fukushima A, Ito T, Fujii H, Kishitani S, Kitashiba H, Nishio T (2011)
DNA Res. 18: 401–411.
An EST-SSR linkage map of Raphanus sativus and comparative genomics of the Brassicaceae.
Shirasawa K, Oyama M, Hirakawa H, Sato S, Tabata S, Fujioka T, Kimizuka-Takagi C, Sasamoto S, Watanabe A, Kato M, Kishida Y, Kohara M, Takahashi C, Tsuruoka H, Wada T, Sakai T, Isobe S. (2011)
DNA Res. 18: 221-232.