Draft sequences of the radish (Raphanus sativus L.) genome.
Radish (Raphanus sativus L., n = 9) is one of the major vegetables in Asia. Since the genomes of Brassica and related species including radish underwent genome rearrangement, it is quite difficult to perform functional analysis based on the reported genomic sequence of Brassica rapa. Therefore, we performed genome sequencing of radish. Short reads of genomic sequences of 191.1 Gb were obtained by next-generation sequencing (NGS) for a radish inbred line, and 76,592 scaffolds of ≥ 300 bp were constructed along with the bacterial artificial chromosome-end sequences. Finally, the whole draft genomic sequence of 402 Mb spanning 75.9% of the estimated genomic size and containing 61,572 predicted genes was obtained. Subsequently, 221 single nucleotide polymorphism markers and 768 PCR-RFLP markers were used together with the 746 markers produced in our previous study for the construction of a linkage map. The map was combined further with another radish linkage map constructed mainly with expressed sequence tag-simple sequence repeat markers into a high-density integrated map of 1,166 cM with 2,553 DNA markers. A total of 1,345 scaffolds were assigned to the linkage map, spanning 116.0 Mb. Bulked PCR products amplified by 2,880 primer pairs were sequenced by NGS, and SNPs in eight inbred lines were identified.
Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan.
Hiroyasu
H
Kitashiba
Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan.
Feng
F
Li
Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan.
Hideki
H
Hirakawa
Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan.
Takahiro
T
Kawanabe
Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan.
Zhongwei
Z
Zou
Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan.
Yoichi
Y
Hasegawa
Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan.
Kaoru
K
Tonosaki
Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan.
Sachiko
S
Shirasawa
Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan.
Aki
A
Fukushima
Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan.
Shuji
S
Yokoi
Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan.
Yoshihito
Y
Takahata
National Institute of Vegetable and Tea Science, 360, Kusawa, Ano, Tsu, Mie 514-2392, Japan.
Tomohiro
T
Kakizaki
National Institute of Vegetable and Tea Science, 360, Kusawa, Ano, Tsu, Mie 514-2392, Japan.
Masahiko
M
Ishida
Plant Breeding Experimental Station, Takii Seed Co. Ltd, Kohsei, Kohka-gun, Shiga 520-20, Japan.
Shunsuke
S
Okamoto
Plant Breeding Experimental Station, Takii Seed Co. Ltd, Kohsei, Kohka-gun, Shiga 520-20, Japan.
Koji
K
Sakamoto
Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan.
Kenta
K
Shirasawa
Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan.
Satoshi
S
Tabata
Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan nishio@bios.tohoku.ac.jp.
Takeshi
T
Nishio
D029741:Brassica rapa / Q000235:genetics; D005819:Genetic Markers; D018745:Genome, Plant; D020641:Polymorphism, Single Nucleotide; D031224:Raphanus / Q000235:genetics*; D017422:Sequence Analysis, DNA
D005819:Genetic Markers
draft sequence; high-density genetic map; radish