A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B.
BACKGROUND
A complete genome sequence is an essential tool for the genetic improvement of wheat. Because the wheat genome is large, highly repetitive and complex due to its allohexaploid nature, the International Wheat Genome Sequencing Consortium (IWGSC) chose a strategy that involves constructing bacterial artificial chromosome (BAC)-based physical maps of individual chromosomes and performing BAC-by-BAC sequencing. Here, we report the construction of a physical map of chromosome 6B with the goal of revealing the structural features of the third largest chromosome in wheat.


RESULTS
We assembled 689 informative BAC contigs (hereafter reffered to as contigs) representing 91% of the entire physical length of wheat chromosome 6B. The contigs were integrated into a radiation hybrid (RH) map of chromosome 6B, with one linkage group consisting of 448 loci with 653 markers. The order and direction of 480 contigs, corresponding to 87% of the total length of 6B, were determined. We also characterized the contigs that contained a part of the nucleolus organizer region or centromere based on their positions on the RH map and the assembled BAC clone sequences. Analysis of the virtual gene order along 6B using the information collected for the integrated map revealed the presence of several chromosomal rearrangements, indicating evolutionary events that occurred on chromosome 6B.


CONCLUSIONS
We constructed a reliable physical map of chromosome 6B, enabling us to analyze its genomic structure and evolutionary progression. More importantly, the physical map should provide a high-quality and map-based reference sequence that will serve as a resource for wheat chromosome 6B.
Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. kobafumi@affrc.go.jp.
Fuminori
F
Kobayashi
Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. jzwu@nias.affrc.go.jp.|Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. jzwu@nias.affrc.go.jp.
Jianzhong
J
Wu
Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. kanamo@affrc.go.jp.
Hiroyuki
H
Kanamori
Bioinformatics Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. tstanaka@affrc.go.jp.
Tsuyoshi
T
Tanaka
Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. skatagiri@affrc.go.jp.
Satoshi
S
Katagiri
Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. wkarasawa@affrc.go.jp.
Wataru
W
Karasawa
Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan. kaneko_satoko@soken.ac.jp.
Satoko
S
Kaneko
Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan. watahoshida@gmail.com.
Shota
S
Watanabe
Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan. ts610821@hotmail.co.jp.
Toyotaka
T
Sakaguchi
Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. hanawayumiko@affrc.go.jp.
Yumiko
Y
Hanawa
Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. fujisawah@affrc.go.jp.
Hiroko
H
Fujisawa
Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. kuritak@affrc.go.jp.
Kanako
K
Kurita
Cereal Science Research Center of Tsukuba, Nisshin Flour Milling Inc., Tsukuba, 300-2611, Japan. abe.chikako@nisshin.com.
Chikako
C
Abe
Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan. masaru_ie@hotmail.com.
Julio C M
JC
Iehisa
Core Research Division, Organization of Advanced Science and Technology, Kobe University, Kobe, 657-8501, Japan. ryohno@people.kobe-u.ac.jp.
Ryoko
R
Ohno
Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ-78371, Olomouc, Czech Republic. safar@ueb.cas.cz.
Jan
J
Šafář
Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ-78371, Olomouc, Czech Republic. simkovah@ueb.cas.cz.
Hana
H
Šimková
Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. mukaiy@affrc.go.jp.
Yoshiyuki
Y
Mukai
Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. bunhamad@athena.ocn.ne.jp.
Masao
M
Hamada
Wheat Breeding Group, NARO Tohoku Agricultural Research Center, Morioka, 020-0198, Japan. saitom@affrc.go.jp.
Mika
M
Saito
Wheat Breeding Group, NARO Tohoku Agricultural Research Center, Morioka, 020-0198, Japan. goro@affrc.go.jp.
Goro
G
Ishikawa
Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. katayose@affrc.go.jp.
Yuichi
Y
Katayose
Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan. endo.takashi.2e@gmail.com.
Takashi R
TR
Endo
Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan. takumi@kobe-u.ac.jp.
Shigeo
S
Takumi
Wheat Breeding Group, NARO Tohoku Agricultural Research Center, Morioka, 020-0198, Japan. tnaka@affrc.go.jp.
Toshiki
T
Nakamura
Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan. kazsato@rib.okayama-u.ac.jp.
Kazuhiro
K
Sato
Kihara Institute for Biological Research, Yokohama City University, Yokohama, 244-0813, Japan. yogihara@yokohama-cu.ac.jp.
Yasunari
Y
Ogihara
Cereal Science Research Center of Tsukuba, Nisshin Flour Milling Inc., Tsukuba, 300-2611, Japan. hayakawa.katsuyuki@nisshin.com.
Katsuyuki
K
Hayakawa
Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ-78371, Olomouc, Czech Republic. dolezel@ueb.cas.cz.
Jaroslav
J
Doležel
Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan. nasushu@kais.kyoto-u.ac.jp.
Shuhei
S
Nasuda
Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. mat@affrc.go.jp.
Takashi
T
Matsumoto
Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. hirokazu@affrc.go.jp.
Hirokazu
H
Handa
D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D032461:Chromosomes, Plant; D019143:Evolution, Molecular; D023061:Gene Order; D015321:Gene Rearrangement; D005819:Genetic Markers; D009697:Nucleolus Organizer Region; D020161:Physical Chromosome Mapping / Q000379:methods*; D014908:Triticum / Q000235:genetics*
D005819:Genetic Markers