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BMC Genomics. 2015 Aug 12;16:595. doi: 10.1186/s12864-015-1803-y.

A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B.

Author information

1
Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. kobafumi@affrc.go.jp.
2
Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. jzwu@nias.affrc.go.jp.
3
Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. jzwu@nias.affrc.go.jp.
4
Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. kanamo@affrc.go.jp.
5
Bioinformatics Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. tstanaka@affrc.go.jp.
6
Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. skatagiri@affrc.go.jp.
7
Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. wkarasawa@affrc.go.jp.
8
Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan. kaneko_satoko@soken.ac.jp.
9
Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan. watahoshida@gmail.com.
10
Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan. ts610821@hotmail.co.jp.
11
Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. hanawayumiko@affrc.go.jp.
12
Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. fujisawah@affrc.go.jp.
13
Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. kuritak@affrc.go.jp.
14
Cereal Science Research Center of Tsukuba, Nisshin Flour Milling Inc., Tsukuba, 300-2611, Japan. abe.chikako@nisshin.com.
15
Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan. masaru_ie@hotmail.com.
16
Core Research Division, Organization of Advanced Science and Technology, Kobe University, Kobe, 657-8501, Japan. ryohno@people.kobe-u.ac.jp.
17
Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ-78371, Olomouc, Czech Republic. safar@ueb.cas.cz.
18
Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ-78371, Olomouc, Czech Republic. simkovah@ueb.cas.cz.
19
Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. mukaiy@affrc.go.jp.
20
Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. bunhamad@athena.ocn.ne.jp.
21
Wheat Breeding Group, NARO Tohoku Agricultural Research Center, Morioka, 020-0198, Japan. saitom@affrc.go.jp.
22
Wheat Breeding Group, NARO Tohoku Agricultural Research Center, Morioka, 020-0198, Japan. goro@affrc.go.jp.
23
Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. katayose@affrc.go.jp.
24
Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan. endo.takashi.2e@gmail.com.
25
Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan. takumi@kobe-u.ac.jp.
26
Wheat Breeding Group, NARO Tohoku Agricultural Research Center, Morioka, 020-0198, Japan. tnaka@affrc.go.jp.
27
Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan. kazsato@rib.okayama-u.ac.jp.
28
Kihara Institute for Biological Research, Yokohama City University, Yokohama, 244-0813, Japan. yogihara@yokohama-cu.ac.jp.
29
Cereal Science Research Center of Tsukuba, Nisshin Flour Milling Inc., Tsukuba, 300-2611, Japan. hayakawa.katsuyuki@nisshin.com.
30
Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ-78371, Olomouc, Czech Republic. dolezel@ueb.cas.cz.
31
Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan. nasushu@kais.kyoto-u.ac.jp.
32
Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. mat@affrc.go.jp.
33
Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. hirokazu@affrc.go.jp.

Abstract

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.

PMID:
26265254
PMCID:
PMC4534020
DOI:
10.1186/s12864-015-1803-y
[Indexed for MEDLINE]
Free PMC Article

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