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

Fuminori Kobayashi,Chikako Abe,Takashi R Endo,Goro Ishikawa,Katsuyuki Hayakawa,Hana Šimková,Yumiko Hanawa,Satoko Kaneko,Tsuyoshi Tanaka,Hirokazu Handa,Shota Watanabe,Toshiki Nakamura,Yasunari Ogihara,Shuhei Nasuda,Shigeo Takumi,Kazuhiro Sato,Satoshi Katagiri,Wataru Karasawa,Kanako Kurita,Jaroslav Doležel,Takashi Matsumoto,Toyotaka Sakaguchi,Masao Hamada,Jan Šafář,Jianzhong Wu,Ryoko Ohno,Julio C M Iehisa,Yūichi Katayose ,Mika Sillanpää ,Hideyuki Fujisawa ,Yukinori Mukai ,Hajime Kanamori

doi:10.1186/s12864-015-1803-y

Abstract

BackgroundA 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.ResultsWe 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.ConclusionsWe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1803-y) contains supplementary material, which is available to authorized users.

Highlights

A complete genome sequence is an essential tool for the genetic improvement of wheat
A stepwise method was used to improve the quality of the contigs in the assembly, which was initially defined during the physical map construction of chromosome 3B [20] and modified for the Whole Genome Profiling (WGP) fingerprints [32]
Using the 6B-specific parameters at final cut-off values of 1e−12 and 1e−11, which were determined based on the balance among the number of contigs, the number of Q-contigs and the coverage of the physical map, we constructed the first physical maps of 6BS and 6BL with 1069 and 514 contigs, respectively (Additional file 3 and Fig. 1; the URGI site of the wheat physical map viewer, https://urgi.versailles.inra.fr/ gb2/gbrowse/wheat_phys_pub/)

Summary

Introduction

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. Common wheat (Triticum aestivum L.) is an allohexaploid species with three distinct genomes, A, B and D, which have been defined by genome analysis [1]. Wheat has been widely used in cytogenetics because of the high visibility of its chromosomes, complex features, such as its large size, high repeat content and polyploidy, have hampered molecular approaches to date, whole-genome sequencing. Recent technological advances have paved the way for genomic approaches that work for even complex genomes, such as wheat. Wholegenome sequences of the common wheat cultivar ‘Chinese Spring’ (CS), wild diploid wheat Triticum urartu (A genome progenitor of common wheat) and wild diploid goat grass Aegilops tauschii (D genome progenitor of common wheat) were analyzed using next-generation sequencing (NGS) technology [11,12,13]

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Results

Conclusion