PuSH - Publication Server of Helmholtz Zentrum München: Whole Genome Profiling (WGP™) and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A.

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Poursarebani, N.* ; Nussbaumer, T. ; Šimková, H.* ; Safar, J.* ; Witsenboer, H.* ; van Oeveren, J.* ; International Wheat Genome Sequencing Consortium (Schnurbusch, T.) ; Dolezel, J.* ; Mayer, K.F.X. ; Stein, N.*

Whole Genome Profiling (WGP™) and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A.

Plant J. 79, 334-347 (2014)

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Bread wheat (Triticum aestivum L.) is the most important staple food crop for 35% of the world's population. International efforts are underway to facilitate an increase in wheat production of which the International Wheat Genome Sequencing Consortium (IWGSC) plays an important role. As part of this effort, we have developed a sequence-based physical map of wheat chromosome 6A utilizing Whole Genome Profiling (WGP(™) ). The Bacterial Artificial Chromosome (BAC) contig assembly tools FingerPrinted Contig (FPC) and Linear Topological Contig (LTC) were used and their contig assemblies were compared. A detailed investigation of the contigs structure revealed that LTC created a highly robust assembly compared to those formed by FPC. The LTC assemblies contained 1217 contigs for the short and 1113 contigs for long arm, with an L50 of 1 Mb. To facilitate in silico anchoring, WGP tags underlying BAC contigs were extended by wheat and wheat progenitor genome sequence information. Sequence data were used for in silico anchoring against genetic markers with known sequences, of which almost 79% of the physical map could be anchored. Moreover, the assigned sequence information led to "decoration" of the respective physical map with 3359 anchored genes. Thus, this robust and genetically anchored physical map will serve as a framework for sequencing of wheat chromosome 6A and is of immediate use for map-based isolation of agronomically important genes/Quantitative Trait Loci located on this chromosome.

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Publication type Article: Journal article

Document type Scientific Article

Corresponding Author

Keywords Bac Contigs ; Bread Wheat Chromosome 6a ; Fingerprinted Contigs (fpc) ; Linear Topological Contigs (ltc) ; Whole Genome Profiling (wgp™) ; Anchored Physical Map; Fusarium Head Blight; Triticum-aestivum; Provides Insights; Cereal Genomes; Climate-change; Draft Genome; Resistance; Evolution; Barley; Recombination

ISSN (print) / ISBN 0960-7412

e-ISSN 1365-313X

Journal Plant Journal, The

Quellenangaben Volume: 79, Issue: 2, Pages: 334-347

Publisher Wiley

Publishing Place Hoboken

Non-patent literature Publications

Reviewing status Peer reviewed

Institute(s) Research Unit Plant Genome and Systems Biology (PGSB)