NDLI: Whole-genome profiling and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A

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Whole-genome profiling and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A

Content Provider	PubMed Central
Author	Naser, Poursarebani Nussbaumer, Thomas Šimková, Hana Šafář, Jan Witsenboer, Hanneke Van, Oeveren Jan Doležel, Jaroslav Mayer, Klaus Fx Stein, Nils Schnurbusch, Thorsten
Copyright Year	2014
Abstract	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 using 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 with those formed by fpc. The ltc assemblies contained 1217 contigs for the short arm and 1113 contigs for the 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 the ‘decoration’ of the respective physical map with 3359 anchored genes. Thus, this robust and genetically anchored physical map will serve as a framework for the 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.
Related Links	http://dx.doi.org/10.1111/tpj.12550
Ending Page	347
Page Count	14
Starting Page	334
File Format	PDF
ISSN	09607412
e-ISSN	1365313X
Journal	The Plant Journal
Issue Number	2
Volume Number	79
Language	English
Publisher	BlackWell Publishing Ltd
Publisher Date	2014-07-01
Access Restriction	Open
Rights Holder	BlackWell Publishing Ltd
Subject Keyword	Plant Science Genetics Cell Biology Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Cell Biology Genetics Plant Science

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