Analysis of the bread wheat genome using whole-genome shotgun sequencing

Rachel Brenchley, Manuel Spannagl, Matthias Pfeifer, Gary L. A. Barker, Rosalinda D’Amore, Alexandra M. Allen, Neil McKenzie, Melissa Kramer, Arnaud Kerhornou, Dan Bolser, Suzanne Kay, Darren Waite, Martin Trick, Ian Bancroft, Yong Gu, Naxin Huo, Ming-Cheng Luo, Sunish Sehgal, Bikram Gill, Sharyar Kianian, Olin Anderson, Paul Kersey, Jan Dvorak, W. Richard McCombie, Anthony Hall (), Klaus F. X. Mayer (), Keith J. Edwards (), Michael W. Bevan () and Neil Hall ()
Additional contact information
Rachel Brenchley: Centre for Genome Research, University of Liverpool, Liverpool L69 7ZB, UK
Manuel Spannagl: MIPS/IBIS, Helmholtz- Zentrum München, 85764 Neuherberg, Germany
Matthias Pfeifer: MIPS/IBIS, Helmholtz- Zentrum München, 85764 Neuherberg, Germany
Gary L. A. Barker: School of Biological Sciences, University of Bristol, Bristol BS8 1UG, UK
Rosalinda D’Amore: Centre for Genome Research, University of Liverpool, Liverpool L69 7ZB, UK
Alexandra M. Allen: School of Biological Sciences, University of Bristol, Bristol BS8 1UG, UK
Neil McKenzie: John Innes Centre, Norwich NR4 7UH, UK
Melissa Kramer: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
Arnaud Kerhornou: European Bioinformatics Institute, Hinxton CB10 1SD, UK
Dan Bolser: European Bioinformatics Institute, Hinxton CB10 1SD, UK
Suzanne Kay: Centre for Genome Research, University of Liverpool, Liverpool L69 7ZB, UK
Darren Waite: John Innes Centre, Norwich NR4 7UH, UK
Martin Trick: John Innes Centre, Norwich NR4 7UH, UK
Ian Bancroft: John Innes Centre, Norwich NR4 7UH, UK
Yong Gu: USDA Western Regional Laboratory
Naxin Huo: USDA Western Regional Laboratory
Ming-Cheng Luo: University of California
Sunish Sehgal: Kansas State University
Bikram Gill: Kansas State University
Sharyar Kianian: North Dakota State University
Olin Anderson: USDA Western Regional Laboratory
Paul Kersey: European Bioinformatics Institute, Hinxton CB10 1SD, UK
Jan Dvorak: University of California
W. Richard McCombie: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
Anthony Hall: Centre for Genome Research, University of Liverpool, Liverpool L69 7ZB, UK
Klaus F. X. Mayer: MIPS/IBIS, Helmholtz- Zentrum München, 85764 Neuherberg, Germany
Keith J. Edwards: School of Biological Sciences, University of Bristol, Bristol BS8 1UG, UK
Michael W. Bevan: John Innes Centre, Norwich NR4 7UH, UK
Neil Hall: Centre for Genome Research, University of Liverpool, Liverpool L69 7ZB, UK

Nature, 2012, vol. 491, issue 7426, 705-710

Abstract: Abstract Bread wheat (Triticum aestivum) is a globally important crop, accounting for 20 per cent of the calories consumed by humans. Major efforts are underway worldwide to increase wheat production by extending genetic diversity and analysing key traits, and genomic resources can accelerate progress. But so far the very large size and polyploid complexity of the bread wheat genome have been substantial barriers to genome analysis. Here we report the sequencing of its large, 17-gigabase-pair, hexaploid genome using 454 pyrosequencing, and comparison of this with the sequences of diploid ancestral and progenitor genomes. We identified between 94,000 and 96,000 genes, and assigned two-thirds to the three component genomes (A, B and D) of hexaploid wheat. High-resolution synteny maps identified many small disruptions to conserved gene order. We show that the hexaploid genome is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded gene families that could be associated with crop productivity. Our analyses, coupled with the identification of extensive genetic variation, provide a resource for accelerating gene discovery and improving this major crop.

Date: 2012
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DOI: 10.1038/nature11650

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