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 KianianOlin Anderson, Paul Kersey, Jan Dvorak, W. Richard McCombie, Anthony Hall, Klaus F.X. Mayer, Keith J. Edwards, Michael W. Bevan, Neil Hall

Research output: Contribution to journalArticle

702 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)705-710
Number of pages6
JournalNature
Volume491
Issue number7426
DOIs
StatePublished - Nov 29 2012

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    Brenchley, R., Spannagl, M., Pfeifer, M., Barker, G. L. A., D'Amore, R., Allen, A. M., McKenzie, N., Kramer, M., Kerhornou, A., Bolser, D., Kay, S., Waite, D., Trick, M., Bancroft, I., Gu, Y., Huo, N., Luo, M. C., Sehgal, S., Gill, B., ... Hall, N. (2012). Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature, 491(7426), 705-710. https://doi.org/10.1038/nature11650