• Open Access

Single nucleotide polymorphism discovery from wheat next-generation sequence data

Authors

  • Kaitao Lai,

    1. School of Agriculture and Food Science, University of Queensland, Brisbane, QLD, Australia
    2. Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
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  • Chris Duran,

    1. Biomatters Ltd., Auckland, New Zealand
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  • Paul J. Berkman,

    1. School of Agriculture and Food Science, University of Queensland, Brisbane, QLD, Australia
    2. Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
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  • Michał T. Lorenc,

    1. School of Agriculture and Food Science, University of Queensland, Brisbane, QLD, Australia
    2. Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
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  • Jiri Stiller,

    1. CSIRO Plant Industry, Brisbane, Qld, Australia
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  • Sahana Manoli,

    1. School of Agriculture and Food Science, University of Queensland, Brisbane, QLD, Australia
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  • Matthew J. Hayden,

    1. Department of Primary Industries, Victorian AgriBiosciences Centre, Bundoora, Vic., Australia
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  • Kerrie L. Forrest,

    1. Department of Primary Industries, Victorian AgriBiosciences Centre, Bundoora, Vic., Australia
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  • Delphine Fleury,

    1. Australian Centre for Plant Functional Genomics, University of Adelaide, Urrbrae, SA, Australia
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  • Ute Baumann,

    1. Australian Centre for Plant Functional Genomics, University of Adelaide, Urrbrae, SA, Australia
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  • Manuel Zander,

    1. School of Agriculture and Food Science, University of Queensland, Brisbane, QLD, Australia
    2. Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
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  • Annaliese S. Mason,

    1. School of Agriculture and Food Science, University of Queensland, Brisbane, QLD, Australia
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  • Jacqueline Batley,

    1. School of Agriculture and Food Science, University of Queensland, Brisbane, QLD, Australia
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  • David Edwards

    Corresponding author
    1. School of Agriculture and Food Science, University of Queensland, Brisbane, QLD, Australia
    2. Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
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(Tel +61 (0) 7 3346 7084; fax +61 (0) 7 3365 1176; email Dave.Edwards@uq.edu.au)

Summary

Single nucleotide polymorphisms (SNPs) are the most abundant type of molecular genetic marker and can be used for producing high-resolution genetic maps, marker-trait association studies and marker-assisted breeding. Large polyploid genomes such as wheat present a challenge for SNP discovery because of the potential presence of multiple homoeologs for each gene. AutoSNPdb has been successfully applied to identify SNPs from Sanger sequence data for several species, including barley, rice and Brassica, but the volume of data required to accurately call SNPs in the complex genome of wheat has prevented its application to this important crop. DNA sequencing technology has been revolutionized by the introduction of next-generation sequencing, and it is now possible to generate several million sequence reads in a timely and cost-effective manner. We have produced wheat transcriptome sequence data using 454 sequencing technology and applied this for SNP discovery using a modified autoSNPdb method, which integrates SNP and gene annotation information with a graphical viewer. A total of 4 694 141 sequence reads from three bread wheat varieties were assembled to identify a total of 38 928 candidate SNPs. Each SNP is within an assembly complete with annotation, enabling the selection of polymorphism within genes of interest.

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