Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content

Authors

  • Pilar Hernandez,

    1. Instituto de Agricultura Sostenible (IAS-CSIC), Alameda del Obispo s/n, 14080 Córdoba, Spain
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  • Mihaela Martis,

    1. Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
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  • Gabriel Dorado,

    1. Departamento de Bioquímica y Biología Molecular, Campus Rabanales C6-1-E17, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, 14071 Córdoba, Spain
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  • Matthias Pfeifer,

    1. Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
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  • Sergio Gálvez,

    1. Departamento de Lenguajes y Ciencias de la Computación, ETSI Informática, Campus de Teatinos, Universidad de Málaga, Bulevar Louis Pasteur 35, 29071 Málaga, Spain
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  • Sebastian Schaaf,

    1. Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
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  • Nicolás Jouve,

    1. Departamento de Biología Celular y Genética, Universidad de Alcalá, Campus Universitario, 28871 Alcalá de Henares, Madrid, Spain
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  • Hana Šimková,

    1. Centre of the Haná Region for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, 77200 Olomouc, Czech Republic
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  • Miroslav Valárik,

    1. Centre of the Haná Region for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, 77200 Olomouc, Czech Republic
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  • Jaroslav Doležel,

    1. Centre of the Haná Region for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, 77200 Olomouc, Czech Republic
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  • Klaus F.X. Mayer

    Corresponding author
    1. Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
      (fax +49 89 3187 2225; e-mail k.mayer@helmholtz-muenchen.de).
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(fax +49 89 3187 2225; e-mail k.mayer@helmholtz-muenchen.de).

Summary

Wheat is the third most important crop for human nutrition in the world. The availability of high-resolution genetic and physical maps and ultimately a complete genome sequence holds great promise for breeding improved varieties to cope with increasing food demand under the conditions of changing global climate. However, the large size of the bread wheat (Triticum aestivum) genome (approximately 17 Gb/1C) and the triplication of genic sequence resulting from its hexaploid status have impeded genome sequencing of this important crop species. Here we describe the use of mitotic chromosome flow sorting to separately purify and then shotgun-sequence a pair of telocentric chromosomes that together form chromosome 4A (856 Mb/1C) of wheat. The isolation of this much reduced template and the consequent avoidance of the problem of sequence duplication, in conjunction with synteny-based comparisons with other grass genomes, have facilitated construction of an ordered gene map of chromosome 4A, embracing ≥85% of its total gene content, and have enabled precise localization of the various translocation and inversion breakpoints on chromosome 4A that differentiate it from its progenitor chromosome in the A genome diploid donor. The gene map of chromosome 4A, together with the emerging sequences of homoeologous wheat chromosome groups 4, 5 and 7, represent unique resources that will allow us to obtain new insights into the evolutionary dynamics between homoeologous chromosomes and syntenic chromosomal regions.

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