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The Plant Genome Abstract - Original Research

Exploiting the Repetitive Fraction of the Wheat Genome for High-Throughput Single-Nucleotide Polymorphism Discovery and Genotyping


This article in TPG

  1. Vol. 9 No. 1
    unlockOPEN ACCESS
    Received: Sept 01, 2015
    Accepted: Oct 20, 2015
    Published: February 5, 2016

    * Corresponding author(s): etienne.paux@clermont.inra.fr
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  1. Nelly Cubizollesabl,
  2. Elodie Reyabm,
  3. Frédéric Chouletab,
  4. Hélène Rimbertab,
  5. Christel Laugierabl,
  6. François Balfouriera,
  7. Jacques Bordesab,
  8. Charles Poncetab,
  9. Peter Jackc,
  10. Chris Jamesc,
  11. Jan Gielend,
  12. Odile Argillierd,
  13. Jean-Pierre Jaubertiee,
  14. Jérôme Auzanneaue,
  15. Antje Rohdef,
  16. Pieter B.F. Ouwerkerkf,
  17. Viktor Korzung,
  18. Sonja Kollersg,
  19. Laurent Guerreirohn,
  20. Delphine Hourcadei,
  21. Olivier Robertj,
  22. Pierre Devauxj,
  23. Anna-Maria Mastrangelok,
  24. Catherine Feuilletabo,
  25. Pierre Sourdilleab and
  26. Etienne Paux *ab
  1. a Institut National de la Recherche Agronomique , Joint Research Unit 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 Chemin de Beaulieu, F-63039 Clermont-Ferrand, France
    b Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 Chemin de Beaulieu, F-63177 Aubière Cedex, France
    l current address: Biogemma, Route d’Ennezat, F-63720 Chappes, France
    m current address: Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelu° 31, CZ-78371 Olomouc, Czech Republic
    c RAGT Seeds Ltd., Grange Rd., Ickleton, Essex, CB10 1TA, UK
    d Syngenta France, 12 Chemin de l’Hobit, F-31790 Saint Sauveur, France
    e Agri-Obtentions, Chemin de la Petite Minière, F-78280 Guyancourt, France
    f B. CropScience NV, Innovation Center Technologiepark 38, B-9052 Ghent, Belgium
    g KWS LOCHOW GMBH, Ferdinand-von-Lochow-Straße 5, D-29303 Bergen, Germany
    h ARVALIS – Institut du Végétal, Station Expérimentale, F-91720 Boigneville, France
    n current address: RAGT 2n, Rue Emile Singla, BP 3331, F-12033 Rodez, France
    i ARVALIS – Institut du Végétal, 6 Chemin de la Côté Vieille, F-31450 Baziège, France
    j Florimond Desprez, BP 41, F-59242 Cappelle-en-Pévèle, France
    k Council for Agricultural Research and Economics – Cereal Research Centre, S.S. 673 km 25.200, I-71122 Foggia, Italy
    o current address: Bayer CropScience, 3500 Paramount Pkwy., Morrisville, NC 27560, USA


Transposable elements (TEs) account for more than 80% of the wheat genome. Although they represent a major obstacle for genomic studies, TEs are also a source of polymorphism and consequently of molecular markers such as insertion site-based polymorphism (ISBP) markers. Insertion site-based polymorphisms have been found to be a great source of genome-specific single-nucleotide polymorphism (SNPs) in the hexaploid wheat (Triticum aestivum L.) genome. Here, we report on the development of a high-throughput SNP discovery approach based on sequence capture of ISBP markers. By applying this approach to the reference sequence of chromosome 3B from hexaploid wheat, we designed 39,077 SNPs that are evenly distributed along the chromosome. We demonstrate that these SNPs can be efficiently scored with the KASPar (Kompetitive allele-specific polymerase chain reaction) genotyping technology. Finally, through genetic diversity and genome-wide association studies, we also demonstrate that ISBP-derived SNPs can be used in marker-assisted breeding programs.

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