The Wheat Black Jack: Advances Towards Sequencing the 21 Chromosomes of Bread Wheat

  • Frédéric Choulet
  • Mario Caccamo
  • Jonathan Wright
  • Michael Alaux
  • Hana Šimková
  • Jan Šafář
  • Philippe Leroy
  • Jaroslav Doležel
  • Jane Rogers
  • Kellye Eversole
  • Catherine Feuillet


Despite its socio-economic importance and the overall recognition that a reference genome sequence has great value for crop improvement, sequencing the wheat genome has long been considered “impossible” because of the sequencing cost and bioinformatic challenges associated with the assembly of the mostly repetitive 17 Gb hexaploid genome. In the past 5 years, however, new platforms and technologies have emerged that enabled the launching of an international effort to tackle the bread wheat genome sequence using a chromosome-by-chromosome approach. In this chapter, we review the features of the wheat genome as well as the tools and technologies that can be used to sequence, assemble, and annotate a large, complex, polyploid genome. We describe the strategies and current status of the efforts towards achieving a reference sequence for the 21 chromosomes of bread wheat. Finally, we present the databases that were established to support the integration of the sequence information with other genetic and biological information.


Wheat Polyploid Chromosome Flow sorting Physical map Genome sequence Next generation sequencing Assembly Annotation Transposable elements Database Data integration 



The authors want to thank Hadi Quesneville, Daphné Verdelet, Kirsley Chennen for their feedback on wheat databases. H.Š., J.Š. and J.D. are supported by the Ministry of Education, Youth and Sports of the Czech Republic, the European Regional Development Fund (Operational Programme Research and Development for Innovations No. ED0007/01/01) and by the Czech Science Foundation (award no. P501/10/1740). F. C., P. L. and C. F. are supported by the European Community’s Seventh Framework Programme TriticeaeGenome (grant agreement n°FP7–212019), the Agence Nationale de la Recherche grant ANR(09-GENM-025), FranceAgriMer (201006-015-104) and the competitiveness cluster “Céréales Vallée” (


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Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Frédéric Choulet
    • 1
    • 2
  • Mario Caccamo
    • 3
  • Jonathan Wright
    • 3
  • Michael Alaux
    • 4
  • Hana Šimková
    • 5
  • Jan Šafář
    • 5
  • Philippe Leroy
    • 1
    • 2
  • Jaroslav Doležel
    • 5
  • Jane Rogers
    • 3
  • Kellye Eversole
    • 6
  • Catherine Feuillet
    • 1
    • 2
  1. 1.Genetics, Diversity and Ecophysiology of CerealsINRA Joint Research Unit 1095 GeneticsClermont-FerrandFrance
  2. 2.Genetics, Diversity and Ecophysiology of CerealsUniversity Blaise Pascal Joint Research Unit 1095 GeneticsClermont-FerrandFrance
  3. 3.The Genome Analysis Centre, Norwich Research ParkColneyUK
  4. 4.INRA Centre de Versailles-GrignonUnité de Recherche en Génomique-InfoVersaillesFrance
  5. 5.Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental BotanyOlomoucCzech Republic
  6. 6.International Wheat Genome Sequencing ConsortiumEversole AssociatesBethesdaUSA

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