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Tracing the ancestry of modern bread wheats

Nature Genetics volume 51, pages 905–911 (2019)Cite this article

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Abstract

For more than 10,000 years, the selection of plant and animal traits that are better tailored for human use has shaped the development of civilizations. During this period, bread wheat (Triticum aestivum) emerged as one of the world’s most important crops. We use exome sequencing of a worldwide panel of almost 500 genotypes selected from across the geographical range of the wheat species complex to explore how 10,000 years of hybridization, selection, adaptation and plant breeding has shaped the genetic makeup of modern bread wheats. We observe considerable genetic variation at the genic, chromosomal and subgenomic levels, and use this information to decipher the likely origins of modern day wheats, the consequences of range expansion and the allelic variants selected since its domestication. Our data support a reconciled model of wheat evolution and provide novel avenues for future breeding improvement.

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Fig. 1: Wheat genome diversity map.
Fig. 2: Geographical components of the panel structure.
Fig. 3: Temporal evolution of wheat diversity.
Fig. 4: Model of reticulated evolution.

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Data Availability

All data analyzed and generated during this study are included in this published article and its supplementary information files (6 tables and 13 figures) and are available online at https://urgi.versailles.inra.fr/download/iwgsc/IWGSC_RefSeq_Annotations/v1.0/iwgsc_refseqv1.0_Whealbi_GWAS.zip (the catalog of imputed and non-imputed variants as a vcf file and passport information for the 487 genotypes as an .xls file). The Whealbi SNP data are open access and can be viewed in the IWGSC reference genome browser54 at https://urgi.versailles.inra.fr/jbrowseiwgsc/gmod_jbrowse/?data=myData%2FIWGSC_RefSeq_v1.0. The sequence data are available at NCBI under the accession number PRJNA524104.

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Acknowledgements

The authors wish to thank the INRA Biological Resources Center on small grain cereals (https://www6.ara.inra.fr/umr1095_eng/Teams/Research/Biological-Resources-Centre) for providing seeds and passport data, and for establishing a wheat biorepository. The authors thank the Federal ex situ Genbank Gatersleben, Germany (IPK), the N. I. Vavilov All-Russian Research Institute of Plant Industry, Russia (VIR), Centre for Genetic Resources, WUR, Netherlands (CGN), Kyoto University, National Bioresource Project, Japan (NBRP), the Australian Winter Cereal Collection Tamworth, Australia (AWCC), the National Plant Germplasm System, USA (USDA-ARS), the International Center for Agriculture Research in the Dry Areas (ICARDA), the Max Planck Institute for Plant Breeding Research Cologne, Germany (MPIPZ), Germplasm Resource Unit at the John Innes Centre UK (JIC) and the Wheat and Barley Legacy for Breeding Improvement (WHEALBI) consortium for providing plant material and passport data. The research leading to these results has received funding from the European Community’s Seventh Framework Programme (FP7/ 2007–2013) under grant agreement FP7- 613556, Whealbi project (http://www.whealbi.eu/project/). R.W. and J.R. also acknowledge support from the Scottish Government Research Program and R.W. from the University of Dundee. H.O. acknowledges support from Çukurova University (FUA-2016–6033). K.F.X.M. acknowledges support from the German Federal Ministry of Food and Agriculture (2819103915) and the DFG (SFB924). T.L. acknowledges supports from the Agence Nationale pour la Recherche (BirdIslandGenomic project 14-CE02-0002), European Research Council (TREEPEACE project, grant agreement 339728) and the bioinformatics platform from Toulouse Midi-Pyrénées (Bioinfo Genotoul) for providing computing and storage resources. J.S. acknowledges support from the Région Auvergne-Rhône-Alpes and FEDER Fonds Européens de Développement Régional (23000816 SRESRI 2015), the CPER contrat de plan État-région (23000892 SYMBIOSE 2016) and AgreenSkills fellowship (applicant ID 4146).

Author information

Author notes

  1. These authors contributed equally: Caroline Pont, Thibault Leroy, Michael Seidel, Alessandro Tondelli, Wandrille Duchemin, David Armisen, Daniel Lang, Daniela Bustos-Korts.

  2. These authors jointly supervised this work: Luigi Cattivelli, Georg Haberer, Gilles Charmet, Jérôme Salse.

  3. A list of members and affiliations appears in the Supplementary Note.

Authors and Affiliations

  1. INRA-Université Clermont Auvergne, Clermont-Ferrand, France

    Caroline Pont, Wandrille Duchemin, David Armisen, Nadia Goué, François Balfourier, Gilles Charmet & Jérôme Salse

  2. INRA-Université de Bordeaux, Cestas, France

    Thibault Leroy

  3. ISEM, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, Montpellier, France

    Thibault Leroy

  4. PGSB, Helmholtz Center Munich, Neuherberg, Germany

    Michael Seidel, Daniel Lang, Manuel Spannagl, Klaus F. X. Mayer & Georg Haberer

  5. Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy

    Alessandro Tondelli & Luigi Cattivelli

  6. Wageningen University & Research, Biometris, Applied Statistics, Wageningen, the Netherlands

    Daniela Bustos-Korts & Fred van Eeuwijk

  7. Plateforme Auvergne Bioinformatique, Mésocentre, Université Clermont Auvergne, Aubière, France

    Nadia Goué

  8. Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary

    Márta Molnár-Láng

  9. KWS UK Ltd, Thriplow, UK

    Jacob Lage

  10. Global Crop Diversity Trust, Bonn, Germany

    Benjamin Kilian

  11. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany

    Benjamin Kilian & Nils Stein

  12. University of Çukurova, Faculty of Agriculture, Department of Field Crops, Adana, Turkey

    Hakan Özkan

  13. Earlham Institute, Norwich Research Park, Norwich, UK

    Darren Waite

  14. NIAB, Huntingdon Road, Cambridge, UK

    Sarah Dyer

  15. URGI, INRA, Université Paris-Saclay, Versailles, France

    Thomas Letellier & Michael Alaux

  16. The James Hutton Institute, Invergowrie, Dundee, UK

    Joanne Russell & Robbie Waugh

  17. Department of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland

    Beat Keller

  18. School of Life Sciences, Technical University Munich, Weihenstephan, Germany

    Klaus F. X. Mayer

  19. The University of Dundee, Division of Plant Sciences, School of Life Sciences, Dundee, UK

    Robbie Waugh

  20. School of Agriculture, Food and Wine, University of Adelaide, Adelaide, South Australia, Australia

    Robbie Waugh

Authors
  1. Caroline Pont
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  2. Thibault Leroy
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  3. Michael Seidel
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  4. Alessandro Tondelli
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  5. Wandrille Duchemin
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  6. David Armisen
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  7. Daniel Lang
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  8. Daniela Bustos-Korts
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  9. Nadia Goué
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  12. Jacob Lage
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  15. Darren Waite
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  16. Sarah Dyer
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  17. Thomas Letellier
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  18. Michael Alaux
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  19. Joanne Russell
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  20. Beat Keller
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  21. Fred van Eeuwijk
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  22. Manuel Spannagl
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  23. Klaus F. X. Mayer
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  24. Robbie Waugh
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  25. Nils Stein
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  26. Luigi Cattivelli
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  27. Georg Haberer
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  28. Gilles Charmet
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  29. Jérôme Salse
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Consortia

Wheat and Barley Legacy for Breeding Improvement (WHEALBI) consortium

Contributions

F.B., B.K. and N.S. carried out panel constitution and distribution. S.D., J.R. and R.W. carried out exome sequencing. D.W., M.Se., M.Sp. and G.H. carried out variant (SNP and indel) calling. C.P., D.A., N.G., M.Se., D.L. and W.D. carried out variant analysis. D.L., W.D., M.Se., C.P., N.G. and G.H. carried out phylogenetic analyis. T.L., C.P. and D.A. carried out diversity analysis and selection footprints. A.T., D.B.K., C.P., H.O., M.M., F.E. and L.C. carried out field experiments and GWAS. B.K., J.R., K.F.X.M., R.W., N.S., L.C., G.H., G.C. and J.S. conceived and supervised the study and prepared the article.

Corresponding author

Correspondence to Jérôme Salse.

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Supplementary Information

Supplementary Tables 1–7 and Supplementary Figures 1–13

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Pont, C., Leroy, T., Seidel, M. et al. Tracing the ancestry of modern bread wheats. Nat Genet 51, 905–911 (2019). https://doi.org/10.1038/s41588-019-0393-z

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