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A saturated SNP linkage map for the orange wheat blossom midge resistance gene Sm1

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SNP markers were developed for the OWBM resistance gene Sm1 that will be useful for MAS. The wheat Sm1 region is collinear with an inverted syntenic interval in B. distachyon.

Abstract

Orange wheat blossom midge (OWBM, Sitodiplosis mosellana Géhin) is an important insect pest of wheat (Triticum aestivum) in many growing regions. Sm1 is the only described OWBM resistance gene and is the foundation of managing OWBM through host genetics. Sm1 was previously mapped to wheat chromosome arm 2BS relative to simple sequence repeat (SSR) markers and the dominant, sequence characterized amplified region (SCAR) marker WM1. The objectives of this research were to saturate the Sm1 region with markers, develop improved markers for marker-assisted selection (MAS), and examine the synteny between wheat, Brachypodium distachyon, and rice (Oryza sativa) in the Sm1 region. The present study mapped Sm1 in four populations relative to single nucleotide polymorphisms (SNPs), SSRs, Diversity Array Technology (DArT) markers, single strand conformation polymorphisms (SSCPs), and the SCAR WM1. Numerous high quality SNP assays were designed that mapped near Sm1. BLAST delineated the syntenic intervals in B. distachyon and rice using gene-based SNPs as query sequences. The Sm1 region in wheat was inverted relative to B. distachyon and rice, which suggests a chromosomal rearrangement within the Triticeae lineage. Seven SNPs were tested on a collection of wheat lines known to carry Sm1 and not to carry Sm1. Sm1-flanking SNPs were identified that were useful for predicting the presence or absence of Sm1 based upon haplotype. These SNPs will be a major improvement for MAS of Sm1 in wheat breeding programs.

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Abbreviations

Aug/HWA:

Augusta/Hard White Alpha

DArT:

Diversity Arrays Technology

DH:

Doubled haploid

Herm/Skal:

Hermann/Skalmeje

KASP:

Kompetitive Allele-Specific PCR

MAS:

Marker-assisted selection

OWBM:

Orange wheat blossom midge

Rob/Pet:

Robigus/Petrus

Rob/Sham:

Robigus/Shamrock

SCAR:

Sequence characterized amplified region

SSCP:

Single strand conformation polymorphism

SSR:

Simple sequence repeat

SNP:

Single nucleotide polymorphism

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Acknowledgments

The authors thank technical staff from the participating labs for their contributions to this research. The authors thank Mike Taylor, Limagrain GmbH, for providing seeds of the DH population Hermann x Skalmeje and Saatzucht Streng-Engelen GmbH & Co. KG, Saatzucht Josef Breun GmbH & Co. KG, Syngenta Seeds GmbH, and Limagrain GmbH for conducting field trials as well as the Gemeinschaft zur Förderung der privaten deutschen Pflanzenzüchtung (GFP) for coordination. MK, FY, CP, AS, PF, IW, JT, and CM were funded by AAFC Agriflex project 2521, the Canadian Wheat Alliance, and as part of CTAG and CTAG2, Genome Prairie projects funded by Genome Canada, Saskatchewan Ministry of Agriculture, and Western Grain Research Foundation. CL, JS, PF, SB, DH, PS, LD, OR, and CU were funded by the French FSOV (Fonds de Soutien à l’Obtention Végétale) under grants FSOV2010L and FSOV2014C. SH, ES, IK, DP, MK, JF, WF, and FO were funded by the German Federal Ministry of Food and Agriculture (BMEL, FKZ 2814302507). Based upon research contributions from the National Research Council of Canada, this publication was given the contribution number NRCC #56179.

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Authors and Affiliations

  1. Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada

    Mulualem T. Kassa, Frank M. You, Ian L. Wise, Julian B. Thomas & Curt A. McCartney

  2. National Research Council, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada

    Mulualem T. Kassa, Andrew G. Sharpe & Pierre R. Fobert

  3. Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI), Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany

    Sabrina Haas, Edgar Schliephake, Ilona Krämer, Dragan Perovic & Frank Ordon

  4. John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK

    Clare Lewis, James Simmonds & Cristobal Uauy

  5. Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada

    Curtis J. Pozniak

  6. Deutsche Saatveredelung AG (DSV), Lippstadt, Nordrhein-Westfalen, Germany

    Michael Koch

  7. Limagrain UK Ltd, Rothwell, UK

    Paul Fenwick & Simon Berry

  8. Arvalis, Institut du Végétal. 6 chemin de la Côte Vieille, 31450, Baziege, France

    Delphine Hourcade

  9. Syngenta France, Ferme de Moyencourt, 78910, Orgerus, France

    Patrice Senellart

  10. RAGT 2n, Rout e d’Epincy, 28150, Louville la Chenard, France

    Laure Duchalais

  11. Bioplante Florimond Desprez, BP41, 59242, Cappelle en Pévèle, France

    Olivier Robert

  12. Saaten-Union Biotec GmbH, Leopoldshoehe, Germany

    Jutta Förster

  13. Department of Plant Breeding, Research Center for BioSystems, Land Use and Nutrition (IFZ), Giessen University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany

    Wolfgang Friedt

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  1. Mulualem T. Kassa
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  2. Sabrina Haas
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  3. Edgar Schliephake
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  4. Clare Lewis
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  5. Frank M. You
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  6. Curtis J. Pozniak
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  7. Ilona Krämer
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  8. Dragan Perovic
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  9. Andrew G. Sharpe
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  10. Pierre R. Fobert
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  11. Michael Koch
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  12. Ian L. Wise
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  13. Paul Fenwick
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  14. Simon Berry
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  15. James Simmonds
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  16. Delphine Hourcade
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  17. Patrice Senellart
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  18. Laure Duchalais
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  19. Olivier Robert
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  20. Jutta Förster
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  21. Julian B. Thomas
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  22. Wolfgang Friedt
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  23. Frank Ordon
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  24. Cristobal Uauy
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  25. Curt A. McCartney
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Correspondence to Curt A. McCartney.

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Communicated by A. Zhang.

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Kassa, M.T., Haas, S., Schliephake, E. et al. A saturated SNP linkage map for the orange wheat blossom midge resistance gene Sm1 . Theor Appl Genet 129, 1507–1517 (2016). https://doi.org/10.1007/s00122-016-2720-4

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