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Chromosomal genomics facilitates fine mapping of a Russian wheat aphid resistance gene

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Abstract

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Making use of wheat chromosomal resources, we developed 11 gene-associated markers for the region of interest, which allowed reducing gene interval and spanning it by four BAC clones.

Abstract

Positional gene cloning and targeted marker development in bread wheat are hampered by high complexity and polyploidy of its nuclear genome. Aiming to clone a Russian wheat aphid resistance gene Dn2401 located on wheat chromosome arm 7DS, we have developed a strategy overcoming problems due to polyploidy and enabling efficient development of gene-associated markers from the region of interest. We employed information gathered by GenomeZipper, a synteny-based tool combining sequence data of rice, Brachypodium, sorghum and barley, and took advantage of a high-density linkage map of Aegilops tauschii. To ensure genome- and locus-specificity of markers, we made use of survey sequence assemblies of isolated wheat chromosomes 7A, 7B and 7D. Despite the low level of polymorphism of the wheat D subgenome, our approach allowed us to add in an efficient and cost-effective manner 11 new gene-associated markers in the Dn2401 region and narrow down the target interval to 0.83 cM. Screening 7DS-specific BAC library with the flanking markers revealed a contig of four BAC clones that span the Dn2401 region in wheat cultivar ‘Chinese Spring’. With the availability of sequence assemblies and GenomeZippers for each of the wheat chromosome arms, the proposed strategy can be applied for focused marker development in any region of the wheat genome.

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Acknowledgments

We thank Prof. B.S. Gill and Prof. Adam Lukaszewski for providing seeds of the wheat ditelosomic lines. We are grateful to Hong Wang and Jeff Rudolph for RWA screening of the mapping population and Jarmila Číhalíková, Romana Šperková, Zdeňka Dubská and Jana Dostálová for the assistance with chromosome sorting and BAC library screening, and Dr. Frank Peairs for the use of the CSU Insectary and for providing aphids. We also thank Andreas Petzold and Stefan Taudien for 454 sequencing and assembling BAC clones. This work was supported by the Czech Science Foundation (Award No. P501/12/2554), Ministry of Education, Youth and Sports of the Czech Republic (National Program of Sustainability I, Grant award LO1204), and Australian Research Council (Projects LP0882095, LP0883462 and DP0985953). Partial support for RWA screening was provided by USDA Cooperative Agreement no. 2010-34205-21350.

Conflict of interest

The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic

    Helena Staňková, Miroslav Valárik, Zuzana Tulpová, Marie Kubaláková, Jaroslav Doležel & Hana Šimková

  2. Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA

    Nora L. V. Lapitan

  3. USAID/Bureau for Food Security, 1300 Pennsylvania Ave. NW, Washington, DC, 20523, USA

    Nora L. V. Lapitan

  4. CSIRO Plant Industry, Brisbane, QLD, 4072, Australia

    Paul J. Berkman

  5. School of Plant Biology, University of Western Australia, Perth, WA, 6009, Australia

    Jacqueline Batley & David Edwards

  6. Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia

    David Edwards

  7. Department of Plant Sciences, University of California, Davis, CA, 95616, USA

    Ming-Cheng Luo

  8. Department Genebank, AG Genome Diversity, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, Seeland (OT), 06466, Gatersleben, Germany

    Nils Stein

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  1. Helena Staňková
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  2. Miroslav Valárik
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  3. Nora L. V. Lapitan
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  4. Paul J. Berkman
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  5. Jacqueline Batley
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  6. David Edwards
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  7. Ming-Cheng Luo
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  8. Zuzana Tulpová
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  9. Marie Kubaláková
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  10. Nils Stein
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  11. Jaroslav Doležel
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  12. Hana Šimková
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Correspondence to Hana Šimková.

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Communicated by H.-Q. Ling.

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Staňková, H., Valárik, M., Lapitan, N.L.V. et al. Chromosomal genomics facilitates fine mapping of a Russian wheat aphid resistance gene. Theor Appl Genet 128, 1373–1383 (2015). https://doi.org/10.1007/s00122-015-2512-2

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