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Development of wild barley-derived DArT markers and their integration into a barley consensus map

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Abstract

Wild barley-specific genomic libraries were developed for the purpose of creating a ‘comprehensive’ genomic representation of the primary Hordeum genepool capable of more robust genotyping of barley. In order to enrich for wild barley-specific sequences in the DArT libraries, suppression subtraction hybridization (SSH) was performed using cultivated barley as the subtraction driver and wild barley as the tester. Four doubled-haploid populations were genotyped with the comprehensive barley DArT array, including two from wild × cultivated crosses (Damon/Harrington and Shechem/Harrington) and two from cultivated × cultivated crosses (Albacete/Barbarrouse and TX9425/Naso Nijo). Analysis of genotyping data revealed that the SSH process was somewhat ineffective at enriching for unique sequences in this application of DArT marker development. However, the addition of markers derived from wild barley proved to be an effective means for increasing the number of polymorphic markers obtainable from a single DArT assay. Genetic maps of the four component populations were developed and 607 newly developed DArT markers were integrated with a barley consensus map to create a new synthetic map of the barley genome containing 3542 markers. This significantly increased the resolution of the consensus map and improved the power of the map to provide a reference for profiling genetic diversity within the primary Hordeum genepool. The improvement in the genotyping capability of the comprehensive DArT genomic representation and the higher resolution of the synthetic map facilitates an even greater flexibility of DArT markers to be utilized as a fast, high-throughput platform for molecular marker-based barley breeding.

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Acknowledgments

This research was funded in part by the Lieberman-Okinow Endowment at the University of Minnesota. We are grateful to Edie Paul and Geneflow, Inc. for providing us with the use of Phenomap software for map synthesis. We are also grateful to J. Carling and M. Evers of Triticarte Pty. Ltd. (DArT) for their efforts in array development and genotyping. We thank Joy K. Roy for providing data used in selection of wild barley accessions for array development.

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Authors and Affiliations

  1. Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN, 55108, USA

    B. P. Alsop & B. J. Steffenson

  2. Triticarte P/L and DArT P/L, PO Box 7141, Yarralumla, Canberra, ACT, 2600, Australia

    P. Wenzl & A. Kilian

  3. Centre UdL-IRTA, Universidad de Lleida, 25198, Lleida, Spain

    A. Farre & I. Romagosa

  4. Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China

    J. M. Wang

  5. Tasmanian Institute of Agricultural Research, University of Tasmania, PO Box 46, Kings Meadows, TAS, 7249, Australia

    M. X. Zhou

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  1. B. P. Alsop
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Correspondence to B. J. Steffenson.

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Alsop, B.P., Farre, A., Wenzl, P. et al. Development of wild barley-derived DArT markers and their integration into a barley consensus map. Mol Breeding 27, 77–92 (2011). https://doi.org/10.1007/s11032-010-9415-3

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  • DOI: https://doi.org/10.1007/s11032-010-9415-3

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