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Development and assessment of simple PCR markers for SNP genotyping in barley

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Abstract

Simple molecular marker assays underpin routine plant breeding and research activities in many laboratories worldwide. With the rapid growth of single nucleotide polymorphism (SNP) resources for many important crop plants, the availability of routine, low-tech marker assays for genotyping SNPs is of increased importance. In this study, we demonstrate that temperature-switch PCR (TSP) supports the rapid development of robust, allele-specific PCR markers for codominant SNP genotyping on agarose gel. A total of 87 TSP markers for assessing gene diversity in barley were developed and used to investigate the efficacy for marker development, assay reliably and genotyping accuracy. The TSP markers described provide good coverage of the barley genome, are simple to use, easy to interpret and score, and are amenable to assay automation. They provide a resource of informative SNP markers for assessing genetic relationships among individuals, populations and gene pools of cultivated barley (Hordeum vulgare L.) and its wild relative H. spontaneum K. Koch. TSP markers provide opportunities to use available SNP resources for marker-assisted breeding and plant genetic research, and to generate information that can be integrated with SNP data from different sources and studies. TSP markers are expected to provide similar advantages for any animal or plant species.

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Author information

Author notes

  1. Matthew J. Hayden

    Present address: Primary Industries Research Victoria, Victorian AgriBioscience Center, La Trobe Research and Development Park, Bundoora, VIC, 3082, Australia

  2. T. Tabone

    Present address: Ludwig Institute for Cancer Research, Royal Melbourne Hospital, PO Box 2008, Parkville, VIC, 3050, Australia

Authors and Affiliations

  1. Molecular Plant Breeding Co-operative Research Centre, Glen Osmond, SA, 5064, Australia

    Matthew J. Hayden, T. Tabone & D. E. Mather

  2. School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, 5064, Australia

    Matthew J. Hayden, T. Tabone & D. E. Mather

Authors
  1. Matthew J. Hayden
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  2. T. Tabone
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  3. D. E. Mather
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Corresponding author

Correspondence to Matthew J. Hayden.

Additional information

Communicated by P. Hayes.

M. J. Hayden and T. Tabone contributed equally to this work.

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Hayden, M.J., Tabone, T. & Mather, D.E. Development and assessment of simple PCR markers for SNP genotyping in barley. Theor Appl Genet 119, 939–951 (2009). https://doi.org/10.1007/s00122-009-1101-7

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  • DOI: https://doi.org/10.1007/s00122-009-1101-7

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