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Efficient validation of single nucleotide polymorphisms in plants by allele-specific PCR, with an example from barley

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Abstract

Although the increasing number of expressed sequence tags (ESTs) from the public domain has facilitated the detection of single nucleotide polymorphisms (SNPs), further validation is needed before they can be used as markers. For SNP validation, we have compared 2 independent methods: (1) the primer extension method followed by capillary electrophoresis on an ABI PRISM 3100 Genetic Analyzer and (2) nested PCR followed by agarose-based visualization. We present an assessment of the efficiency and costs associated with these methods, based on a sample of barley cultivars.

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Abbreviations

AS-PCR:

allele-specific PCR

SNP:

single nucleotide polymorphism

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Authors and Affiliations

  1. Agriculture and Agri-Food Canada (AAFC) Central Experimental Farm, K1A 0C6, Ottawa, ON, Canada

    V. D. Soleimani & B. R. Baum

  2. Ottawa-Carleton Institute of Biology, University of Ottawa, 30 Marie Curie, K1N 6N5, Ottawa, ON, Canada

    V. D. Soleimani & D. A. Johnson

Authors
  1. V. D. Soleimani
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  2. B. R. Baum
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  3. D. A. Johnson
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Correspondence to B. R. Baum.

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Soleimani, V.D., Baum, B.R. & Johnson, D.A. Efficient validation of single nucleotide polymorphisms in plants by allele-specific PCR, with an example from barley. Plant Mol Biol Rep 21, 281–288 (2003). https://doi.org/10.1007/BF02772803

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