dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics

Authors

  • Michael M. Neff,

    1. Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA,, Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA, and, Department of Physics, Georgia Institute of Technology, 837 State St. NW, Atlanta GA, 30332, USA
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  • Joseph D. Neff,

    1. Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA,, Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA, and, Department of Physics, Georgia Institute of Technology, 837 State St. NW, Atlanta GA, 30332, USA
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  • Joanne Chory,

    1. Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA,, Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA, and, Department of Physics, Georgia Institute of Technology, 837 State St. NW, Atlanta GA, 30332, USA
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  • Alan E. Pepper

    1. Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA,, Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA, and, Department of Physics, Georgia Institute of Technology, 837 State St. NW, Atlanta GA, 30332, USA
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Summary

PCR-based detection of single nucleotide polymorphisms is a powerful tool for the plant geneticist. Cleaved amplified polymorphic sequence analysis is the most widely used approach for the detection of single nucleotide polymorphisms. However, this technique is limited to mutations which create or disrupt a restriction enzyme recognition site. This paper presents a modification of this technique where mismatches in a PCR primer are used to create a polymorphism based on the target mutation. This technique is useful for following known mutations in segregating populations and genetic mapping of isolated DNAs used for positional based cloning of new genes. In addition, a computer program has been developed that facilitates the design of these PCR primers.

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