A robust method for detecting single-nucleotide changes as polymorphic markers by PCR

Plant J. 1998 May;14(3):381-5. doi: 10.1046/j.1365-313x.1998.00123.x.


Numerous techniques in plant molecular genetic analysis, such as mapping and positional cloning techniques, rely on the availability of molecular markers that can differentiate between alleles at a particular locus. PCR-based cleaved amplified polymorphic sequences (CAPS) markers have been widely used as a means of rapidly and reliably detecting a single-base change that creates a unique restriction site in one of a pair of alleles. However, the majority of single-nucleotide changes do not create such sites and thus cannot be used to create CAPS markers. In this paper, a modification of the CAPS technique that allows detection of most single-nucleotide changes by utilizing mismatched PCR primers is described. The mismatches in the PCR primers, in combination with the single-nucleotide change, create a unique restriction site in one of the alleles.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Base Sequence
  • DNA Primers
  • Deoxyribonucleases, Type II Site-Specific
  • Genetic Markers*
  • Point Mutation*
  • Polymerase Chain Reaction*
  • Polymorphism, Genetic*
  • Restriction Mapping


  • DNA Primers
  • Genetic Markers
  • endodeoxyribonuclease MwoI
  • Deoxyribonucleases, Type II Site-Specific