title: A robust method for detecting single-nucleotide changes as polymorphic markers by PCR.
abstract: 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.
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison 53706, USA.
authors.forename: S D
authors.initials: SD
authors.lastname: Michaels
authors.forename: R M
authors.initials: RM
authors.lastname: Amasino
mesh_terms: D001483:Base Sequence; D017931:DNA Primers; D015252:Deoxyribonucleases, Type II Site-Specific; D005819:Genetic Markers; D017354:Point Mutation; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D015183:Restriction Mapping
chemical_list: D017931:DNA Primers; D005819:Genetic Markers; C060413:endodeoxyribonuclease MwoI; D015252:Deoxyribonucleases, Type II Site-Specific