Efficient Genetic Mapping of Single Nucleotide Polymorphisms Based Upon DNA Mismatch Digestion

A single-strand specific (sss) nuclease, found in extracts of celery juice, can be used to digest heteroduplex DNA and hence identify heterozygous single nucleotide polymorphism (SNP) sites in PCR products. Here we show this method can be used to map specific genes with relative simplicity and low cost. A particular nucleotide substitution does not need to be identified, and in fact, a priori knowledge of the presence of a SNP is not required, as the entire length of the PCR product is interrogated for the presence of SNPs. This characteristic enables application of this technique to genomes that are not well characterized with regard to SNP polymorphism, and for rapidly placing particular genes onto linkage maps. While this technique is best suited for mapping markers in a backcross configuration, we show that in an F₂ configuration, where alternative homozygotes cannot be discerned by this technique, data are still relatively informative about linkage.