SNP2RFLP: a computational tool to facilitate genetic mapping using benchtop analysis of SNPs

Abstract

Genome-wide analysis of single nucleotide polymorphism (SNP) markers is an extremely efficient means for genetic mapping of mutations or traits in mice. However, this approach often defines a relatively large recombinant interval. To facilitate the refinement of this interval, we developed the program SNP2RFLP. This program can be used to identify region-specific SNPs in which the polymorphic nucleotide creates a restriction fragment length polymorphism (RFLP) that can be readily assayed at the benchtop using restriction enzyme digestion of SNP-containing PCR products. The program permits user-defined queries that maximize the informative markers for a particular application. This facilitates fine-mapping in a region containing a mutation of interest, which should prove valuable to the mouse genetics community. SNP2RFLP and further details are publicly available at http://genetics.bwh.harvard.edu/snp2rflp/ .

Fig. 1

A SNP2FRLP-identified RFLP assay used to identify mice carrying a mapped ENU-induced mutation. PCR products of 195 bp encompassing SNP rs37311177 on chromosome 13 were amplified from tail DNA isolated from individual mice and digested with the restriction enzyme MseI. Samples included AJ, FVB strain controls (underlined), and five experimental samples. AJ polymorphism at this SNP creates an RFLP that is not present in the FVB genome

Fig. 2

A screen shot of three informative SNPs returned by SNP2RFLP. The restriction enzyme recognition sites (bold) cut at the SNP position (bold, blue) in the sequence. The genotype of the SNP for each strain is shown. The suggested primers found by Primer3 are highlighted in red along the sequence