Designing a CAP Marker From a SNP Using the SGN CAPS Designer

One method for SNP detection is to create a cleaved amplified polymorphic (CAP) marker. A CAP marker is a simple PCR-based molecular marker assay visualized by agarose gel electrophoresis.

This tutorial provides a general explanation of a CAP marker and demonstrates how to design a CAP marker from a previously identified SNP using the Sol Genomics Network CAPS designer tool. In the event that the slideshare tutorial does not work, the tutorial is also attached as a pdf at the bottom of the page.

References Cited

• Ilic, K., T. Berleth, and N. J. Provart. 2004. BlastDigester – a web-based program for efficient CAPS marker design. Trends in Genetics 20: 280–283. (Available at: http://dx.doi.org/10.1016/j.tig.2004.04.012) (verified 11 May 2012).
• Konieczny, A., and F. M. Ausubel. 1993. A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant Journal 4: 403–410. (Available online at: http://dx.doi.org/10.1046/j.1365-313X.1993.04020403.x) (verified 11 May 2012).
• Thiel, T., R. Kota, I. Grosse, N. Stein, and A. Graner. 2004. SNP2CAPS: A SNP and INDEL analysis tool for CAPS marker development. Nucleic Acids Research 32: e5. (Available online at: http://dx.doi.org/10.1093/nar/gnh006) (verified 11 May 2012).

External Links

• CAPS Designer [Online]. Sol Genomics Network. Boyce Thompson Institute. Available at: http://solgenomics.net/tools/caps_designer/caps_input.pl (verified 11 May 2012).
• Cleaved amplified polymorphic sequences [Online]. U.S. National Library of Medicine, National Institutes of Health. Available at: http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/TechCAPS.shtml (verified 11 May 2012).
• Provart, N. BlastDigester. [Online]. The Bio-Array Resource for Plant Biology, University of Toronto. Available at: http://bar.utoronto.ca/ntools/cgi-bin/ntools_blast_digester.cgi (verified 11 May 2012).
• SNP2CAPS [Online]. Plant Genome Resources Center, Leibniz Institute of Plant Genetics and Crop Plant Research. Available at: http://pgrc.ipk-gatersleben.de/snp2caps/ (verified 11 May 2012).

Additional Resources

• Designing CAPS and dCAPS markers using dCAPS finder
• Overview of traditional molecular markers
• Molecular markers as size and sequence variants
• Molecular marker assays
• Genotyping DNA sequence variation (SNP) by conversion to size variation (CAP)
• Genotyping with molecular markers: Scoring a CAP marker on an agarose gel

Funding Statement

Development of this lesson was supported in part by the National Institute of Food and Agriculture (NIFA) Solanaceae Coordinated Agricultural Project, agreement 2009-85606-05673, administered by Michigan State University. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the United States Department of Agriculture.

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