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

Authors:

Matthew Robbins, The Ohio State University; Heather L. Merk, The Ohio State University

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 (SGN) CAPS designer tool.

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

Additional Resources

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.

Attachments:

SGN CAPS Designer Tutorial.pdf (431.48 KB)

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The Polymerase Chain Reaction (PCR)

Author:

Matthew Robbins, The Ohio State University

This module provides an overview of the polymerase chain reaction (PCR), describes PCR using an analogy to photocopying a book, provides links to animations describing PCR, and provides examples of analysis of PCR products.

Introduction

The polymerase chain reaction (PCR) is a procedure that mimics the cellular process of DNA replication using the machinery of heat-resistant bacteria in a cyclic manner, resulting in several million copies of a specific DNA sequence that can then be visualized through electrophoresis and staining with a dye. PCR is commonly used in plant genetics and molecular breeding to copy a specific DNA fragment from the genome of an individual as a step in the process of  molecular marker assisted selection. The use of PCR to copy a specific portion of a genome is analogous to photocopying a specific page of a book. Table 1 illustrates this analogy by comparing the component required to copy DNA by PCR to those needed to photocopy a page of a book.

Table 1. Comparing components in PCR to photocopying a page in a book.

Photocopier items PCR components
The book The entire genome
(called the DNA template)
The page A portion of the genome (fragment) we are interested in
A bookmark Primers that “mark” the specific fragment
The copy machine

The enzyme that copies DNA
(called a polymerase)

Paper and toner

The four bases that make up DNA
(called nucleotides)

In the same way that a bookmark identifies the specific page to photocopy out of a book, PCR primers identify the specific fragment to be copied from the entire genome. In order to copy a page, the photocopier uses the paper and toner to make the copy. Similarly, the polymerase requires nucleotides to produce a replicate of the original DNA fragment.

Resources on PCR

To understand in more detail how these components function in PCR, the Plant and Soil Sciences eLibrary at the University of Nebraska-Lincoln has an informative lesson on PCR including an animation of the process:

Screenshot of the PCR animation from the Plant and Soil Sciences eLibrary
Photo credit: Plant and Soil Science eLibrary

Another animation on PCR can be found at the Dolan DNA Learning Center, part of The Cold Spring Harbor Laboratory.

Screenshot of the introdction to the PCR animation at the Dolan DNA Learning Center
Photo credit: The Dolan DNA Learning Center

The Genetics Science Learning Center at the University of Utah also has an animation on PCR.

Screenshot of the PCR tutorial at the Genetic Science Learning Center
Photo credit: The Genetics Science Learning Center

Analyzing PCR products

When using PCR for genotyping, the amplified DNA fragments can be analyzed several different ways. DNA amplified by PCR can be:

External Links

Additional Resources

For some PCR related entertainment, we recommend “The PCR Song“. With lyrics such as “PCR, when you need to find out who’s your Daddy; PCR, when you need to solve a crime…” this video produced by BioRad features characterizations of famous and not-so-famous folk singers. If you like the musical theme, the “GTCA Song” song rocks to the tune of YMCA while reviewing the biochemistry of PCR.

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.

Mention of specific companies is not intended for promotion purposes.

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