Converting SNPs to CAPS and dCAPS Marker Using dCAPS Finder

Plant Breeding and Genomics January 31, 2012 Print Friendly and PDF

Author:

Sungwoo Lee, The Ohio State University

This tutorial provides an overview of CAPS and dCAPS markers as well as the steps required to design CAPS and dCAPS markers from previously identified SNPs using dCAPS finder software.

Introduction

Single Nucleotide Polymorphism (SNP) markers can be converted to Cleaved/Cut Amplified Polymorphic Sequence (CAPS) markers if the polymorphism alters a restriction enzyme cutting site. If a polymorphic restriction enzyme cutting site is inserted, the markers are referred to as derived CAPS (dCAPS). This tutorial introduces users to dCAPS finder software, which can be used to design CAPS and dCAPS markers. 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

  • Lee, S. H., D. R. Walker, P. B. Cregan, and H. R. Boerma. 2004. Comparison of four flow cytometric SNP detection assays and their use in plant improvement. Theoretical and Applied Genetics 110: 167–174. (Available online at: dx.doi.org/10.1007/s00122-004-1827-1) (verified 12 Jan 2011).
  • Neff, M. M., E. Turk, and M. Kalishman. 2002. Web-based primer design for single nucleotide polymorphism analysis. Trends in Genetics 18: 613–615. (Available online at: http://dx.doi.org/10.1016/S0168-9525(02)02820-2) (verified 10 Jan 2011).
  • Neff, M. M., J. D. Neff, J. Chory, and A. E. Pepper. 1998. dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: Experimental applications in arabidopsis thaliana genetics. Plant Journal 14: 387–392. (Available online at: http://dx.doi.org/10.1046/j.1365-313X.1998.00124.x) (verified 10 Jan 2011).

External Link

Additional Resource

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:

Designing CAPS and dCAPS Tutorial.pdf (1.66 MB)

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USDA / NIFA

This work is supported by the USDA National Institute of Food and Agriculture, New Technologies for Ag Extension project.