Plant Molecular Biology Reporter

, Volume 19, Issue 2, pp 137–149 | Cite as

Efficient protocols for CAPS-based mapping inArabidopsis

  • Lars O. Baumbusch
  • Ina K. Sundal
  • D. Wayne Hughes
  • Glenn A. Galau
  • Kjetill S. Jakobsen


Positional cloning continues to be an essential method for gene identification and characterisation. The introduction of PCR-based techniques such as Amplified Fragment Length Polymorphism (AFLP), Simple Sequence Length Polymorphisms (SSLP) and Cleaved Amplified Polymorphic Sequences (CAPS) has greatly increased the efficiency of gene mapping in arabidopsis. To develop the CAPS marker approach further, we have altered several critical mapping parameters. Efficiency was improved by using a small volume of dry seed for DNA extraction instead of the commonly used vegetative tissue. Reproducibility of PCR reactions was enhanced by faster and reduced protocols for PCR and restriction enzyme digestion and optimisation of PCR conditions for over 50 CAPS primer pairs. Finally, the density of genetic markers was increased by providing polymorphic information for all CAPS markers in arabidopsis ecotypes Wassilewskija (Ws), Columbia (Col) and Cape Verde Islands (Cvi).

Key words

Arabidopsis CAPS DNA extraction ecotype polymorphisms gene mapping PCR conditions 



amplified fragment length polymorphism


cleaved amplified polymorphic sequences


restriction fragment length polymorphism


simple sequence length polymorphism. Ecotypes forArabidopsis thaliana






Cape Verde Islands












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Copyright information

© International Society for Plant Molecular Biology 2001

Authors and Affiliations

  • Lars O. Baumbusch
    • 1
  • Ina K. Sundal
    • 1
  • D. Wayne Hughes
    • 2
  • Glenn A. Galau
    • 2
  • Kjetill S. Jakobsen
    • 1
  1. 1.Division of Molecular BiologyUniversity of OsloOsloNorway
  2. 2.Department of BotanyUniversity of GeorgiaAthensUSA

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