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PCR Analysis of SSR Polymorphisms in Plants Using Agarose Gels

  • Michele Morgante
  • Antonella Pfeiffer
  • Irena Jurman
  • Gianpaolo Paglia
  • Angelo M. Olivieri
Chapter

Abstract

The alleles of microsatellite (SSR) loci are identified by PCR amplifications of genomic DNA using primer pairs which flank the microsatellite repeats (see also Chapter 11.1. We try to use a single set of amplification and reaction conditions for all the primer pairs, without any optimization of these conditions. This is a necessity when large numbers of primers have to be screened and used. A single locus is normally amplified. More than one locus may be amplified if the genome is polyploid or if non-specific annealing occurs due to bad primer design, poor sequence data or homology of the primers with repeated sequence elements. The fragments obtained from the PCR amplification must be separated from one another to identify polymorphisms in SSRs.

Keywords

Microsatellite Repeat Ethidium Bromide Solution Shadow Band Repeat Sequence Element Mononucleotide SSRs 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Morgante, M. and Olivieri, A. M. (1993). PCR-amplified microsatellites as markers in plant genetics. Plant Journal 3: 175–182.CrossRefGoogle Scholar
  2. 2.
    Litt, M., Hauge, X. and Sharma, V. (1993). Shadow Bands Seen When Typing Polymorphic Dinucleotide Repeats: Some Causes and Cures. BioTechniques 15: 280–284.Google Scholar
  3. 3.
    Odelberg, S. J. and White, R. (1993). A Method for Accurate Amplification of Polymorphic CA Repeat Sequences. PCR Methods and Applications 3: 7–12.Google Scholar
  4. 4.
    Mellersh, C. and Sampson, J. (1993). Simplifying Detection of Microsatellite Length Polymorphisms. BioTechniques 15: 582–584.Google Scholar

Copyright information

© Chapman & Hall 1998

Authors and Affiliations

  • Michele Morgante
  • Antonella Pfeiffer
  • Irena Jurman
  • Gianpaolo Paglia
  • Angelo M. Olivieri

There are no affiliations available

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