Plant Molecular Biology Reporter

, Volume 26, Issue 3, pp 255–262 | Cite as

Insertions–Deletions in a Microsatellite Flanking Region May Be Resolved by Variation in Stuttering Patterns

Article

Abstract

Microsatellites or simple sequence repeats (SSRs) may display polymerase-chain-reaction-amplified fragment lengths mismatching the patterns expected from repeat copy number variation. We sequenced alleles of a nuclear dinucleotide SSR locus in two oak species which showed 2- and 1-bp length differences between alleles and three types of stuttering patterns in fragment length analysis. In accordance with the variation in stuttering, we identified three allele classes characterized by insertions–deletions in the flanking regions and overlapping repeat copy number ranges. Different alleles could thus only be safely separated when considering these stuttering patterns. Our results raise the question of how to adequately delimit alleles when such size homoplasy is present. We advise to thoroughly characterize SSR sequence variation during marker development and to carefully place primer sites along flanking regions to facilitate automated allele scoring and to minimize labor-intensive visual inspection.

Keywords

Allele calling Flanking region Fragment length analysis Nuclear microsatellite Nucleotide substitutions Simple sequence repeat Size homoplasy Stuttering pattern 

Abbreviations

bp

base pair

FLA

fragment length analysis

indel

insertion–deletion

nSSR

nuclear simple sequence repeat

PCR

polymerase chain reaction

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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Felix Gugerli
    • 1
  • Sabine Brodbeck
    • 1
  • Rolf Holderegger
    • 1
  1. 1.Ecological Genetics and EvolutionWSL Swiss Federal Research InstituteBirmensdorfSwitzerland

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