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.
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Abbreviations
- bp:
-
base pair
- FLA:
-
fragment length analysis
- indel:
-
insertion–deletion
- nSSR:
-
nuclear simple sequence repeat
- PCR:
-
polymerase chain reaction
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Acknowledgements
This work was carried out in the framework of the European project Oakflow (CT-FAIR 2000-00960), which was financially supported by the Swiss Federal Office for Education and Science (BBW 99.0838). We thank Christoph Sperisen for providing technical support and an anonymous referee for helpful comments on the manuscript.
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Gugerli, F., Brodbeck, S. & Holderegger, R. Insertions–Deletions in a Microsatellite Flanking Region May Be Resolved by Variation in Stuttering Patterns. Plant Mol Biol Rep 26, 255–262 (2008). https://doi.org/10.1007/s11105-008-0034-7
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DOI: https://doi.org/10.1007/s11105-008-0034-7