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Microsatellite Development

Dr. Jörg Plieske

Microsatellite markers (also referred to as Simple Sequence Repeats, SSR) are based on the amplification of short (2-6 base pairs) tandem repeat sequences. They can be obtained either by sequencing prescreened cloned DNA fragments or through bioinformatic mining of genomic or cDNA sequence databases. Microsatellite markers show a higher level of polymorphism than most other marker systems because variation in the repeat number occurs easily through slippage during DNA replication and/or unequal crossing over. Unlike most other marker systems, microsatellites are a multiallelic system, which makes them ideal for the analysis of closely related lines or varieties. Microsatellite markers are currently the main marker system for many field crop and vegetable plants.

Besides its analysis capacities, TraitGenetics also offers development of microsatellite markers for any eukaryotic plant species within a reasonable time frame. For microsatellite development, we use specialized genomic libraries yielding a high number of functional microsatellite markers. These libraries are arrayed using robotic equipment and can be screened with a variety of microsatellite motifs. Strict quality controls during marker development and testing ensure the reliability of our markers in routine applications such as genetic mapping, marker assisted selection or population genetics. TraitGenetics has been involved in the development of several thousand microsatellite markers from various crop species (e.g. wheat, rapeseed, barley, sugar beet).



 Identification of microsatellite containing clones: a plasmid library arrayed on a membrane is hybridized to a microsatellite motive as synthetic probe. Positive clones are visible as duplicate spots

MS Development

 A microsatellite motif (CT) in a DNA sequence


Identification of oligonucleotide primers for amplification of a microsatellite containing sequence



Analysis of wheat varieties with a multiallelic microsatellite marker
using capillary electrophoresis (ABI 3100)

Large scale Projects at TraitGenetics

For nearly ten years now TraitGenetics successfully performes large scale projects for major crop plants. Besides our activities to establish high quality sets of publicly available markers, we extended the genetic maps of wheat and rapeseed with more than 1.000 microsatellite markers developed in-house. With a selection of approximately 200 mapped markers of high quality and suitability for genotyping we created marker databases for more than thousand currently grown varieties, older varieties and important germplasm for both wheat and rapeseed.
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