Molecular Markers

Microsatellites Markers (SSR)

Microsatellites or simple sequence repeats (SSRs) are a relatively new class of DNA markers of short runs of tandemly repeated sequence motifs evenly distributed throughout eucaryotic genomes. Due to the high rate of variation in the number of repeat units, the polymorphism level shown by SSRs is high. Furthermore SSRs are easy to analyse by means of PCR, using flanking unique sequence primers. These features make microsatellites suitable markers for several application in genetic analysis. A major limitation of SSRs is the time and cost required to isolate and characterise each locus when pre-existing DNA sequence is not available. Typically, this process requires the construction and screening of a genomic library of size-selected DNA fragments with SSR-specific probes, followed by DNA sequencing of isolated positive clone, PCR primer synthesis and testing. Only after that the copy number, informativeness and chromosomal position of SSR loci can be determined. Significant cost and time saving can be made if library screening is reduced. In our project we therefore applied a technique for the construction of small insert libraries enriched for SSRs.

In the frame of a ProInno co-operation project we developed microsatellite markers for the identification of Osteospermum and Dimorphoteca varieties for which there was no pre-existingDNA sequence information. The variety Orange Symphony was used as reference variety when establishing the library enriched for SSRs. Up to now we identified 26 SSRs SSR-containing fragments are amplified via PCR using primer pairs complementary to the flanking regions, and result in polymorphisms due to different fragment length after gel electrophoresis thus enabling the differentiation of varietes.


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