Microsatellite Genotyping

Microsatellites or tandem repeats are repeating sequences of short DNA stretches (usually 1-6 bp long). Microsatellites are polymorphic DNA loci present throughout the whole genome. Microsatellite genotyping is a widely accepted tool for a variety of applications such as linkage mapping studies, association studies, and identification of organisms.

We use ABI3730 capillary electrophoresis platform for microsatellite genotyping. Our standard microsatellite set for whole genome linkage analysis projects is Applied Biosystems Linkage Mapping Set v2.5 MD10 with approximately 385 markers. Fine mapping markers can also be selected with the research groups.

In a microsatellite project, microsatellite loci are amplified by PCR using fluorescently labeled forward and unlabeled reverse primers. The PCR amplicons are separated by size using electrophoresis, and in our case ABI3730 capillary electrophoresis, and the dye labeled products are identified by fluorescence detection. We use the GeneMapper® Software by Applied Biosystems to size and genotype the alleles.