text: what are ssr markers?   in 1989, weber & may and litt & luty discover microsatellite sequences, demonstrate their high level of polymorphism due to variations in the number of tandem repeats (1 - typical heterozygosities in cattle), abundance and even distribution across the genome.   microsatellites are genotyped using the polymerase chain reaction (1 ) using primers targetted to the unique sequences flanking the microsatellite motif. pcr can easily be semi-automated (1 )   the resulting pcr products are separated according to size by gel electrophoresis using either agarose gels or more commonly (because of their higher resolution) denaturing polyacrylamide gels (page) (1 ).   pcr products are visualized by:  direct staining (ethidium bromide or silverstaining)(1 )  autoradiography:  the pcr products are labeled either by incorporation of [a -p 32 or 33] dntps (1 )or [a -s 35] dnts during the pcr amplification (1 )(labels the two strands), or by using one end-labeled primer (labels one strand). primers are end-labeled using [g -p 32 ]atp and t4 polynucleotide kinase (1 ) .  after gel electrophoresis, an x-ray film is exposed to the gel revealing the position of the pcr products as black spots. a photon of light or a b particle or g ray released from a radioactive molecule "activate" silver bromide crystals on the film emulsion. this renders them capable of being reduced through the developing process to form silver metal (a "grain"). the silver grains on the film form the image.  co-amplification and/or co-loading of multiples microsatellites allows for multiplex genotyping (2-4 systems).  fluorescence labeling:  the pcr products are labeled either by using primers or dntps which are tagged with an appropriate fluorophore, a chemical group which fluoresces when exposed to a specific wavelength of light. popular fluorophores used in direct labeling include fluorescein, a pale green fluorescent dye, rhodamine, a red fluorescent dye, and amino methyl coumarin, a blue fluorescent dye. fluorophoes are characterized by their excitation and emission spectra.  the pcr products are detected during migration using automatic sequencers. (1 )  co-amplification and/or co-loading of multiples microsatellites allows for multiplex genotyping (up to 20 systems). (1 )  software packages allow for semi-automated data capture (1 ).   microsatellite profiles are often difficult to read due to artefactual bands, which result from (1 ):   the differential migration of the two dna strands in denaturing acrylamide gels  the "+ a" activity of the taq polymerase generating x + 1 bands  slippage of the taq polymerase during polymerization generating ? +4, +2, -2, -4, ? "stutter" bands  non denatured secondary structures adopted by the pcr products.