The plant genome comprises of both highly conserved single copy (functional) sequences and the rapidly evolving high copy, repeated DNA sequences. The repetitive DNA, which may account for about 90% of the total genomic DNA in plants serve as powerful molecular markers because of the extensive sequence variation. One of the major classes of the repeat DNA is microsatellites (SSR) which are tandem repeats of 2-10 nucleotides.

The regions flanking the microsatellites are generally conserved among genotypes of a particular species, across species within a genus and rarely even across the genus. These conserved sequences are utilized to amplify individual SSR loci. These markers are referred to as STMS. The polymorphism revealed by markers is due to variation in the length of SSR at a given locus.

Advantages:

Because of their locus specific nature and presence of high information content, the co-dominant markers find extensive use in linkage mapping and tagging of genes. STMS markers have been developed in a large number of crop species using the genomic library approach.

Limitations:

These markers require precise DNA sequence information for each marker locus for designing a pair of identifying primers. The initial development of these markers therefore requires cloning and sequencing thus making the process labor intensive and expensive. But once the locus specific primers have been designed the approach becomes rapid and cost effective.