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Sequence tagged sites (STS)

This is a general term for markers that are developed with sequence-specific primers, usually for a particular genome region or type of region. Some knowledge of DNA sequence is necessary, obviously, but in many cases this is already publicly available. If you find the sequence of a gene you are interested in online or in a publication, you could design primers specific for that sequence, and try to amplify the sequence in your own germplasm.

For example, a search of the NCBI* database for the term “rice blast resistance” results in many sequences, one of which is a gene that is 3458 base pairs (bp) long,  the first ~500 of which are shown below.

Either manually or using a primer design software program, primers could be developed which would amplify a fragment of this gene from rice genomic DNA.