Inter Simple Sequence Repeats (ISSR)


ISSRs are DNA fragments of about 100-3000 bp located between adjacent, oppositely oriented microsatellite regions. ISSRs are amplified by PCR using microsatellite core sequences as primers with a few selective nucleotides as anchors into the non-repeat adjacent regions (16-18 bp). About 10-60 fragments from multiple loci are generated simultaneously, separated by gel electrophoresis and scored as the presence or absence of fragments of particular size. Techniques related to ISSR analysis are Single Primer Amplification Reaction (SPAR) that uses a single primer containing only the core motif of a microsatellite, and Directed Amplification of Minisatellite-region DNA (DAMD) that uses a single primer containing only the core motif of a minisatellite.


The main advantage of ISSRs is that no sequence data for primer construction are needed. Because the analytical procedures include PCR, only low quantities of template DNA are required. Furthermore, ISSRs are randomly distributed throughout the genome.


Because ISSR is a multilocus technique, disadvantages include the possible non-homology of similar sized fragments. Moreover, ISSRs, like RAPDs, can have reproducibility problems.


Because of the multilocus fingerprinting profiles obtained, ISSR analysis can be applied in studies involving genetic identity, parentage, clone and strain identification, and taxonomic studies of closely related species. In addition, ISSRs are considered useful in gene mapping studies.

Suggested reading

Application of inter simple sequence repeat (ISSR) markers to plant genetics Godwin, I.D., Aitken, E.A.B. and Smith, L.W. (1997). Electrophoresis, 18: 1524-1528. doi:10.1002/elps.1150180906.

Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification Zietkiewicz, E., Rafalski, A. and Labuda, D. (1994). Genomics, 20: 176-183.