Sequence Characterized Amplified Region (SCAR)


SCARs are DNA fragments amplified by the PCR using specific 15-30 bp primers, designed from nucleotide sequences established from cloned RAPD fragments linked to a trait of interest. By using longer PCR primers, SCARs do not face the problem of low reproducibility generally encountered with RAPDs. Obtaining a codominant marker may be an additional advantage of converting RAPDs into SCARs, although SCARs may exhibit dominance when one or both primers partially overlap the site of sequence variation. Length polymorphisms are detected by gel electrophoresis.


The main advantage of SCARs is that they are quick and easy to use. In addition, SCARs have a high reproducibility and are locus-specific. Due to the use of PCR, only low quantities of template DNA are required.


Disadvantages include the need for sequence data to design the PCR primers.


SCARs are locus specific and have been applied in gene mapping studies and marker assisted selection.

Suggested reading

Development of reliable PCR based markers linked to downy mildew resistance genes in lettuce Paran, I. and Michelmore, R.W. (1993). Theoretical and Applied Genetics, 85: 985-993.