Cleaved Amplified Polymorphic Sequence (CAPS)


CAPS are DNA fragments amplified by PCR using specific 20-25 bp primers, followed by digestion of the PCR products with a restriction enzyme. Subsequently, length polymorphisms resulting from variation in the occurrence of restriction sites are identified by gel electrophoresis of the digested products. CAPS have also been referred to as PCR-Restriction Fragment Length Polymorphism (PCR-RFLP).


Advantages of CAPS include the involvement of PCR requiring only low quantities of template DNA, the codominance of alleles and the high reproducibility. Compared to RFLPs, CAPS analysis does not include the laborious and technically demanding steps of Southern blot hybridization and radioactive detection procedures.


In comparison with RFLP analysis, CAPS polymorphisms are more difficult to find because of the limited size of the amplified fragments (300-1800 bp). Furthermore, sequence data are needed to design the PCR primers.


CAPS markers have been applied predominantly in gene mapping studies.

Suggested reading

A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers Konieczny, A. and Ausubel, F.M. (1993). The Plant Journal, 4: 403-410. doi:10.1046/j.1365-313X.1993.04020403.x.

PCR-based RFLP analysis of DNA sequence diversity in the gastric pathogen Helicobacter pylori Akopyanz, N., Bukanov, N., Westblom, T.U. and Berg, D.E. (1992). Nucleic Acid Research, 20: 6221-6225. doi:10.1093/nar/20.23.6221.