The complexity of eukaryotic nuclear DNA is sufficiently high that by chance pairs of sites complementary to single octa- or deca- nucleotide sequences may occur in correct orientation and close enough to one another for PCR amplification. The RAPD marker system (Williams et al. 1990) makes use of random decamer primers for PCR at low stringency conditions (36-46oC) for the amplification of such loci. The fragments generated are 300-2000bp in size and the fingerprint contains polymorphic and/or monomrphic bands.

Advantages:

• No prior sequence information is required
• Simple and inexpensive technique
• RAPDs can be easily detected on Agarose gels after ethidium bromide staining
• No need of radioactivity Only small quantity of template DNA is required

Limitations:

• Reproducibility of RAPD assay varies with minor changes in the experimental conditions .
• Number of loci detected per assay are limited (5-10)