Although the RAPD method is relatively fast, cheap and easy to perform in comparison with
other methods that have been used as DNA markers, the issue of reproducibility has been of
much concern since the publication of the technique. In fact, ordinary PCR is also sensitive to
changes in reaction conditions, but the RAPD reaction is far more sensitive than conventional
PCR because of the length of a single and arbitrary primer used to amplify anonymous regions
of a given genome. This reproducibility problem is usually the case for bands with lower
intensity. The reason for bands with high or lower intensity is still not known. Perhaps some
primers do not perfectly match the priming sequence, amplification in some cycles might not
occur, and therefore bands remain fainter. The chance of these kinds of bands being sensitive
to reaction conditions of course would be higher than those with higher intensity amplified with
primers perfectly matching the priming sites. The most important factor for reproducibility of
the RAPD profile has been found to be the result of inadequately prepared template DNA (59).
Differences between the template DNA concentration of 2 individualsÕ DNA samples result in the
loss or gain of some bands (60).
Since RAPD amplification is directed with a single, arbitrary and short oligonucleotide
primer, DNA from virtually from all sources is amenable to amplification. Therefore, DNA from
the genome in question may include contaminant DNA from infections and parasites in the
material from which the DNA has been isolated. Special care is needed for keeping out the DNA
to be amplified from other sources of DNA.