Sequencing of RAPD Markers

Abstract

Although the random amplified polymorphic DNA (RAPD) methodology, described by Williams et al. (1990) and Welsh and McClelland (1990), has been extensively used for many purposes, very little is known about the nucleotide sequence of RAPD markers and the primer binding sites within the target genome. It may be assumed that RAPD amplification is initiated at many sites which are imperfectly complementary to the primer sequence and which form short inverted repeats separated in the target genome by 0.2–3 kb. Moreover, some RAPD bands could result from self-priming events due to hairpin loop formation at the 3’ terminus of the initially amplified products. Such events should produce large inverted repeats. Determination of the nucleotide sequence of RAPD products could help in understanding the molecular mechanisms generating RAPD patterns and highlight novel applications of this methodology. The molecular nature of the polymorphisms detected in RAPD amplification has yet to be described. This would require DNA sequencing of several genomic primer binding sites from a number of polymorphic bands. Determining the nucleotide sequence of RAPD products might permit identification and study of those DNA regions of target genomes that were preferentially amplified.