PCR with arbitrary primers: approach with care

New techniques have recently been described that employ the polymerase chain reaction (PCR) to amplify arbitrary regions of a genome using a single primer. The techniques reveal polymorphisms in insect taxa that lack allozyme variation and, for the first time, permit genetic polymorphisms to be rapidly analysed in small arthropods (e.g. mites, endoparasitic wasps). The methods have been used in identification of sub-species and cryptic species, and have applications in population genetics and genetic fingerprinting. They are fairly inexpensive, do not require the use of radioactivity, are relatively simple to learn and can easily be adapted to most laboratories. However, their application is not without technical problems and practical limitations. The purpose of this note is to indicate the critical factors to consider before launching into their use. We chiefly emphasize that most polymorphisms revealed by these methods segregate as dominant markers. Furthermore, application of these techniques requires extensive standardization and may not prove to be reproducible among various laboratories especially those employing different types of thermal cyclers. There are some unique features of these polymorphisms to consider when using them in genetic fingerprinting. In addition, because the techniques amplify arbitrary regions of genomes, similarly sized fragments amplified between two species may not be homologous. This argument and empirical observations suggest that PCR with arbitrary primers will have limited application in molecular systematics above the intraspecific level.