Genetic Analysis with Random Amplified Polymorphic DNA Markers

Publisher Summary This chapter presents experimental protocols for random amplified polymorphic DNA (RAPD) assays and applications, emphasizing their use for genetic analysis in plants. It describes a novel type of genetic marker that is based on DNA amplification but requires no knowledge of target DNA sequence. These markers, called “RAPD markers” are generated by the amplification of random DNA segments with the single primers of arbitrary nucleotide sequence. RAPD markers can be used for genetic mapping applications as well as for genetic diagnostics. The assay is nonradioactive, requires only nanogram quantities of DNA, and is applicable to a broad range of species. The chapter compares restriction fragment length polymorphism (RFLP) and RAPD assays. RAPD markers provide the geneticist with a new tool to explore the genetics of sexually reproducing organisms, with applications in gene mapping, population genetics, molecular systematics, and marker-assisted selection in plant and animal breeding. In most cases, data can be generated faster and with less labor than by previous methods. The process can be set up in a small laboratory and there is no need to use radioactive isotopes, making it accessible to a broad range of biologists.