ABSTRACT
This chapter discusses the use of polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) in fungal systematics, with an emphasis on current methods. The PCR reaction produces sufficient DNA to be directly sequenced or visualized in agarose gels following staining with ethidium bromide. The most precise method for detecting polymorphisms between PCR products is the determination and the comparison of their nucleotide sequences. The PCR products obtained from different strains can be digested with restriction endonucleases and the profiles compared. The restriction fragments can be separated by electrophoresis in agarose or acrylamide gels, using simple and inexpensive equipment and well-established protocols. Electrophoretic patterns generated by PCR/RFLP analysis can be compared to quantify the variations between strains, to estimate their relationships, and to represent them in a dendrogram or tree. The similarity matrix or distance matrix is displayed as a dendrogram representing the relationships among the strains.
