A-1910A: The Use of AFLP Techniques for DNA Fingerprinting in Plants

In the last fifteen years, three devastating fungal diseases of Theobroma cacao, the chocolate tree, have enveloped virtually all areas of cocoa production in Central and South America. One of the common mechanisms for dealing with plant disease problems, particularly in areas with minimal resources for application of fungicides, has been the use of genetically resistant germplasm lines. Unfortunately, cocoa is a commodity that has an extended breeding of six years from seed to podbearing mature tree. Partially due to this long period, the tree has been maintained in a state of wild cultivation for almost 400 years without a great deal of crop improvement characteristic of other modern cultivated crops. As a result, there is very little information regarding the genetic diversity of the international cocoa germplasm collections. DNA fingerprinting, a tool that has been widely used in forensic science, is also useful in a variety of applications with plants. It is used to identify genetic diversity within breeding populations, to positively identify and differentiate accessions, cultivars, and species that might be difficult to characterize due to similar morphological characteristics or indistinct traits, and to identify plants containing genes of interest such as the confirmation of transformation events. A number of molecular tools and procedures are being employed to establish DNA fingerprinting profiles and each of these procedures has its strengths and weaknesses. Amplified restriction Fragment Length Polymorphic (AFLP) DNA analysis, which is the focus of this report, is a useful procedure for DNA fingerprinting, especially when very little information is known about the genome of the plant under study. AFLP DNA analysis of plants is a useful procedure for quickly assessing the genetic background of selected lines or populations. AFLP techniques produce a much higher percentage of polymorphic bands per analysis than the earlier procedures of RFLP (restriction fragment length polymorphisms) or RAPD analysis (random amplified polymorphisms). For example, in a comparative study of AFLP, RFLP, and RAPD analysis of inbred lines of soybean, Lin et al. (1996) reported that AFLP gave a number of discriminatory polymorphic bands or probes that was 8 to 10 times higher than the other two procedures (see Table 1).