DNA based diagnostics has become increasingly utilised in the agriculture sector both in the diagnosis of pathogens and pests as well as in molecular marker assisted breeding. Most DNA diagnostic tests for plant pathogens are based on specific amplification of the genomic material(either DNA or RNA) from the pathogen using the polymerase chain reaction or PCR and the subsequent detection of the amplified product. The simplest method of detection of the amplified product is agarose or polyacrylamide gel

electrophoresis. More sophisticated platforms have been developed particularly for the detection of multiple pathogens most of which are based on arrays.

The most important characteristics of a diagnostic protocol are that the protocol is both sensitive and specific. Thus, the major reasons that PCR diagnostics have become popularfor pathogen detection are that very small concentrations of the target organism can be detected and the specificity can be varied from highly specific to broad. However, there are a number of disadvantages that must be overcome for a PCR based diagnostic test to be sufficiently robust for it to be used in a clinical environment. The disadvantage of PCR is that it is prone to both false positive and false negative results.

False positives usually result from (a) poor primer design or amplification conditions such that organisms other than the target organism are amplified or (b) contamination of either the original sample or reagents involved in the procedure. False negatives usually result from (a) poor primer design or amplification conditions in that there are variants within the population of the target organism which are not amplified, (b) poor extraction of DNA from the sample material, ie insufficient DNA is extracted or (c) contaminants in the DNA sample that inhibit the amplification. Three laboratory were identified and examined for merit and validity.