Detection of fungi on the basis of visual examination of morphology is highly selective and species-specific identification of fungi and spores is therefore difficult. Molecular techniques present several advantages over the traditional ones and, most importantly, nucleic acid sequences unique to particular organisms can generally be found. As these techniques do not rely on phenotypic examination, gene expression is not required and identification times can be reduced significantly. In the fungi, molecular markers can be derived from both variable and conserved regions of the nuclear and mitochondrial genome, and different markers have been used to define populations at all levels from an individual isolate upwards. Some methods have the potential for the detection of specific genomic DNA sequences directly from initial plant samples, thereby eliminating the requirement to isolate and culture the fungus. Specific molecular markers, probes, and primers have commonly been developed from a variety of DNA sequences including randomly cloned genomic DNA fragments and specific regions such as genes coding for ribosomal RNA (rRNA), virulence factors, and insertion sequences.
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