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This document discusses the methodologies and gene targets involved in molecular diagnostics for plant associated pests and pathogens. It explores the capabilities and limitations of molecular diagnostics in a routine laboratory as well as the propensity for these tests to be used to identify cryptic or new organisms. A case study is presented that details the methods used to identify an emerging bacterial pathogen of corn in Nebraska. The most successful method for identifying pests and pathogens is through sequence analysis of target genes or gene sequences. The limitations of this method are the result of yet too poorly supplemented databases from which to compare unknown sequences. The success of molecular diagnostics depends on the addition of verified specimens to publicly available DNA sequence databases. Diagnoses made in a routine laboratory may be supplemented by molecular data.
