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* Abstract The advent of molecular biology in general and the polymerase chain reaction in particular have greatly facilitated genomic analyses of microorganisms, provide enhanced capability to characterize and classify strains, and facilitate research to assess the genetic diversity of populations. The diversity of large populations can be assessed in a relatively efficient manner using rep-PCR-, AFLP-, and AP-PCR/RAPD-- based genomic fingerprinting methods, especially when combined with computer-- assisted pattern analysis. Genetic diversity maps provide a framework to understand the taxonomy, population structure, and dynamics of phytobacteria and provide a highresolution framework to devise sensitive, specific, and rapid methods for pathogen detection, plant disease diagnosis, as well as management of disease risk. A variety of PCR-based fingerprinting protocols such as rDNA-based PCR, ITS-PCR, ARDRA, T-RFLPs, and tRNA-PCR have been devised, and numerous innovative approaches using specific primers have been adopted to enhance both the detection and identification of phytobacteria. PCR-based protocols, combined with computer-based analysis, have provided novel fundamental knowledge of the ecology and population dynamics of bacterial pathogens, and present exciting new opportunities for basic and applied studies in plant pathology.
Key Words population structure, polymerase chain reaction, genomic fingerprinting, informatics, disease management, phylogeny
INTRODUCTION
The advent of molecular biology has caused a significant shift in the types of approaches used to characterize and identify plant pathogens and to devise disease management strategies. This shift is driven by both technology and ecology, and has occurred in parallel with significant changes in agricultural production methods, as highlighted by advances in precision agriculture and ecologically based pest management approaches (EBPM). Whereas precision agriculture has been driven primarily by technology and requires massive data sets and a suite of information technologies to design crop-production strategies (118), EBPM is biointensive and requires detailed knowledge of multilevel interactions between parasitic and beneficial organisms and their plant hosts (69, 89).
Likewise, technological advances in molecular biology have radically changed our capacity to rapidly characterize and track microorganisms. Complete genomic DNA sequences of 18 microorganisms to date, and an additional 56 under way (35, and WWW sites therein), have provided an extensive framework for a new era of microbial genetics, classification, and identification. These genomic approaches have also generated molecular tools for rapid and high-resolution pathogen detection and...