The three Ds of PCR-based genomic analysis of phytobacteria: Diversity, detection, and disease diagnosis

The advent of molecular biology in general and the polymerase chain reactio n in particular have greatly facilitated genomic analyses of microorganisms , provide enhanced capability to characterize and classify strains, and fac ilitate research to assess the genetic diversity of populations. The divers ity of large populations can be assessed in a relatively efficient manner u sing 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 s tructure, and dynamics of phytobacteria and provide a high-resolution frame work to devise sensitive, specific, and rapid methods for pathogen detectio n, plant disease diagnosis, as well as management of disease risk. A variet y of PCR-based fingerprinting protocols such as rDNA-based PCR, ITS-PCR, AR DRA, T-RFLPs, and tRNA-PCR have been devised, and numerous innovative appro aches using specific primers have been adopted to enhance both the detectio n and identification of phytobacteria. PCR-based protocols, combined with c omputer-based analysis, have provided novel fundamental knowledge of the ec ology and population dynamics of bacterial pathogens, and present exciting new opportunities for basic and applied studies in plant pathology.