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

• Published in: Annual review of phytopathology Vol. 37; pp. 81 - 125
• Main Authors: Louws, F.J, Rademaker, J.L.W, De Bruijn, F.J
• Format: Journal Article
• Language: English
• Published: Palo Alto, CA Annual Reviews 01.01.1999; Annual Reviews, Inc
• Subjects: amplified fragment length polymorphism; amplified ribosomal dna restriction analysis; Bacterial plant pathogens; Biological and medical sciences; detection; disease control; disease diagnosis; DNA fingerprinting; evaluation; Fundamental and applied biological sciences. Psychology; Generalities. Techniques. Transmission, epidemiology, ecology. Antibacterial substances, control; genetic techniques and protocols; genetic variation; identification; literature reviews; molecular sequence data; nucleotide sequences; phylogeny; Phytopathology. Animal pests. Plant and forest protection; plant diseases and disorders; plant pathogenic bacteria; polymerase chain reaction; population structure; random amplified polymorphic DNA technique; restriction fragment length polymorphism; restriction mapping; ribosomal DNA; risk reduction; Plant pathogen; Genetic marker; Taxonomy; Experimental method; Pest and disease control; Chemotaxonomy; Review; Epidemiology; Random amplified polymorphic DNA marker; Strain; Polymerase chain reaction; Restriction fragment length polymorphism; Bacteria; Specific identification; Diagnosis; Detection
• ISSN: 0066-4286; 1545-2107
• DOI: 10.1146/annurev.phyto.37.1.81

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 high-resolution 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.