ARS | Publication request: DNA FINGERPRINTING OF FUNGAL AND PLANT GENOMES USING CAPILLARY ELECTROPHORESIS

Submitted to: American Phytopathological Society Potomac Division Meeting
Publication Type: Abstract Only
Publication Acceptance Date: August 1, 2006
Publication Date: August 1, 2006
Citation: Mischke, B.S., Oneill, N.R., Zhang, D. 2005. DNA fingerprinting of fungal and plant genomes using capillary electrophoresis. American Phytopathological Society Potomac Division Meeting. 95:S170.

Technical Abstract: Automated Capillary Electrophoresis (ACE) can be used to determine and characterize the DNA fragments that establish DNA fingerprints and profiles. This analytical separation technique supports high throughput analysis for the various molecular procedures that can be employed to determine identity and relationships based on DNA differences. We have used Simple Sequence Repeat (SSR) markers in the chocolate tree, Theobroma cacao, to identify germplasm held in collections at several tropical locations, to demonstrate the limited genetic diversity of some collections compared to others, and to examine the origin of accessions. If sufficient prior knowledge is available for a genome, SSR analysis is a straightforward procedure to perform, and results are easily scored with ACE. However the multistep procedure to generate markers by Amplifed Fragment Length Polymorphism (AFLP) and analysis of the results by ACE are significanly more involved. Using AFLP, which requires no prior sequence information about a particular genome, we have successfully differentiated species, subspecies and populations of Erythroxylum coca, the source of cocaine. AFLP results with fungal plant pathogens have been easier to achieve and require fewer primer combinations than higher plants. Our results have demonstrated associations of polymorphic markers in vegetative compatibility groups in Sclerotinia homoeocarpa and revealed population structure in Ophiosphaerella agrostis and in the species group that includes Stemphylium herbarum, S. vesicarium, and S. alfalfae. Issues in interpretation of AFLP analysis will be discussed.