DNA microarrays on agarose-coated glass slides for plant pathogen identification

Agarose-coated glass slides were used as a platform for microarray analysis applied to plant pathogen identification. The agarose substrate combines the desirable features of fluorescence detection and high DNA immobilization capacity, in contrast to nylon membranes, which are unsuitable for fluorescent detection, and standard glass microarray slides, which have a low capacity for immobilization. Oligonucleotide probes were immobilized on the agarose substrate, then hybridized to fluorescently labeled sample DNA. Agarose concentration and hybridizing DNA length affected hybridization efficiency. Probes arrayed on the agarose distinguished Didymella bryoniae and Botrytis cinerea from each other with no cross reaction. No interference from other common greenhouse plant pathogens was found. Results compared favorably with those obtained on nylon membranes, and surpassed those achieved on the commercially available glass substrate. Agarose-coated slides are easily produced, and with the use of a manual arrayer, are an inexpensive alternative to commercial microarrays for small scale applications.