title: Development of a DNA Microarray-Based Assay for the Detection of Sugar Beet Root Rot Pathogens.
abstract: Sugar beet root rot diseases that occur during the cropping season or in storage are accompanied by high yield losses and a severe reduction of processing quality. The vast diversity of microorganism species involved in rot development requires molecular tools allowing simultaneous identification of many different targets. Therefore, a new microarray technology (ArrayTube) was applied in this study to improve diagnosis of sugar beet root rot diseases. Based on three marker genes (internal transcribed spacer, translation elongation factor 1 alpha, and 16S ribosomal DNA), 42 well-performing probes enabled the identification of prevalent field pathogens (e.g., Aphanomyces cochlioides), storage pathogens (e.g., Botrytis cinerea), and ubiquitous spoilage fungi (e.g., Penicillium expansum). All probes were proven for specificity with pure cultures from 73 microorganism species as well as for in planta detection of their target species using inoculated sugar beet tissue. Microarray-based identification of root rot pathogens in diseased field beets was successfully confirmed by classical detection methods. The high discriminatory potential was proven by Fusarium species differentiation based on a single nucleotide polymorphism. The results demonstrate that the ArrayTube constitute an innovative tool allowing a rapid and reliable detection of plant pathogens particularly when multiple microorganism species are present.
authors.affiliation: First, second, and fourth authors: Institute of Sugar Beet Research, Holtenser Landstr. 77, 37079 Göttingen, Germany; and third author: Alere Technologies GmbH, Löbstedter Str. 105, 07743 Jena, Germany, and InfectoGnostics Research Campus Jena, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Liebe
authors.affiliation: First, second, and fourth authors: Institute of Sugar Beet Research, Holtenser Landstr. 77, 37079 Göttingen, Germany; and third author: Alere Technologies GmbH, Löbstedter Str. 105, 07743 Jena, Germany, and InfectoGnostics Research Campus Jena, Germany.
authors.forename: Daniela S
authors.initials: DS
authors.lastname: Christ
authors.affiliation: First, second, and fourth authors: Institute of Sugar Beet Research, Holtenser Landstr. 77, 37079 Göttingen, Germany; and third author: Alere Technologies GmbH, Löbstedter Str. 105, 07743 Jena, Germany, and InfectoGnostics Research Campus Jena, Germany.
authors.forename: Ralf
authors.initials: R
authors.lastname: Ehricht
authors.affiliation: First, second, and fourth authors: Institute of Sugar Beet Research, Holtenser Landstr. 77, 37079 Göttingen, Germany; and third author: Alere Technologies GmbH, Löbstedter Str. 105, 07743 Jena, Germany, and InfectoGnostics Research Campus Jena, Germany.
authors.forename: Mark
authors.initials: M
authors.lastname: Varrelmann
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000302:isolation & purification; D027461:Beta vulgaris / Q000382:microbiology*; D005658:Fungi / Q000235:genetics* / Q000302:isolation & purification; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009868:Oomycetes / Q000235:genetics* / Q000302:isolation & purification; D010935:Plant Diseases / Q000382:microbiology*; D013045:Species Specificity