Application Guide - QIAxcel Advanced

82 QIAxcel Advanced Application Guide 10/2016 ISSR-PCR fingerprinting of plant pathogen strains using the QIAxcel® system and BioNumerics® Steve Baeyen1 , Joanna Zaluga2 , Paul De Vos2 , Martine Maes1 1 Plant-Crop Protection, Institute for Agricultural and Fisheries Research (ILVO), Burg. Van Gansberghelaan 96, B-9820 Merelbeke, Belgium 2 Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium Introduction The causal organism of bacterial canker in tomato plants is the seed-borne pathogen Clavibacter michiganensis subsp. michiganensis (1). It is a quarantine organism under the European Union Plant Health legislation (2). It poses serious economic risks in tomato cultivation, as epidemics can result from the spread of contaminated seed and transmission of the pathogen to seedlings and plants (3). In this study, ISSR sequences of individual C. michiganensis subsp. michiganensis strains were amplified using ISSR-PCR and analyzed using the QIAxcel Advanced System. ISSR stands for Inter Simple Sequence Repeat and refers to the genome regions between microsatellite loci. It is a rapid and inexpensive genotyping technique with a wide range of applications, including the characterization of genetic relatedness among the organisms of a population (4). ISSR profiling is as reproducible as AFLP, but more cost effective (5). The QIAxcel Advanced System ScreenGel® software is fully compatible with BioNumerics software. Using the QIAxcel plugin, raw data files from the QIAxcel software can be imported as densitometric curve files (with the file extensions .xml and .csv) or peak table files (with the file extensions .xdr). BioNumerics Plug-in v1.0 makes it possible to link any sample information (e.g., sample names) provided in ScreenGel (v1.0.1.0) to entries in a BioNumerics database. After ISSR fingerprints have been imported, they can be reliably normalized. Automated peak-calling algorithms allow rapid assignment of bands. Optionally, the software can exclude interfering primer dimers by discarding all peaks below or above a certain peak height. Since the BioNumerics platform allows the storage of genomic and phenotypic biological data in one program, it also enables the combination of fingerprint patterns obtained using ISSR-PCR

Pages Overview