title: Development of a specific PCR assay for the detection of Rhizoctonia solani AG 1-IB using SCAR primers.
abstract: OBJECTIVE
  The aim of this study was to develop a specific and sensitive identification method for Rhizoctonia solani AG 1-IB isolates based on phylogenetic relationships of R. solani AG-1 subgroups using rDNA-internal transcribed spacer (rDNA-ITS) sequence analysis.
  
  
  RESULTS
  A neighbour-joining tree analysis of 40 rDNA-ITS sequences demonstrated that R. solani AG-1 isolates cluster separately in six subgroups IA, IB, IC, ID, IE and IF. A molecular marker was generated from a random amplified polymorphic DNA fragment (RAPD). After conversion into a sequence-characterized amplified region (SCAR), a specific primer set for identification of subgroup AG 1-IB was designed for use in a polymerase chain reaction (PCR). The primer pair amplified a single DNA product of 324 bp.
  
  
  CONCLUSIONS
  R. solani AG-1 subgroups were discriminated by sequence analysis of the ITS region. The designed SCAR primer pair allowed an unequivocal and rapid detection of R. solani AG 1-IB in plant and soil samples.
  
  
  CONCLUSIONS
  Sequence analysis of the rDNA-ITS region can be used for differentiation of subgroups within AG-1. The use of the developed SCAR primer set allowed a reliable and fast identification of R. solani AG 1-IB and provides a powerful tool for disease diagnosis.
authors.affiliation: Institute of Vegetable and Ornamental Crops IGZ, Grossbeeren/Erfurt e.V., Germany. grosch@igzev.de
authors.forename: R
authors.initials: R
authors.lastname: Grosch
authors.forename: J H M
authors.initials: JH
authors.lastname: Schneider
authors.forename: A
authors.initials: A
authors.lastname: Peth
authors.forename: A
authors.initials: A
authors.lastname: Waschke
authors.forename: P
authors.initials: P
authors.lastname: Franken
authors.forename: A
authors.initials: A
authors.lastname: Kofoet
authors.forename: S H
authors.initials: SH
authors.lastname: Jabaji-Hare
mesh_terms: D001483:Base Sequence; D017931:DNA Primers / Q000235:genetics; D004271:DNA, Fungal / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000235:genetics*; D016533:Mycological Typing Techniques / Q000379:methods; D010802:Phylogeny; D010944:Plants / Q000382:microbiology; D016133:Polymerase Chain Reaction / Q000379:methods*; D019105:Random Amplified Polymorphic DNA Technique / Q000379:methods; D012232:Rhizoctonia / Q000235:genetics / Q000302:isolation & purification*; D017422:Sequence Analysis, DNA / Q000379:methods; D012988:Soil Microbiology; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D017931:DNA Primers; D004271:DNA, Fungal; D021903:DNA, Ribosomal Spacer