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Development of a specific PCR assay for the detection of Rhizoctonia solani AG 1‐IB using SCAR primers
Author(s) -
Grosch R.,
Schneider J.H.M.,
Peth A.,
Waschke A.,
Franken P.,
Kofoet A.,
JabajiHare S.H.
Publication year - 2007
Publication title -
journal of applied microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.889
H-Index - 156
eISSN - 1365-2672
pISSN - 1364-5072
DOI - 10.1111/j.1365-2672.2006.03125.x
Subject(s) - rhizoctonia solani , primer (cosmetics) , rapd , polymerase chain reaction , biology , ribosomal dna , phylogenetic tree , sequence analysis , genetics , microbiology and biotechnology , internal transcribed spacer , dna , botany , gene , genetic diversity , chemistry , population , medicine , environmental health , organic chemistry
Aims: 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. Methods and 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. Significance and Impact of the Study: 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.