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Molecular tools to investigate Rhizoctonia solani distribution in soil
Author(s) -
Budge G. E.,
Shaw M. W.,
Colyer A.,
Pietravalle S.,
Boonham N.
Publication year - 2009
Publication title -
plant pathology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.928
H-Index - 85
eISSN - 1365-3059
pISSN - 0032-0862
DOI - 10.1111/j.1365-3059.2009.02139.x
Subject(s) - rhizoctonia solani , biology , dna extraction , internal transcribed spacer , ribosomal dna , soil water , extraction (chemistry) , soil test , veterinary medicine , polymerase chain reaction , botany , microbiology and biotechnology , horticulture , ribosomal rna , chromatography , chemistry , genetics , phylogenetics , ecology , gene , medicine
Real‐time PCR protocols were developed to detect and discriminate 11 anastomosis groups (AGs) of Rhizoctonia solani using ribosomal internal transcribed spacer (ITS) regions (AG‐1‐IA, AG‐1‐IC, AG‐2‐1, AG‐2‐2, AG‐4HGI+II, AG‐4HGIII, AG‐8) or β‐tubulin (AG‐3, AG‐4HGII, AG‐5 and AG‐9) sequences. All real‐time assays were target group specific, except AG‐2‐2, which showed a weak cross‐reaction with AG‐2 tabac . In addition, methods were developed for the high throughput extraction of DNA from soil and compost samples. The DNA extraction method was used with the AG‐2‐1 assay and shown to be quantitative with a detection threshold of 10 −7 g of R. solani per g of soil. A similar DNA extraction efficiency was observed for samples from three contrasting soil types. The developed methods were then used to investigate the spatial distribution of R. solani AG‐2‐1 in field soils. Soil from shallow depths of a field planted with Brassica oleracea tested positive for R. solani AG‐2‐1 more frequently than soil collected from greater depths. Quantification of R. solani inoculum in field samples proved challenging due to low levels of inoculum in naturally occurring soils. The potential uses of real‐time PCR and DNA extraction protocols to investigate the epidemiology of R. solani are discussed.