PCR-Based Methods — A Promising Tool for Detection and Identification of Fungi in Soil

Lübeck, Mette; Lübeck, Peter Stephensen

doi:10.1007/978-94-009-1698-2_16

Cited by 9 publications

(6 citation statements)

References 39 publications

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“…The developed PCR assay does not allow a quantification of target DNA. Detection of a small amount of target organisms in an environment requires a high level of sensitivity (Lübeck and Lübeck 1996). Future work will be devoted to developing a PCR quantitative assay with higher sensitivity for determining the infection level in plant and soil samples.…”

Section: Discussionmentioning

confidence: 99%

Development of a specific PCR assay for the detection of Rhizoctonia solani AG 1-IB using SCAR primers

et al. 2007

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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.

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Section: Discussionmentioning

confidence: 99%

Development of a specific PCR assay for the detection of Rhizoctonia solani AG 1-IB using SCAR primers

et al. 2007

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“…Future work will include sequencing of the fragments to design specific primers that selectively amplify the 0.7kb marker. This could be used more directly for monitoring the presence of such an isolate in soil assays where total DNA is extracted from soil and amplified with such primers ( Lübeck and Lübeck, 1996).…”

Section: Discussionmentioning

confidence: 99%

Characterization of Trichoderma Isolates from Philippine Rice Fields by UP‐PCR and rDNA‐ITS1 Analysis: Identification of UP‐PCR Markers

Cumagun¹,

Hockenhull

Lübeck³

2000

Journal of Phytopathology

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Forty‐two isolates of Trichoderma from rice fields in four provinces in the Philippines were characterized using rDNA‐ITS1 analysis and universally primed polymerase chain reaction (UP‐PCR). Two groups were clearly distinguishable on the basis of length and restriction pattern of the internal transcribed spacer (ITS) region of the ribosomal DNA and UP‐PCR banding profiles using UP primer, L45. The 40 isolates comprising the largest group were very similar with respect to their UP‐PCR banding profiles and were assigned to Trichoderma harzianum Rifai following morphological identification of four of the isolates. The two isolates belonging to the second group were identified as Trichodermaviride Pers. ex. Gray on the basis of their morphology, rDNA‐ITS1 analysis and distinct UP‐PCR banding profiles. One of the T. harzianum isolates with good cellulolytic and competitive saprophytic abilities was analysed using single and pair‐wise combinations of UP primers in order to distinguish it from the remaining 41 isolates. A suitable diagnostic marker was identified and this marker will be valuable for monitoring the isolate in field tests.

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“…Several molecular tools are available to study populations of ectomycorrhizal fungi (Lubeck & Lubeck 1996), some of which are rapid and require low quantities of DNA template. A useful tool is the analysis of PCR‐amplified polymorphic ribosomal DNA loci (Henrion et al 1994; Selosse et al 1996).…”

Section: Introductionmentioning

confidence: 99%

Temporal persistence and spatial distribution of an American inoculant strain of the ectomycorrhizal basidiomycete Laccaria bicolor in a French forest plantation

et al. 1998

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Selected strains of ectomycorrhizal fungi, such as the basidiomycete Laccaria bicolor, are currently being used as inoculants in nurseries to improve growth of forest trees after outplanting. Information is needed on the survival of these introduced strains in forests and their impact on indigenous biodiversity. Dissemination and persistence of an American strain, L. bicolor S238N, were studied 10 years after outplanting in a Douglas fir plantation located at Saint‐Brisson (Morvan, France). About 430 Laccaria spp. sporophores were collected over 3 years. Inheritance of nuclear ribosomal DNA, as well as RAPD markers, was characterized in L. bicolor S238N, using a haploid progeny set of 91 monokaryons. More than 50 markers were identified (19 heterozygous and 33 homozygous or cytoplasmic markers), which unambiguously confirmed that the introduced strain was still present in the inoculated plots. Neither selfing (P < 0.0008) nor introgression with indigenous strains was detected although in vitro interfertility between the American strain and indigenous L. bicolor was identified. No ingress of the introduced genet into adjacent uninoculated plots colonized by various local Laccaria genets was detected. It is proposed that the spatial distributions identified have developed through mycelial propagation of the introduced strain and intraspecific competition with native genets. Although longer‐term data is still lacking, the stability of the inoculant strain and the limited disturbance to indigenous populations described support large‐scale nursery production of this host‐fungal combination.

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PCR-Based Methods — A Promising Tool for Detection and Identification of Fungi in Soil

Cited by 9 publications

References 39 publications

Development of a specific PCR assay for the detection of Rhizoctonia solani AG 1-IB using SCAR primers

Development of a specific PCR assay for the detection of Rhizoctonia solani AG 1-IB using SCAR primers

Characterization of Trichoderma Isolates from Philippine Rice Fields by UP‐PCR and rDNA‐ITS1 Analysis: Identification of UP‐PCR Markers

Temporal persistence and spatial distribution of an American inoculant strain of the ectomycorrhizal basidiomycete Laccaria bicolor in a French forest plantation

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