Back to Search
Start Over
DNA barcode, multiplex PCR and qPCR assay for diagnosis of pathogens infecting pulse crops to facilitate safe exchange and healthy conservation of germplasm.
- Source :
-
Archives of microbiology [Arch Microbiol] 2021 Jul; Vol. 203 (5), pp. 2575-2589. Date of Electronic Publication: 2021 Mar 08. - Publication Year :
- 2021
-
Abstract
- The DNA barcodes were developed from ITS region for the identification of fungal plant pathogens namely, Alternaria alternata and A. tenuissima both causing leaf spots, Ascochyta rabiei causing Ascochyta blight, Fusarium oxysporum f. sp. ciceris causing wilt, Macrophomina phaseolina causing dry root rot, Rhizoctonia solani causing web blight and wet root rot, Sclerotium (Athelia) rolfsii causing collar rot, Sclerotinia sclerotiorum causing stem rot and Cercospora canescens and Pseudocercospora cruenta both causing leaf spots in pulse crops. Barcode compliance for A. alternata (DBTPQ001-18), A. tenuissima (DBTPQ002-18), A. rabiei (DBTPQ003-18), F. oxysporum f. sp. ciceris (DBTPQ004-18), M. phaseolina (DBTPQ005-18), R. solani (DBTPQ006-18), S. rolfsii (DBTPQ007-18), S. sclerotiorum (DBTPQ008-18), C. canescens (DBTPQ009-18) and P. cruenta (DBTPQ029-20) have been generated based on the Barcode of Life Data System (BOLD) system. In addition to ITS, other genomic regions were also explored and on the basis of sequence variation they were ranked as TEF-α > SSU > LSU > β-tubulin. These genes could be considered for secondary barcode and phylogenetic relatedness. ITS-based markers for the detection of A. alternata (BAA2aF and BAA2aR) and R. solani (BRS17cF and BRS17cR) were developed which provided 400 bp and 220 bp amplicons, respectively. While, for F. oxysporum f. sp. ciceris, COX1-based marker (FOCox1F and FOCox3R) was developed which amplified 150 bp. The markers proved highly specific and sensitive with detection limit of 0.0001 ng of template DNA using qPCR and simultaneously detected these three pathogens. The DNA barcodes and diagnostics developed are suitable for quick and reliable detection of these pathogens during quarantine processing and field diagnostics.
- Subjects :
- Alternaria classification
Alternaria genetics
Alternaria isolation & purification
Ascomycota classification
Ascomycota genetics
Ascomycota isolation & purification
DNA, Fungal genetics
Fungi genetics
Fungi isolation & purification
Fusarium classification
Fusarium genetics
Fusarium isolation & purification
Multiplex Polymerase Chain Reaction
Phylogeny
Real-Time Polymerase Chain Reaction
Rhizoctonia classification
Rhizoctonia genetics
Rhizoctonia isolation & purification
Crops, Agricultural microbiology
DNA Barcoding, Taxonomic
Fabaceae microbiology
Fungi classification
Plant Diseases microbiology
Polymerase Chain Reaction
Subjects
Details
- Language :
- English
- ISSN :
- 1432-072X
- Volume :
- 203
- Issue :
- 5
- Database :
- MEDLINE
- Journal :
- Archives of microbiology
- Publication Type :
- Academic Journal
- Accession number :
- 33683395
- Full Text :
- https://doi.org/10.1007/s00203-021-02259-w