DNA microarray-based detection and identification of bacterial and viral pathogens of maize

Abstract

We describe the construction and evaluation of DNA microarray for simultaneous detection and identification of five microbial pathogens of maize: Pantoea ananatis, P. agglomerans, Enterobacter cloaceae subsp. dissolvens, Maize dwarf mosaic virus (MDMV) and Sugarcane mosaic virus (SCMV). Unlike other DNA microarrays described, our microarray comprises probes targeting the whole genomes of the tested pathogens. Control probes are complementary to genomes of closely related microorganisms that are nonpathogenic to maize and against maize and human genome sequences in order to avoid the potential false-positive results. Obtained results indicate that the fluorescence signals from pathogen and control probes are well distinguished in all performed experiments. The microarray's performance was compared with classical PCR-based pathogen detection method, and the versatility of the assay was tested in silico.

Current and emerging trends in techniques for plant pathogen detection

“…Several arrays have been developed to detect bacterial, fungal and viral plant pathogens ( Lievens et al., 2003 ; Zhang et al., 2008 ; Narayanasamy, 2011 ; Charlermroj et al., 2013 ; Úrbez-Torres et al., 2015 ; Krawczyk et al., 2017 ; Bhat and Rao, 2020 ; Aslam et al., 2022 ). Commercial kits are also available, such as a macro-array that is able to detect 8 potato viruses simultaneously (BIOREBA).…”

Recent Advances in Molecular Diagnostics of Fungal Plant Pathogens: A Mini Review

“…Hybridized probe-cDNA systems can be detected and quantified using fluorophore, silver, or chemiluminescence-labeled targets to define the comparative abundance of transcripts in the sample ( Guigó, 2013 ). Advancement of DNA microarray technology has led high throughput and multiple detection of various phytopathogens including viruses, viroids, bacteria, and fungi ( Tiberini and Barba, 2012 ; Musser et al., 2014 ; Nam et al., 2014 ; Krawczyk et al., 2017 ). PCR primers and florescent probes for targeting fungal potato pathogens Rhizoctonia solani , Spongospora subterranea ( ITS region), Alternaria solani , A. alternata ( Alt_a1 gene), Fusarium sp.…”

Next-generation DNA sequencing of Panax samples revealed new genotypes: Burrows-Wheeler Aligner, Python-based abundance and clustering analysis

“…There are many genetic methods available that use single nucleotide polymorphisms (SNPs), e.g., nucleic acid test (NAT) using probe-PCR product strand hybridization [ [4] , [5] , [6] , [7] , [8] ], qPCR [ [9] , [10] , [11] ], and lesion induced DNA amplification (LIDA) [ [12] , [13] , [14] ]. These techniques, which are effective when the DNA samples have known single nucleotide polymorphisms (SNPs), require considerable optimization.…”