Oligonucleotide microarray-based detection and identification of 10 major tomato viruses

Optimization and improvement of oligonucleotide microarray-based detection of tomato viruses and pospiviroids

“…In order to simplify the cDNA labeling step, a modified protocol with a shorter time (reduction of the labeling time from 18 h to 2 h, with a saving of 16 h), was compared with the previous protocol (Pasquini et al, 2007;Tiberini et al, 2010) in terms of the specificity and signal intensity of the hybridization. The evaluation of the labeling efficiency was based on the formula reported previously by calculating the total number of dye molecules incorporated per 1000 nucleotides.…”

“…The hybridizations, including scanning and slide stripping, were carried out according to Tiberini et al (2010) following the manufacturer's instructions by increasing the hybridization temperature from 42 • C to 50 • C.…”

“…The chip was divided into four sub-arrays, each with the oligonucleotide set of 429 virus and viroid probes including internal and negative controls, according to Tiberini et al (2010). It enabled four different, independent and simultaneous hybridization events to be performed.…”

“…They are powerful and useful methods for parallel, high-throughput experimentation in molecular biological research (Shoemaker et al, 2001). Various microarray platforms for plant virus detection have been developed, using different solid support (surfaces or beads) and oligonucleotide probe synthesis (Abdullahi et al, 2005(Abdullahi et al, , 2011Nicolaisen, 2011;Engel et al, 2010;Tiberini et al, 2010;Zhang et al, 2010;Wei et al, 2009;Pasquini et al, 2007Pasquini et al, , 2010Lenz et al, 2008;Bystricka et al, 2005;Deyong et al, 2005;Boonham et al, 2003;Bystrická et al, 2003;Lee et al, 2003). Oligonucleotide probes were first synthesized and then spotted onto a glass slide; alternatively, probes are synthesized directly onto the array surface.…”

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

“…The DNA microarrays were used for detection of potato viruses (Bystřická et al 2003), cucurbit-infecting tobamoviruses (Lee et al 2003), plum pox virus (Pasquini et al 2008), grapevine viruses (Nicolaisen 2011) and for detection of a number of plant viruses in a multiplex assay (Engel et al 2010). Other microarray studies involve both complex detection of a wide range pathogens (Zhang et al 2013) and targeted identification of pathogens in a particular plant host, e.g., tomato (Tiberini et al 2010) or potato (Fessehaie et al 2003). Nevertheless, there is no specific DNA microarray available for detection of microbial pathogens of maize (Zea mays).…”