Sensitive and selective detection of DNA fragments associated with Ganoderma boninense by DNA-nanoparticle conjugate hybridisation

Abstract

A colourimetric assay for the detection of DNA fragments associated with the oil palm pathogen Ganoderma boninense and other fungi DNA is reported. The assay is based on the aggregation of DNA-nanoparticle conjugates in the presence of complementary DNA from the target organism. Here, various designs of DNAnanoparticle conjugates were evaluated, and it was found that the best design gave a visually observable colour change with as little as 2 pmol of doublestranded DNA analyte even in the presence of a large excess of a mixture of noncomplementary DNA. Overall, this label-free system is rapid, sensitive, selective, simple in design, and easy to carry out. It does not require specialist equipment or specialist training for the interpretation of the results, and therefore has the potential to be deployed for agricultural diagnostics in the field.

Classification of basal stem rot using deep learning: a review of digital data collection and palm disease classification methods

“…BSR infection causes an estimated economic loss of RM 225 million to 2.2 billion per annum . BSR can potentially destroy 860,610 hectares worth of oil palm plantations by year 2040 ( Bharudin et al, 2022 ; Rani et al, 2020 ; Olaniyi & Szulczyk, 2020 ).…”

“…Many approaches to manage BSR were discussed in chapter II of this review article, which include physical, chemical and biocontrol. Physical control is expensive as it requires huge labor and manpower, which with the shortage of labor it is even more difficult to physically control the spread of BSR ( Siddiqui et al, 2021 ; Rani et al, 2020 ; Ho et al, 2016 ). Chemical and biocontrol methods often have biosafety concerns, and most methods are proven inadequate to significantly control the spread of BSR ( Siddiqui et al, 2021 ; Nurazah et al, 2021 ).…”

“…The plant disease mentioned that has severely impacted the growth of the industry is called the basal stem rot (BSR). BSR has directly caused a significant reduction in the yearly harvest of the oil palm ( Rani et al, 2020 ).…”

“…As a result, Rani et al (2020) estimated that BSR causes an RM 225 million economic loss in Malaysia per annum . Bharudin et al (2022) estimated that the economic loss is up to USD 500 million (about RM 2.2 billion) per annum .…”

“…Therefore, detection method that is quantitative, sensitive and selective need to be developed to detect BSR at the early phase. The solution should also be affordable, having high tolerance towards hostile environmental conditions and not requiring specialized equipment or training ( Rani et al, 2020 ).…”