Assessing the effect of sample storage time on viral detection using a rapid and cost-effective CTAB-based extraction...

Area of Science:

• Plant Pathology
• Molecular Biology
• Biotechnology

Background:

• Cassava leaf samples degrade rapidly during storage and transport.
• Obtaining quality DNA/RNA is essential for plant virus epidemiology and disease control.
• Low-cost, efficient methods are needed, especially for remote areas and developing countries.

Purpose of the Study:

• To investigate the effect of sample storage duration on nucleic acid (N.A.) quality for virus detection.
• To optimize and test a simple, rapid, and cost-effective CTAB-based approach (M3) for N.A. extraction.
• To compare M3 with two existing CTAB-based methods (M1 and M2).

Main Methods:

• Optimized a CTAB-based method (M3) for N.A. extraction.
• Tested M3 alongside M1 and M2 using fresh and stored cassava leaves (1-56 months).
• Quantified DNA/RNA using Nanodrop and agarose gel electrophoresis; estimated degradation rates.

Main Results:

• Method M3 extracted higher DNA concentrations for short-term storage (1-8 months).
• M3 and M2 yielded high DNA concentrations for long-term storage (26-56 months).
• M3 and M2 produced high-quality DNA from fresh samples; RT-PCR detected viruses from M3-extracted RNA.

Conclusions:

• The optimized CTAB method (M3) is cost-effective, quick, and simple for processing fresh and dry cassava samples.
• This method aids in timely decisions for plant disease management and surveillance.
• It enables efficient N.A. extraction for plant virus diagnostics in resource-limited settings.