Evaluation of three different DNA extraction methods for the detection of Pepper yellow leaf curl virus (PepYLCV) by Polymerase Chain Reaction

Abstract

Abstract Pepper yellow leaf curl virus (PepYLCV) from the genus Begomovirus infecting Chili pepper plant can cause significant yield losses. PepYLCV infection can lead the development of mosaic yellow, mottled pattern and yellowing leaves, which can be challenging in disease management and control. Developing effective detection methods for PepYLCV is a critical disease management and crop loss mitigation. The Begomovirus viruses have extremely low viral concentrations and are limited to the phloem and vascular system. DNA extraction is an important step in PepYLCV detection. This study aimed to evaluate the efficiency of three DNA extraction methods: phenol-based extraction, CTAB-based extraction, and the GeneJET Plant Genomic DNA Purification Kit (Thermo Scientific™). These methods were evaluated for their performance to identified the presence of PepYLCV DNA and provide accurate results for further analyses. DNA samples were extracted from two varieties including Red Habanero and F8 012328-6-2-1-1-3-1, and were subsequently amplified using Krusty Homer’s primers. The results showed that all three extraction methods possess the capability to identify PepYLCV. Based on the results, DNA extraction employing the CTAB-based method yields DNA with higher concentration and purity levels. Additionally, this method proves to be cost-effective and proficient in generating higher DNA concentrations.