Comparative study of DNA extraction methods for Dendrobium bantimurung orchids using commercial kits and a modified CTAB method

Abstract

Genomic DNA extraction is a critical step in plant molecular studies, particularly in species rich in secondary metabolites that may interfere with DNA isolation and downstream analyses. Dendrobium bantimurung is an orchid species containing high levels of phenolic compounds; therefore, it requires an effective DNA extraction method. This study aimed to compare the effectiveness of a modified CTAB method with two commercial DNA extraction kits, Geneaid and Vazyme, for genomic DNA isolation from D. bantimurung plantlets. DNA was extracted from the leaf and root tissues of six-month-old plantlets. DNA quality and quantity were evaluated by DNA concentration, purity ratios (A260/280 and A260/230), agarose gel electrophoresis, and PCR amplification with ITS primers. The results showed that the modified CTAB method produced the highest DNA quality and the most successful PCR amplification compared with the commercial kits. However, the kit-based methods offered advantages in terms of speed and practicality. These findings indicate that the modified CTAB method is more suitable for genomic DNA extraction from D. bantimurung, whereas commercial kits require further optimization to improve their performance.