Evaluation of USM Biotech DNA extraction method for selected agricultural crops in comparison with existing methods

Abstract

Different DNA extraction protocols have been used in plant DNA extraction. However, no comparative analysis has been done to determine their efficiency, cost effectiveness and time requirement for the extraction. Three (3) established protocols and the USM Biotech modified protocols were used in this study. It aimed to evaluate the efficiency of the four DNA extraction protocols in terms of DNA yield, purity and processing time; to determine and compare the cost of sample analysis per protocol and to assess which protocol is universally applicable in extracting DNA of selected agricultural crops (banana, cacao, durian, mango and rubber). The experiment was carried out in 4X5 factorial arranged in Complete Randomized Design (CRD), Factor A as protocols and Factor B as crops used. Results of the study showed that among four (4) protocols, the protocol developed by Ferdous et al. (2012) was the most cost effective. It was the least expensive and fastest method of extracting DNA resulting to high genomic DNA yield. Likewise, University of Southern Mindanao (USM) Biotech modified protocol was found to be another efficient, economical and effective method of extracting DNA with sufficient amount of DNA yields. The protocol developed by Ray et al. (2016) produced the highest DNA yield; however, it was the most time-consuming method among the four (4) protocols. The Diversity Array Technology (DArT) protocol on the other hand, was the most expensive method among the four protocols because it required the use of expensive reagents and liquid nitrogen.