Genomic DNA Extraction Methods for Optimal Quality DNA Recovery from Tomato Yellow Leaf Curl Virus (TYLCV)

Abstract

High quality DNA is essential for numerous downstream applications, especially PCR. Currently, various protocols for plant DNA extraction already exists, many of which are modifications of the CTAB method, aiming to enhance the extraction process and improve the quality and yield of DNA. This study primarily focuses in comparing three DNA extraction protocols commonly used to detect Tomato Yellow Leaf Curl Virus on infected tomato plants. Ten tomato leaf samples that were treated with liquid nitrogen were used in the experiment. Based on the results, the CTAB method has the highest DNA concentration mean of 1718.01ng/µL and it’s the only protocol that passed the purity ratio of A260/280 with an average value of 1.96 (range: 1.74-2.12) and a value of 1.45 on purity ratio of A260/230. Interestingly, despite its superior DNA quality, the CTAB method had the lowest number of samples that successfully amplified the A2 gene. This occurrence needs further investigation to identify what causes the contrasting results. In this case, the commercial kit and the NaOH produced better results in amplifying the viral A2 gene of the Tomato Yellow Leaf Curl Virus. Further optimization on the DNA extraction protocol is highly encouraged to produce high qualityDNA extract that will effectively amplify the viral gene and produce distinct PCR bands.