Soybean oil has recently emerged as the most widely consumed genetically modified (GM) vegetable oil globally. DNA-based methods offer considerable advantages for monitoring GM-derived products; however, their efficacy strongly depends on the quality and quantity of extracted DNA. Owing to intensive processing, refined oils typically contain extremely low concentrations of severely fragmented DNA, making DNA extraction highly challenging. To address this issue, we introduce an innovative magnetic bead-based DNA extraction protocol specifically tailored to refined soybean oils. Optimal DNA adsorption was achieved using 300 nm carboxyl (-COOH)-modified magnetic beads under optimized conditions, including 1 M guanidine isothiocyanate (GITC) buffer at pH 6.0, combined with ethanol at a 1:1 ratio. Subsequently, we developed a cetyltrimethylammonium bromide (CTAB)-magnetic bead method in which DNA was efficiently transferred from the oil phase to the aqueous phase, concentrated via precipitation, resuspended in GITC buffer, and finally purified using magnetic beads. Comparative evaluations using nested polymerase chain reaction (PCR) and real-time PCR confirmed that this method significantly outperformed traditional CTAB-based methods (CTAB alone, CTAB-hexane) and two representative silica membrane-based extraction kits. Spike recovery experiments further demonstrated its superior efficacy, achieving a DNA recovery rate of 76.37%. The proposed protocol is simple, user-friendly, cost-effective, and highly efficient, markedly reducing reliance on large volumes of organic solvents (e.g., hexane and chloroform) and minimizing the required centrifugation steps. This novel method established an effective approach for DNA extraction from refined vegetable oils, facilitating the development of rapid and reliable GM detection.

Soybean is the most widely cultivated genetically modified (GM) crop worldwide, making the detection of GM soybean oil a critical issue for food safety and trade compliance. Such detection depends on whether DNA survives oil processing, yet how processing affects DNA in refined oil has remained unclear. Here, we tracked DNA mass and gene integrity along a complete industrial soybean oil processing chain, from seed to deodorized oil, and compared three degumming methods at laboratory scale. DNA mass dropped sharply during crude oil extraction and degumming, the larger part of the loss occurring between the meal and the crude oil, leaving refined oils with extremely low levels (2.60 × 10⁻² to 7.43 × 10⁻¹ ng/g). During degumming, most DNA moved from crude oil into the oil sediment, with removal efficiency decreasing in the order enzymatic > acid > hydration degumming, in line with phospholipid removal. The lectin and cp4 epsps genes degraded mainly during solvent extraction and deodorization. These findings reveal where GM DNA is lost or destroyed along the chain, show that fragments below 200 bp survive to fully refined oil, and identify enzymatic degumming as the most effective treatment for removing DNA (at the lab scale). Testing of refined soybean oil therefore requires short amplicons, and a negative result obtained with longer targets does not demonstrate the absence of GM material.