This study aimed to establish a highly specific and sensitive quantitative assay for transgenic maize CC-2, independently developed in China, using droplet digital polymerase chain reaction (ddPCR). Primers and probes were designed to target the specific insertion sequence of the CC-2 event. The reaction conditions were systematically optimized. A duplex ddPCR system was successfully developed, enabling the simultaneous detection of the endogenous gene and the CC-2 event-specific fragment. The verification results demonstrated that this method exhibited no cross-amplification in various non-target genetically modified (GM) events, confirming its high specificity; a linear response was achieved covering the range from 20 to 20000 copies for the genomic DNA of CC-2, and the limit of detection (LOD) and limit of quantification (LOQ) were found to be 10 and 20 copies, respectively. In a blind test, the method demonstrated high repeatability and accuracy for samples containing varying concentrations of the event, meeting both national and international standards for the quantitative analysis of genetically modified organisms (GMO). The ddPCR method provides a robust technical foundation for the commercial cultivation of transgenic maize CC-2 and the regulatory monitoring of its products.

Using genetically modified (GM) soybean MON87705 containing the figwort mosaic virus 35S promoter (FMV 35S) as a marker gene, a quantitative method for detecting transgenic crops was established based on real-time fluorescent quantitative polymerase chain reaction (real-time PCR) and digital polymerase chain reaction (dPCR). The amplification system was tested by real-time PCR, revealing that the developed method was highly specific to FMV 35S. By determining quantitative parameters using duplex droplet digital PCR (ddPCR), it was found that within the genomic DNA concentration range of 0.005–20 ng/mL, the measured copy number of the target gene had a good linear correlation with the theoretical copy number; the limit of detection (LOD) and the limit of quantification (LOQ) of dPCR for FMV 35S were as low as 5 copies and 0.1%, respectively. Blind samples with different contents of MON87705 were tested on two dPCR platforms, indicating that accurate, reliable and reproducible results were obtained in the duplex and triple detection using a combination of internal reference genes and foreign specific fragments. Therefore, the quantitative dPCR method, which can meet the parameter requirements of the quantitative detection standard for genetically modified components with improved detection efficiency, represents an accurate and simple technology for the quantitative detection of genetically modified crops.