Duplex digital droplet PCR for the determination of non-Basmati rice in Basmati rice (Oryza sativa) on the base of a deletion in the fragrant gene

Due to its higher trade value, a broad range of adulterations of Basmati rice with cheaper rice varieties can be found on the market. A duplex digital droplet PCR (ddPCR) assay was developed to test rice samples, labeled as “Basmati,” for their authenticity. The new ddPCR assay is based on the real-time PCR (rtPCR) method published previously. It showed to be able to screen for non-Basmati rice contents in the range of 1 % or higher. As digital PCR does not require calibrators for the quantification, the method is more economic, compared to rtPCR or microsatellite analysis (MA). It is also less time-consuming than MA and an alternative method for the verification of rtPCR results. Comparing results gained by all three methods revealed best correlation between ddPCR and MA.