In Ecuador, the cocoa bean clone CCN-51 is grown for bulk cocoa bean use, whereas the "Arriba Nacional" variety is highly valued for its fine cocoa flavour. An assay based on in-vitro use of CRISPR-Cpf1, which is suitable for AT-rich targets, such as the chloroplast genome (cpGenome), was developed to give a rapid differentiation between the two cocoa varieties. Two assay systems were used to digest both Arriba and CCN-51. The results were tested qualitatively by agarose gel electrophoresis, and quantitatively by capillary gel electrophoresis. Using this assay, admixtures containing 5% CCN-51 (P < 0.01) in Arriba and 10% Arriba (P < 0.05) in CCN-51were reliably detected. The application to processed cocoa products was also successful.
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