title: DNA-based differentiation of the Ecuadorian cocoa types CCN-51 and Arriba based on sequence differences in the chloroplast genome.
abstract: Two cocoa types, Arriba and CCN-51, are being cultivated in Ecuador. With regard to the unique aroma, Arriba is considered a fine cocoa type, while CCN-51 is a bulk cocoa because of its weaker aroma. Because it is being assumed that Arriba is mixed with CCN-51, there is an interest in the analytical differentiation of the two types. Two methods to identify CCN-51 adulterations in Arriba cocoa were developed on the basis of differences in the chloroplast DNA. On the one hand, a different repeat of the sequence TAAAG in the inverted repeat region results in a different length of amplicons for the two cocoa types, which can be detected by agarose gel electrophoresis, capillary gel electrophoresis, and denaturing high-performance liquid chromatography. On the other hand, single nucleotide polymorphisms (SNPs) between the CCN-51 and Arriba sequences represent restriction sites, which can be used for restriction fragment length polymorphism analysis. A semi-quantitative analysis based on these SNPs is feasible. A method for an exact quantitation based on these results is not realizable. These sequence variations were confirmed for a comprehensive cultivar collection of Arriba and CCN-51, for both bean and leaf samples.
authors.affiliation: Hamburg School of Food Science, Institut für Lebensmittelchemie, Universität Hamburg , Grindelallee 117, 20146 Hamburg, Germany.
authors.forename: Luise
authors.initials: L
authors.lastname: Herrmann
authors.forename: Ilka
authors.initials: I
authors.lastname: Haase
authors.forename: Maike
authors.initials: M
authors.lastname: Blauhut
authors.forename: Nadine
authors.initials: N
authors.lastname: Barz
authors.forename: Markus
authors.initials: M
authors.lastname: Fischer
mesh_terms: D001483:Base Sequence; D002099:Cacao / Q000145:classification* / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D016002:Discriminant Analysis; D004484:Ecuador; D014644:Genetic Variation; D054628:Genome, Chloroplast; D008969:Molecular Sequence Data; D018515:Plant Leaves / Q000145:classification / Q000235:genetics; D012150:Polymorphism, Restriction Fragment Length; D020641:Polymorphism, Single Nucleotide; D012639:Seeds / Q000145:classification / Q000235:genetics
chemical_list: D018744:DNA, Plant
keywords: Arriba; CCN-51; Theobroma cacao; chloroplast genome; inverted repeat region