Molecular diagnostics of Conopomorpha cramerella (Snellen) (Lepidoptera: Gracillaridae)

The cocoa pod borer (CPB) moth, Conopomorpha cramerella (Snellen) is one of the most injurious pests of cocoa in South-East Asia. Identification relies upon tedious morphological procedures such as genitalia dissection for adults, and there are no keys for larvae or pupae. We used the COI barcode region as an alternative diagnostic method to confirm species identification of all three stages, that is, larvae, pupae and adults. Specimens were collected using various methods, including pheromone traps and direct removal of larvae from a range of fruits such as taun, cocoa and rambutan. The surveys took place in 2008–2009 in Papua New Guinea, Malaysia and Indonesia. Three Molecular Operational Taxonomic Units were detected: two Conopomorpha (Gracillaridae) species (one being CPB) and one undetermined Stathmopodidae. DNA analysis confirmed the presence of CPB at all sites, regardless of the collection method. Seven distinct haplotypes of CPB were found in total with haplotype CPB_COI_A representing 95% of the CPB samples. The remaining haplotypes diverged from CPB_COI_A by less than 0.3% and were found in cocoa and rambutan. The undetermined Conopomorpha species could not be identified using this approach due to this species not having reference DNA sequences represented in public DNA databases. We recommend using this molecular method for monitoring purposes.