Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions.

BACKGROUND: Theobroma cacao L., is a tree originated from the tropical rainforest of South America. It is one of the major cash crops for many tropical countries. T. cacao is mainly produced on smallholdings, providing resources for 14 million farmers. Disease resistance and T. cacao quality improvement are two important challenges for all actors of cocoa and chocolate production. T. cacao is seriously affected by pests and fungal diseases, responsible for more than 40% yield losses and quality improvement, nutritional and organoleptic, is also important for consumers. An international collaboration was formed to develop an EST genomic resource database for cacao. RESULTS: Fifty-six cDNA libraries were constructed from different organs, different genotypes and different environmental conditions. A total of 149,650 valid EST sequences were generated corresponding to 48,594 unigenes, 12,692 contigs and 35,902 singletons. A total of 29,849 unigenes shared significant homology with public sequences from other species.Gene Ontology (GO) annotation was applied to distribute the ESTs among the main GO categories.A specific information system (ESTtik) was constructed to process, store and manage this EST collection allowing the user to query a database.To check the representativeness of our EST collection, we looked for the genes known to be involved in two different metabolic pathways extensively studied in other plant species and important for T. cacao qualities: the flavonoid and the terpene pathways. Most of the enzymes described in other crops for these two metabolic pathways were found in our EST collection.A large collection of new genetic markers was provided by this ESTs collection. CONCLUSION: This EST collection displays a good representation of the T. cacao transcriptome, suitable for analysis of biochemical pathways based on oligonucleotide microarrays derived from these ESTs. It will provide numerous genetic markers that will allow the construction of a high density gene map of T. cacao. This EST collection represents a unique and important molecular resource for T. cacao study and improvement, facilitating the discovery of candidate genes for important T. cacao trait variation.

Inhibition of Phytophthora species, agents of cocoa black pod disease, by secondary metabolites of Trichoderma species.

Cocoa production is affected by the black pod disease caused by several Phytophthora species that bring, about each year, an estimated loss of 44% of world production. Chemical control remains expensive and poses an enormous risk of poisoning for the users and the environment. Biocontrol by using antagonistic microorganisms has become an alternative to the integrated control strategy against this disease. Trichoderma viride T7, T. harzanium T40, and T. asperellum T54, which showed in vivo and in vitro antagonistic activity against P. palmivora, were cultured and mycelia extracted. Inhibition activity of crude extracts was determined, and then organic compounds were isolated and characterized. The in vitro effect of each compound on the conidia germination and mycelia growth of four P. palmivora, two P. megakaria, and one P. capsici was evaluated. T. viride that displayed best activities produced two active metabolites, viridin and gliovirin, against P. palmivora and P. megakaria strains. However, no activity against P. capsici was observed. Besides being active separately, these two compounds have a synergistic effect for both inhibitions, mycelia growth and conidia germination. These results provide the basis for the development of a low-impact pesticide based on a mixture of viridin and gliovirine.

Numerous clones resistant to Phytophthora palmivora in the "Guiana" genetic group of Theobroma cacao L.

Cocoa black pod rot, a disease caused by Stramenopiles of the genus Phytophthora, and particularly by the pan-tropical species P. palmivora, causes serious production losses worldwide. In order to reduce the impact of these pests and diseases, preference is given to genetic control using resistant varieties and, to that end, breeders seek sources of resistance in wild cocoa trees. For instance, surveys of spontaneous cocoa trees in French Guiana between 1985 and 1995 led to the collection of abundant plant material forming a particular genetic group (the "Guiana" group). Following numerous one-off studies demonstrating the merits of this group as a source of resistance to Phytophthora, this article presents the results of a comprehensive study assessing the resistance of 186 "Guiana" clones in relation to the Guianan strain (GY 27) of P. palmivora. This study, undertaken in French Guiana, using an efficient methodology (ten series of tests and a statistical test adapted to the ordinal nature of the data) confirmed that the "Guiana" genetic group does indeed constitute an important source of resistance to P. palmivora, though with some variations depending on the demes of origin. Numerous clones (59) proved to be as resistant as the SCAVINA 6 resistance control, whilst nine were statistically more resistant. The "Resistant" and "Moderately Resistant" Guianan clones totalled 108 (58% of the total tested). Some of the clones more resistant than SCAVINA 6 could be incorporated into numerous cocoa breeding programmes, particularly those that also display other notable qualities. The same applies for numerous other clones equivalent to SCAVINA 6, especially the "elite"' clones GU 134-B, GU 139-A and GU 285-A.