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

Argout Xavier, Fouet Olivier, Wincker Patrick, Gramacho Karina Peres, Legavre Thierry, Sabau Xavier, Risterucci Ange-Marie, Da Silva Corinne, Cascardo Julio Cezar M., Allègre Mathilde, Kuhn David N., Verica Joseph, Courtois Brigitte, Loor Rey Gaston, Babin Régis, Sounigo Olivier, Ducamp Michel, Guiltinan Mark J., Ruiz Manuel, Alemanno Laurence, Machado Regina, Phillips Wilbert, Schnell Raymond J., Gilmour Martin, Rosenquist Eric, Butler David R., Maximova Siela N., Lanaud Claire. 2008. 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. BMC Genomics, 9 (512), 19 p.

Type d'url non précisé : http://www.biomedcentral.com/1471-2164/9/512

Résumé : 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. 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. 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.

Mots-clés Agrovoc : Theobroma cacao, adn, séquence nucléotidique, transcription, collection de matériel génétique, expression des gènes, génie génétique, résistance aux maladies, marqueur génétique

Classification Agris : F30 - Génétique et amélioration des plantes
H20 - Maladies des plantes

Champ stratégique Cirad : Axe 1 (2005-2013) - Intensification écologique

Auteurs et affiliations

• Argout Xavier, CIRAD-BIOS-UMR DAP (FRA) ORCID: 0000-0002-0100-5511
• Fouet Olivier, CIRAD-BIOS-UMR DAP (FRA) ORCID: 0000-0001-8547-1474
• Wincker Patrick, Centre national de séquençage (FRA)
• Gramacho Karina Peres, CEPLAC (BRA)
• Legavre Thierry, CIRAD-BIOS-UMR DAP (FRA)
• Sabau Xavier, CIRAD-BIOS-UMR DAP (FRA)
• Risterucci Ange-Marie, CIRAD-BIOS-UMR DAP (FRA)
• Da Silva Corinne, Centre national de séquençage (FRA)
• Cascardo Julio Cezar M., UESC (BRA)
• Allègre Mathilde, CIRAD-BIOS-UMR DAP (FRA)
• Kuhn David N., USDA (USA)
• Verica Joseph, Pennsylvania State University (USA)
• Courtois Brigitte, CIRAD-BIOS-UMR DAP (FRA) ORCID: 0000-0003-2118-7102
• Loor Rey Gaston, INIAP (ECU)
• Babin Régis, CIRAD-BIOS-UPR Bioagresseurs de pérennes (CMR) ORCID: 0000-0002-3753-1193
• Sounigo Olivier, CIRAD-BIOS-UPR Bioagresseurs de pérennes (CMR) ORCID: 0000-0001-6278-8903
• Ducamp Michel, CIRAD-BIOS-UMR BGPI (FRA)
• Guiltinan Mark J., Pennsylvania State University (USA)
• Ruiz Manuel, CIRAD-BIOS-UMR DAP (FRA) ORCID: 0000-0001-8153-276X
• Alemanno Laurence
• Machado Regina, Masterfoods (BRA)
• Phillips Wilbert, CATIE (CRI)
• Schnell Raymond J., USDA (USA)
• Gilmour Martin, MARS Confectionery (GBR)
• Rosenquist Eric, USDA (USA)
• Butler David R., UWI (TTO)
• Maximova Siela N., Pennsylvania State University (USA)
• Lanaud Claire, CIRAD-BIOS-UMR DAP (FRA) ORCID: 0000-0001-6411-7310

Source : Cirad - Agritrop (https://agritrop.cirad.fr/548501/)

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