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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
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, Volume 9, Article 512, Year 2008
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Description
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. © 2008 Argout et al; licensee BioMed Central Ltd.
Authors & Co-Authors
Argout, Xavier
France, Paris
Cirad
Fouet, Olivier
France, Paris
Cirad
Wincker, Patrick
France, Evry
Genoscope - Centre National de Séquençage
Peres Gramacho, Karina
Brazil, Itabuna
Ceplac
Legavre, Thierry
France, Paris
Cirad
Sabau, Xavier
France, Paris
Cirad
Risterucci, Ange Marie
France, Paris
Cirad
da Silva, Corinne D.
France, Evry
Genoscope - Centre National de Séquençage
Cascardo, Julio
Brazil, Ilheus
Universidade Estadual de Santa Cruz
Allegre, Mathilde
France, Paris
Cirad
Kuhn, David N.
United States, Washington, D.c.
Usda Agricultural Research Service
Verica, Joseph
United States, University Park
Pennsylvania State University
Courtois, Brigitte
France, Paris
Cirad
Loor, Gaston
Unknown Affiliation
Babin, Régis
Cameroon, Yaounde
Ministry of Scientific Research and Innovation-cameroon
France, Paris
Cirad
Sounigo, Olivier
Cameroon, Yaounde
Ministry of Scientific Research and Innovation-cameroon
France, Paris
Cirad
Ducamp, Michel
France, Montpellier
Plant Health Institute Montpellier
Guiltinan, Mark J.
United States, University Park
Pennsylvania State University
Ruiz, Manuel
France, Paris
Cirad
Alemanno, Laurence
France, Paris
Cirad
Machado, Regina
Unknown Affiliation
Phillips, W.
Costa Rica, Turrialba
Catie - Centro Agronómico Tropical de Investigación y Enseñanza
Schnell, Ray
United States, Washington, D.c.
Usda Agricultural Research Service
Gilmour, Martin
United States, Mclean
Mars Incorporated
Rosenquist, Eric
United States, Washington, D.c.
Usda Agricultural Research Service
Butler, David R.
Trinidad and Tobago, St Augustine
The University of the West Indies, St. Augustine Campus
Maximova, Siela N.
United States, University Park
Pennsylvania State University
Lanaud, Claire
France, Paris
Cirad
Statistics
Citations: 131
Authors: 28
Affiliations: 11
Identifiers
Doi:
10.1186/1471-2164-9-512
e-ISSN:
14712164
Research Areas
Genetics And Genomics
Noncommunicable Diseases