Open Access Methodology article

The 'PUCE CAFE' Project: the First 15K Coffee Microarray, a New Tool for Discovering Candidate Genes correlated to Agronomic and Quality Traits

Isabelle Privat1*, Amélie Bardil4, Aureliano Bombarely Gomez3, Dany Severac2, Christelle Dantec2, Ivanna Fuentes2, Lukas Mueller3, Thierry Joët5, David Pot6, Séverine Foucrier1, Stéphane Dussert5, Thierry Leroy5, Laurent Journot2, Alexandre de Kochko5, Claudine Campa5, Marie-Christine Combes4, Philippe Lashermes4 and Benoit Bertrand4

Author Affiliations

1 Nestlé R&D Tours, 101 Avenue Gustave Eiffel, Notre Dame d'Oé, BP 49716, 37097 Tours Cedex 2, France

2 Montpellier Genomix, IGF, 141 rue de la Cardonille, 34094 Montpellier Cedex 05, France

3 Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, New York 14853-1801, USA

4 IRD-CIRAD, UMR RPB, BP 64501, 34394 Montpellier, France

5 IRD, UMR DIAPC, BP 64501, 34394 Montpellier, France

6 CIRAD avenue Agropolis, 34398 Montpellier Cedex 5, France

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BMC Genomics 2011, 12:5  doi:10.1186/1471-2164-12-5

Published: 5 January 2011



Understanding the genetic elements that contribute to key aspects of coffee biology will have an impact on future agronomical improvements for this economically important tree. During the past years, EST collections were generated in Coffee, opening the possibility to create new tools for functional genomics.


The "PUCE CAFE" Project, organized by the scientific consortium NESTLE/IRD/CIRAD, has developed an oligo-based microarray using 15,721 unigenes derived from published coffee EST sequences mostly obtained from different stages of fruit development and leaves in Coffea Canephora (Robusta). Hybridizations for two independent experiments served to compare global gene expression profiles in three types of tissue matter (mature beans, leaves and flowers) in C. canephora as well as in the leaves of three different coffee species (C. canephora, C. eugenoides and C. arabica). Microarray construction, statistical analyses and validation by Q-PCR analysis are presented in this study.


We have generated the first 15 K coffee array during this PUCE CAFE project, granted by Génoplante (the French consortium for plant genomics). This new tool will help study functional genomics in a wide range of experiments on various plant tissues, such as analyzing bean maturation or resistance to pathogens or drought. Furthermore, the use of this array has proven to be valid in different coffee species (diploid or tetraploid), drastically enlarging its impact for high-throughput gene expression in the community of coffee research.