The 'PUCE CAFE' project: The first 15K coffee microarray, a new tool for discovering candidate genes correlated to agronomic and quality traits

Privat Isabelle, Bardil Amélie, Bombarely Gomez Aureliano, Severac Dany, Dantec Christelle, Fuentes Ivanna, Mueller Lukas, Joët Thierry, Pot David, Foucrier Séverine, Dussert Stéphane, Leroy Thierry, Journot Laurent, De Kochko Alexandre, Campa Claudine, Combes Marie-Christine, Lashermes Philippe, Bertrand Benoît. 2011. The 'PUCE CAFE' project: The first 15K coffee microarray, a new tool for discovering candidate genes correlated to agronomic and quality traits. BMC Genomics, 12 (5), 14 p.

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Abstract : Background: 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. Results: 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. Conclusion: 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. (Résumé d'auteur)

Mots-clés Agrovoc : Coffea canephora, Coffea arabica, Coffea eugenioides

Mots-clés géographiques Agrovoc : Éthiopie, Kenya, Congo

Classification Agris : F30 - Plant genetics and breeding
F60 - Plant physiology and biochemistry

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

Auteurs et affiliations

  • Privat Isabelle, Centre de recherches Nestlé (FRA)
  • Bardil Amélie, CIRAD-BIOS-UMR RPB (FRA)
  • Bombarely Gomez Aureliano, Boyce Thompson Institute for Plant Research (USA)
  • Severac Dany, Montpellier Génopole Microarray Facility (FRA)
  • Dantec Christelle, Montpellier Génopole Microarray Facility (FRA)
  • Fuentes Ivanna, Montpellier Génopole Microarray Facility (FRA)
  • Mueller Lukas, Boyce Thompson Institute for Plant Research (USA)
  • Joët Thierry, IRD (REU)
  • Pot David, CIRAD-BIOS-UMR DAP (FRA) ORCID: 0000-0001-6144-8448
  • Foucrier Séverine, Centre de recherches Nestlé (FRA)
  • Dussert Stéphane, IRD (FRA)
  • Leroy Thierry, CIRAD-BIOS-UMR DAP (FRA)
  • Journot Laurent, Montpellier Génopole Microarray Facility (FRA)
  • De Kochko Alexandre, IRD (FRA)
  • Campa Claudine, IRD (FRA)
  • Combes Marie-Christine, IRD (FRA)
  • Lashermes Philippe, IRD (FRA)
  • Bertrand Benoît, CIRAD-BIOS-UMR RPB (FRA)

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