title: The 'PUCE CAFE' Project: the first 15K coffee microarray, a new tool for discovering candidate genes correlated to agronomic and quality traits.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Nestlé R&D Tours, 101 Avenue Gustave Eiffel, Notre Dame d'Oé, BP 49716, 37097 Tours Cedex 2, France. isabelle.privat@rdto.nestle.com
authors.forename: Isabelle
authors.initials: I
authors.lastname: Privat
authors.forename: Amélie
authors.initials: A
authors.lastname: Bardil
authors.forename: Aureliano Bombarely
authors.initials: AB
authors.lastname: Gomez
authors.forename: Dany
authors.initials: D
authors.lastname: Severac
authors.forename: Christelle
authors.initials: C
authors.lastname: Dantec
authors.forename: Ivanna
authors.initials: I
authors.lastname: Fuentes
authors.forename: Lukas
authors.initials: L
authors.lastname: Mueller
authors.forename: Thierry
authors.initials: T
authors.lastname: Joët
authors.forename: David
authors.initials: D
authors.lastname: Pot
authors.forename: Séverine
authors.initials: S
authors.lastname: Foucrier
authors.forename: Stéphane
authors.initials: S
authors.lastname: Dussert
authors.forename: Thierry
authors.initials: T
authors.lastname: Leroy
authors.forename: Laurent
authors.initials: L
authors.lastname: Journot
authors.forename: Alexandre
authors.initials: A
authors.lastname: de Kochko
authors.forename: Claudine
authors.initials: C
authors.lastname: Campa
authors.forename: Marie-Christine
authors.initials: MC
authors.lastname: Combes
authors.forename: Philippe
authors.initials: P
authors.lastname: Lashermes
authors.forename: Benoit
authors.initials: B
authors.lastname: Bertrand
mesh_terms: D000383:Agriculture / Q000379:methods*; D003069:Coffee / Q000235:genetics*; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D023281:Genomics / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction
chemical_list: D003069:Coffee