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

International audienceBackground : Understanding the genetic elements that contribute to key aspects of coffee biology will have animpact on future agronomical improvements for this economically important tree. During the past years, ESTcollections 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 anoligo-based microarray using 15,721 unigenes derived from published coffee EST sequences mostly obtained fromdifferent stages of fruit development and leaves inCoffea Canephora (Robusta). Hybridizations for two independentexperiments served to compare global gene expression profiles in three types of tissue matter (mature beans, leaves and flowers) inC. canephoraas well as in the leaves of three different coffee species (C. canephora, C.eugenoidesandC. arabica). Microarray construction, statistical analyses and validation by Q-PCR analysis arepresented 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 ofexperiments 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