Abstract
BackgroundUnderstanding 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.ResultsThe "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.ConclusionWe 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.
Highlights
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
Our results reveal that this new tool applies to high-throughput gene expression analyses in various Coffea species
The use of the array has proven to be valid for genomic studies on different plant tissues
Summary
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. Two of these species Coffea canephora (robusta) and Coffea arabica, are widely cultivated for the production of coffee beverages. The former is diploid (2n = 2× = 22) and allogamous, the latter, allotetraploid (2n = 4× = 44) and preferentially autogamous. In terms of cup quality, consumers appreciate C. arabica (Arabica) more due to its taste, which is less bitter and more flavourful compared with C. canephora (Robusta) While it is not widely known, coffee is one of the most valuable international exchange commodities in agricultural trade. Over 25 million people worldwide are linked to coffee cultivation and processing Despite these economic aspects, coffee research suffers from a lack of both scientific and financial investment. Coffee researchers have only limited access to the plethora of genomic resources available for most major crop species
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