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High-throughput sequencing of cDNA shows that cv. Rubi and IAPAR59 of Coffea Arabica have different molecular response to water privation

Vidal R.O., Alekcevetch J.C., Leroy T., De Bellis F., Pot D., Rodrigues G.C., Carazzolle M.F., Pereira G.A.G., Andrade A.C., Marraccini P.. 2013. In : Proceedings of the 24th International Conference on Coffee Science, San José, Costa Rica, 12th-16th November 2012. Paris : ASIC, p. 562-568. International Conference on Coffee Science. 24, 2012-11-11/2012-11-16, San José (Costa Rica).

It is well known that drought periods affect coffee plant development, leading to plant death and abortion of developing fruits in case of severe drought. In relation to coffee genetic diversity, several works reported the identification of plants of C. canephora conilon susceptible or tolerant to drought which were analyzed at the physiological level and also used to identify candidate genes underlying stress responses. Even narrow, a genetic diversity for drought tolerance also exist in the species C. arabica. In addition to the identification of undiscovered transcripts, the recent development of low-cost, high throughput next-generation (NGS) sequencing technologies now opens the way to perform expression profiling and to identify gene presenting differential expression patterns by comparing the frequency of reads obtained after sequencing. In order to initiate such kind of approach in coffee, RNA of meristematic tissues from Iapar59 (I59, drought tolerant) and Rubi (R, drought sensible) cultivars of C. arabica grown under field-grown with (I) or without (NI) irrigation were extracted and used to generate cDNA that were further sequenced. The sequencing data revealed 282.213, 135.304, 345.751 and 230.064 reads obtained from I59-I, I59-NI, R-I and R-NI samples, respectively, totalizing more than 255Mb. These data was compared with all available transcriptome Coffea data, including the EST sequences from both Coffea arabica and C. canephora. The results of these comparisons will be presented as well as the preliminary data of an electronic northern performed in order to identify differentially expressed genes between the two cultivars in both conditions (NI or I). General numbers show that Rubi has a more intense molecular response to drought, with many genes over-expressed. Also functional analysis of biological processes shows an enrichment of stress response genes in Rubi non-irrigated while in I59 there is a decrease in expression in genes related to carbohydrate metabolism and cell wall organization. It is worth noting the number of genes up-regulated in Rubi non irrigated (NI) and involved with drought stress response, like RD22, PDIR10 (dirigent-like protein), MYB and caffeine synthase for example, while these genes were not detected under this stress in I59. In other hand, many drought genes related to drought-stress tolerance were detected in the I59 cultivar involved in biosynthetic process such as sugar transporters, some proteins related with abiotic stress tolerance (i.e. osmotins), water channel protein, LEA proteins (implicated in detoxification and alleviation of cellular damage during dehydration) and heat shock proteins (HSPs). In the I59 cultivar, genes coding for enzymes involved in the ABA synthesis (isopentenyl diphosphate isomerase, geranylgeranyl reductase), which causes stomatal closure, precursor and enzymes, were also 1 highly expressed. Q-PCR experiments were also performed and allowed to confirm the data obtained in silico for several genes. These results will be presented and discussed.

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