Identification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars

Souto Mofatto Luciana, De Araújo Carneiro Fernanda, Gomes Vieira Natalia, Duarte Karoline Estefani, Vidal Ramon Oliveira, Alekcevetch Jean Carlos, Guitton Cotta Michelle, Verdeil Jean-Luc, Lapeyre-Montes Fabienne, Lartaud Marc, Leroy Thierry, De Bellis Fabien, Pot David, Costa Rodrigues Gustavo, Falsarella Carazzolle Marcelo, Guimarães Pereira Gonçalo Amarante, Carvalho Andrade Alan, Marraccini Pierre. 2016. Identification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars. BMC Plant Biology, 16 (94), 18 p.

Journal article ; Article de recherche ; Article de revue à facteur d'impact Revue en libre accès total
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Mofatto et al. BMC Plant Biology 2016.pdf

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Quartile : Q1, Sujet : PLANT SCIENCES

Additional Information : Jeux de données enregistrés : The reads were submitted to GenBank and to the BioProject/NCBI database under the accession number PRJNA282394. (liens pas encore actifs).

Abstract : Background: Drought is a widespread limiting factor in coffee plants. It affects plant development, fruit production, bean development and consequently beverage quality. Genetic diversity for drought tolerance exists within the coffee genus. However, the molecular mechanisms underlying the adaptation of coffee plants to drought are largely unknown. In this study, we compared the molecular responses to drought in two commercial cultivars (IAPAR59, drought-tolerant and Rubi, drought-susceptible) of Coffea arabica grown in the field under control (irrigation) and drought conditions using the pyrosequencing of RNA extracted from shoot apices and analysing the expression of 38 candidate genes. Results: Pyrosequencing from shoot apices generated a total of 34.7 Mbp and 535,544 reads enabling the identification of 43,087 clusters (41,512 contigs and 1,575 singletons). These data included 17,719 clusters (16,238 contigs and 1,575 singletons) exclusively from 454 sequencing reads, along with 25,368 hybrid clusters assembled with 454 sequences. The comparison of DNA libraries identified new candidate genes (n = 20) presenting differential expression between IAPAR59 and Rubi and/or drought conditions. Their expression was monitored in plagiotropic buds, together with those of other (n = 18) candidates genes. Under drought conditions, up-regulated expression was observed in IAPAR59 but not in Rubi for CaSTK1 (protein kinase), CaSAMT1 (SAM-dependent methyltransferase), CaSLP1 (plant development) and CaMAS1 (ABA biosynthesis). Interestingly, the expression of lipid-transfer protein (nsLTP) genes was also highly up-regulated under drought conditions in IAPAR59. This may have been related to the thicker cuticle observed on the abaxial leaf surface in IAPAR59 compared to Rubi. Conclusions: The full transcriptome assembly of C. arabica, followed by functional annotation, enabled us to identify differentially expressed genes related to drought conditions. Using these data, candidate genes were selected and their differential expression profiles were confirmed by qPCR experiments in plagiotropic buds of IAPAR59 and Rubi under drought conditions. As regards the genes up-regulated under drought conditions, specifically in the drought-tolerant IAPAR59, several corresponded to orphan genes but also to genes coding proteins involved in signal transduction pathways, as well as ABA and lipid metabolism, for example. The identification of these genes should help advance our understanding of the genetic determinism of drought tolerance in coffee. (Résumé d'auteur)

Mots-clés Agrovoc : Coffea arabica, Tolérance à la sécheresse, Gène, Identification, Expression des gènes, Transcription, Coffea canephora

Mots-clés géographiques Agrovoc : Espirito Santo, Brésil

Mots-clés complémentaires : Séquencage

Classification Agris : F30 - Plant genetics and breeding
H50 - Miscellaneous plant disorders
F60 - Plant physiology and biochemistry

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

  • Souto Mofatto Luciana, UNICAMP (BRA)
  • De Araújo Carneiro Fernanda, UFLA (BRA)
  • Gomes Vieira Natalia, EMBRAPA (BRA)
  • Duarte Karoline Estefani, EMBRAPA (BRA)
  • Vidal Ramon Oliveira, UNICAMP (BRA)
  • Alekcevetch Jean Carlos, EMBRAPA (BRA)
  • Guitton Cotta Michelle, CIRAD-BIOS-UMR AGAP (FRA)
  • Verdeil Jean-Luc, CIRAD-BIOS-UMR AGAP (FRA)
  • Lapeyre-Montes Fabienne, CIRAD-BIOS-UMR AGAP (FRA)
  • Lartaud Marc, CIRAD-BIOS-UMR AGAP (FRA)
  • Leroy Thierry, CIRAD-BIOS-UMR AGAP (FRA)
  • De Bellis Fabien, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-7070-7691
  • Pot David, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-6144-8448
  • Costa Rodrigues Gustavo, EMBRAPA (BRA)
  • Falsarella Carazzolle Marcelo, UNICAMP (BRA)
  • Guimarães Pereira Gonçalo Amarante, UNICAMP (BRA)
  • Carvalho Andrade Alan, EMBRAPA (BRA)
  • Marraccini Pierre, CIRAD-BIOS-UMR AGAP (BRA) ORCID: 0000-0001-7637-6811

Source : Cirad-Agritrop (

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