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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

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

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Author(s):
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Mofatto, Luciana Souto [1] ; Carneiro, Fernanda de Arajo [2] ; Vieira, Natalia Gomes [2] ; Duarte, Karoline Estefani [2] ; Vidal, Ramon Oliveira [1] ; Alekcevetch, Jean Carlos [2] ; Cotta, Michelle Guitton [2] ; Verdeil, Jean-Luc [3] ; Lapeyre-Montes, Fabienne [3] ; Lartaud, Marc [3] ; Leroy, Thierry [3] ; De Bellis, Fabien [3] ; Pot, David [3] ; Rodrigues, Gustavo Costa [4] ; Carazzolle, Marcelo Falsarella [1] ; Guimaraes Pereira, Goncalo Amarante [1] ; Andrade, Alan Carvalho [2, 5] ; Marraccini, Pierre [3, 2]
Total Authors: 18
Affiliation:
[1] Univ Estadual Campinas, Inst Biol, Dept Genet & Evolucao, LGE, Cidade Univ Zeferino Vaz, BR-13083970 Campinas, SP - Brazil
[2] Embrapa Recursos Genet & Biotecnol LGM NTBio, Parque Estacao Bio, CP 02372, BR-70770917 Brasilia, DF - Brazil
[3] CIRAD, UMR AGAP, F-34398 Montpellier - France
[4] Univ Estadual Campinas, Embrapa Informat Agr, Ave Andre Tosello 209, CP 6041, BR-13083886 Campinas, SP - Brazil
[5] Embrapa Cafe, INOVACAFE, Campus UFLA, BR-37200000 Lavras, MG - Brazil
Total Affiliations: 5
Document type: Journal article
Source: BMC PLANT BIOLOGY; v. 16, APR 19 2016.
Web of Science Citations: 16
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. (AU)

FAPESP's process: 13/08293-7 - CCES - Center for Computational Engineering and Sciences
Grantee:Munir Salomao Skaf
Support Opportunities: Research Grants - Research, Innovation and Dissemination Centers - RIDC