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Tropical Plant Biology

, Volume 11, Issue 1–2, pp 31–48 | Cite as

Nucleotide Diversity of the Coding and Promoter Regions of DREB1D, a Candidate Gene for Drought Tolerance in Coffea Species

  • Gabriel Sergio Costa Alves
  • Luana Ferreira Torres
  • Sinara Oliveira de Aquino
  • Tharyn Reichel
  • Luciana Perreira Freire
  • Natalia Gomes Vieira
  • Felipe Vinecky
  • Dominique This
  • David Pot
  • Hervé Etienne
  • Luciano Vilela Paiva
  • Pierre Marraccini
  • Alan Carvalho Andrade
Article
  • 217 Downloads

Abstract

Climate change is posing a major challenge to coffee production worldwide leading to a need for the development of coffee cultivars with increased drought tolerance. In several plant species, the use of DREB genes in crop improvement has achieved promising results to desiccation tolerance engineering. Recent studies reported CcDREB1D specific patterns of expression in Coffea canephora and functional evidence of this gene involvement in drought stress responses. However, knowledge on natural diversity of this gene is largely unknown. In this context, this study aimed at evaluating the sequence variability of the DREB1D gene in several Coffea genotypes. Nucleotide variation in promoters and coding regions of this gene were evaluated in a population consisting of 38 genotypes of C. canephora, C. arabica and C. eugenioides, most of them characterized by different phenotypes (tolerance vs. susceptibility) in relation to drought. The genetic diversity of the loci revealed different haplotypes for the promoter and coding regions. In particular, our findings suggest association between drought tolerance and the genetic variations on DREB1D promoter regions, but not with those from its corresponding coding regions. Gene expression studies revealed up-regulated expression of DREB1D gene upon drought mainly in leaves of drought-tolerant clones of C. canephora, and in response to drought, high, and low temperatures in leaves of C. arabica, suggesting a key role of this gene in coffee responses to abiotic stress.

Keywords

Coffee DREB1D Drought stress Genetic diversity Haplotype Promoter 

Notes

Acknowledgments

This work was carried out under the Embrapa-CIRAD scientific cooperation project entitled “Genetic determinism of drought tolerance in coffee”. The authors acknowledge the financial support from the Consórcio Pesquisa Café, Instituto Nacional de Ciência e Tecnologia – Café (Conselho Nacional de Desenvolvimento Cientifico e Tecnologico/Fundação de Amparo à Pesquisa do Estado de Minas Gerais) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/Comité Français d’Évaluation de la Coopération Universitaire et Scientifique avec le Brésil (Project 407-2012/University of Lavras and Montpellier SupAgro). The authors would like to thank Drs Aymbiré Francisco Almeida da Fonseca, Maria Amélia Gava Ferrão and Romário Gava Ferrão from the INCAPER Institute, the Centre National de la Recherche Agronomique (CNRA, Dr. Hyacinthe Legnate) - Divo (Ivory Coast) and the Coffee Research Center (NARO-COREC, Pascal Musoli) - Mukono (Uganda) for providing plant material to extract genomic DNA. They also acknowledge Dr. Thierry Leroy for providing genomic DNA and Peter Biggins (CIRAD UMR AGAP) for their discussions and critical reading of the manuscript.

Author Contribution Statement

P.M., H.E., L.V.P. and A.C.A. designed the study. G.S.C.A., L.P.F., N.G.V., F.V. performed DNA amplifications and sequencing. L.F.T., S.O.A. and T.R. performed expression studies. G.S.C.A., D.T. and D.P. were responsible for the bioinformatic processing of the data. G.S.C.A., D.T., D.P., P.M. and A.C.A. wrote the manuscript. All the authors read and approved the final version of the manuscript.

Compliance with Ethical Standards

Conflict of Interest

We confirm that this work is original and has not been published elsewhere nor is currently under consideration for publication elsewhere. The authors declare that they have no conflict of interest.

Ethical Standard

The authors declare that the experiments comply with the current laws of Brazil.

Supplementary material

12042_2018_9199_MOESM1_ESM.docx (109 kb)
Supplementary file 1 Nucleotide alignments of DREB1D promoter haplotypes. The consensus sequence (see Figure 2) is used as a reference in upper part of alignments. The nucleotides are numbered (on the right) of each lane using the first nucleotide (+1, white letter in black box) of the DREB1D mRNA sequence. The ATG start codon of the DREB1D-coding sequence is also indicated. For each accession, HP numbers are indicated. (DOCX 109 kb)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Gabriel Sergio Costa Alves
    • 1
    • 2
  • Luana Ferreira Torres
    • 2
    • 6
  • Sinara Oliveira de Aquino
    • 1
    • 2
  • Tharyn Reichel
    • 2
  • Luciana Perreira Freire
    • 1
    • 2
  • Natalia Gomes Vieira
    • 1
    • 2
  • Felipe Vinecky
    • 1
    • 2
  • Dominique This
    • 3
  • David Pot
    • 4
  • Hervé Etienne
    • 5
  • Luciano Vilela Paiva
    • 2
  • Pierre Marraccini
    • 1
    • 4
    • 5
  • Alan Carvalho Andrade
    • 1
    • 6
  1. 1.Embrapa Recursos Genéticos e Biotecnologia (LGM), Parque EBBrasíliaBrazil
  2. 2.Universidade Federal de Lavras, Campus UFLALavrasBrazil
  3. 3.Montpellier SupAgro, UMR AGAPMontpellierFrance
  4. 4.CIRAD, UMR AGAPMontpellierFrance
  5. 5.CIRAD, UMR IPMEMontpellierFrance
  6. 6.Embrapa Café, INOVACAFÉ, UFLALavrasBrazil

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