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

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

doi:10.1007/s12042-018-9199-x

Cited by 15 publications

(7 citation statements)

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“…In coffee, several TFs have been previously observed to respond to drought exposure. For instance, a wide-throughout transcriptomic study found only 22 probable responsive TFs, namely from the Myb superfamily [29], being the overexpression of TFs, including the DREB gene family also reported [74][75][76]. Likewise, in our study, four TFs were found to be significantly up-regulated in CL153 under drought (ERF027, DREB1D, DREB1A, and NAC055 in both water deficits) and three others in Icatu (TF15 under the two water deficits, plus basic leucine zipper 6 under MWD, and zipper 5 under SWD) suggesting their involvement in the drought-response tolerance of these genotypes.…”

Section: Drought-responsiveness Transcription Factorsmentioning

confidence: 99%

Understanding the Impact of Drought in Coffea Genotypes: Transcriptomic Analysis Supports a Common High Resilience to Moderate Water Deficit but a Genotype Dependent Sensitivity to Severe Water Deficit

et al. 2021

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Water scarcity is the most significant factor limiting coffee production, although some cultivars can still have important drought tolerance. This study analyzed leaf transcriptomes of two coffee cultivars with contrasting physiological responses, Coffea canephora cv. CL153 and Coffea. arabica cv. Icatu, subjected to moderate (MWD) or severe water deficits (SWD). We found that MWD had a low impact compared with SWD, where 10% of all genes in Icatu and 17% in CL153 reacted to drought, being mainly down-regulated upon stress. Drought triggered a genotype-specific response involving the up-regulation of reticuline oxidase genes in CL153 and heat shock proteins in Icatu. Responsiveness to drought also included desiccation protectant genes, but primarily, aspartic proteases, especially in CL153. A total of 83 Transcription Factors were found engaged in response to drought, mainly up-regulated, especially under SWD. Together with the enrollment of 49 phosphatases and 272 protein kinases, results suggest the involvement of ABA-signaling processes in drought acclimation. The integration of these findings with complementing physiological and biochemical studies reveals that both genotypes are more resilient to moderate drought than previously thought and suggests the existence of post-transcriptional mechanisms modulating the response to drought.

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Section: Drought-responsiveness Transcription Factorsmentioning

confidence: 99%

Understanding the Impact of Drought in Coffea Genotypes: Transcriptomic Analysis Supports a Common High Resilience to Moderate Water Deficit but a Genotype Dependent Sensitivity to Severe Water Deficit

et al. 2021

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“…Since DREB 1 /CBF (dehydration responsive element binding/C-repeat binding factor) encoding genes in abiotic stress have important roles in responding to abiotic stress, nucleotide diversity of DREB 1 gene has been characterized in several plants [53–57]. In 126 wheat lines, the nucleotide diversity π and θ values of wheat DREB gene on 1A chromosome were 0.180 and 0.392, respectively [27], which were much higher than the values detected in A genome T .…”

Section: Discussionmentioning

confidence: 99%

“…urartu . DREB 1 A nucleotide diversity was calculated from the 126 wheat lines that were developed by the International Maize and Wheat Improvement Center from entries in the elite spring wheat yield trial, semiarid wheat yield trial, and high temperature wheat yield trial [57]. These lines, during the breeding procedure, might suffer different natural selection pressure, resulting in the wide range of diversity of this gene.…”

Section: Discussionmentioning

confidence: 99%

Nucleotide diversity patterns at the DREB1 transcriptional factor gene in the genome donor species of wheat (Triticum aestivum L)

Sun

Chun

et al. 2019

PLoS ONE

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Bread wheat (AABBDD) originated from the diploid progenitor Triticum urartu (AA), a relative of Aegilops speltoides (BB), and Ae . tauschii (DD). The DREB 1 transcriptional factor plays key regulatory role in low-temperature tolerance. The modern breeding strategies resulted in serious decrease of the agricultural biodiversity, which led to a loss of elite genes underlying abiotic stress tolerance in crops. However, knowledge of this gene’s natural diversity is largely unknown in the genome donor species of wheat. We characterized the dehydration response element binding protein 1 ( DREB 1) gene-diversity pattern in Ae . speltoides , Ae . tauschii , T . monococcum and T . urartu . The highest nucleotide diversity value was detected in Ae . speltoides , followed by Ae . tauschii and T . monococcum . The lowest nucleotide diversity value was observed in T . urartu . Nucleotide diversity and haplotype data might suggest no reduction of nucleotide diversity during T . monococcum domestication. Alignment of the 68 DREB 1 sequences found a large-size (70 bp) insertion/deletion in the accession PI486264 of Ae . speltoides , which was different from the copy of sequences from other accessions of Ae . speltoides , suggesting a likely existence of two different ancestral Ae . speltoides forms. Implication of sequences variation of Ae . speltoides on origination of B genome in wheat was discussed.

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“…Association studies will also benefit from the sequencing of the C. canephora reference genome (Denoeud et al, 2014). Efforts to unravel the molecular mechanisms of coffee in response to drought stress have been accomplished elsewhere by (Mofatto et al, 2016, Vieira et al, 2013, Marraccini et al, 2012, Alves et al, 2018 and it is important that we conduct related studies with Ugandan C. canephora diversity to understand the molecular mechanisms and gene expressions in regard to drought stress.…”

Section: Future Research Perspectivesmentioning

confidence: 99%

Genetic diversity and phenotypic variation of wild, feral and cultivated Coffea canephora in relation to drought stress

Kiwuka

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Catherine Kiwuka (2020). Genetic diversity and phenotypic variation of wild, feral and cultivated Coffea canephora in relation to drought stress. PhD thesis, Wageningen University, The Netherlands, with summaries in English and Dutch, 180 pp.Coffea canephora Pierre ex A. Froehner (Robusta coffee) is an important crop sustaining millions of livelihoods in its production zone which is predominated by poor countries. Like the other commercially important coffee species, Coffea arabica, the production of Coffea canephora is threatened by the prevailing intense and frequent drought spells reported to be increasing in relation to climate change. There is thus an urgent need to develop drought resilient C. canephora cultivars especially for poor farmers who often lack irrigation options.Availability of C. canephora intraspecific diversity and occurrence of wild populations across an environmental gradient may indicate presence of valuable genetic material, which could be used directly as a new variety or as a parent in breeding climate resilient varieties. This thesis explored: (i) the genetic diversity of Ugandan Robusta coffee; (ii) linkages between allelic variation and environmental variables; (iii) phenotypic variation in drought tolerance and (iv) phenotypic plasticity to shifts in water availability and its relationship with drought tolerance.Results showed that: Uganda's C. canephora differentiates into five geographically delimited groups, and there is substantial phenotypic variation in relation to their response to water availability across locations and genetic groups but no significant phenotypic variation along the level of cultivation status. We observed a trade-off between drought tolerance and growth in ample water conditions. Drought tolerance of the genotypes was negatively associated to an index that indicated wetness of the climate at their locations suggesting some degree of local adaptation. Finally, our results also showed a negative correlation between plasticity in response to changes in water availability and drought tolerance. Generally, our study revealed the comprehensive genetic structure of Uganda's C. canephora, its differential response in to drought stress, growth-tolerance trade-off, plasticity-tolerance trade-off, the link between δ 13 C discrimination and water-use efficiency, and the probable implications of the findings to developing drought tolerant cultivars. Our findings can be used in further studies like association studies to identify putatively adapted genotypes and in breeding programs to develop climate resilient cultivars. Table of contents Chapter General introduction 1 Chapter Genetic diversity of native and cultivated Uganda's Coffea canephora 19 Pierre ex A. Froehner. A perspective into potential utilization and conservation of the diversity Chapter Intraspecific variation in growth response to drought stress across 51 geographic locations and genetic groups in Coffea canephora Pierre ex A. Froehner Chapter Phenotypic and genotypic variation in trait plastic response...

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

Cited by 15 publications

References 58 publications

Understanding the Impact of Drought in Coffea Genotypes: Transcriptomic Analysis Supports a Common High Resilience to Moderate Water Deficit but a Genotype Dependent Sensitivity to Severe Water Deficit

Understanding the Impact of Drought in Coffea Genotypes: Transcriptomic Analysis Supports a Common High Resilience to Moderate Water Deficit but a Genotype Dependent Sensitivity to Severe Water Deficit

Nucleotide diversity patterns at the DREB1 transcriptional factor gene in the genome donor species of wheat (Triticum aestivum L)

Genetic diversity and phenotypic variation of wild, feral and cultivated Coffea canephora in relation to drought stress

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