Differential fine-tuning of gene expression regulation in coffee leaves by CcDREB1D promoter haplotypes under water deficit

Alves, Gabriel Sergio Costa; Torres, Luana Ferreira; Déchamp, Eveline; Breitler, Jean‐Christophe; Joët, Thierry; Gatineau, Frédéric; Andrade, Alan Carvalho; Bertrand, Benoît; Marraccini, Pierre; Etienne, Hervé

doi:10.1093/jxb/erx166

Cited by 27 publications

(33 citation statements)

References 78 publications

(94 reference statements)

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“…We also found three DREB related genes with increased transcripts at T3. The sequence of one of these T = 3 induced genes (DREB-1D (Alves et al 2017)) is nearly identical to CcDREB1a that we have shown earlier to be induced at T = 3 by qRT-PCR ( Fig. 3).…”

Section: Identification Of Genes With Strong Differential Expression supporting

confidence: 61%

“…Two of these had significant UP expression at day 9 (Cc8_g13960, FC = 7.85 and Cc2_g03430, FC = 5.51),with DNA sequence analysis showing the latter gene is the well characterized drought stress regulated gene CcDREB-1D (Alves et al 2017). Recent detailed studies of the CcDREB-1D gene in different varieties found variety-specific promotor variations linked to phenotypic differences in drought tolerance , and further work found that haplotype specific CcDREB-1D promoters can influence the type and level of a reporter gene's response to water and temperature-related stresses (Alves et al 2017;de Aquino et al 2018). Although both DREBs noted here had very low transcript levels without a water deficit, and high levels under a strong water deficit (day 9), they appeared to react differently after re-watering, with the transcript levels falling faster for Cc8_g13960 versus Cc2_g03430 (DREB-1D), suggesting these two genes may have some differences in function.…”

Section: Discussionmentioning

confidence: 99%

“…The first notable set of genes found were members of the DREB transcription factor family (Lata and Prasad 2011). Two of these had significant UP expression at day 9 (Cc8_g13960, FC = 7.85 and Cc2_g03430, FC = 5.51),with DNA sequence analysis showing the latter gene is the well characterized drought stress regulated gene CcDREB-1D (Alves et al 2017). Recent detailed studies of the CcDREB-1D gene in different varieties found variety-specific promotor variations linked to phenotypic differences in drought tolerance , and further work found that haplotype specific CcDREB-1D promoters can influence the type and level of a reporter gene's response to water and temperature-related stresses (Alves et al 2017;de Aquino et al 2018).…”

Section: Discussionmentioning

confidence: 99%

“…For the high temperature control plants, only a very weak induction of CcDH1a was detected, with the highest level of transcripts seen at day 6. CcDREB1a encodes a coffee drought inducible Dehydration-Responsive-Element-Binding transcription factor of the APETALA2 (AP2) gene family (Alves et al 2017). The data in Fig.…”

Section: Comparison Of Leaf Gene Expression Changes For Plants Subjecmentioning

confidence: 99%

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Temperature Impacts the Response of Coffea canephora to Decreasing Soil Water Availability

Thioune

Strickler

Gallagher

et al. 2020

Tropical Plant Biol.

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Climate change is expected to result in more frequent periods of both low rainfall and above normal temperatures for many coffee growing regions. To understand how coffee reacts to such change, we studied the physiological and gene expression responses of the clonal variety C. canephora FRT07 exposed to water deficits under two different temperature regimes. Variations in the timedependent impact of water deficits on leaf stomatal conductance and carbon assimilation were significantly different under the 27°C and 27°C/42°C conditions examined. The physiological responses 24 h after re-watering were also different for both conditions. Expression analysis of genes known to respond to water deficits indicated that drought-related signaling occurred at both temperatures. Deeper insights into the response of coffee to water deficits was obtained by RNASeq based whole transcriptome profiling of leaves from early, late, and recovery stages of the 27°C experiment. This yielded expression data for 13,642 genes and related differential expression analysis uncovered 362 and 474 genes with increased and decreased expression, respectively, under mild water deficits, and 1627 genes and 2197 genes, respectively, under more severe water deficits. The data presented, from a single clonal coffee variety, serves as an important reference point for future comparative physiological/ transcriptomic studies with clonal coffee varieties with different sensitivities to water deficits and high temperatures. Such comparative analyses will help predict how different coffee varieties respond to changing climatic conditions, and may facilitate the identification of alleles associated with high and low tolerance to water deficits, enabling faster breeding of more climatesmart coffee trees.

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Section: Identification Of Genes With Strong Differential Expression supporting

confidence: 61%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Comparison Of Leaf Gene Expression Changes For Plants Subjecmentioning

confidence: 99%

See 2 more Smart Citations

Temperature Impacts the Response of Coffea canephora to Decreasing Soil Water Availability

Thioune

Strickler

Gallagher

et al. 2020

Tropical Plant Biol.

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“…The CAATBOX1 motif was the most abundant motif in the 18 VviERF6L upstream regions (Additional File 14), which may play a role in tissue specific gene expression [61] and contribute to VviERF6L expression across the broad range of tissues observed in the meta-data analysis. The MYB1AT motif is present in dehydration responsive genes like RD22 [62]. This motif was present in all VviERF6L promoters, but with fewer repetitions, supporting the transcriptomic data that ERF6Ls are only responding to severe water stress (Fig.…”

Section: Individual Vvierf6ls Had Unique Gene Expressionsupporting

confidence: 78%

VviERF6Ls: an expanded clade in Vitis responds transcriptionally to abiotic and biotic stresses and berry development

Toups

Cochetel

Gray

et al. 2020

Preprint

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Background VviERF6Ls are an uncharacterized gene clade in Vitis with only distant Arabidopsis orthologs. Preliminary data indicated these transcription factors may play a role in berry development and extreme abiotic stress responses. To better understand this highly duplicated, conserved clade, additional members of the clade were identified in four Vitis genotypes. A meta-data analysis was performed on publicly available microarray and RNA-Seq data (confirmed and expanded with RT-qPCR), and a Vitis VviERF6L1 overexpression line was established and characterized with phenotyping and RNA-Seq. Results A total of 18 PN40024 VviERF6Ls were identified; additional VviERF6Ls were identified in Cabernet Sauvignon, Chardonnay, and Carménère. The amino acid sequences of VviERF6Ls were found to be highly conserved. VviERF6L transcripts were detected in numerous plant organs and were differentially expressed in response to numerous abiotic stresses including water deficit, salinity, and cold as well as biotic stresses such as red blotch virus, N. parvum , and E. necator . VviERF6Ls were differentially expressed across stages of berry development, peaking in the pre-veraison/veraison stage, and retaining conserved expression patterns across different vineyards, years, and Vitis cultivars. Co-expression network analysis identified a scarecrow-like transcription factor and a calmodulin-like gene with highly similar expression profiles to the VviERF6L clade. Overexpression of VviERF6L1 in a Seyval Blanc background did not result in detectable morphological phenotypes. Genes differentially expressed in response to VviERF6L1 overexpression were associated with abiotic and biotic stress responses. Conclusions VviERF6Ls represent a large and distinct clade of ERF transcription factors in grapevine. The high conservation of protein sequence between these 18 transcription factors may indicate these genes originate from a duplication event in Vitis . Despite high sequence similarity and similar expression patterns, VviERF6Ls demonstrate unique levels of expression supported by similar but heterogeneous promoter sequences. VviERF6L gene expression differed between Vitis species, cultivars and organs including roots, leaves and berries. These genes respond to berry development and abiotic and biotic stresses. VviERF6L1 overexpression in Vitis vinifera results in differential expression of genes related to phytohormone and immune system signaling. Further investigation of this interesting gene family is warranted.

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Gene Expression in Coffee

Marraccini

2020

Progress in Botany

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Differential fine-tuning of gene expression regulation in coffee leaves by CcDREB1D promoter haplotypes under water deficit

Abstract: Fine-tuning of DREB1D expression in stomatal guard cells under water deficit is mediated differentially by promoter haplotypes from sensitive and tolerant coffee genotypes.

Cited by 27 publications

References 78 publications

Temperature Impacts the Response of Coffea canephora to Decreasing Soil Water Availability

Temperature Impacts the Response of Coffea canephora to Decreasing Soil Water Availability

VviERF6Ls: an expanded clade in Vitis responds transcriptionally to abiotic and biotic stresses and berry development

Gene Expression in Coffee

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