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

IbMYB73 targets abscisic acid-responsive IbGER5 to regulate root growth and stress tolerance in sweet potato

Root development influences plant responses to environmental conditions, and well-developed rooting enhances plant survival under abiotic stress. However, the molecular and genetic mechanisms underlying root development and abiotic stress tolerance in plants remain unclear. In this study, we identified the MYB transcription factor-encoding gene IbMYB73 by cDNA-amplified fragment length polymorphism and RNA-seq analyses. IbMYB73 expression was greatly suppressed under abiotic stress in the roots of the salt-tolerant sweet potato (Ipomoea batatas) line ND98, and its promoter activity in roots was significantly reduced by abscisic acid (ABA), NaCl, and mannitol treatments. Overexpression of IbMYB73 significantly inhibited adventitious root growth and abiotic stress tolerance, whereas IbMYB73-RNAi plants displayed the opposite pattern. IbMYB73 influenced the transcription of genes involved in the ABA pathway. Furthermore, IbMYB73 formed homodimers and activated the transcription of ABA-responsive protein IbGER5 by binding to an MYB binding sites I motif in its promoter. IbGER5 overexpression significantly inhibited adventitious root growth and abiotic stress tolerance concomitantly with a reduction in ABA content, while IbGER5-RNAi plants showed the opposite effect. Collectively, our results demonstrated that the IbMYB73-IbGER5 module regulates ABA-dependent adventitious root growth and abiotic stress tolerance in sweet potato, which provides candidate genes for the development of elite crop varieties with well-developed root-mediated abiotic stress tolerance.

Reliable reference genes and abiotic stress marker genes in Klebsormidium nitens

Microalgae have recently emerged as a key research topic, especially as biological models. Among them, the green alga Klebsormidium nitens, thanks to its particular adaptation to environmental stresses, represents an interesting photosynthetic eukaryote for studying the transition stages leading to the colonization of terrestrial life. The tolerance to different stresses is manifested by changes in gene expression, which can be monitored by quantifying the amounts of transcripts by RT-qPCR. The identification of optimal reference genes for experiment normalization was therefore necessary. In this study, using four statistical algorithms followed by the RankAggreg package, we determined the best reference gene pairs suitable for normalizing RT-qPCR data in K. nitens in response to three abiotic stresses: high salinity, PEG-induced dehydration and heat shock. Based on these reference genes, we were able to identify marker genes in response to the three abiotic stresses in K. nitens.

Multiplex CRISPR/Cas9-mediated knockout of the phytoene desaturase gene in Coffea canephora

Coffea canephora (2n = 2x = 22 chromosomes) is a species with extensive genetic diversity and desirable agronomic traits for coffee breeding programs. However, obtaining a new coffee cultivar through conventional breeding techniques may require more than 30 years of crossing cycles and selection, which hampers the effort of keeping up with market demands and rapidly proposing more resilient to climate change varieties. Although, the application of modern biotechnology tools such as precision genetic engineering technologies may enable a faster cultivar development process. Therefore, we aimed to validate the CRISPR/Cas9 system to generate mutations on a selected genotype of C. canephora, the clone 14. Embryogenic calli and a multiplex binary vector containing two sgRNAs targeting different exons of the CcPDS gene were used. The sgRNAs were under the C. canephora U6 promoter regulation. The target gene encodes phytoene desaturase, an enzyme essential for photosynthesis involved in β-carotene biosynthesis. Somatic seedlings and embryos with albino, variegated and green phenotypes regenerated after Agrobacterium tumefaciens-mediated genetic transformation were analyzed by verifying the insertion of the Cas9 gene and later by sequencing the sgRNAs target regions in the genome of Robusta modified seedlings. Among them, 77% had the expected mutations, and of which, 50% of them had at least one target with a homozygous mutation. The genotype, temperature of co-cultivation with the bacteria, and light intensity used for subsequent embryo regeneration appeared to strongly influence the successful regeneration of plants with a mutated CcPDS gene in the Coffea genus.

The biological feasibility and social context of gene-edited, caffeine-free coffee

Coffee, especially the species Coffea arabica and Coffea canephora, is one of the world’s most consumed beverages. The consumer demand for caffeine-free coffee is currently being met through chemical decaffeination processes. However, this method leads to loss of beverage quality. In this review, the feasibility of using gene editing to produce caffeine-free coffee plants is reviewed. The genes XMT (7-methylxanthosine methyltransferase) and DXMT (3,7-dimethylxanthine methyltransferase) were identified as candidate target genes for knocking out caffeine production in coffee plants. The possible effect of the knock-out of the candidate genes was assessed. Using Agrobacterium tumefaciens-mediated introduction of the CRISPR-Cas system to Knock out XMT or DXMT would lead to blocking caffeine biosynthesis. The use of CRISPR-Cas to genetically edit consumer products is not yet widely accepted, which may lead to societal hurdles for introducing gene-edited caffeine-free coffee cultivars onto the market. However, increased acceptance of CRISPR-Cas/gene editing on products with a clear benefit for consumers offers better prospects for gene editing efforts for caffeine-free coffee.

Fine-Tuning Cold Stress Response Through Regulated Cellular Abundance and Mechanistic Actions of Transcription Factors

Inflictions caused by cold stress can result in disastrous effects on the productivity and survival of plants. Cold stress response in plants requires crosstalk between multiple signaling pathways including cold, heat, and reactive oxygen species (ROS) signaling networks. CBF, MYB, bHLH, and WRKY families are among the TFs that function as key players in the regulation of cold stress response at the molecular level. This review discusses some of the latest understanding on the regulation of expression and the mechanistic actions of plant TFs to address cold stress response. It was shown that the plant response consists of early and late responses as well as memory reprogramming for long-term protection against cold stress. The regulatory network can be differentiated into CBF-dependent and independent pathways involving different sets of TFs. Post-transcriptional regulation by miRNAs, control during ribosomal translation process, and post-translational regulation involving 26S proteosomic degradation are processes that affect the cellular abundance of key regulatory TFs, which is an important aspect of the regulation for cold acclimation. Therefore, fine-tuning of the regulation by TFs for adjusting to the cold stress condition involving the dynamic action of protein kinases, membrane ion channels, adapters, and modifiers is emphasized in this review.

Comparative Phenotypic and Transcriptomic Analysis Reveals Key Responses of Upland Cotton to Salinity Stress During Postgermination

To understand the molecular mechanisms of salinity tolerance during seed germination and post-germination stages, this study characterized phenotypic and transcriptome responses of two cotton cultivars during salinity stress. The two cultivars were salt-tolerant (ST) LMY37 and salt-sensitive (SS) ZM12, with the former exhibiting higher germination rate, growth, and primary-root fresh weight under salinity stress. Transcriptomic comparison revealed that up-regulation of differentially expressed genes (DEGs) was the main characteristic of transcriptional regulation in ST, while SS DEGs were mainly down-regulated. GO and KEGG analyses uncovered both common and specific responses in ST and SS. Common processes, such as reactive oxygen species (ROS) metabolism and cell wall biosynthesis, may be general responses to salinity in cotton. In contrast, DEGs involved in MAPK-signaling pathway activated by ROS, carotenoid biosynthesis pathway and cysteine and methionine metabolism pathway [producing the precursors of stress hormone abscisic acid (ABA) and ethylene (ET), respectively] as well as stress tolerance related transcription factor genes, showed significant expression differences between ST and SS. These differences might be the molecular basis leading to contrasting salinity tolerance. Silencing of GhERF12, an ethylene response factor gene, caused higher salinity sensitivity and increased ROS accumulation after salinity stress. In addition, peroxidase (POD) and superoxide dismutase (SOD) activity obviously declined after silencing GhERF12. These results suggest that GhERF12 is involved in salinity tolerance during early development. This study provides a novel and comprehensive perspective to understand key mechanisms of salinity tolerance and explores candidate genes that may be useful in developing stress-tolerant crops through biotechnology.

Transcriptomic Leaf Profiling Reveals Differential Responses of the Two Most Traded Coffee Species to Elevated [CO2]

As atmospheric [CO₂] continues to rise to unprecedented levels, understanding its impact on plants is imperative to improve crop performance and sustainability under future climate conditions. In this context, transcriptional changes promoted by elevated CO₂ (eCO₂) were studied in genotypes from the two major traded coffee species: the allopolyploid Coffea arabica (Icatu) and its diploid parent, C. canephora (CL153). While Icatu expressed more genes than CL153, a higher number of differentially expressed genes were found in CL153 as a response to eCO₂. Although many genes were found to be commonly expressed by the two genotypes under eCO₂, unique genes and pathways differed between them, with CL153 showing more enriched GO terms and metabolic pathways than Icatu. Divergent functional categories and significantly enriched pathways were found in these genotypes, which altogether supports contrasting responses to eCO₂. A considerable number of genes linked to coffee physiological and biochemical responses were found to be affected by eCO₂ with the significant upregulation of photosynthetic, antioxidant, and lipidic genes. This supports the absence of photosynthesis down-regulation and, therefore, the maintenance of increased photosynthetic potential promoted by eCO₂ in these coffee genotypes.

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

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 Vitis VviERF6L1 overexpression lines were 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.

Full moonlight-induced circadian clock entrainment in Coffea arabica

BACKGROUND

It is now well documented that moonlight affects the life cycle of invertebrates, birds, reptiles, and mammals. The lunisolar tide is also well-known to alter plant growth and development. However, although plants are known to be very photosensitive, few studies have been undertaken to explore the effect of moonlight on plant physiology.

RESULTS

Here for the first time we report a massive transcriptional modification in Coffea arabica genes under full moonlight conditions, particularly at full moon zenith and 3 h later. Among the 3387 deregulated genes found in our study, the main core clock genes were affected.

CONCLUSIONS

Moonlight also negatively influenced many genes involved in photosynthesis, chlorophyll biosynthesis and chloroplast machinery at the end of the night, suggesting that the full moon has a negative effect on primary photosynthetic machinery at dawn. Moreover, full moonlight promotes the transcription of major rhythmic redox genes and many heat shock proteins, suggesting that moonlight is perceived as stress. We confirmed this huge impact of weak light (less than 6 lx) on the transcription of circadian clock genes in controlled conditions mimicking full moonlight.

An Altered Circadian Clock Coupled with a Higher Photosynthesis Efficiency Could Explain the Better Agronomic Performance of a New Coffee Clone When Compared with a Standard Variety

In a context where climate change is threatening coffee productivity, the management of coffee leaf rust is a challenging issue. Major resistant genes, which have been used for many years, are systematically being overcome by pathogens. Developing healthy plants, able to defend themselves and be productive even when attacked by the pathogen, should be part of a more sustainable alternative approach. We compared one hybrid (GPFA124), selected for its good health in various environments including a reduced rust incidence, and the cv. 'Caturra', considered as a standard in terms of productivity and quality but highly susceptible to rust, for phenotypic variables and for the expression of genes involved in the circadian clock and in primary photosynthetic metabolism. The GPFA124 hybrid showed increased photosynthetic electron transport efficiency, better carbon partitioning, and higher chlorophyll content. A strong relationship exists between chlorophyll a fluorescence and the expression of genes related to the photosynthetic electron transport chain. We also showed an alteration of the amplitude of circadian clock genes in the clone. Our work also indicated that increased photosynthetic electron transport efficiency is related to the clone's better performance. Chlorophyll a fluorescence measurement is a good indicator of the coffee tree's physiological status for the breeder. We suggest a connection between the circadian clock and carbon metabolism in coffee tree.

Coffee Somatic Embryogenesis: How Did Research, Experience Gained and Innovations Promote the Commercial Propagation of Elite Clones From the Two Cultivated Species?

Since the 1990s, somatic embryogenesis (SE) has enabled the propagation of selected varieties, Arabica F1 hybrid and Robusta clones, originating from the two cultivated coffee species, Coffea arabica and Coffea canephora, respectively. This paper shows how mostly empirical research has led to successful industrial transfers launched in the 2000s in Latin America, Africa, and Asia. Coffee SE can be considered as a model for other woody perennial crops for the following reasons: (i) a high biological efficiency has been demonstrated for propagated varieties at all developmental stages, and (ii) somaclonal variation is understood and mastered thanks to intensive research combining molecular markers and field observations. Coffee SE is also a useful model given the strong economic constraints that are specific to this species. In brief, SE faced four difficulties: (i) the high cost of SE derived plants compared to the cost of seedlings of conventional varieties, (ii) the logistic problems involved in reaching small-scale coffee growers, (iii) the need for certification, and (iv) the lack of solvency among small-scale producers. Nursery activities were professionalized by introducing varietal certification, quality control with regard to horticultural problems and somaclonal variation, and sanitary control for Xylella fastidiosa. In addition, different technology transfers were made to ensure worldwide dissemination of improved F1 Arabica hybrids and Robusta clones. Innovations have been decisive for successful scaling-up and reduction of production costs, such as the development of temporary immersion bioreactors for the mass production of pre-germinated embryos, their direct sowing on horticultural soil, and the propagation of rejuvenated SE plants by rooted mini-cuttings. Today, SE is a powerful tool that is widely used in coffee for biotechnological applications including propagation and genetic transformation. Basic research has recently started taking advantage of optimized SE protocols. Based on -omics methodologies, research aims to decipher the molecular events involved in the key developmental switches of coffee SE. In parallel, a high-throughput screening of active molecules on SE appears to be a promising tool to speed-up the optimization of SE protocols.

Identification of a seed maturation protein gene from Coffea arabica (CaSMP) and analysis of its promoter activity in tomato

A seed maturation protein gene (CaSMP) from Coffea arabica is expressed in the endosperm of yellow/green fruits. The CaSMP promoter drives reporter expression in the seeds of immature tomato fruits. In this report, an expressed sequence tag-based approach was used to identify a seed-specific candidate gene for promoter isolation in Coffea arabica. The tissue-specific expression of the cognate gene (CaSMP), which encodes a yet uncharacterized coffee seed maturation protein, was validated by RT-qPCR. Additional expression analysis during coffee fruit development revealed higher levels of CaSMP transcript accumulation in the yellow/green phenological stage. Moreover, CaSMP was preferentially expressed in the endosperm and was down-regulated during water imbibition of the seeds. The presence of regulatory cis-elements known to be involved in seed- and endosperm-specific expression was observed in the CaSMP 5'-upstream region amplified by genome walking (GW). Additional histochemical analysis of transgenic tomato (cv. Micro-Tom) lines harboring the GW-amplified fragment (~ 1.4 kb) fused to uidA reporter gene confirmed promoter activity in the ovule of immature tomato fruits, while no activity was observed in the seeds of ripening fruits and in the other organs/tissues examined. These results indicate that the CaSMP promoter can be used to drive transgene expression in coffee beans and tomato seeds, thus representing a promising biotechnological tool.

Physiological and Agronomic Performance of the Coffee Crop in the Context of Climate Change and Global Warming: A Review

Coffee is one of the most important global crops and provides a livelihood to millions of people living in developing countries. Coffee species have been described as being highly sensitive to climate change, as largely deduced from modeling studies based on predictions of rising temperatures and changing rainfall patterns. Here, we discuss the physiological responses of the coffee tree in the context of present and ongoing climate changes, including drought, heat, and light stresses, and interactions between these factors. We also summarize recent insights on the physiological and agronomic performance of coffee at elevated atmospheric CO₂ concentrations and highlight the key role of CO₂ in mitigating the harmful effects of heat stress. Evidence is shown suggesting that warming, per se, may be less harmful to coffee suitability than previously estimated, at least under the conditions of an adequate water supply. Finally, we discuss several mitigation strategies to improve crop performance in a changing world.

Juvenile Coffee Leaves Acclimated to Low Light Are Unable to Cope with a Moderate Light Increase

The understorey origin of coffee trees and the strong plasticity of Coffea arabica leaves in relation to contrasting light environments have been largely shown. The adaptability of coffee leaves to changes in light was tested under controlled conditions by increasing the illumination rate on C. arabica var. Naryelis seedlings acclimated to low light conditions and observing leaf responses at three different developmental stages (juvenile, growing and mature). Only mature leaves proved capable of adapting to new light conditions. In these leaves, different major mechanisms were found to contribute to maintaining a good photosynthetic level. With increased illumination, a high photosynthetic response was conserved thanks to fast nitrogen remobilization, as indicated by SPAD values and the photorespiration rate. Efficient photoprotection was accompanied by a great ability to export sucrose, which prevented excessive inhibition of the Calvin cycle by hexose accumulation. In contrast, in younger leaves, increased illumination caused photodamage, observable even after 9 days of treatment. One major finding was that young coffee leaves rely on the accumulation of chlorogenic acids, powerful antioxidant phenolic compounds, to deal with the accumulation of reactive oxygen species rather than on antioxidant enzymes. Due to a lack of efficient photoprotection, a poor ability to export sucrose and inadequate antioxidant protection, younger leaves seemed to be unable to cope with increased illumination. In these leaves, an absence of induced antioxidant enzyme activity was accompanied, in growing leaves, by an absence of antioxidant synthesis or, in juvenile leaves, inefficient synthesis of flavonoids because located in some epidermis cells. These observations showed that coffee leaves, at the beginning of their development, are not equipped to withstand quick switches to higher light levels. Our results confirm that coffee trees, even selected for full sunlight conditions, remain shade plants possessing leaves able to adapt to higher light levels only when mature.