Overexpression of water-responsive genes promoted by elevated CO2 reduces ROS and enhances drought tolerance in Coffea species

Drought is a major constraint to plant growth and productivity worldwide and will aggravate as water availability becomes scarcer. Although elevated air [CO2] might mitigate some of these effects in plants, the mechanisms underlying the involved responses are poorly understood in woody economically important crops such as Coffea. This study analyzed transcriptome changes in Coffea canephora cv. CL153 and C. arabica cv. Icatu exposed to moderate (MWD) or severe water deficits (SWD) and grown under ambient (aCO2) or elevated (eCO2) air [CO2]. We found that changes in expression levels and regulatory pathways were barely affected by MWD, while the SWD condition led to a down-regulation of most differentially expressed genes (DEGs). eCO2 attenuated the impacts of drought in the transcripts of both genotypes but mostly in Icatu, in agreement with physiological and metabolic studies. A predominance of protective and reactive oxygen species (ROS)-scavenging-related genes, directly or indirectly associated with ABA signaling pathways, was found in Coffea responses, including genes involved in water deprivation and desiccation, such as protein phosphatases in Icatu, and aspartic proteases and dehydrins in CL153, whose expression was validated by qRT-PCR. The existence of a complex post-transcriptional regulatory mechanism appears to occur in Coffea explaining some apparent discrepancies between transcriptomic, proteomic, and physiological data in these genotypes.info:eu-repo/semantics/publishedVersio

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

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.info:eu-repo/semantics/publishedVersio

A Transcriptomic Approach to Understanding the Combined Impacts of Supra-Optimal Temperatures and CO2 Revealed Different Responses in the Polyploid Coffea arabica and Its Diploid Progenitor C. canephora

Understanding the effect of extreme temperatures and elevated air (CO2) is crucial for mitigating the impacts of the coffee industry. In this work, leaf transcriptomic changes were evaluated in the diploid C. canephora and its polyploid C. arabica, grown at 25 C and at two supra-optimal temperatures (37 C, 42 C), under ambient (aCO2) or elevated air CO2 (eCO2). Both species expressed fewer genes as temperature rose, although a high number of differentially expressed genes (DEGs) were observed, especially at 42 C. An enrichment analysis revealed that the two species reacted differently to the high temperatures but with an overall up-regulation of the photosynthetic machinery until 37 C. Although eCO2 helped to release stress, 42 C had a severe impact on both species. A total of 667 photosynthetic and biochemical related-DEGs were altered with high temperatures and eCO2, which may be used as key probe genes in future studies. This was mostly felt in C. arabica, where genes related to ribulose-bisphosphate carboxylase (RuBisCO) activity, chlorophyll a-b binding, and the reaction centres of photosystems I and II were down-regulated, especially under 42 C, regardless of CO2. Transcriptomic changes showed that both species were strongly affected by the highest temperature, although they can endure higher temperatures (37 C) than previously assumed.info:eu-repo/semantics/publishedVersio

Primary metabolite profile changes in coffea spp. Promoted by single and combined exposure to drought and elevated co2 concentration

info:eu-repo/grantAgreement/FCT/OE/PD%2FBD%2F113475%2F2015/PT PD/00035/2013 CRA-RED-00053-16Climate change scenarios pose major threats to many crops worldwide, including coffee. We explored the primary metabolite responses in two Coffea genotypes, C. canephora cv. Conilon Clone 153 and C. arabica cv. Icatu, grown at normal (aCO2) or elevated (eCO2) CO2 concentrations of 380 or 700 ppm, respectively, under well-watered (WW), moderate (MWD), or severe (SWD) water deficit conditions, in order to assess coffee responses to drought and how eCO2 can influence such responses. Primary metabolites were analyzed with a gas chromatography time-of-flight mass spectrometry metabolomics platform (GC-TOF-MS). A total of 48 primary metabolites were identified in both genotypes (23 amino acids and derivatives, 10 organic acids, 11 sugars, and 4 other metabolites), with differences recorded in both genotypes. Increased metabolite levels were observed in CL153 plants under single and combined conditions of aCO2 and drought (MWD and SWD), as opposed to the observed decreased levels under eCO2 in both drought conditions. In contrast, Icatu showed minor differences under MWD, and increased levels (especially amino acids) only under SWD at both CO2 concentration conditions, although with a tendency towards greater increases under eCO2. Altogether, CL153 demonstrated large impact under MWD, and seemed not to benefit from eCO2 in either MWD and SWD, in contrast with Icatu.publishersversionpublishe

Next-Generation Proteomics Reveals a Greater Antioxidative Response to Drought in Coffea arabica Than in Coffea canephora

Drought is a major threat to coffee, compromising the quality and quantity of its production. We have analyzed the core proteome of 18 Coffea canephora cv. Conilon Clone 153 and C. arabica cv. Icatu plants and assessed their responses to moderate (MWD) and severe (SWD) water deficits. Label-free quantitative shotgun proteomics identified 3000 proteins in both genotypes, but less than 0.8% contributed to ca. 20% of proteome biomass. Proteomic changes were dependent on the severity of drought, being stronger under SWD and with an enrolment of different proteins, functions, and pathways than under MWD. The two genotypes displayed stress-responsive proteins under SWD, but only C. arabica showed a higher abundance of proteins involved in antioxidant detoxification activities. Overall, the impact of MWD was minor in the two genotypes, contrary to previous studies. In contrast, an extensive proteomic response was found under SWD, with C. arabica having a greater potential for acclimation/resilience than C. canephora. This is likely supported by a wider antioxidative response and an ability to repair photosynthetic structures, being crucial to develop new elite genotypes that assure coffee supply under water scarcity levelsinfo:eu-repo/semantics/publishedVersio

Mitigation of the Negative Impact of Warming on the Coffee Crop: The Role of Increased Air [CO2] and Management Strategies

Crop sustainability can be threatened by new environmental challenges regarding predicted climate changes and global warming. Therefore, the study of real biological impacts of future environmental conditions (e.g., increased air [CO2], supra-optimal temperature and water scarcity) on crop plants, as well as the re-evaluation of management procedures and strategies, must be undertaken in order to improve crop adaptation and promote mitigation of negative environmental impacts, thus affording crop resilience. Coffee is a tropical crop that is grown in more than 80 countries, making it one of the world’s most traded agricultural products, while involving millions of people worldwide in the whole chain of value. It has been argued that this crop will be highly affected by climate changes, resulting in decreases in both suitable areas for cultivation and productivity, as well as impaired beverage quality in the near future. Here, we report recent findings regarding coffee species exposure to combined supra-optimal air temperatures and enhanced air [CO2], and impacts of drought stress on the crop. Ultimately, we discuss key strategies to improve coffee performance in the context of new environmental scenarios. The recent findings clearly show that high [CO2] has a positive impact on coffee plants, increasing their tolerance to high temperatures. This has been related to a better plant vigor, to the triggering of protective mechanisms, and to a higher functional status of the photosynthetic machinery. Even so, coffee plant is expected to suffer from water scarcity in a changing world. Therefore, discussion is focused on some important management strategies (e.g., shade systems, crop management and soil covering and terracing), which can be implemented to improve coffee performance and sustain coffee production in a continually changing environment

Lipid profile adjustments may contribute to warming acclimation and to heat impact mitigation by elevated [CO2] in Coffea spp

This work was supported by European Union, Program Horizon 2020, call H2020-SFS-2016-2, action RIA, and Portuguese national funds from Fundacao para a Ciencia e a Tecnologia (project PTDC/ASP-AGR/31257/2017; Funding from CNPq (fellowships to E. Campostrini, F.L. Partelli, and F.M. DaMatta) is also acknowledged.An unexpected heat resilience, and the mitigation of heat impacts by elevated [CO2] were recently reported in Coffea spp. Plants must maintain membrane fluidity and integrity to cope with temperature changes, which requires an adequate lipid dynamics. This work provides the lipid profile (galactolipids, GL; phospholipids, PL; sulfolipids, SL) of chloroplast membranes, and the expression of a set of genes related to lipid metabolism in Coffea arabica L. (cv. Icatu and IPR108) and C. canephora cv. Conilon CL153, under elevated [CO2] (380 or 700 μL L−1), heat (25/20, 31/25, 37/30 and 42/34 °C, day/night) and their interaction. Major membrane lipids alterations, different among genotypes, included: A) responsiveness of total fatty acids (TFAs) synthesis to [CO2] (except IPR108) and heat (except CL153); stronger remodeling (unsaturation degree) in the 700-plants from 37/30 °C to 42/34 °C, coordinated at transcriptional level with the down-regulation of fatty acid desaturase FAD3 gene (C. arabica) and up-regulation of lipoxygenase genes LOX5A (CL153 and Icatu) and LOX5B (Icatu) at the highest temperature; B) quantitative and qualitative modifications in GL (monogalactosyldiacylglycerol, MGDG; digalactosyldiacylglycerol, DGDG), PL (phosphatidylcholine, PC; phosphatidylglycerol, PG), and SL (sulfoquinovosyldiacylglycerol, SQDG) classes, prompted by heat, elevated [CO2], and, especially, the interaction, in CL153 and Icatu. Overall membrane enrichment with MGDG and DGDG as a result of heat and [CO2] interaction in these genotypes, but at the highest temperature only in Icatu the high [CO2] maintained greater contents and unsaturation values of these GLs than in the 380-plants. C) Among PL classes, PG seems to play an active role in heat acclimation of C. arabica genotypes, increasing in 700-plants at 42/34 °C. Globally, Icatu often showed changes closer to those of heat tolerant cv. CL153 than to cv. IPR108. Overall, lipid profile adjustments in chloroplast membranes, from TFAs bulk until FA unsaturation within each class, are expected to contribute to long-term acclimation to climate changes in coffee plant.publishersversionpublishe

Transcriptomic leaf profiling reveals differential responses of the two most traded coffee species to elevated [co2]

PTDC/ASP-AGR/31257/2017 UIDB/00239/2020 UIDP/04035/2020 UID/AGR/04129/2020 UIDB/04551/2020 CRA-RED-00053-16As 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.publishersversionpublishe

High-resolution shotgun proteomics reveals that increased air [CO2] amplifies the acclimation response of coffea species to drought regarding antioxidative, energy, sugar, and lipid dynamics

Funding Information: This work received funding support from the European Union's Horizon 2020 research and innovation program (grant agreement No 727934 , project BreedCAFS), and from national funds from Fundação para a Ciência e a Tecnologia, I.P. (FCT) , Portugal, through the project PTDC/ASP-AGR/31257/2017 , and the research units UIDB/00239/2020 ( CEF ), and UIDP/04035/2020 (GeoBioTec) and under the Scientific Employment Stimulus - Individual Call (CEEC Individual) - 2021.01107.CEECIND/CP1689/CT0001 (IM) . Fellowships from the Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brazil (CNPq) , (to F.M. DaMatta and F.L. Partelli), and Fundação de Amparo à Pesquisa do Estado de Minas Gerais, Brazil (FAPEMIG, projects CRA-RED-00053-16 and APQ 01512-18 , to F.M. DaMatta) are also greatly acknowledged. Publisher Copyright: © 2022 Elsevier GmbHAs drought threatens crop productivity it is crucial to characterize the defense mechanisms against water deficit and unveil their interaction with the expected rise in the air [CO2]. For that, plants of Coffea canephora cv. Conilon Clone 153 (CL153) and C. arabica cv. Icatu grown under 380 (aCO2) or 700 μL L−1 (eCO2) were exposed to moderate (MWD) and severe (SWD) water deficits. Responses were characterized through the activity and/or abundance of a selected set of proteins associated with antioxidative (e.g., Violaxanthin de-epoxidase, Superoxide dismutase, Ascorbate peroxidases, Monodehydroascorbate reductase), energy/sugar (e.g., Ferredoxin-NADP reductase, NADP-dependent glyceraldehyde-3-phosphate dehydrogenase, sucrose synthase, mannose-6-phosphate isomerase, Enolase), and lipid (Lineolate 13S-lipoxygenase) processes, as well as with other antioxidative (ascorbate) and protective (HSP70) molecules. MWD caused small changes in both genotypes regardless of [CO2] level while under the single imposition to SWD, only Icatu showed a global reinforcement of most studied proteins supporting its tolerance to drought. eCO2 alone did not promote remarkable changes but strengthened a robust multi-response under SWD, even supporting the reversion of impacts already observed by CL153 at aCO2. In the context of climate changes where water constraints and [CO2] levels are expected to increase, these results highlight why eCO2 might have an important role in improving drought tolerance in Coffea species.publishersversionpublishe