GeoBioSciences GeoTechnologies and GeoEngineering

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Protective Responses at the Biochemical and Molecular Level Differ between a Coffea arabica L. Hybrid and Its Parental Genotypes to Supra-Optimal Temperatures and Elevated Air [CO2]

Publication . Vinci, Gabriella; Marques, Isabel; Rodrigues, Ana P.; Martins, Sónia; Leitão, António E.; Semedo, Magda C.; Silva, Maria J.; Lidon, Fernando C.; DaMatta, Fábio; Ribeiro-Barros, Ana I.; Ramalho, José C.

Climate changes with global warming associated with rising atmospheric [CO2] can strongly impact crop performance, including coffee, which is one of the most world’s traded agricultural commodities. Therefore, it is of utmost importance to understand the mechanisms of heat tolerance and the potential role of elevated air CO2 (eCO2) in the coffee plant response, particularly regarding the antioxidant and other protective mechanisms, which are crucial for coffee plant acclimation. For that, plants of Coffea arabica cv. Geisha 3, cv. Marsellesa and their hybrid (Geisha 3 Marsellesa) were grown for 2 years at 25/20 C (day/night), under 400 (ambient CO2, aCO2) or 700 L (elevated CO2, eCO2) CO2 L-1, and then gradually submitted to a temperature increase up to 42/30 C, followed by recovery periods of 4 (Rec4) and 14 days (Rec14). Heat (37/28 C and/or 42/30 C) was the major driver of the response of the studied protective molecules and associated genes in all genotypes. That was the case for carotenoids (mostly neoxanthin and lutein), but the maximal (a + b) carotenes pool was found at 37/28 C only in Marsellesa. All genes (except VDE) encoding for antioxidative enzymes (catalase, CAT; superoxide dismutases, CuSODs; ascorbate peroxidases, APX) or other protective proteins (HSP70, ELIP, Chape20, Chape60) were strongly upregulated at 37/28 C, and, especially, at 42/30 C, in all genotypes, but with maximal transcription in Hybrid plants. Accordingly, heat greatly stimulated the activity of APX and CAT (all genotypes) and glutathione reductase (Geisha3, Hybrid) but not of SOD. Notably, CAT activity increased even at 42/30 C, concomitantly with a strongly declined APX activity. Therefore, increased thermotolerance might arise through the reinforcement of some ROS-scavenging enzymes and other protective molecules (HSP70, ELIP, Chape20, Chape60). Plants showed low responsiveness to single eCO2 under unstressed conditions, while heat promoted changes in aCO2 plants. Only eCO2 Marsellesa plants showed greater contents of lutein, the pool of the xanthophyll cycle components (V + A + Z), and b-carotene, compared to aCO2 plants at 42/30 C. This, together with a lower CAT activity, suggests a lower presence of H2O2, likely also associated with the higher photochemical use of energy under eCO2. An incomplete heat stress recovery seemed evident, especially in aCO2 plants, as judged by the maintenance of the greater expression of all genes in all genotypes and increased levels of zeaxanthin (Marsellesa and Hybrid) relative to their initial controls. Altogether, heat was the main response driver of the addressed protective molecules and genes, whereas eCO2 usually attenuated the heat response and promoted a better recovery. Hybrid plants showed stronger gene expression responses, especially at the highest temperature, when compared to their parental genotypes, but altogether, Marsellesa showed a greater acclimation potential. The reinforcement of antioxidative and other protective molecules are, therefore, useful biomarkers to be included in breeding and selection programs to obtain coffee genotypes to thrive under global warming conditions, thus contributing to improved crop sustainability

2022Journal article

Open access

Genomic evaluation of Coffea arabica and its wild relative Coffea racemosa in Mozambique: settling resilience keys for the Coffee crop in the context of climate change

Publication . Tapaça, Inocência da Piedade Ernesto; Mavuque, Lopes; Corti, Riccardo; Pedrazzani, Samuele; Maquia, Ivete S. A.; Tongai, Castigo; Partelli, Fábio Luiz; Ramalho, José C.; Marques, Isabel; Ribeiro-Barros, Ana I.

Climate change is negatively affecting the coffee value chain, with a direct effect on approximately 100 million people from 80 countries. This has been attributed to the high vulnerability of the two-mainstream species, Coffea arabica and Coffea canephora, to extreme weather events, with notable uneven increases in market prices. Taking into account the narrow genetic plasticity of the commercial coffee cultivars, wild-relatives and underutilized Coffea species are valuable genetic resources. In this work, we have assessed the occurrence of Coffea species in to understand the degree of genetic relationships between Coffea species in the country, as well as the patterns of genetic diversity, differentiation, and genetic structure. Only one wild species was found, C. racemosa, which showed a high level of genetic separation with C. arabica, based on plastid, as well as SSR and SNP analysis. C. arabica presented low levels of diversity likely related to their autogamous nature, while the allogamous C. racemosa presented higher levels of diversity and heterozygosity. The analysis of the functional pathways based on SNPs suggests that the stress signaling pathways are more robust in this species. This novel approach shows that it is vital to introduce more resilient species and increase genomic diversity in climate-smart practices.

2023Journal article

Open access

Salt Stress Tolerance in Casuarina glauca: Insights from the Branchlets Transcriptome

Publication . Fernandes, Isabel; Paulo, Octávio S.; Marques, Isabel; Sarjkar, Indrani; Sen, Arnab; Graça, Inês; Pawlowski, Katharina; Ramalho, José C.; Ribeiro-Barros, Ana I.

Climate change and the accelerated rate of population growth are imposing a progressive degradation of natural ecosystems worldwide. In this context, the use of pioneer trees represents a powerful approach to reverse the situation. Among others, N2-fixing actinorhizal trees constitute important elements of plant communities and have been successfully used in land reclamation at a global scale. In this study, we have analyzed the transcriptome of the photosynthetic organs of Casuarina glauca (branchlets) to unravel the molecular mechanisms underlying salt stress tolerance. For that, C. glauca plants supplied either with chemical nitrogen (KNO3 +) or nodulated by Frankia (NOD+) were exposed to a gradient of salt concentrations (200, 400, and 600 mM NaCl) and RNA-Seq was performed. An average of ca. 25 million clean reads was obtained for each group of plants, corresponding to 86,202 unigenes. The patterns of differentially expressed genes (DEGs) clearly separate two groups: (i) control- and 200 mM NaCl-treated plants, and (ii) 400 and 600 mM NaCltreated plants. Additionally, although the number of total transcripts was relatively high in both plant groups, the percentage of significant DEGs was very low, ranging from 6 (200 mM NaCl/NOD+) to 314 (600 mM NaCl/KNO3 +), mostly involving down-regulation. The vast majority of up-regulated genes was related to regulatory processes, reinforcing the hypothesis that some ecotypes of C. glauca have a strong stress-responsive system with an extensive set of constitutive defense mechanisms, complemented by a tight mechanism of transcriptional and post-transcriptional regulation. The results suggest that the robustness of the stress response system in C. glauca is regulated by a limited number of genes that tightly regulate detoxification and protein/enzyme stability, highlighting the complexity of the molecular interactions leading to salinity tolerance in this species

2022Journal article

Open access

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

Publication . Marques, Isabel; Gouveia, Duaret; Gaillard, Jean-Charles; Martins, Sónia; Semedo, Magda C.; Lidon, Fernando C.; DaMatta, Fábio M.; Ribeiro-Barros, Ana I.; Armengaud, Jean; Ramalho, José C.

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 levels

2022Journal article

Open access

Diversity of leaf stomatal traits among Coffea canephora Pierre ex A. Froehner genotypes

Publication . Dubberstein, Danielly; Oliveira, Marcos Goes; Aoyama, Elisa Mitsuko; Guilhen, José Henrique; Ferreira, Adésio; Marques, Isabel; Ramalho, José C.; Partelli, Fábio Luiz

Leaf morpho-anatomical characteristics directly reflect photosynthetic performance and the ability to adapt to different environmental conditions. The study of biometric traits is essential for the selection of promising plant materials for breeding purposes. To identify new varieties of coffee plants with desirable traits for genetic improvement programs, this study investigated the variability of leaf morpho-anatomical traits in 43 genotypes of Coffea canephora (as the species under study is hypostomatous). Seven leaf characteristics were used: epidermal cell density (ECD), stomatal length (SL), stomatal width (SW), stomatal density (SD), stomatal size (SS), stomatal index (SI), and stomatal length/width. Morphological traits (plant height, internodal distance, and leaf area) and grain production were also assessed. The data analyzed multivariate analysis of variance grouped by the unweighted pair group the arithmetic mean hierarchical method, and data were also subjected to a Pearson linear correlation and principal component analyses (PCAs). The results showed wide morphological variability reflecting six morphological groups, which is relevant for the genetic divergence analysis and for breeding purposes, as the results have the potential to identify superior genotypes. Within the groups, genotypes were mainly separated by the number of epidermal cells and the number and size of the stomata, reflecting a high genetic heterogeneity within genotypes. Positive and negative correlations were found, with levels of significance ranging from weak to strong among the analyzed traits. The highest correlation levels were found for SL SS, SW SS, and SI SD. In addition, the PCA indicated that plant height, distance between nodes, and leaf area were positively correlated and associated. The greater the number and width of stomata, the higher the rate of gas exchange. Both characteristics are favorable for the development and production of coffee plants, explaining the positive correlation observed in this study. These results emphasize the usefulness of trait evaluations for the identification and breeding of genotypes to compose new C. canephora cultivars suitable for changing environments

2021Journal article

Open access