24 results on '"Leran, Sophie"'
Search Results
2. The Nitrate Transporter Family Protein LjNPF8.6 Controls the N-Fixing Nodule Activity
- Author
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Valkov, Vladimir Totev, Rogato, Alessandra, Alves, Ludovico Martins, Sol, Stefano, Noguero, Mélanie, Léran, Sophie, Lacombe, Benoit, and Chiurazzi, Maurizio
- Published
- 2017
3. Global transcriptome profiling reveals differential regulatory, metabolic and hormonal networks during somatic embryogenesis in Coffea arabica
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Awada, Rayan, Lepelley, Maud, Breton, David, Charpagne, Aline, Campa, Claudine, Berry, Victoria, Georget, Frederic, Breitler, Jean-Christophe, Leran, Sophie, Djerrab, Doaa, Martinez-Seidel, Federico, Descombes, Patrick, Crouzillat, Dominique, Bertrand, Benoît, Etienne, Hervé, Awada, Rayan, Lepelley, Maud, Breton, David, Charpagne, Aline, Campa, Claudine, Berry, Victoria, Georget, Frederic, Breitler, Jean-Christophe, Leran, Sophie, Djerrab, Doaa, Martinez-Seidel, Federico, Descombes, Patrick, Crouzillat, Dominique, Bertrand, Benoît, and Etienne, Hervé
- Abstract
Background: Somatic embryogenesis (SE) is one of the most promising processes for large-scale dissemination of elite varieties. However, for many plant species, optimizing SE protocols still relies on a trial and error approach. We report the first global scale transcriptome profiling performed at all developmental stages of SE in coffee to unravel the mechanisms that regulate cell fate and totipotency. Results: RNA-seq of 48 samples (12 developmental stages × 4 biological replicates) generated 90 million high quality reads per sample, approximately 74% of which were uniquely mapped to the Arabica genome. First, the statistical analysis of transcript data clearly grouped SE developmental stages into seven important phases (Leaf, Dedifferentiation, Primary callus, Embryogenic callus, Embryogenic cell clusters, Redifferentiation and Embryo) enabling the identification of six key developmental phase switches, which are strategic for the overall biological efficiency of embryo regeneration. Differential gene expression and functional analysis showed that genes encoding transcription factors, stress-related genes, metabolism-related genes and hormone signaling-related genes were significantly enriched. Second, the standard environmental drivers used to control SE, i.e. light, growth regulators and cell density, were clearly perceived at the molecular level at different developmental stages. Third, expression profiles of auxin-related genes, transcription factor-related genes and secondary metabolism-related genes were analyzed during SE. Gene co-expression networks were also inferred. Auxin-related genes were upregulated during dedifferentiation and redifferentiation while transcription factor-related genes were switched on from the embryogenic callus and onward. Secondary metabolism-related genes were switched off during dedifferentiation and switched back on at the onset of redifferentiation. Secondary metabolites and endogenous IAA content were tightly linked with the
- Published
- 2023
4. Microscopic analysis of root cellular architecture in different coffee species: a preliminary comparison of the main phenotypical traits in controlled conditions
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Crisafulli, Paola, Bordeaux, Mélanie, Georget, Frederic, Lefort, Eveline, Leran, Sophie, Neumann, Kerstin, Navarini, Luciano, Crisafulli, Paola, Bordeaux, Mélanie, Georget, Frederic, Lefort, Eveline, Leran, Sophie, Neumann, Kerstin, and Navarini, Luciano
- Published
- 2023
5. Addressing climate change in coffee farming: development of a methodology to select for drought tolerance in coffee varieties
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Darracq, Olivier, Leran, Sophie, Aberkane, Hafid, Palacios, Algenis, Castillo, Jonny, Bordeaux, Mélanie, Marie, Lison, Arigoni, Fabrizio, Etienne, Hervé, Bertrand, Benoît, Marraccini, Pierre, Darracq, Olivier, Leran, Sophie, Aberkane, Hafid, Palacios, Algenis, Castillo, Jonny, Bordeaux, Mélanie, Marie, Lison, Arigoni, Fabrizio, Etienne, Hervé, Bertrand, Benoît, and Marraccini, Pierre
- Published
- 2023
6. Description of an Arabica coffee ideotype for agroforestry cropping systems: A guideline for breeding more resilient new varieties
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Breitler, Jean-Christophe, Etienne, Hervé, Leran, Sophie, Marie, Lison, Bertrand, Benoît, Breitler, Jean-Christophe, Etienne, Hervé, Leran, Sophie, Marie, Lison, and Bertrand, Benoît
- Abstract
Climate change (CC) is already impacting Arabica coffee cultivation in the intertropical zone. To deal with this situation, it is no longer possible to manage this crop using industrial agriculture techniques, which has been the main strategy implemented since the Green Revolution. Developing a more sustainable agriculture system that respects people and the environment is essential to guarantee future generations' access to natural resources. In the case of Arabica coffee, the solution has been found. Agroforestry is proposed as an ecosystem-based strategy to mitigate and adapt to CC. At least 60% of Arabica coffee is produced in agroforestry systems (AFSs), which are the most sustainable way to produce coffee. Nevertheless, AFS coffee cultivation is currently uncompetitive partly because all modern varieties, selected for full-sun intensive cropping systems, have low yields in shaded environments. Here we review the reasons why agroforestry is part of the solution to CC, and why no breeding work has been undertaken for this cropping system. Based on the literature data, for breeding purposes we also define for the first time one possible coffee ideotype required for AFS coffee cultivation. The four main traits are: (1) productivity based on F1 hybrid vigor, tree volume and flowering intensity under shade; (2) beverage quality by using wild Ethiopian accessions as female progenitors and selecting for this criterion using specific biochemical and molecular predictors; (3) plant health to ensure good tolerance to stress, especially biotic; and (4) low fertilization to promote sustainable production. For each of these traits, numerous criteria with threshold values to be achieved per trait were identified. Through this research, an ecosystem-based breeding strategy was defined to help create new F1 hybrid varieties within the next 10 years.
- Published
- 2022
7. Shade effects on yield across different Coffea arabica cultivars — how much is too much? A meta-analysis
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Koutouleas, Athina, Sarzynski, Thuan, Bertrand, Benoît, Bordeaux, Mélanie, Skovmand Bosselmann, Aske, Campa, Claudine, Etienne, Hervé, Turreira-Garcia, Nerea, Leran, Sophie, Markussen, Bo, Marraccini, Pierre, Cochicho Ramalho, José, Vaast, Philippe, Raebild, Anders, Koutouleas, Athina, Sarzynski, Thuan, Bertrand, Benoît, Bordeaux, Mélanie, Skovmand Bosselmann, Aske, Campa, Claudine, Etienne, Hervé, Turreira-Garcia, Nerea, Leran, Sophie, Markussen, Bo, Marraccini, Pierre, Cochicho Ramalho, José, Vaast, Philippe, and Raebild, Anders
- Abstract
The coffee research community has maintained a long ongoing debate regarding the implications of shade trees in coffee production. Historically, there has been contrasting results and opinions on this matter, thus recommendations for the use of shade (namely in coffee agroforestry systems) are often deemed controversial, particularly due to potential yield declines and farmers' income. This study is one of the first demonstrating how several Coffea arabica cultivars respond differently to shade with respect to yield. By standardising more than 200 coffee yield data from various in-field trials, we assembled the so-called “Ristretto” data pool, a one of a kind, open-source dataset, consolidating decades of coffee yield data under shaded systems. With this standardised dataset, our meta-analysis demonstrated significant genotypic heterogeneity in response to shade, showing neutral, inverted U-shaped and decreasing trends between yield and shade cover amongst 18 different cultivars. These findings encourage the examination of C. arabica at the cultivar level when assessing suitability for agroforestry systems. Comparison of productivity is also encouraged across a range of low to moderate shade levels (10–40%), in order to help elucidate potential unknown optimal shade levels for coffee production.
- Published
- 2022
8. Study of circadian regulation of primary metabolism in coffee plant is key to develop coffee varieties adapted to climate change
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Breitler, Jean-Christophe, Toniutti, Lucile, Djerrab, Doaa, Leran, Sophie, Campa, Claudine, Etienne, Hervé, and Bertrand, Benoît
- Subjects
food and beverages - Abstract
RATIONALE - The circadian clock (CC) is a critical regulator to optimize the plant physiology and metabolism to the correct time of the day, providing plants with the ability to anticipate daily and seasonal environmental changes. Plant transcriptome is massively modulated by the CC which is an integrator of many environmental cues. Through several experiments we show here how the CC of Arabica is modulated by the environment and how the genetic background can also modulate the CC with huge impact on primary metabolism. METHODS RNA sequencing was systematically used to study gene expression over 24h in combination with metabolomical and physiological analysis. Then we have integrated information of multiple circadian RNA-seq diurnal time-course in order to estimate the fraction of the Arabica transcriptome that is circadian regulated. Comparison of all the rhythmic genes identified in coffee genome with those of Arabidopsis thaliana revealed they are identical at almost 90%. RESULTS - We present how photoperiod, full-moon light, and thermos-cycles, led to changes in transcript abundance of thousand of genes during the diurnal cycle altered the CC amplitude which in cascade modify the expression of thousand of rythmic genes. Moreover, we will explain how the genetic background can change the CC and the implication in terms of primary metabolism, physiological behaviour and disease resistance. In this presentation we pay special attention to three major genes of the core clock for which we recall how important they are for the regulation of the transcriptome and in fine on the development of the plant and the major agronomic traits. CONCLUSIONS & PERSPECTIVES - Variations in the environment and/or genetic background have a major impact on the rhythmicity and daily amplitude of expression of a large number of Arabica coffee genes. The same trends as in model plants (notably Arabidopsis) are found here. The study of variations in the expression of the main core clock genes is fundamental and needs to be refined. A major question that needs to be addressed is: can we find allelic variation in circadian genes in the Arabica species and can we use it to breed news varieties with higher performances.
- Published
- 2021
9. Photoperiod-dependent transcriptional modifications in key metabolic pathways in Coffea arabica
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Djerrab, Doaa, Bertrand, Benoît, Breitler, Jean-Christophe, Leran, Sophie, Dechamp, Eveline, Campa, Claudine, Barrachina, Célia, Conejero, Geneviève, Etienne, Hervé, Sulpice, Ronan, Djerrab, Doaa, Bertrand, Benoît, Breitler, Jean-Christophe, Leran, Sophie, Dechamp, Eveline, Campa, Claudine, Barrachina, Célia, Conejero, Geneviève, Etienne, Hervé, and Sulpice, Ronan
- Abstract
Photoperiod length induces in temperate plants major changes in growth rates, morphology and metabolism with, for example, modifications in the partitioning of photosynthates to avoid starvation at the end of long nights. However, this has never been studied for a tropical perennial species adapted to grow in a natural photoperiod close to 12 h/12 h all year long. We grew Coffea arabica L., an understorey perennial evergreen tropical species in its natural 12 h/12 h and in a short 8 h/16 h photoperiod, and we investigated its responses at the physiological, metabolic and transcriptomic levels. The expression pattern of rhythmic genes, including core clock genes, was affected by changes in photoperiod. Overall, we identified 2859 rhythmic genes, of which 89% were also rhythmic in Arabidopsis thaliana L. Under short-days, plant growth was reduced, and leaves were thinner with lower chlorophyll content. In addition, secondary metabolism was also affected with chlorogenic acid and epicatechin levels decreasing, and in agreement, the genes involved in lignin synthesis were overexpressed and those involved in the flavanol pathway were underexpressed. Our results show that the 8 h/16 h photoperiod induces drastic changes in morphology, metabolites and gene expression, and the responses for gene expression are similar to those observed in the temperate annual A. thaliana species. Short photoperiod induces drastic changes in gene expression, metabolites and leaf structure, some of these responses being similar to those observed in A. thaliana.
- Published
- 2021
10. Unravelling the metabolic and hormonal machinery during key steps of somatic embryogenesis: A case study in coffee
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Awada, Rayan, Campa, Claudine, Gibault, Estelle, Dechamp, Eveline, Georget, Frederic, Lepelley, Maud, Abdallah, Cécile, Erban, Alexander, Martinez-Seidel, Federico, Kopka, Joachim, Legendre, Laurent, Leran, Sophie, Conejero, Geneviève, Verdeil, Jean-Luc, Crouzillat, Dominique, Breton, David, Bertrand, Benoît, Etienne, Hervé, Awada, Rayan, Campa, Claudine, Gibault, Estelle, Dechamp, Eveline, Georget, Frederic, Lepelley, Maud, Abdallah, Cécile, Erban, Alexander, Martinez-Seidel, Federico, Kopka, Joachim, Legendre, Laurent, Leran, Sophie, Conejero, Geneviève, Verdeil, Jean-Luc, Crouzillat, Dominique, Breton, David, Bertrand, Benoît, and Etienne, Hervé
- Abstract
RATIONALE - Somatic embryogenesis (SE) is one of the most promising processes for large-scale dissemination of elite varieties. However, whatever the species considered, SE research still remains essentially empirical resulting in many drawbacks to fulfil market demands, especially due to an overall slow technical progress over the last 20 years. Knowledge about the molecular events involved in the key steps of the SE process is urgently needed to pilot the optimization of SE protocols. In this study, we took advantage of the latest metabolomics technologies and applied them to one of the most advanced and reliable large-scale SE processes, the one developed for coffee. METHODS - Sampling covered 15 key developmental stages. Five independent leaf introductions were carried out with more than 4,000 leaf explants and a total of 25 independent cell lines. All obtained cell lines were high-yielding and time-synchronized during embryo regeneration enabling a successful sampling. Primary metabolites, secondary metabolites and phytohormones were quantified using GC-MS, HPLC and UPLC- MS/MS respectively. A robust statistical method was used to identify metabolic pathway changes associated with the main developmental phases and phase switches. Histological analysis and cell imaging were also required to characterize developmental stages and associate metabolic profiles with cell structure organization. Lastly, comparing Arabica embryogenic and non-embryogenic calli enabled the identification of metabolic markers of the embryogenic capacity. RESULTS - Statistical analysis performed on 104 metabolites revealed that massive re-configuration of metabolic pathways induced SE. During initial dedifferentiation, a sharp decrease in phenolic compounds and caffeine levels was observed while auxins, cytokinins and ethylene levels were at their highest. Totipotency reached its highest expression during the callus stages when a shut-off in hormonal and metabolic pathways related to sugar
- Published
- 2021
11. Functional characterization of the arabidopsis abscisic acid transporters NPF4.5 and NPF4.6 in xenopus oocytes
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Leran, Sophie, Noguero, Mélanie, Corratgé-Faillie, Claire, Boursiac, Yann, Brachet, Chantal, Lacombe, Benoit, Leran, Sophie, Noguero, Mélanie, Corratgé-Faillie, Claire, Boursiac, Yann, Brachet, Chantal, and Lacombe, Benoit
- Abstract
Few proteins have been characterized as abscisic acid transporters. Several of them are NRT1/PRT Family (NPF) transporters which have been characterized in yeast using reporter systems. Because several members of the NPF4 subfamily members were identified in yeast as ABA transporters, here, we screened for ABA transport activity the seven members of the NPF4 subfamily in Xenopus oocytes using cRNA injection and 3H-ABA accumulation. The ABA transport capacities of NPF4.2, NPF4.5, NPF4.6, and NPF4.7 were confirmed. The transport properties of NPF4.5 and NPF4.6 were studied in more detail. Both ABA transporter activities are pH-dependent and slightly pH-dependent apparent Km around 500 μM. There is no competitive inhibition of the ABA-analogs pyrabactin and quinabactin on ABA accumulation demonstrating a different selectivity compared to the ABA receptors. Functional expression of these ABA transporters in Xenopus oocyte is an opportunity to start structure–function studies and also to identify partner proteins of these hormone transporters.
- Published
- 2020
12. Full moonlight-induced circadian clock entrainment in Coffea arabica
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Breitler, Jean-Christophe, Djerrab, Doaa, Leran, Sophie, Toniutti, Lucile, Guittin, Charlie, Severac, Dany, Pratlong, M., Dereeper, Alexis, Etienne, Hervé, Bertrand, Benoît, Breitler, Jean-Christophe, Djerrab, Doaa, Leran, Sophie, Toniutti, Lucile, Guittin, Charlie, Severac, Dany, Pratlong, M., Dereeper, Alexis, Etienne, Hervé, and Bertrand, Benoît
- Abstract
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.
- Published
- 2020
13. De nouvelles variétés pour des systèmes caféiers agroforestiers innovants
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Bertrand, Benoît, Breitler, Jean-Christophe, Georget, Frederic, Penot, Eric, Bordeaux, Mélanie, Marraccini, Pierre, Leran, Sophie, Campa, Claudine, Bonato, Olivier, Villain, Luc, Etienne, Hervé, UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Département Environnements et Sociétés (Cirad-ES), Innovation et Développement dans l'Agriculture et l'Alimentation (UMR Innovation), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Côte, F.X. (ed.), Poirier-Magona, E. (ed.), Perret, S. (ed.), Roudier, P. (ed.), Rapidel, B. (ed.), and Thirion, M.C. (ed.)
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SELECTION ,[SDV.SA]Life Sciences [q-bio]/Agricultural sciences ,AMERIQUE LATINE ,F08 - Systèmes et modes de culture ,MEXIQUE ,PEROU ,F30 - Génétique et amélioration des plantes ,CAFE ,COSTA RICA ,Variété ,AMELIORATION VARIETALE ,Adaptabilité ,BIODIVERSITE ,AGROFORESTERIE ,COMMERCIALISATION ,CAFEIER ,EMBRYOGENESE SOMATIQUE ,Coffea arabica ,COLOMBIE ,BRESIL ,HYBRIDATION ,NICARAGUA - Published
- 2019
14. A global approach to decipher molecular basis of coffee tree adaptation to shade
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Duangsodsri, Teerarat, Leran, Sophie, Villegas, A.M., Vestalys, I., Artins, A., Etienne, Hervé, Breitler, Jean-Christophe, Villain, Luc, Bertrand, Benoît, and Campa, Claudine
- Subjects
P40 - Météorologie et climatologie ,F08 - Systèmes et modes de culture ,fungi ,Arbre d'ombrage ,food and beverages ,adaptation aux changements climatiques ,Coffea arabica ,Agroforesterie ,F30 - Génétique et amélioration des plantes ,Marqueur génétique - Abstract
Culture under shade in AgroForestry Systems (AFS) is proposed to face the predicted negative effects of climate change on coffee plants. To decipher the molecular mechanisms involved in coffee tree adaptation to lower light, cultivars breaded for intensive full sun production systems have been grown under shade and full sun, in Mexico and Colombia. Leaves have been harvested for biochemical and transcriptomic comparative analyses. A common biochemical and transcriptomic response is observed in mature leaves of two years-old juvenile trees of C. arabicavar. Marsellesa cultivated in Mexico at different altitudes and of six-years old producing trees of eight different Arabica genotypes cultivated in Colombia. HPLC analysis showed a significant decrease in phenolic content under shade, especially glycosylated flavonoids involved in light protection. Transcriptomic analyses showed that 70% of the under-expressed genes under shade are heat shock proteins involved in temperature but also in various abiotic stress responses. Overall, our results show that Arabica culture under shade limits the biological costs for the plant, due to stresses. This energy saving opens new question: are the resources more allocated to primary metabolism, bean production and homeostasis? We are currently testing these genes and metabolites as markers to predict the adaptation to AFS and associated abiotic stresses.
- Published
- 2019
15. The agroecological transition of agricultural systems in the global South
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Bertrand, Benoît, Breitler, Jean-Christophe, Georget, Frederic, Penot, Eric, Bordeaux, Mélanie, Marraccini, Pierre, Leran, Sophie, Campa, Claudine, Bonato, Olivier, Villain, Luc, Etienne, Hervé, Côte, F.X. (ed.), Poirier-Magona, E. (ed.), Perret, S. (ed.), Roudier, P. (ed.), Rapidel, B. (ed.), and Thirion, M.C. (ed.)
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SELECTION ,F08 - Systèmes et modes de culture ,agroécologie ,Agroforesterie ,F30 - Génétique et amélioration des plantes ,K01 - Foresterie - Considérations générales ,CAFE ,Semence ,AMELIORATION VARIETALE ,amélioration génétique ,AGROFORESTERIE ,BIODIVERSITE ,COMMERCIALISATION ,EMBRYOGENESE SOMATIQUE ,CAFEIER ,Coffea arabica ,HYBRIDATION ,Système de culture ,Biodiversité - Published
- 2019
16. Coffee somatic embryogenesis, a model to decipher fundamental mechanisms associated to totipotency, somaclonal variation and photo-autotrophy acquisition
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Etienne, Hervé, Breitler, Jean-Christophe, Bertrand, Benoît, Dechamp, Eveline, Marraccini, Pierre, Leran, Sophie, Campa, Claudine, Duangsodsri, Teerarat, Georget, Frederic, and Awada, Rayan
- Abstract
Nowadays coffee somatic embryogenesis (SE) can be considered as a model for woody perennial crops as its industrial application already allowed the dissemination of 50 millions of elite plants in the two cultivated species. The process works with high biological efficiency is observed at all developmental stages and somaclonal variation is mastered. Current research beneficiates from this regeneration model as well as from the progress of coffee genomics and biotechnologies, focuses on two distinct objectives. The recent advances of this research and their respective outputs are reviewed and discussed in this presentation. The first objective is to develop basic research based on-omics methodologies to decipher the fondamental mechanisms associated to cell reprogramming by focusing on two examples: i) Taking advantage of optimized SE protocols, we will unravel totipotency mechanisms and molecular events involved in the key developmental switches occurring during cell dedifferentiation/redifferentiation. A multi approach characterization through cell imaging, massive transcriptomic, epigenetic and metabolomic analyzes is applied at all the key developmental stages from the leaf explant to torpedo-shaped embryos (7 well characterized developmental stages). Big data integration and a system biology approach will provide a thorough knowledge of the expression of totipotency. ii) Coffee embryos acquire the capacity to photosynthetize very early in their developmental process (at the cotyledonary stage). Understanding the events leading to the acquisition of photo-autotrophy is also being studied by ecophysiological and molecular approaches applied to torpedo and cotyledonary-shaped embryo cultures under contrasted light, C02 and sugar conditions. Otherwise, the second objective is to provide - through technological approaches - powerful tools to accelerate the optimization of coffee breeding: i) The high-throughput molecular screening method has been recently developed by Nestle that allows to miniaturize the SE process and opens the way to study the biological effect of new active molecules on particular developmental switches' efficiency. It will also allow the development of miniaturized EMS (Ethyl Methyl Sulphate) mutant banks by simplifying their setting up and further management. ii) The genome editing of coffee genome by the Crispr/Cas9 technology recently described by using embryogenic tissues transformation gives us the possibility to rapidly and precisely manipulate plant genomes to introduce a trait of agronomic interest.
- Published
- 2019
17. New varieties for innovative agroforestry coffee systems
- Author
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Bertrand, Benoît, Breitler, Jean-Christophe, Georget, Frederic, Penot, Eric, Bordeaux, Mélanie, Marraccini, Pierre, Leran, Sophie, Campa, Claudine, Bonato, Olivier, Villain, Luc, Etienne, Hervé, Bertrand, Benoît, Breitler, Jean-Christophe, Georget, Frederic, Penot, Eric, Bordeaux, Mélanie, Marraccini, Pierre, Leran, Sophie, Campa, Claudine, Bonato, Olivier, Villain, Luc, and Etienne, Hervé
- Published
- 2019
18. Unravelling the metabolic and hormonal machinery during key steps of somatic embryogenesis: A case study in coffee
- Author
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Awada, Rayan, Campa, Claudine, Gibault, Estelle, Dechamp, Eveline, Georget, Frederic, Lepelley, Maud, Abdallah, Cécile, Erban, Alexander, Martinez-Seidel, Federico, Kopka, Joachim, Legendre, Laurent, Leran, Sophie, Conejero, Geneviève, Verdeil, Jean-Luc, Crouzillat, Dominique, Breton, David, Bertrand, Benoît, Etienne, Hervé, Awada, Rayan, Campa, Claudine, Gibault, Estelle, Dechamp, Eveline, Georget, Frederic, Lepelley, Maud, Abdallah, Cécile, Erban, Alexander, Martinez-Seidel, Federico, Kopka, Joachim, Legendre, Laurent, Leran, Sophie, Conejero, Geneviève, Verdeil, Jean-Luc, Crouzillat, Dominique, Breton, David, Bertrand, Benoît, and Etienne, Hervé
- Abstract
Somatic embryogenesis (SE) is one of the most promising processes for large-scale dissemination of elite varieties. However, for many plant species, optimizing SE protocols still relies on a trial-and-error approach. Using coffee as a model plant, we report here the first global analysis of metabolome and hormone dynamics aiming to unravel mechanisms regulating cell fate and totipotency. Sampling from leaf explant dedifferentiation until embryo development covered 15 key stages. An in-depth statistical analysis performed on 104 metabolites revealed that massive re-configuration of metabolic pathways induced SE. During initial dedifferentiation, a sharp decrease in phenolic compounds and caffeine levels was also observed while auxins, cytokinins and ethylene levels were at their highest. Totipotency reached its highest expression during the callus stages when a shut-off in hormonal and metabolic pathways related to sugar and energetic substance hydrolysis was evidenced. Abscisic acid, leucine, maltotriose, myo-inositol, proline, tricarboxylic acid cycle metabolites and zeatin appeared as key metabolic markers of the embryogenic capacity. Combining metabolomics with multiphoton microscopy led to the identification of chlorogenic acids as markers of embryo redifferentiation. The present analysis shows that metabolite fingerprints are signatures of cell fate and represent a starting point for optimizing SE protocols in a rational way.
- Published
- 2019
19. Creating new coffee varieties to cope with climate changes: current knowledge and future challenges
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Marraccini, Pierre, De Aquino Oliveira, Sinara, Torres, Luana F., Alves, G.C.S., Breitler, Jean-Christophe, Campa, Claudine, Leran, Sophie, Villain, Luc, Georget, Frederic, De Kochko, Alexandre, Poncet, Valérie, Andrade, Alan Carvalho, Etienne, Hervé, and Bertrand, Benoît
- Abstract
Like many other crops, coffee production is threatened by climate changes. Therefore, research on coffee adaptation to abiotic stresses as well as alternative faster breeding programs are priorities in many coffee growing countries. During the last decade, studies have been focused on identifying the physiological, molecular and genetic determinisms of coffee drought‐tolerance, mainly on C. canephora. By comparing drought‐tolerant and ‐susceptible clones, several candidate genes (like CcDREB1D) were highlighted. Recent studies demonstrated that CcDREB1D promoter haplotypes differentially regulate the expression of this gene under drought (and other abiotic stresses), mainly in leaf guard cells. In order to predict the adaptedness of C. canephora populations to climate change, statistical analyses are in progress to associate SNPs found in such candidate genes with climate parameters. Regarding C. arabica, new F1 hybrids resulting from conventional varieties crossed with wild Ethiopia accessions were recently created. With high vigor and yield, these hybrids were proved to be better adapted to agroforestry (low light) and full‐sun (high light) conditions than traditional cultivated varieties*. Even though the molecular mechanisms of heterosis in these hybrids are largely unknown, preliminary studies suggested higher homeostasis probably linked to a better regulation of genes involved in the circadian clock. *BREEDCAFS (BREEDing Coffee for AgroForestry Systems) project H2020‐SFS‐2016‐2 supported by EU (www.breedcafs.eu)
- Published
- 2018
20. Revisiting the functional properties of NPF6.3/NRT1.1/CHL1 in xenopus oocytes
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Noguero, Mélanie, Leran, Sophie, Bouguyon, Eléonore, Brachet, Chantal, Tillard, Pascal, Nacry, Philippe, Gojon, Alain, Krouk, Gabriel, and Lacombe, Benoît
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arabidopsis ,xenopus oocyte ,transporteur de nitrate ,transport d'auxine ,patch clamp - Published
- 2018
21. Coffee somatic embryogenesis: How did research, experience gained and innovations promote the commercial propagation of elite clones from the two cultivated species
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Etienne, Hervé, Breton, David, Breitler, Jean-Christophe, Bertrand, Benoît, Dechamp, Eveline, Awada, Rayan, Marraccini, Pierre, Leran, Sophie, Alpizar, Edgardo, Campa, Claudine, Courtel, Philippe, Georget, Frederic, Ducos, Jean-Paul, Etienne, Hervé, Breton, David, Breitler, Jean-Christophe, Bertrand, Benoît, Dechamp, Eveline, Awada, Rayan, Marraccini, Pierre, Leran, Sophie, Alpizar, Edgardo, Campa, Claudine, Courtel, Philippe, Georget, Frederic, and Ducos, Jean-Paul
- Abstract
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
- Published
- 2018
22. The nitrate transporter family protein LjNPF8.6 controls the N-fixing nodule activity
- Author
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Totev Valkov, Vladimir, Rogato, Alessandra, Martins Alves, Ludovico, Sol, Stefano, Noguero, Mélanie, Leran, Sophie, Lacombe, Benoit, Chiurazzi, Maurizio, Totev Valkov, Vladimir, Rogato, Alessandra, Martins Alves, Ludovico, Sol, Stefano, Noguero, Mélanie, Leran, Sophie, Lacombe, Benoit, and Chiurazzi, Maurizio
- Abstract
N-fixing nodules are new organs formed on legume roots as a result of the beneficial interaction with soil bacteria, rhizobia. The nodule functioning is still a poorly characterized step of the symbiotic interaction, as only a few of the genes induced in N-fixing nodules have been functionally characterized. We present here the characterization of a member of the Lotus japonicus nitrate transporter1/peptide transporter family, LjNPF8.6. The phenotypic characterization carried out in independent L. japonicus LORE1 insertion lines indicates a positive role of LjNPF8.6 on nodule functioning, as knockout mutants display N-fixation deficiency (25%) and increased nodular superoxide content. The partially compromised nodule functioning induces two striking phenotypes: anthocyanin accumulation already displayed 4 weeks after inoculation and shoot biomass deficiency, which is detected by long-term phenotyping. LjNPF8.6 achieves nitrate uptake in Xenopus laevis oocytes at both 0.5 and 30 mm external concentrations, and a possible role as a nitrate transporter in the control of N-fixing nodule activity is discussed.
- Published
- 2017
23. Nitrate sensing and uptake in Arabidopsis are enhanced by ABI2, a phosphatase inactived by the stress hormone abcisic acid
- Author
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Leran, Sophie, Edel, Kai H, Pervent, Marjorie, Hashimoto, Kenji, Corratge, Claire, Offenborn, Jan Niklas, Tillard, Pascal, Gojon, Alain, Kudla, Jörg, Lacombe, Benoît, Center for Genomics and Systems Biology, New York University [New York] (NYU), NYU System (NYU), Institut für Biologie und Biotechnologie der Pflanzen, University of Münster, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
- Subjects
arabidopsis ,xenopus oocyte ,viruses ,nitrogène ,assimilation de nitrate ,education ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,transport transmembranaire ,environment and public health ,health care economics and organizations - Abstract
Nitrate sensing and uptake in Arabidopsis are enhanced by ABI2, a phosphatase inactived by the stress hormone abcisic acid. International Congress "Nitrogen 2016" EMBO Conference
- Published
- 2016
24. Leaf Fructose Content Is Controlled by the Vacuolar Transporter SWEET17 in Arabidopsis
- Author
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Chardon, Fabien, Bedu, Magali, Calenge, Fanny, Klemens, Patrick A. W., Spinner, Lara, Clement, Gilles, Chietera, Giorgiana, Leran, Sophie, Ferrand, Marina, Lacombe, Benoit, Loudet, Olivier, Dinant, Sylvie, Bellini, Catherine, Neuhaus, H. Ekkehard, Daniel-Vedele, Francoise, Krapp, Anne, Chardon, Fabien, Bedu, Magali, Calenge, Fanny, Klemens, Patrick A. W., Spinner, Lara, Clement, Gilles, Chietera, Giorgiana, Leran, Sophie, Ferrand, Marina, Lacombe, Benoit, Loudet, Olivier, Dinant, Sylvie, Bellini, Catherine, Neuhaus, H. Ekkehard, Daniel-Vedele, Francoise, and Krapp, Anne
- Abstract
In higher plants, soluble sugars are mainly present as sucrose, glucose, and fructose [1]. Sugar allocation is based on both source-to-sink transport and intracellular transport between the different organelles [2,3] and depends on actual plant requirements [4]. Under abiotic stress conditions, such as nitrogen limitation, carbohydrates accumulate in plant cells [5]. Despite an increasing number of genetic studies [6, 7], the genetic architecture determining carbohydrate composition is poorly known. Using a quantitative genetics approach, we determined that the carrier protein SWEET17 is a major factor controlling fructose content in Arabidopsis leaves. We observed that when SWEET17 expression is reduced, either by induced or natural variation, fructose accumulates in leaves, suggesting an enhanced storage capacity. Subcellular localization of SWEET17-GFP to the tonoplast and functional expression in Xenopus oocytes showed that SWEET17 is the first vacuolar fructose transporter to be characterized in plants. Physiological studies in planta provide evidence that SWEET17 acts to export fructose out of the vacuole. Overall, our results suggest that natural variation in leaf fructose levels is controlled by the vacuolar fructose transporter SWEET17. SWEET17 is highly conserved across the plant kingdom; thus, these findings offer future possibilities to modify carbohydrate partitioning in crops.
- Published
- 2013
- Full Text
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