Sophie Léran

Université de Montpellier

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Hervé Etienne

Institut de Recherche pour le Développement

Jean‐Christophe Breitler

Centre de Coopération Internationale en Recherche Agronomique pour le Développement

Claudine Campa

Institut de Recherche pour le Développement

Benoît Bertrand

Institut de Recherche pour le Développement

Benoı̂t Lacombe

Institut des Sciences des Plantes de Montpellier

Frédéric Georget

Centre de Coopération Internationale en Recherche Agronomique pour le Développement

Alaín Gojon

Institut Agro Montpellier

Doâa Djerrab

Diversité, adaptation et développement des plantes

Rayan Awada

Nestlé (France)

D. Breton

Nestlé (France)

Cooperative Institutions

Université de Montpellier

Centre National de la Recherche Scientifique

Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement

Institut de Recherche pour le Développement

Centre de Coopération Internationale en Recherche Agronomique pour le Développement

Institut Agro Montpellier

Agropolis International

Institut des Sciences des Plantes de Montpellier

Diversité, adaptation et développement des plantes

Laboratoire des Interactions Plantes Micro-Organismes

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A unified nomenclature of NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family members in plants

Trends in Plant Science (2013)

Sophie Léran Kranthi Varala Jean‐Christophe Boyer Maurizio Chiurazzi Nigel M. Crawford

Subfamily

Protein family

Homology

Solute carrier family

Phylogenetic nomenclature

10.1016/j.tplants.2013.08.008

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Citations (584)

Photoperiod-dependent transcriptional modifications in key metabolic pathways in Coffea arabica

Tree Physiology (2020)

Doâa Djerrab Benoît Bertrand Jean‐Christophe Breitler Sophie Léran Eveline Déchamp

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.

10.1093/treephys/tpaa130

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Global transcriptome profiling reveals differential regulatory, metabolic and hormonal networks during somatic embryogenesis in Coffea arabica

BMC Genomics (2023)

Rayan Awada Maud Lepelley D. Breton Aline Charpagne Claudine Campa

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 their respective gene expression. Lastly, comparing Arabica embryogenic and non-embryogenic cell transcriptomes enabled the identification of biological processes involved in the acquisition of embryogenic capacity. Conclusions The present analysis showed that transcript fingerprints are discriminating signatures of cell fate and are under the direct influence of environmental drivers. A total of 23 molecular candidates were successfully identified overall the 12 developmental stages and can be tested in many plant species to optimize SE protocols in a rational way.

Coffea

10.1186/s12864-022-09098-z

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Citations (17)

AtNPF5.5, a nitrate transporter affecting nitrogen accumulation in Arabidopsis embryo

Scientific Reports (2015)

Sophie Léran Bharti Garg Yann Boursiac Claire Corratgé‐Faillie Chantal Brachet

Dipeptide (Leu-Leu) and nitrate transport activities of 26 Arabidopsis NPF (NRT1/PTR Family) proteins were screened in Saccharomyces cerevisiae and Xenopus laevis oocytes, respectively. Dipeptide transport activity has been confirmed for 2 already known dipeptide transporters (AtNPF8.1 and AtNPF8.3) but none of the other tested NPFs displays dipeptide transport. The nitrate transport screen resulted in the identification of two new nitrate transporters, AtNPF5.5 and AtNPF5.10. The localization of the mRNA coding for NPF5.5 demonstrates that it is the first NPF transporter reported to be expressed in Arabidopsis embryo. Two independent homozygous npf5.5 KO lines display reduced total nitrogen content in the embryo as compared to WT plants, demonstrating an effect of NPF5.5 function on the embryo nitrogen content. Finally, NPF5.5 gene produces two different transcripts (AtNPF5.5a and AtNPF5.5b) encoding proteins with different N-terminal ends. Both proteins are able to transport nitrate in xenopus oocytes.

10.1038/srep07962

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Citations (65)

De nouvelles variétés pour des systèmes caféiers agroforestiers innovants

HAL (Le Centre pour la Communication Scientifique Directe) (2019)

B. Bertrand Jean‐Christophe Breitler Frédéric Georget Éric Penot Mélanie Bordeaux

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Additional file 5 of Global transcriptome profiling reveals differential regulatory, metabolic and hormonal networks during somatic embryogenesis in Coffea arabica

Figshare (2023)

Rayan Awada Maud Lepelley D. Breton Aline Charpagne Claudine Campa

Additional file 5: Table S1. List of differentially expressed genes (DEGs) between the 12 developmental stages covering the SE process (10,384 DEGs) and their normalized counts by DESEq2.

Profiling (computer programming)

10.6084/m9.figshare.22616177

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Leaf Fructose Content Is Controlled by the Vacuolar Transporter SWEET17 in Arabidopsis

Current Biology (2013)

G Chardon Magali Bedu Fanny Calenge Patrick A.W. Klemens Lara Spinner

10.1016/j.cub.2013.03.021

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Citations (235)

Nitrate sensing and uptake in Arabidopsis are enhanced by ABI2, a phosphatase inactived by the stress hormone abcisic acid

HAL (Le Centre pour la Communication Scientifique Directe) (2016)

Sophie Léran Kai H. Edel Marjorie Pervent Kenji Hashimoto Claire Corratgé‐Faillie

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

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Early development and gravitropic response of lateral roots inArabidopsis thaliana

Philosophical Transactions of the Royal Society B Biological Sciences (2012)

Soazig Guyomarc’h Sophie Léran Maxime Auzon-Cape Francine Perrine‐Walker Mikaël Lucas

Root system architecture plays an important role in determining nutrient and water acquisition and is modulated by endogenous and environmental factors, resulting in considerable developmental plasticity. The orientation of primary root growth in response to gravity (gravitropism) has been studied extensively, but little is known about the behaviour of lateral roots in response to this signal. Here, we analysed the response of lateral roots to gravity and, consistently with previous observations, we showed that gravitropism was acquired slowly after emergence. Using a lateral root induction system, we studied the kinetics for the appearance of statoliths, phloem connections and auxin transporter gene expression patterns. We found that statoliths could not be detected until 1 day after emergence, whereas the gravitropic curvature of the lateral root started earlier. Auxin transporters modulate auxin distribution in primary root gravitropism. We found differences regarding PIN3 and AUX1 expression patterns between the lateral root and the primary root apices. Especially PIN3, which is involved in primary root gravitropism, was not expressed in the lateral root columella. Our work revealed new developmental transitions occurring in lateral roots after emergence, and auxin transporter expression patterns that might explain the specific response of lateral roots to gravity.

Gravitropism

Lateral root

Columella

Root cap

Polar auxin transport

10.1098/rstb.2011.0231

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Citations (54)

Shade effects on yield across different Coffea arabica cultivars — how much is too much? A meta-analysis

Agronomy for Sustainable Development (2022)

Athina Koutouleas Thuan Sarzynski Benoît Bertrand Mélanie Bordeaux Aske Skovmand Bosselmann

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.

10.1007/s13593-022-00788-2

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Citations (31)