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1. NIRSpredict: a platform for predicting plant traits from near infra-red spectroscopy

Author: Axel Vaillant, Grégory Beurier, Denis Cornet, Lauriane Rouan, Denis Vile, Cyrille Violle, and François Vasseur
Subjects: Arabidopsis thaliana, Functional traits, Genetic variability, Machine learning, Phenomics, Secondary metabolites, Botany, QK1-989
Abstract: Summary Near-infrared spectroscopy (NIRS) has become a popular tool for investigating phenotypic variability in plants. We developed the Shiny NIRSpredict application to get predictions of 81 Arabidopsis thaliana phenotypic traits, including classical functional traits as well as a large variety of commonly measured chemical compounds, based from near-infrared spectroscopy values based on deep learning. It is freely accessible at the following URL: https://shiny.cefe.cnrs.fr/NirsPredict/ . NIRSpredict has three main functionalities. First, it allows users to submit their spectrum values to get the predictions of plant traits from models built with the hosted A. thaliana database. Second, users have access to the database of traits used for model calibration. Data can be filtered and extracted on user’s choice and visualized in a global context. Third, a user can submit his own dataset to extend the database and get part of the application development. NIRSpredict provides an easy-to-use and efficient method for trait prediction and an access to a large dataset of A. thaliana trait values. In addition to covering many of functional traits it also allows to predict a large variety of commonly measured chemical compounds. As a reliable way of characterizing plant populations across geographical ranges, NIRSpredict can facilitate the adoption of phenomics in functional and evolutionary ecology.
Published: 2024
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2. Ecological trade-offs drive phenotypic and genetic differentiation of Arabidopsis thaliana in Europe

Author: Cristina C. Bastias, Aurélien Estarague, Denis Vile, Elza Gaignon, Cheng-Ruei Lee, Moises Exposito-Alonso, Cyrille Violle, and François Vasseur
Subjects: Science
Abstract: Abstract Plant diversity is shaped by trade-offs between traits related to competitive ability, propagule dispersal, and stress resistance. However, we still lack a clear understanding of how these trade-offs influence species distribution and population dynamics. In Arabidopsis thaliana, recent genetic analyses revealed a group of cosmopolitan genotypes that successfully recolonized Europe from its center after the last glaciation, excluding older (relict) lineages from the distribution except for their north and south margins. Here, we tested the hypothesis that cosmopolitans expanded due to higher colonization ability, while relicts persisted at the margins due to higher tolerance to competition and/or stress. We compared the phenotypic and genetic differentiation between 71 European genotypes originating from the center, and the south and north margins. We showed that a trade-off between plant fecundity and seed mass shapes the differentiation of A. thaliana in Europe, suggesting that the success of the cosmopolitan groups could be explained by their high dispersal ability. However, at both north and south margins, we found evidence of selection for alleles conferring low dispersal but highly competitive and stress-resistance abilities. This study sheds light on the role of ecological trade-offs as evolutionary drivers of the distribution and dynamics of plant populations.
Published: 2024
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3. AraDiv: a dataset of functional traits and leaf hyperspectral reflectance of Arabidopsis thaliana

Author: Maria Stefania Przybylska, Cyrille Violle, Denis Vile, J. F. Scheepens, Benoit Lacombe, Xavier Le Roux, Lisa Perrier, Lou Sales-Mabily, Mariette Laumond, Mariona Vinyeta, Pierre Moulin, Gregory Beurier, Lauriane Rouan, Denis Cornet, and François Vasseur
Subjects: Science
Abstract: Abstract Data from functional trait databases have been increasingly used to address questions related to plant diversity and trait-environment relationships. However, such databases provide intraspecific data that combine individual records obtained from distinct populations at different sites and, hence, environmental conditions. This prevents distinguishing sources of variation (e.g., genetic-based variation vs. phenotypic plasticity), a necessary condition to test for adaptive processes and other determinants of plant phenotypic diversity. Consequently, individual traits measured under common growing conditions and encompassing within-species variation across the occupied geographic range have the potential to leverage trait databases with valuable data for functional and evolutionary ecology. Here, we recorded 16 functional traits and leaf hyperspectral reflectance (NIRS) data for 721 widely distributed Arabidopsis thaliana natural accessions grown in a common garden experiment. These data records, together with meteorological variables obtained during the experiment, were assembled to create the AraDiv dataset. AraDiv is a comprehensive dataset of A. thaliana’s intraspecific variability that can be explored to address questions at the interface of genetics and ecology.
Published: 2023
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4. Plant–herbivore interactions: Experimental demonstration of genetic variability in plant–plant signalling

Author: Aurélien Estarague, Cyrille Violle, Denis Vile, Anaïs Hany, Thibault Martino, Pierre Moulin, and François Vasseur
Subjects: Arabidopsis thaliana, Cornu aspersum, genome‐wide association study, herbivory, intraspecific diversity, Evolution, QH359-425
Abstract: Abstract Plant–herbivore interactions mediated by plant–plant signalling have been documented in different species but its within‐species variability has hardly been quantified. Here, we tested if herbivore foraging activity on plants was influenced by a prior contact with a damaged plant and if the effect of such plant–plant signalling was variable across 113 natural genotypes of Arabidopsis thaliana. We filmed the activity of the generalist herbivore Cornu aspersum during 1 h on two plants differing only in a prior contact with a damaged plant or not. We recorded each snails' first choice, and measured its first duration on a plant, the proportion of time spent on both plants and leaf consumption. Overall, plant–plant signalling modified the foraging activity of herbivores in A. thaliana. On average, snails spent more time and consumed more of plants that experienced a prior contact with a damaged plant. However, the effects of plant–plant signalling on snail behaviour was variable: depending on genotype identity, plant–plant signalling made undamaged plants more repellant or attractive to snails. Genome‐wide associations revealed that genes related to stress coping ability and jasmonate pathway were associated to this variation. Together, our findings highlight the adaptive significance of plant–plant signalling for plant–herbivore interactions.
Published: 2023
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5. The global spectrum of plant form and function: enhanced species-level trait dataset

Author: Sandra Díaz, Jens Kattge, Johannes H. C. Cornelissen, Ian J. Wright, Sandra Lavorel, Stéphane Dray, Björn Reu, Michael Kleyer, Christian Wirth, I. Colin Prentice, Eric Garnier, Gerhard Bönisch, Mark Westoby, Hendrik Poorter, Peter B. Reich, Angela T. Moles, John Dickie, Amy E. Zanne, Jérôme Chave, S. Joseph Wright, Serge N. Sheremetiev, Hervé Jactel, Christopher Baraloto, Bruno E. L. Cerabolini, Simon Pierce, Bill Shipley, Fernando Casanoves, Julia S. Joswig, Angela Günther, Valeria Falczuk, Nadja Rüger, Miguel D. Mahecha, Lucas D. Gorné, Bernard Amiaud, Owen K. Atkin, Michael Bahn, Dennis Baldocchi, Michael Beckmann, Benjamin Blonder, William Bond, Ben Bond-Lamberty, Kerry Brown, Sabina Burrascano, Chaeho Byun, Giandiego Campetella, Jeannine Cavender-Bares, F. Stuart Chapin, Brendan Choat, David Anthony Coomes, William K. Cornwell, Joseph Craine, Dylan Craven, Matteo Dainese, Alessandro Carioca de Araujo, Franciska T. de Vries, Tomas Ferreira Domingues, Brian J. Enquist, Jaime Fagúndez, Jingyun Fang, Fernando Fernández-Méndez, Maria T. Fernandez-Piedade, Henry Ford, Estelle Forey, Gregoire T. Freschet, Sophie Gachet, Rachael Gallagher, Walton Green, Greg R. Guerin, Alvaro G. Gutiérrez, Sandy P. Harrison, Wesley Neil Hattingh, Tianhua He, Thomas Hickler, Steven I. Higgins, Pedro Higuchi, Jugo Ilic, Robert B. Jackson, Adel Jalili, Steven Jansen, Fumito Koike, Christian König, Nathan Kraft, Koen Kramer, Holger Kreft, Ingolf Kühn, Hiroko Kurokawa, Eric G. Lamb, Daniel C. Laughlin, Michelle Leishman, Simon Lewis, Frédérique Louault, Ana C. M. Malhado, Peter Manning, Patrick Meir, Maurizio Mencuccini, Julie Messier, Regis Miller, Vanessa Minden, Jane Molofsky, Rebecca Montgomery, Gabriel Montserrat-Martí, Marco Moretti, Sandra Müller, Ülo Niinemets, Romà Ogaya, Kinga Öllerer, Vladimir Onipchenko, Yusuke Onoda, Wim A. Ozinga, Juli G. Pausas, Begoña Peco, Josep Penuelas, Valério D. Pillar, Clara Pladevall, Christine Römermann, Lawren Sack, Norma Salinas, Brody Sandel, Jordi Sardans, Brandon Schamp, Michael Scherer-Lorenzen, Ernst-Detlef Schulze, Fritz Schweingruber, Satomi Shiodera, Ênio Sosinski, Nadejda Soudzilovskaia, Marko J. Spasojevic, Emily Swaine, Nathan Swenson, Susanne Tautenhahn, Ken Thompson, Alexia Totte, Rocío Urrutia-Jalabert, Fernando Valladares, Peter van Bodegom, François Vasseur, Kris Verheyen, Denis Vile, Cyrille Violle, Betsy von Holle, Patrick Weigelt, Evan Weiher, Michael C. Wiemann, Mathew Williams, Justin Wright, and Gerhard Zotz
Subjects: Science
Abstract: Measurement(s) plant trait Technology Type(s) various Factor Type(s) none Sample Characteristic - Organism Tracheophyta Sample Characteristic - Environment natural environment Sample Characteristic - Location global
Published: 2022
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6. A Perspective on Plant Phenomics: Coupling Deep Learning and Near-Infrared Spectroscopy

Author: François Vasseur, Denis Cornet, Grégory Beurier, Julie Messier, Lauriane Rouan, Justine Bresson, Martin Ecarnot, Mark Stahl, Simon Heumos, Marianne Gérard, Hans Reijnen, Pascal Tillard, Benoît Lacombe, Amélie Emanuel, Justine Floret, Aurélien Estarague, Stefania Przybylska, Kevin Sartori, Lauren M. Gillespie, Etienne Baron, Elena Kazakou, Denis Vile, and Cyrille Violle
Subjects: Arabidopsis thaliana, near-infrared spectroscopy (NIRS), multivariate analysis, machine learning, functional traits, metabolomics, Plant culture, SB1-1110
Abstract: The trait-based approach in plant ecology aims at understanding and classifying the diversity of ecological strategies by comparing plant morphology and physiology across organisms. The major drawback of the approach is that the time and financial cost of measuring the traits on many individuals and environments can be prohibitive. We show that combining near-infrared spectroscopy (NIRS) with deep learning resolves this limitation by quickly, non-destructively, and accurately measuring a suite of traits, including plant morphology, chemistry, and metabolism. Such an approach also allows to position plants within the well-known CSR triangle that depicts the diversity of plant ecological strategies. The processing of NIRS through deep learning identifies the effect of growth conditions on trait values, an issue that plagues traditional statistical approaches. Together, the coupling of NIRS and deep learning is a promising high-throughput approach to capture a range of ecological information on plant diversity and functioning and can accelerate the creation of extensive trait databases.
Published: 2022
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7. Natural variation at FLM splicing has pleiotropic effects modulating ecological strategies in Arabidopsis thaliana

Author: Mathieu Hanemian, François Vasseur, Elodie Marchadier, Elodie Gilbault, Justine Bresson, Isabelle Gy, Cyrille Violle, and Olivier Loudet
Subjects: Science
Abstract: FLOWERING LOCUS M (FLM) is known as a repressor of Arabidopsis flowering. Here, the authors show that a single intronic substitution of FLM modulates leaf color and plant growth strategy along the leaf economics spectrum, as well as plays a role in plant adaptation.
Published: 2020
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8. The genetic interaction of REVOLUTA and WRKY53 links plant development, senescence, and immune responses.

Author: Justine Bresson, Jasmin Doll, François Vasseur, Mark Stahl, Edda von Roepenack-Lahaye, Joachim Kilian, Bettina Stadelhofer, James M Kremer, Dagmar Kolb, Stephan Wenkel, and Ulrike Zentgraf
Subjects: Medicine, Science
Abstract: In annual plants, tight coordination of successive developmental events is of primary importance to optimize performance under fluctuating environmental conditions. The recent finding of the genetic interaction of WRKY53, a key senescence-related gene with REVOLUTA, a master regulator of early leaf patterning, raises the question of how early and late developmental events are connected. Here, we investigated the developmental and metabolic consequences of an alteration of the REVOLUTA and WRKY53 gene expression, from seedling to fruiting. Our results show that REVOLUTA critically controls late developmental phases and reproduction while inversely WRKY53 determines vegetative growth at early developmental stages. We further show that these regulators of distinct developmental phases frequently, but not continuously, interact throughout ontogeny and demonstrated that their genetic interaction is mediated by the salicylic acid (SA). Moreover, we showed that REVOLUTA and WRKY53 are keys regulatory nodes of development and plant immunity thought their role in SA metabolic pathways, which also highlights the role of REV in pathogen defence. Together, our findings demonstrate how late and early developmental events are tightly intertwined by molecular hubs. These hubs interact with each other throughout ontogeny, and participate in the interplay between plant development and immunity.
Published: 2022
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9. Natural variation of Arabidopsis thaliana responses to Cauliflower mosaic virus infection upon water deficit.

Author: Sandy E Bergès, François Vasseur, Alexis Bediée, Gaëlle Rolland, Diane Masclef, Myriam Dauzat, Manuella van Munster, and Denis Vile
Subjects: Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5
Abstract: Plant virus pathogenicity is expected to vary with changes in the abiotic environment that affect plant physiology. Conversely, viruses can alter the host plant response to additional stimuli from antagonism to mutualism depending on the virus, the host plant and the environment. Ecological theory, specifically the CSR framework of plant strategies developed by Grime and collaborators, states that plants cannot simultaneously optimize resistance to both water deficit and pathogens. Here, we investigated the vegetative and reproductive performance of 44 natural accessions of A. thaliana originating from the Iberian Peninsula upon simultaneous exposure to soil water deficit and viral infection by the Cauliflower mosaic virus (CaMV). Following the predictions of Grime's CSR theory, we tested the hypothesis that the ruderal character of a plant genotype is positively related to its tolerance to virus infection regardless of soil water availability. Our results showed that CaMV infection decreased plant vegetative performance and annihilated reproductive success of all accessions. In general, water deficit decreased plant performance, but, despite differences in behavior, ranking of accessions tolerance to CaMV was conserved under water deficit. Ruderality, quantified from leaf traits following a previously published procedure, varied significantly among accessions, and was positively correlated with tolerance to viral infection under both well-watered and water deficit conditions, although the latter to a lesser extent. Also, in accordance with the ruderal character of the accession and previous findings, our results suggest that accession tolerance to CaMV infection is positively correlated with early flowering. Finally, plant survival to CaMV infection increased under water deficit. The complex interactions between plant, virus and abiotic environment are discussed in terms of the variation in plant ecological strategies at the intraspecific level.
Published: 2020
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10. Image-based methods for phenotyping growth dynamics and fitness components in Arabidopsis thaliana

Author: François Vasseur, Justine Bresson, George Wang, Rebecca Schwab, and Detlef Weigel
Subjects: Biomass accumulation, Fruit number, Modeling, Image analysis, RGR, Sigmoid, Plant culture, SB1-1110, Biology (General), QH301-705.5
Abstract: Abstract Background The model species Arabidopsis thaliana has extensive resources to investigate intraspecific trait variability and the genetic bases of ecologically relevant traits. However, the cost of equipment and software required for high-throughput phenotyping is often a bottleneck for large-scale studies, such as mutant screening or quantitative genetics analyses. Simple tools are needed for the measurement of fitness-related traits, like relative growth rate and fruit production, without investment in expensive infrastructures. Here, we describe methods that enable the estimation of biomass accumulation and fruit number from the analysis of rosette and inflorescence images taken with a regular camera. Results We developed two models to predict plant dry mass and fruit number from the parameters extracted with the analysis of rosette and inflorescence images. Predictive models were trained by sacrificing growing individuals for dry mass estimation, and manually measuring a fraction of individuals for fruit number at maturity. Using a cross-validation approach, we showed that quantitative parameters extracted from image analysis predicts more 90% of both plant dry mass and fruit number. When used on 451 natural accessions, the method allowed modeling growth dynamics, including relative growth rate, throughout the life cycle of various ecotypes. Estimated growth-related traits had high heritability (0.65
Published: 2018
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11. Nonlinear phenotypic variation uncovers the emergence of heterosis in Arabidopsis thaliana.

Author: François Vasseur, Louise Fouqueau, Dominique de Vienne, Thibault Nidelet, Cyrille Violle, and Detlef Weigel
Subjects: Biology (General), QH301-705.5
Abstract: Heterosis describes the phenotypic superiority of hybrids over their parents in traits related to agronomic performance and fitness. Understanding and predicting nonadditive inheritance such as heterosis is crucial for evolutionary biology as well as for plant and animal breeding. However, the physiological bases of heterosis remain debated. Moreover, empirical data in various species have shown that diverse genetic and molecular mechanisms are likely to explain heterosis, making it difficult to predict its emergence and amplitude from parental genotypes alone. In this study, we examined a model of physiological dominance initially proposed by Sewall Wright to explain the nonadditive inheritance of traits like metabolic fluxes at the cellular level. We evaluated Wright's model for two fitness-related traits at the whole-plant level, growth rate and fruit number, using 450 hybrids derived from crosses among natural accessions of A. thaliana. We found that allometric relationships between traits constrain phenotypic variation in a nonlinear and similar manner in hybrids and accessions. These allometric relationships behave predictably, explaining up to 75% of heterosis amplitude, while genetic distance among parents at best explains 7%. Thus, our findings are consistent with Wright's model of physiological dominance and suggest that the emergence of heterosis on plant performance is an intrinsic property of nonlinear relationships between traits. Furthermore, our study highlights the potential of a geometric approach of phenotypic relationships for predicting heterosis of major components of crop productivity and yield.
Published: 2019
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12. Interact to survive: Phyllobacterium brassicacearum improves Arabidopsis tolerance to severe water deficit and growth recovery.

Author: Justine Bresson, François Vasseur, Myriam Dauzat, Marc Labadie, Fabrice Varoquaux, Bruno Touraine, and Denis Vile
Subjects: Medicine, Science
Abstract: Mutualistic bacteria can alter plant phenotypes and confer new abilities to plants. Some plant growth-promoting rhizobacteria (PGPR) are known to improve both plant growth and tolerance to multiple stresses, including drought, but reports on their effects on plant survival under severe water deficits are scarce. We investigated the effect of Phyllobacterium brassicacearum STM196 strain, a PGPR isolated from the rhizosphere of oilseed rape, on survival, growth and physiological responses of Arabidopsis thaliana to severe water deficits combining destructive and non-destructive high-throughput phenotyping. Soil inoculation with STM196 greatly increased the survival rate of A. thaliana under several scenarios of severe water deficit. Photosystem II efficiency, assessed at the whole-plant level by high-throughput fluorescence imaging (Fv/Fm), was related to the probability of survival and revealed that STM196 delayed plant mortality. Inoculated surviving plants tolerated more damages to the photosynthetic tissues through a delayed dehydration and a better tolerance to low water status. Importantly, STM196 allowed a better recovery of plant growth after rewatering and stressed plants reached a similar biomass at flowering than non-stressed plants. Our results highlight the importance of plant-bacteria interactions in plant responses to severe drought and provide a new avenue of investigations to improve drought tolerance in agriculture.
Published: 2014
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13. Genetic variability and plasticity of plant allometry

Author: François Vasseur, Cyrille Violle, Brian J. Enquist, Denis Vile, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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)-Université de Montpellier (UM), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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), University of Arizona, Santa Fe Institute, Association Nationale de la Recherche et de la Technologie, Grant/Award Number: 0398/2009-09 42 008, H2020 European Research Council, Grant/Award Number: ERC-StG-2020-949843 PHENOVIGOUR, Région Occitanie Pyrénées-Méditerranée, Grant/Award Number: FEDER FSE IEJ 2014- 2020, ANR-17-CE02-0018,AraBreed,Exploration des réponses évolutives des plantes à des changements environnementaux à la lumière des théories écologiques : un test expérimental chez l'espèce modèle Arabidopsis thaliana(2017), and European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015)
Subjects: high temperature, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, water stress, Arabidopsis thaliana, intraspecific trait variability, plasticity, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, growth rate, metabolic scaling theory, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; The metabolic scaling theory (MST) predicts quasi-universal trait-size relationships in plants, characterised by a unique allometric exponent within and across large taxonomic scales. However, recent studies have identified variability in allometric relationships, without a clear understanding of the modulating role played by genetic variation and environment.Here, we investigated (1) the allometric relationships for two central traits of MST, namely total leaf area and plant growth rate, in the model species Arabidopsis thaliana, (2) the variability of plant allometries between genotypes and (3) the plastic responses of plant allometries under water deficit, high temperature and their interaction.Using a population of 120 genotypes, we found that intraspecific allometries adhered on average with MST predictions. However, a broad variability but a moderate plasticity in the allometric exponents was observed across genotypes and environments. Allometric exponents were impacted significantly, yet weakly, by water deficit, but not by high temperature. Moreover, genotypes that deviated from MST predictions exhibited more plasticity in trait-size relationships than genotypes that followed MST predictions.Our study suggests that plant allometry is genetically variable and might be related to different adaptive strategies to cope with stressing conditions. Thus, our results highlights the need of assessing trait-size relationships within species to understand the mechanisms of plant adaptation to contrasted environments.
Published: 2023
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14. Domestication provides durum wheat with protection from locust herbivory

Author: Marie‐Pierre Chapuis, Nicolas Leménager, Cyril Piou, Pierre Roumet, Héloïse Marche, Julia Centanni, Christophe Estienne, Martin Ecarnot, François Vasseur, Cyrille Violle, Elena Kazakou, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, This work was supported by the DINER project, publicly funded by the Labex CEMEB and funds from the French Agricultural Research Centre for International Development (CIRAD). CV was supported by the European Research Council (ERC) Starting Grant Project StG-2014-639706-CONSTRAINTS. We thank the CEFE (Centre d'Ecologie Fonctionnelle et Evolutive) and the CBGP (Centre de Biologie pour la Gestion des Populations) for providing us access to the LabEx CeMEB plateform 'terrain d'expérience CEFE,' 43°38′20.2′′N 3°51′51.0′′E, and the SEPA plateform, respectively., ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), and European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015)
Subjects: Ecology, leaf, nutritional ecology, plant toughness, [SDV]Life Sciences [q-bio], domestication syndrome, Locusta migratoria, functional ecology, Triticum turgidum, cereal crop, pest insects, plant nitrogen content, feeding selection, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation
Abstract: International audience; Lower plant resistance to herbivores following domestication has been suggested as the main cause for higher feeding damage in crops than in wild progenitors. While herbivore compensatory feeding has also been proposed as a possible mechanism for raised damage in crops with low nutritional quality, predictions regarding the effects of plant domestication on nutritional quality for herbivores remain unclear. In particular, data on primary metabolites, even major macronutrients, measured in the organs consumed by herbivores, are scarce. In this study, we used a collection of 10 accessions of wild ancestors and 10 accessions of modern progenies of Triticum turgidum to examine whether feeding damage and selectivity by nymphs of Locusta migratoria primarily depended on five leaf traits related to structural resistance or nutrient profiles. Our results unexpectedly showed that locusts favored wild ancestors over domesticated accessions and that leaf toughness and nitrogen and soluble protein contents increased with the domestication process. Furthermore, the quantitative relationship between soluble protein and digestible carbohydrates was found to poorly meet the specific requirements of the herbivore, in all wheat accessions, both wild and modern. The increase in leaf structural resistance to herbivores in domesticated tetraploid wheat accessions suggested that resource allocation trade-offs between growth and herbivory resistance may have been disrupted by domestication in the vegetative organs of this species. Since domestication did not result in a loss of nutritional quality in the leaves of the tetraploid wheat, our results rather provides evidence for a role of the content of plants in nonnutritive nitrogenous secondary compounds, possibly deterrent or toxic, at least for grasshopper herbivores.
Published: 2023
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15. Ecological and genetic trade-offs driveArabidopsis thalianarange expansion in Europe

Author: Cristina C. Bastias, Aurélien Estarague, Denis Vile, Cheng-Ruei Lee, Moises Exposito-Alonso, Cyrille Violle, and François Vasseur
Abstract: How trade-offs between traits constrain adaptation to contrasted environments is critical to understand the distribution range of a given species. InArabidopsis thaliana, genetic analyses recently revealed that a group of genotypes successfully recolonized Europe from its center after the last glaciation, outcompeting older lineages and leaving them only at the distribution margins, where environmental conditions are more stressing. However, whether trade-offs between traits related to dispersal, competition, and stress tolerance explain the success and persistence of different lineages across the species geographic range remains an open question. Here, we compared the genetic and phenotypic differentiation between 72 ecotypes originating from three geographical groups in Europe (North, South and Center). We measured key traits related to fecundity, dispersal ability, competition tolerance, and stress tolerance, and used genomic data to infer the effect of selection on these traits. We showed that a trade-off between plant fecundity and seed mass constrains the diversification ofA. thalianain Europe. In particular, the success of the cosmopolitan genotypes that recolonized Europe can be explained by their higher dispersal ability at the expense of their competitive ability and stress tolerance. Inversely, peripheral ecotypes exhibited the opposite trait syndrome: high competition and stress tolerance but low dispersal ability. Moreover, peripheral genotypes tend to differentiate from central ones at genes involved in dispersal and competitive traits such as seed mass. Combining ecological and genomic approaches, our study demonstrated the role of key ecological trade-offs as evolutionary drivers of the distribution of plant populations along a geographic gradient.SignificanceAcross geographic gradients, differential adaptive phenotypes among populations can reduce the risk of local extinctions and favor niche dynamics. However, a phenotypic advantage often comes at a cost. For instance, the competition-colonization trade-off is proposed as an important driver of plant interspecific diversity, but its role for local adaptation at the intraspecific level is still unclear. Using the broadly-distributed speciesArabidopsis thaliana, we evaluate how ecological trade-offs have shaped the demography and evolution of central and peripheral populations in its native geographic gradient. Our study demonstrates that the competition-colonization trade-off is responsible of the spatially-structured phenotypic variation ofA. thalianaacross its geographical range. Our study highlights seed mass as a key trait for plant adaptation across environmental conditions.
Published: 2022
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16. Increasing plant group productivity through latent genetic variation for cooperation

Author: Luo S, Samuel E. Wuest, Ueli Grossniklaus, Pascal A. Niklaus, François Vasseur, Nuno D. Pires, Julie Messier, University of Zurich, and Ronald, Pamela C
Subjects: 0106 biological sciences, Crops, Agricultural, Natural resource economics, UFSP13-8 Global Change and Biodiversity, Regulator, Arabidopsis, Locus (genetics), Genetics and Molecular Biology, Biology, 580 Plants (Botany), 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 10126 Department of Plant and Microbial Biology, Genetic variation, Humans, Allele, 10211 Zurich-Basel Plant Science Center, Alleles, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, General Immunology and Microbiology, General Neuroscience, Tragedy of the commons, Genetic Variation, 15. Life on land, Plant Breeding, Phenotype, General Biochemistry, Monoculture, General Agricultural and Biological Sciences, 010606 plant biology & botany
Abstract: Historic yield advances in the major crops have, to a large extent, been achieved by selection for improved productivity of groups of plant individuals such as high-density stands. Research suggests that such improved group productivity depends on “cooperative” traits (e.g., erect leaves, short stems) that—while beneficial to the group—decrease individual fitness under competition. This poses a problem for some traditional breeding approaches, especially when selection occurs at the level of individuals, because “selfish” traits will be selected for and reduce yield in high-density monocultures. One approach, therefore, has been to select individuals based on ideotypes with traits expected to promote group productivity. However, this approach is limited to architectural and physiological traits whose effects on growth and competition are relatively easy to anticipate. Here, we developed a general and simple method for the discovery of alleles promoting cooperation in plant stands. Our method is based on the game-theoretical premise that alleles increasing cooperation benefit the monoculture group but are disadvantageous to the individual when facing noncooperative neighbors. Testing the approach using the model plant Arabidopsis thaliana, we found a major effect locus where the rarer allele was associated with increased cooperation and productivity in high-density stands. The allele likely affects a pleiotropic gene, since we find that it is also associated with reduced root competition but higher resistance against disease. Thus, even though cooperation is considered evolutionarily unstable except under special circumstances, conflicting selective forces acting on a pleiotropic gene might maintain latent genetic variation for cooperation in nature. Such variation, once identified in a crop, could rapidly be leveraged in modern breeding programs and provide efficient routes to increase yields.
Published: 2022

17. Plant-herbivore interactions: experimental demonstration of genetic variability in plant-plant signaling

Author: Aurélien Estarague, Cyrille Violle, Denis Vile, Anaïs Hany, Thibault Martino, Pierre Moulin, and François Vasseur
Abstract: Plant-herbivore interactions mediated by plant-plant signaling were documented in different species. Here, we tested if herbivore foraging activity on plants was influenced by plant’s prior contact with a damaged plant and if the effect of such plant-plant signaling was variable across genotypes.We filmed snails during one hour on two plants differing only in a prior contact with a damaged plant or not. We replicated eight times the experiment on 113 natural genotypes of Arabidopsis thaliana. We recorded snails’ first choice, and measured its first duration on a plant, the proportion of time spent on both plants and leaf consumption.On average, snails spent more time on plants that experienced a prior contact with a damaged plant, and consumed them more. However, plant-plant signaling effect on snail behavior was variable across genotypes. Genome-wide association studies revealed that a small number of genetic polymorphisms related to stress coping ability and jasmonate pathway explained this variation.Plant-plant signaling modified the foraging activity of herbivores in A. thaliana. Depending on the plant genotype, plant-plant signaling made undamaged plants more repulsive or attractive to snails. This finding questions the theoretical basement of the evolution of plant-herbivore interactions mediated by plant-plant signaling.HighlightPlant-plant signaling differently affects snail foraging activity depending on genetic variations in A.thaliana. These findings question the theoretical basement of the evolution of plant-herbivore interactions mediated by plant-plant signaling.
Published: 2022
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18. Do leaf nitrogen resorption dynamics align with the slow‐fast continuum? A test at the intraspecific level

Author: Kevin Sartori, Cyrille Violle, Denis Vile, François Vasseur, Pierre de Villemereuil, Justine Bresson, Lauren Gillespie, Leila Rose Fletcher, Lawren Sack, Elena Kazakou, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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)-Université de Montpellier (UM), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - 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), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), University of California [Los Angeles] (UCLA), University of California (UC), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), and European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015)
Subjects: association genetics, Arabidopsis thaliana, leaf nitrogen, fungi, food and beverages, population genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, resorption, Ecology, Evolution, Behavior and Systematics, resource-use strategies
Abstract: International audience; The links between internal nitrogen recycling through the process of resorption from senescing leaves, whole-plant resource-use strategies and performance remain elusive. Indeed, tests of such potential linkages are hampered by the classical evaluation of plant nitrogen resorption efficiency (REN) based on ‘snapshots’ of leaf nitrogen concentration from adult and senescent leaves. We significantly increased the resolution for measuring leaf nitrogen resorption by non-destructively tracking time courses of nitrogen concentration in leaves of 137 natural Arabidopsis thaliana genotypes native to a wide range of climates across Europe, grown in a greenhouse. In addition to the classical measurement of resorption efficiency, we computed the relative maximum resorption rate of nitrogen (RRN), that is, the amount of nitrogen remobilized by a leaf per unit time and per unit nitrogen, together with slow–fast syndrome traits at the leaf and whole-plant levels. Across genotypes, high rates and efficiencies of nitrogen resorption were associated with low specific leaf area and late flowering. The RRN showed significant heritability, genetic associations and was negatively correlated with the mean annual temperature of the native populations. By contrast, despite the evidence of a correlation with temperature, REN showed lower heritability and no evidence of genetic association, questioning the mechanisms of nitrogen resorption. Overall, our results suggest a much stronger adaptive role for leaf nitrogen resorption than previously uncovered.
Published: 2022
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19. Into the range: a latitudinal gradient or a center-margins differentiation of ecological strategies in Arabidopsis thaliana ?

Author: Denis Vile, François Vasseur, Justine Bresson, Aurélien Estarague, Stéphane Herbette, Cyrille Violle, Moises Exposito-Alonso, Denis Cornet, Grégory Beurier, Lauriane Rouan, Cristina C. Bastias, Kevin Sartori, Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Swedish University of Agricultural Sciences (SLU), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Stanford University, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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)-Université de Montpellier (UM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Carnegie Institution for Science, European Research Council (ERC) Starting Grant Project 'Ecophysiological and biophysical constraints on domestication in crop plants' (Grant ERC-StG-2014- 639706-CONSTRAINTS)., Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: 0106 biological sciences, plant trait-based ecology, Range (biology), Nitrogen, Acclimatization, Species distribution, Population, Arabidopsis, Plant Science, fuctionnal trait, Biology, 010603 evolutionary biology, 01 natural sciences, Intraspecific competition, 03 medical and health sciences, water stress, CSR strategies, interspecific variation, education, Macroecology, 030304 developmental biology, 0303 health sciences, Phenotypic plasticity, education.field_of_study, Ecology, Phenotypic trait, Original Articles, 15. Life on land, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Adaptation, Physiological, Phenotype, phenotopic plasticity, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Adaptation, performance, stress resistance-fecondity trade -off, 010606 plant biology & botany
Abstract: Background and Aims Determining within-species large-scale variation in phenotypic traits is central to elucidate the drivers of species’ ranges. Intraspecific comparisons offer the opportunity to understand how trade-offs and biogeographical history constrain adaptation to contrasted environmental conditions. Here we test whether functional traits, ecological strategies from the CSR scheme and phenotypic plasticity in response to abiotic stress vary along a latitudinal or a center- margins gradient within the native range of Arabidopsis thaliana. Methods We experimentally examined the phenotypic outcomes of plant adaptation at the center and margins of its geographic range using 30 accessions from southern, central and northern Europe. We characterized the variation of traits related to stress tolerance, resource use, colonization ability, CSR strategy scores, survival and fecundity in response to high temperature (34 °C) or frost (- 6 °C), combined with a water deficit treatment. Key Results We found evidence for both a latitudinal and a center-margins differentiation for the traits under scrutiny. Age at maturity, leaf dry matter content, specific leaf area and leaf nitrogen content varied along a latitudinal gradient. Northern accessions presented a greater survival to stress than central and southern accessions. Leaf area, C-scores, R-scores and fruit number followed a center-margins differentiation. Central accessions displayed a higher phenotypic plasticity than northern and southern accessions for most studied traits. Conclusions Traits related to an acquisitive/conservative resource-use trade-off followed a latitudinal gradient. Traits associated with a competition/colonization trade-off differentiated along the historic colonization of the distribution range and then followed a center-margins differentiation. Our findings pinpoint the need to consider the joint effect of evolutionary history and environmental factors when examining phenotypic variation across the distribution range of a species.
Published: 2021
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20. The genetic interaction of REVOLUTA and WRKY53 links plant development, senescence, and immune responses

Author: James M. Kremer, Joachim Kilian, Stephan Wenkel, Ulrike Zentgraf, Jasmin Doll, François Vasseur, Justine Bresson, Bettina Stadelhofer, Edda von Roepenack-Lahaye, Mark Stahl, and Dagmar Kolb
Subjects: Senescence, Metabolic pathway, Immune system, Evolutionary biology, Immunity, Ontogeny, Gene expression, Plant Immunity, Biology, Gene
Abstract: In annual plants, tight coordination of successive developmental events is of primary importance to optimize performance under fluctuating environmental conditions. The recent finding of the genetic interaction of WRKY53, a key senescence-related gene with REVOLUTA, a master regulator of early leaf patterning, raises the question of how early and late developmental events are connected. Here, we investigated the developmental and metabolic consequences of an alteration of the REVOLUTA and WRKY53 gene expression, from seedling to fruiting. Our results show that REVOLUTA critically controls late developmental phases and reproduction while inversely WRKY53 determines vegetative growth at early developmental stages. We further show that these regulators of distinct developmental phases frequently, but not continuously, interact throughout ontogeny and demonstrated that their genetic interaction is mediated by the salicylic acid (SA). Moreover, we showed that REVOLUTA and WRKY53 are keys regulatory nodes of development and plant immunity thought their role in SA metabolic pathways, which also highlights the role of REV in pathogen defence. Together, our findings demonstrate how late and early developmental events are tightly intertwined by molecular hubs. These hubs interact with each other throughout ontogeny, and participate to the interplay between plant development and immunity.
Published: 2021
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21. The genetic interaction of REVOLUTA and WRKY53 links plant development, senescence, and immune responses

Author: Justine Bresson, Jasmin Doll, François Vasseur, Mark Stahl, Edda von Roepenack-Lahaye, Joachim Kilian, Bettina Stadelhofer, James M. Kremer, Dagmar Kolb, Stephan Wenkel, Ulrike Zentgraf, University of Tübingen, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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)-Université de Montpellier (UM), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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), Michigan State University [East Lansing], Michigan State University System, University of Copenhagen = Københavns Universitet (UCPH), Institutional Strategy of the University of Tuebingen (Deutsche Forschungsgemeinschaft, ZUK 63), Alexander von Humboldt Foundation, and Deutsche Forschungsgemeinschaft (CRC1101, B06)
Subjects: DNA-Binding Proteins, Plant Leaves, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Multidisciplinary, Arabidopsis Proteins, Gene Expression Regulation, Plant, Arabidopsis, Immunity, Plant Development, Plants, Genetically Modified, Salicylic Acid
Abstract: In annual plants, tight coordination of successive developmental events is of primary importance to optimize performance under fluctuating environmental conditions. The recent finding of the genetic interaction of WRKY53, a key senescence-related gene with REVOLUTA, a master regulator of early leaf patterning, raises the question of how early and late developmental events are connected. Here, we investigated the developmental and metabolic consequences of an alteration of the REVOLUTA and WRKY53 gene expression, from seedling to fruiting. Our results show that REVOLUTA critically controls late developmental phases and reproduction while inversely WRKY53 determines vegetative growth at early developmental stages. We further show that these regulators of distinct developmental phases frequently, but not continuously, interact throughout ontogeny and demonstrated that their genetic interaction is mediated by the salicylic acid (SA). Moreover, we showed that REVOLUTA and WRKY53 are keys regulatory nodes of development and plant immunity thought their role in SA metabolic pathways, which also highlights the role of REV in pathogen defence. Together, our findings demonstrate how late and early developmental events are tightly intertwined by molecular hubs. These hubs interact with each other throughout ontogeny, and participate in the interplay between plant development and immunity.
Published: 2021
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22. Leaf economics and slow-fast adaptation across the geographic range of Arabidopsis thaliana

Author: Marianne Gerard, Kevin Sartori, Oscar Javier Ayala-Garay, Etienne Baron, Laura Garcia de Jalon, Maria Del Rey Granado, Agathe Chassagneux, Elena Kazakou, Denis Vile, François Vasseur, Diane Masclef, Nick P. Rowe, Cyrille Violle, Ananda Christophe, Erwan Harscouet, Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-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)-Institut de Recherche pour le Développement (IRD [France-Sud]), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), INRA Dpt EA grant, European Research Council (ERC) (‘CONSTRAINTS’: grant ERC-StG-2014-639706-CONSTRAINTS), French Agency for Research (ANR grant ANR-17-CE02-0018-01, ‘AraBreed’), ANR-17-CE02-0018,AraBreed,Exploration des réponses évolutives des plantes à des changements environnementaux à la lumière des théories écologiques : un test expérimental chez l'espèce modèle Arabidopsis thaliana(2017), European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015), 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), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: 0301 basic medicine, allocation de ressources, media_common.quotation_subject, Biodiversité et Ecologie, Arabidopsis, lcsh:Medicine, Biology, Plant Physiological Phenomena, Article, Life history theory, Biodiversity and Ecology, adaptation au climat, 03 medical and health sciences, Plant evolution, 0302 clinical medicine, écologie fonctionnelle, Plant ecology, lcsh:Science, media_common, 2. Zero hunger, Functional ecology, Multidisciplinary, Ecology, Geography, arabidopsis thaliana, fungi, lcsh:R, Longevity, Ecological genetics, food and beverages, Interspecific competition, 15. Life on land, Arid, Plant Leaves, 030104 developmental biology, Natural variation in plants, Habitat, comparaison intraspécifique, 13. Climate action, lcsh:Q, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Slow Growing, 030217 neurology & neurosurgery
Abstract: International audience; Life history strategies of most organisms are constrained by resource allocation patterns that follow a 'slow-fast continuum'. It opposes slow growing and long-lived organisms with late investment in reproduction to those that grow faster, have earlier and larger reproductive effort and a short longevity. In plants, the Leaf Economics Spectrum (LES) depicts a leaf-level trade-off between the rate of carbon assimilation and leaf lifespan, as stressed in functional ecology from interspecific comparative studies. However, it is still unclear how the LES is connected to the slow-fast syndrome. Interspecific comparisons also impede a deep exploration of the linkage between Les variation and adaptation to climate. Here, we measured growth, morpho-physiological and life-history traits, at both the leaf and whole-plant levels, in 378 natural accessions of Arabidopsis thaliana. We found that the Les is tightly linked to variation in whole-plant functioning, and aligns with the slow-fast continuum. A genetic analysis further suggested that phenotypic differentiation results from the selection of different slow-fast strategies in contrasted climates. slow growing and long-lived plants were preferentially found in cold and arid habitats while fast growing and short-lived ones in more favorable habitats. Our findings shed light on the role of the slow-fast continuum for plant adaptation to climate. More broadly, they encourage future studies to bridge functional ecology, genetics and evolutionary biology to improve our understanding of plant adaptation to environmental changes. Investigations of the genetic and phenotypic differentiation of plant lineages along environmental gradients is crucial for the understanding of plant evolutionary responses to current and future climate variations. As plants cannot simultaneously optimize competing eco-physiological functions, an important question is how plant adaptation occurs under the influence of major trade-offs between traits. The slow-fast continuum is a pervasive trade-off between resource allocation to growth, reproduction and survival , spread across the tree of life 1. The slow end of this continuum is characterized by slow growing, long-lived species and low reproductive output, while species at the fast end reach reproductive maturity faster and produce more offsprings. In plants, the leaf economics spectrum (LES hereafter) 2-4 is thought to reflect the physiological basis of the slow-fast continuum 4. The LES arrays plant species along a continuum of leaf trait syndromes going from short-lived leaves with fast metabolism to the reverse syndrome 3. Core LES traits include leaf dry mass per area (LMA), leaf lifespan (LLS) and net photosynthetic rate per mass unit (A mass) 3,5-7. LES traits are widely used in comparative ecology to infer whole-plant ecological strategies 4,8-12. However, the extent to which leaf-level resource economics reflects whole-plant physiology, performance, and ultimately fitness, is still under debate 13. Many processes can lead to a mismatch between LES and whole-plant functioning 14 , including the impact of self-shading among leaves and resource allocation patterns, such as carbon investment in non-photosynthetic tissues 15,16. To gain insights into the robustness of the slow-fast continuum at different organizational levels, we need
Published: 2019
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23. Natural variation at FLM splicing has pleiotropic effects modulating ecological strategies in Arabidopsis thaliana

Author: Justine Bresson, Elodie Marchadier, Mathieu Hanemian, Cyrille Violle, Isabelle Gy, Olivier Loudet, François Vasseur, Elodie Gilbault, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), European Project: 243359,EC:FP7:ERC,ERC-2009-StG,DECODE(2010), European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - 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), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro
Subjects: 0301 basic medicine, Arabidopsis, General Physics and Astronomy, 02 engineering and technology, Gene Expression Regulation, Plant, lcsh:Science, education.field_of_study, Multidisciplinary, Temperature, food and beverages, Genetic Pleiotropy, 021001 nanoscience & nanotechnology, Phenotype, 0210 nano-technology, Plant genetics, RNA Splicing, Science, Quantitative Trait Loci, Population, MADS Domain Proteins, Locus (genetics), Biology, Article, Evolutionary genetics, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Plant development, Genetic variation, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Allele, education, Alleles, Arabidopsis Proteins, Human evolutionary genetics, fungi, Genetic Variation, General Chemistry, Quantitative genetics, 15. Life on land, biology.organism_classification, Introns, Plant Leaves, Natural variation in plants, 030104 developmental biology, Evolutionary biology, lcsh:Q
Abstract: Investigating the evolution of complex phenotypes and the underlying molecular bases of their variation is critical to understand how organisms adapt to their environment. Applying classical quantitative genetics on a segregating population derived from a Can-0xCol-0 cross, we identify the MADS-box transcription factor FLOWERING LOCUS M (FLM) as a player of the phenotypic variation in plant growth and color. We show that allelic variation at FLM modulates plant growth strategy along the leaf economics spectrum, a trade-off between resource acquisition and resource conservation, observable across thousands of plant species. Functional differences at FLM rely on a single intronic substitution, disturbing transcript splicing and leading to the accumulation of non-functional FLM transcripts. Associations between this substitution and phenotypic and climatic data across Arabidopsis natural populations, show how noncoding genetic variation at a single gene might be adaptive through pleiotropic effects., FLOWERING LOCUS M (FLM) is known as a repressor of Arabidopsis flowering. Here, the authors show that a single intronic substitution of FLM modulates leaf color and plant growth strategy along the leaf economics spectrum, as well as plays a role in plant adaptation.
Published: 2020
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24. Weeds: Against the Rules?

Author: Jonathan Storkey, Guillaume Fried, Lucie Mahaut, Pierre-Olivier Cheptou, François Bretagnolle, François Vasseur, Cyrille Violle, François Munoz, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité entomologie et plantes invasives, Laboratoire de la Santé des Végétaux, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire Interdisciplinaire de Physique [Saint Martin d’Hères] (LIPhy ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Rothamsted Research, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, French Foundation for Research on Biodiversity (FRB, European Research Council (ERC) starting grant project ‘Ecophysiological and Biophysical Constraints on Domestication in Crop Plants’ (grant ERC-StG-2014-639706-CONSTRAINTS), the FRB, and the European Development Fund (EDF) in the context of CESAB project ‘Causes and Consequences of Functional Rarity from Local to Global Scales’ (FREE)., Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - 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), Unité entomologie et plantes invasives (LSV Montpellier), Laboratoire de la santé des végétaux (LSV), Biotechnology and Biological Sciences Research Council (BBSRC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Biogéosciences [UMR 6282] (BGS), and Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Plant Weeds, Plant Science, Biology, Ecological systems theory, eco-evolutionary dynamics, 01 natural sciences, Novel ecosystem, 03 medical and health sciences, Anthropocene, ecological novelty, Humans, Natural (music), functional trait, Ecosystem, Ecology, Community assembly, business.industry, Eco-evolutionary dynamics, Novelty, Agriculture, Environmental ethics, 15. Life on land, Ecology and Evolutionary Biology, Biological Evolution, Functional trait, 030104 developmental biology, 13. Climate action, community assembly, Evolutionary ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, 010606 plant biology & botany
Abstract: International audience; Establishing laws of plant and ecosystems functioning has been an overarching objective of functional and evolutionary ecology. However, most theories neglect the role of human activities in creating novel ecosystems characterized by species assemblages and environmental factors that are not observed in natural systems. We argue that agricultural weeds, as an emblematic case of such an ‘ecological novelty’, constitute an original and underutilized model for challenging current concepts in ecology and evolution. We highlight key aspects of weed ecology and evolutionary biology that can help to test and recast ecological and evolutionary laws in a changing world. We invite ecologists to seize upon weeds as a model system to improve our understanding of the short-term and long-term dynamics of ecological systems in the Anthropocene.
Published: 2020
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25. Genomic basis and evolutionary potential for extreme drought adaptation in Arabidopsis thaliana

Author: George Wang, Wei Ding, Hernán A. Burbano, François Vasseur, Detlef Weigel, and Moises Exposito-Alonso
Subjects: 0301 basic medicine, Mediterranean climate, Arabidopsis thaliana, Range (biology), Climate Change, Species distribution, Adaptation, Biological, Arabidopsis, Climate change, drought, Biology, GWA, Models, Biological, Article, polygenic adaptation, environmental niche models, Evolution, Molecular, 03 medical and health sciences, Ecology, Evolution, Behavior and Systematics, Genetic diversity, Natural selection, Ecology, Genetic heterogeneity, fungi, Global warming, Genetic Variation, food and beverages, Plant community, Biological Evolution, image processing, Droughts, Population decline, 030104 developmental biology, Evolutionary biology, Adaptation, random forest, Genome, Plant, Genome-Wide Association Study
Abstract: Because earth is currently experiencing unprecedented climate change, it is important to predict how species will respond to it. However, geographically-explicit predictive studies frequently ignore that species are comprised of genetically diverse individuals that can vary in their degree of adaptation to extreme local environments; properties that will determine the species’ ability to withstand climate change. Because an increase in extreme drought events is expected to challenge plant communities with global warming, we carried out a greenhouse experiment to investigate which genetic variants predict surviving an extreme drought event and how those variants are distributed across EurasianArabidopsis thalianaindividuals. Genetic variants conferring higher drought survival showed signatures of polygenic adaptation, and were more frequently found in Mediterranean and Scandinavian regions. Using geoenvironmental models, we predicted that Central European populations might lag behind in adaptation by the end of the 21stcentury. Further analyses showed that a population decline could nevertheless be compensated by natural selection acting efficiently over standing variation or by migration of adapted individuals from populations at the margins of the species’ distribution. These findings highlight the importance of within-species genetic heterogeneity in facilitating an evolutionary response to a changing climate.One-sentence summary“Future genetic changes inA. thalianapopulations can be forecast by combining climate change models with genomic predictions based on experimental phenotypic data.”
Published: 2017
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26. Secondary metabolites have more influence than morphophysiological traits on litter decomposability across genotypes of Arabidopsis thaliana

Author: Denis Vile, François Vasseur, Nick P. Rowe, Etienne Baron, Kevin Sartori, Elena Kazakou, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-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)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), 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)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: 0106 biological sciences, 0301 basic medicine, Genotype, Arabidopsis thaliana, Physiology, caractère fonctionnel, Climate, variabilité génétique, Arabidopsis, Secondary Metabolism, dégradration de la litière, Plant Science, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, Intraspecific competition, Gene ontology, Environment, Functional traits, Litter decomposability, Natural variation, Leaf economics spectrum, Glucosinolates, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, natural variation, Genetic variability, functional traits, glucosinolates, Genetic association, 2. Zero hunger, Natural selection, Vegetal Biology, biology, leaf economics spectrum, Genetic Variation, glucosinolate, Interspecific competition, 15. Life on land, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, litter decomposability, Genetic architecture, Plant Leaves, 030104 developmental biology, métabolite secondaire, Evolutionary biology, Trait, gene ontology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, environment, Biologie végétale, 010606 plant biology & botany, Genome-Wide Association Study
Abstract: International audience; Although interspecific variation in plant phenotype is recognised to impact afterlife processes such as litter decomposability, it is still unclear which traits and selection pressures explain these relationships. Examining intraspecific variation is crucial to identify and compare trait effects on decomposability, and investigate the potential role of natural selection. We studied the genetic variability and relationships between decomposability, plant traits typically related to decomposability at species level (morphophysiological traits), and leaf metabolites among a set of genotypes of Arabidopsis thaliana grown under controlled conditions. We also investigated correlations between decomposability and environmental variables at genotypes collection site. We investigated the genetic architecture of decomposability with genome-wide association studies (GWAS). There was large genetic variability in decomposability that was correlated with precipitation. Morphophysiological traits had a minor effect, while secondary metabolites, especially glucosinolates, were correlated with decomposability. Consistently, GWAS suggested that genes and metabolites related to the composition of cell membranes and envelopes control the variation of decomposability across genotypes. Our study suggests that decomposability varies within species as a result of metabolic adaptation to climate. Our findings highlight that subtle variations of defence-related metabolites like glucosinolates may strongly influence after-life processes such as decomposability.
Published: 2019
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27. Transcriptional natural variation at FLM induces synergistic pleiotropy in Arabidopsis thaliana

Author: Justine Bresson, Elodie Marchadier, Mathieu Hanemian, Cyrille Violle, Isabelle Gy, Olivier Loudet, François Vasseur, and Elodie Gilbault
Subjects: 0106 biological sciences, Genetics, 0303 health sciences, education.field_of_study, biology, fungi, Population, food and beverages, Locus (genetics), Quantitative genetics, 15. Life on land, biology.organism_classification, 01 natural sciences, Phenotype, 03 medical and health sciences, Arabidopsis, RNA splicing, Genetic variation, Allele, education, 030304 developmental biology, 010606 plant biology & botany
Abstract: Investigating the evolution of complex phenotypes and the underlying molecular bases of their variation is critical to understand how organisms adapt to the environment. We used leaf growth as a model trait as it is highly integrative of internal and external cues and relies on functions at different levels of the plant organization. Applying classical quantitative genetics on a recombinant inbred line population derived from a Can-0 x Col-0 cross, we identified the MADS-box transcription factor FLOWERING LOCUS M (FLM) as a player of the phenotypic variation for leaf growth and colour. Interestingly, we showed that allelic variation at FLM modulates plant growth strategy along the leaf economics spectrum, a trade-off between resource acquisition and resource conservation observable across thousands of plant species. We demonstrated that the functional differences at FLM relies on a single intronic substitution, disturbing transcript splicing and leading to a low expression of the active FLM transcript. Using phenotypic and climatic data across Arabidopsis natural populations, our work shows how noncoding genetic variation of a single gene may be adaptive through synergistic pleiotropy.
Published: 2019
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28. Non-linear phenotypic variation uncovers the emergence of heterosis in Arabidopsis thaliana

Author: Dominique de Vienne, Detlef Weigel, Louise Fouqueau, Cyrille Violle, François Vasseur, Thibault Nidelet, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Max Planck Institute for Developmental Biology, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-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)-Institut de Recherche pour le Développement (IRD [France-Sud]), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Sciences Pour l'Oenologie (SPO), 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)-Université Montpellier 1 (UM1)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), French Agency for Research (ANR) [ANR-17-CE020-0018-01], European Research Council (ERC) (AdG IMMUNEMESIS) [340602], European Research Council (ERC) (StG CONSTRAINTS) [639706], Agreenskills fellowship programme - EU's Seventh Framework Programme [3215 FP7-609398], ANR-17-CE02-0018,AraBreed,Exploration des réponses évolutives des plantes à des changements environnementaux à la lumière des théories écologiques : un test expérimental chez l'espèce modèle Arabidopsis thaliana(2017), European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015), 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 de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Université Montpellier 1 (UM1)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Vasseur, François, and Weigel, Detlef
Subjects: 0301 basic medicine, Animal breeding, Genotype, QH301-705.5, Heterosis, Population, Arabidopsis, Biology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Hybrid Vigor, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Biology (General), Allele, education, Crosses, Genetic, Hybrid, 2. Zero hunger, education.field_of_study, Vegetal Biology, General Immunology and Microbiology, Models, Genetic, General Neuroscience, 15. Life on land, Phenotype, Primer, 030104 developmental biology, Genetic distance, Biological Variation, Population, Evolutionary biology, Hybridization, Genetic, hétérosis, Allometry, General Agricultural and Biological Sciences, Biologie végétale, 030217 neurology & neurosurgery
Abstract: Recognition and exploitation of hybrid vigor or heterosis among individual crosses of plants and animals has a long and distinguished history. Its manifestation is influenced by a combination of genetic, epigenetic, phenotypic, and environmental factors. Although heterosis is known to be governed by both dominant and epistatic gene action, its expression is greatly influenced by nonlinear interaction among epigenetic and phenotypic (phenomic) components. The magnitude of heterosis is generally inferred post hoc by the phenotypic performance of hybrids among laboriously made individual crosses. The expression of dominance, however, is nonlinear at the cellular level and obeys the principles underlying metabolic flux. Then, is it possible to exploit these relationships to predict heterosis? Vasseur and colleagues have indeed demonstrated the feasibility of such an approach in a series of experiments taking integrated biochemical and computational approaches, as well as testing these results on large samples of model organisms. The results offer promise toward phenomic prediction of heterosis across a wide array of organisms., A recent study applies allometric models to test Sewall Wright’s 85 year-old conjecture on the expression of dominance among traits that contribute to productivity and Darwinian fitness in Arabidopsis thaliana. This Primer explores the wide-ranging implications for agriculture and human health.
Published: 2019
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29. Climate as a driver of adaptive variations in ecological strategies in Arabidopsis thaliana

Author: Elena Kazakou, Kevin Sartori, Cyrille Violle, Etienne Baron, Florian Fort, Denis Vile, François Vasseur, Eric Garnier, Jules Segrestin, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-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)-Institut de Recherche pour le Développement (IRD [France-Sud]), Département Biologie et Ecologie, Centre National de la Recherche Scientifique (CNRS), INRA, CNRS, the French Agency for Research (ANR grant ANR-17-CE02-0018-01, 'AraBreed' ), European Research Council (ERC) ('CONSTRAINTS': grant ERC-StG-2014-639706-CONSTRAINTS)., ANR-17-CE02-0018,AraBreed,Exploration des réponses évolutives des plantes à des changements environnementaux à la lumière des théories écologiques : un test expérimental chez l'espèce modèle Arabidopsis thaliana(2017), European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015), 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), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3)
Subjects: 0106 biological sciences, CSR classification, Specific leaf area, Arabidopsis thaliana, Range (biology), Climate, [SDE.MCG]Environmental Sciences/Global Changes, Adaptation, Biological, Arabidopsis, Trait–environment relationships, Plant Science, Ecological strategy, Biology, 010603 evolutionary biology, 01 natural sciences, Genetic diversity, Life history theory, 03 medical and health sciences, Africa, Northern, Ruderal species, Adaptive differentiation, Biomass, Life History Traits, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Natural selection, Grime triangle, Ecology, fungi, Interspecific competition, 15. Life on land, biology.organism_classification, Latitudinal gradient, Europe, Plant Leaves, Functional trait, Trait, Adaptation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Research in Context, 010606 plant biology & botany, QST–FST
Abstract: Background and aimsThe ‘CSR classification’ categorizes plant species between stress-tolerators, ruderals (R) and competitors (C). Initially proposed as a general framework to describe ecological strategies at the interspecific level, this scheme has recently been used to investigate the variation of strategies within species. For instance, ample variation along the S-R axis was found in Arabidopsis thaliana, with stress-tolerator accessions predominating in hot and dry regions.MethodsIn this study, the range of CSR strategies within A. thaliana was evaluated across 426 accessions originating from North Africa to Scandinavia. A position in the CSR strategy space was allocated for every accession based on three functional traits: leaf area, leaf dry matter content (LDMC) and specific leaf area (SLA). Results were related to climate at origin and compared to a previous study performed on the same species. Furthermore, the role of natural selection in phenotypic differentiation between lineages was investigated with Qst-Fst comparisons, using the large genetic information available for this species.Key resultsSubstantial variation in ecological strategies along the S-R axis was found in A. thaliana. By contrast with previous findings, stress-tolerator accessions predominated in cold climates, notably Scandinavia, where late flowering was associated with traits related to resource conservation such as high LDMC and low SLA. Because of trait plasticity, variations in CSR classification to growth conditions were also observed for the same genotypes.ConclusionsThere is a latitudinal gradient of ecological strategies in A. thaliana as a result of within-species adaptation to climate. Our study also underlines the importance of growth conditions and of the methodology used for trait measurement, notably age versus stage measurement, to infer the strength and direction of trait-environment relationships. Taken together, this highlights the potential and limitations of the CSR classification to explain functional adaptation to the environment.
Published: 2018
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30. Adaptive diversification of growth allometry in the plant Arabidopsis thaliana

Author: Oscar Javier Ayala-Garay, Cyrille Violle, Brian J. Enquist, Denis Vile, George Wang, François Vasseur, Moises Exposito-Alonso, Detlef Weigel, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Division of Geriatric Medicine and Gerontology, Johns Hopkins University School of Medicine, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-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)-Institut de Recherche pour le Développement (IRD [France-Sud]), Department of Molecular Biology [Tübingen], Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, European Research Council (ERC-StG-CONSTRAINTS), European Project: 340602,EC:FP7:ERC,ERC-2013-ADG,IMMUNEMESIS(2014), 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), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3)
Subjects: 0301 basic medicine, 0106 biological sciences, croissance végétale, Evolution, Climate Change, Local adaptation, Metabolic theory of ecology, Tree allometry, Arabidopsis, modèle allométrique, Biology, Balancing selection, 010603 evolutionary biology, 01 natural sciences, Intraspecific competition, 03 medical and health sciences, Stress, Physiological, GWAS, analyse génomique, Stabilizing selection, Scaling, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Multidisciplinary, Vegetal Biology, Fitness trade-off, Abiotic stress, Arabidopsis Proteins, arabidopsis thaliana, food and beverages, 15. Life on land, Biological Sciences, Models, Theoretical, Metabolic scaling theory, Adaptation, Physiological, Biological Evolution, 030104 developmental biology, Evolutionary biology, [SDE]Environmental Sciences, équation allométrique, Allometry, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, human activities, Biologie végétale
Abstract: Significance Are there biological constants unifying phenotypic diversity across scales? Metabolic scaling theory (MST) predicts mathematical regularity and constancy in the allometric scaling of growth rate with body size across species. Here we show that adaptation to climate in Arabidopsis thaliana is associated with local strains that substantially deviate from the values predicted by MST. This deviation can be linked to increased stress tolerance at the expense of seed production, and it occurs through selection on genes that are involved in the abiotic stress response and are geographically correlated with climatic conditions. This highlights the evolutionary role of allometric diversification and helps establish the physiological bases of plant adaptation to contrasting environments., Seed plants vary tremendously in size and morphology; however, variation and covariation in plant traits may be governed, at least in part, by universal biophysical laws and biological constants. Metabolic scaling theory (MST) posits that whole-organismal metabolism and growth rate are under stabilizing selection that minimizes the scaling of hydrodynamic resistance and maximizes the scaling of resource uptake. This constrains variation in physiological traits and in the rate of biomass accumulation, so that they can be expressed as mathematical functions of plant size with near-constant allometric scaling exponents across species. However, the observed variation in scaling exponents calls into question the evolutionary drivers and the universality of allometric equations. We have measured growth scaling and fitness traits of 451 Arabidopsis thaliana accessions with sequenced genomes. Variation among accessions around the scaling exponent predicted by MST was correlated with relative growth rate, seed production, and stress resistance. Genomic analyses indicate that growth allometry is affected by many genes associated with local climate and abiotic stress response. The gene with the strongest effect, PUB4, has molecular signatures of balancing selection, suggesting that intraspecific variation in growth scaling is maintained by opposing selection on the trade-off between seed production and abiotic stress resistance. Our findings suggest that variation in allometry contributes to local adaptation to contrasting environments. Our results help reconcile past debates on the origin of allometric scaling in biology and begin to link adaptive variation in allometric scaling to specific genes.
Published: 2018
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31. Multivariate genetic analysis of plant responses to water deficit and high temperature revealed contrasting adaptive strategies

Author: Denis Vile, François Vasseur, Christine Granier, Myriam Dauzat, Thibaut Bontpart, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), and Vile, Denis
Subjects: water use efficiency, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0106 biological sciences, Arabidopsis thaliana, QTL, Physiology, Arabidopsis, Plant Science, 01 natural sciences, variance génétique, Gene–environment interaction, Transpiration, 2. Zero hunger, Principal Component Analysis, 0303 health sciences, education.field_of_study, Vegetal Biology, Ecotype, déficit hydrique, Phenology, Temperature, efficacité d'utilisation de l'eau, food and beverages, Antagonistic pleiotropy, Genotype by environment interactions, G-matrix, Mixed-effects model, Water use efficiency, Adaptation, Physiological, Agricultural sciences, interaction génotype environnement, Phenotype, pleiotropie, écophysiologie végétale, Research Paper, Genotype, Quantitative Trait Loci, Population, Plant Development, Environment, Quantitative trait locus, Biology, Models, Biological, 03 medical and health sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, photosynthèse, Water-use efficiency, education, Alleles, 030304 developmental biology, photosynthesis, Water, 15. Life on land, Genetic architecture, Agronomy, Multivariate Analysis, Gene-Environment Interaction, Factor Analysis, Statistical, Sciences agricoles, Biologie végétale, 010606 plant biology & botany
Abstract: Summary Plants need to control transpiration and photosynthesis tightly in order to grow under drought and high temperature. Contrasting genetic-by-environment interactions are exploited by Arabidopsis thaliana to improve stress tolerance., How genetic factors control plant performance under stressful environmental conditions is a central question in ecology and for crop breeding. A multivariate framework was developed to examine the genetic architecture of performance-related traits in response to interacting environmental stresses. Ecophysiological and life history traits were quantified in the Arabidopsis thaliana Ler×Cvi mapping population exposed to constant soil water deficit and high air temperature. The plasticity of the genetic variance–covariance matrix (G-matrix) was examined using mixed-effects models after regression into principal components. Quantitative trait locus (QTL) analysis was performed on the predictors of genotype effects and genotype by environment interactions (G×E). Three QTLs previously identified for flowering time had antagonistic G×E effects on carbon acquisition and the other traits (phenology, growth, leaf morphology, and transpiration). This resulted in a size-dependent response of water use efficiency (WUE) to high temperature but not soil water deficit, indicating that most of the plasticity of carbon acquisition and WUE to temperature is controlled by the loci that control variation of development, size, growth, and transpiration. A fourth QTL, MSAT2.22, controlled the response of carbon acquisition to specific combinations of watering and temperature irrespective of plant size and development, growth, and transpiration rate, which resulted in size-independent plasticity of WUE. These findings highlight how the strategies to optimize plant performance may differ in response to water deficit and high temperature (or their combination), and how different G×E effects could be targeted to improve plant tolerance to these stresses.
Published: 2014
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32. Genetic architecture of nonadditive inheritance in Arabidopsis thaliana hybrids

Author: Dominik G. Grimm, Carmen Martín Pizarro, Karsten M. Borgwardt, François Vasseur, Eunyoung Chae, Anette Habring-Müller, Detlef Weigel, Daniel Koenig, Danelle K. Seymour, and Barbara Rakitsch
Subjects: 0301 basic medicine, Arabidopsis thaliana, Heterosis, Population, Arabidopsis, Genome-wide association study, Crosses, half diallel, Diallel cross, 03 medical and health sciences, Genetic, Genetic variation, Hybrid Vigor, heterosis, Genetics, GWAS, education, Hybridization, Crosses, Genetic, Hybrid, education.field_of_study, Multidisciplinary, biology, fungi, Human Genome, food and beverages, Genetic Variation, biology.organism_classification, Genetic architecture, 030104 developmental biology, Phenotype, PNAS Plus, Hybridization, Genetic
Abstract: Significance Hybrid progeny of inbred parents are often more fit than their parents. Such hybrid vigor, or heterosis, is the focus of many plant breeding programs, and the rewards are evident. Hybrid maize has for many decades accounted for the majority of seed planted each year in North America and Europe. Despite the prevalence of this phenomenon and its agricultural importance, the genetic basis of heterotic traits is still unclear. We have used a large collection of first-generation hybrids in Arabidopsis thaliana to characterize the genetics of heterosis in this model plant. We have identified loci that contribute substantially to hybrid vigor and show that a subset of these exhibits classical dominance, an important finding with direct implications for crop improvement. , The ubiquity of nonparental hybrid phenotypes, such as hybrid vigor and hybrid inferiority, has interested biologists for over a century and is of considerable agricultural importance. Although examples of both phenomena have been subject to intense investigation, no general model for the molecular basis of nonadditive genetic variance has emerged, and prediction of hybrid phenotypes from parental information continues to be a challenge. Here we explore the genetics of hybrid phenotype in 435 Arabidopsis thaliana individuals derived from intercrosses of 30 parents in a half diallel mating scheme. We find that nonadditive genetic effects are a major component of genetic variation in this population and that the genetic basis of hybrid phenotype can be mapped using genome-wide association (GWA) techniques. Significant loci together can explain as much as 20% of phenotypic variation in the surveyed population and include examples that have both classical dominant and overdominant effects. One candidate region inherited dominantly in the half diallel contains the gene for the MADS-box transcription factor AGAMOUS-LIKE 50 ( AGL50 ), which we show directly to alter flowering time in the predicted manner. Our study not only illustrates the promise of GWA approaches to dissect the genetic architecture underpinning hybrid performance but also demonstrates the contribution of classical dominance to genetic variance.
Published: 2016

33. Arabidopsis growth under prolonged high temperature and water deficit: independent or interactive effects?

Author: Justine Bresson, Marjorie Pervent, Christine Granier, Bertrand Muller, Denis Vile, François Vasseur, Thierry Simonneau, and Michaël Belluau
Subjects: 2. Zero hunger, 0106 biological sciences, 0303 health sciences, Biomass (ecology), biology, Specific leaf area, Physiology, Phenology, food and beverages, Plant Science, 15. Life on land, biology.organism_classification, 01 natural sciences, 6. Clean water, Water deficit, 03 medical and health sciences, Agronomy, Productivity (ecology), Arabidopsis, Arabidopsis thaliana, 030304 developmental biology, 010606 plant biology & botany, Stomatal density
Abstract: High temperature (HT) and water deficit (WD) are frequent environmental constraints restricting plant growth and productivity. These stresses often occur simultaneously in the field, but little is known about their combined impacts on plant growth, development and physiology. We evaluated the responses of 10 Arabidopsis thaliana natural accessions to prolonged elevated air temperature (30 °C) and soil WD applied separately or in combination. Plant growth was significantly reduced under both stresses and their combination was even more detrimental to plant performance. The effects of the two stresses were globally additive, but some traits responded specifically to one but not the other stress. Root allocation increased in response to WD, while reproductive allocation, hyponasty and specific leaf area increased under HT. All the traits that varied in response to combined stresses also responded to at least one of them. Tolerance to WD was higher in small-sized accessions under control temperature and HT and in accessions with high biomass allocation to root under control conditions. Accessions that originate from sites with higher temperature have less stomatal density and allocate less biomass to the roots when cultivated under HT. Independence and interaction between stresses as well as the relationships between traits and stress responses are discussed.
Published: 2011
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34. Changes in light intensity reveal a major role for carbon balance in Arabidopsis responses to high temperature

Author: Denis Vile, François Vasseur, and Florent Pantin
Subjects: 0106 biological sciences, Limiting factor, 0303 health sciences, biology, Physiology, fungi, food and beverages, Plant Science, 15. Life on land, biology.organism_classification, Photosynthesis, 01 natural sciences, 03 medical and health sciences, Shade avoidance, Light intensity, Arabidopsis, Botany, Arabidopsis thaliana, Sugar, 030304 developmental biology, 010606 plant biology & botany, Transpiration
Abstract: High temperature (HT) is a major limiting factor for plant productivity. Because some responses to HT, notably hyponasty, resemble those encountered in low light (LL), we hypothesized that plant responses to HT are under the control of carbon balance. We analysed the interactive effects of HT and irradiance level on hyponasty and a set of traits related to plant growth in natural accessions of Arabidopsis thaliana and mutants affected in heat dissipation through transpiration (NCED6-OE, ost2) and starch metabolism (pgm). HT induced hyponasty, reduced plant growth and modified leaf structure. LL worsened the effects of HT, while increasing light restored trait values close to levels observed at control temperature. Leaf temperature per se did not play a major role in the observed responses. By contrast, a major role of carbon balance was supported by hyponastic growth of pgm, as well as morphological, physiological (photosynthesis, sugar and starch contents) and transcriptional data. Carbon balance could be a common sensor of HT and LL, leading to responses specific of the shade avoidance syndrome. Hyponasty and associated changes in plant traits could be key traits conditioning plant performance under competition for light, particularly in warm environments.
Published: 2011
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35. Testing models for the leaf economics spectrum with leaf and whole-plant traits in [i]Arabidopsis thaliana[/i]

Author: Benjamin Blonder, Brian J. Enquist, Bill Shipley, Cyrille Violle, Denis Vile, François Vasseur, Environmental Change Institute, University of Oxford, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Département de Biologie, Université de Sherbrooke (UdeS), Department of Ecology and Evolutionary Biology [University of Arizona], University of Arizona, Santa Fe Institute, European Project: 221060, University of Oxford [Oxford], Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Sherbrooke University, Department of Ecology and Evolutionary Biology, 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)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-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)-Institut de Recherche pour le Développement (IRD [France-Sud]), and Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: Venation network, genotype, [SDV]Life Sciences [q-bio], Arabidopsis, Vascular patterning, Plant Biology, Plant Science, structural equation modelling, vein density, Structural equation modeling, cytoplasm–cell wall partitioning, Inbred strain, Botany, Arabidopsis thaliana, modélisation structurelle, Leaf economics spectrum, assimilation du carbone, Plant traits, Research Articles, Ecotype, biology, leaf economics spectrum, venation network, arabidopsis thaliana, système vasculaire, biology.organism_classification, plateforme de phénotypage, nervure, Cytoplasm-cell wall partitioning, Structural equation modelling, Vein density, Trait, paroi cellulaire
Abstract: The LES is a global set of patterns that describes correlations between functional traits (e.g. carbon assimilation rate, lifespan) that determine terrestrial resource fluxes. Several classes of models have been proposed to explain the LES, but none have been extensively tested against each other with fine-scale data. Here we assemble a large set of genotypes of Arabidopsis thaliana that show variation in leaf functional traits. We show that no extant theory for the LES is supported, but that some leaf venation networks likely play a role in driving the pattern. Our study provides a roadmap for the measurements that could generate further insight into this fundamental ecological pattern., The leaf economics spectrum (LES) describes strong relationships between multiple functional leaf traits that determine resource fluxes in vascular plants. Five models have been proposed to explain these patterns: two based on patterns of structural allocation, two on venation networks and one on resource allocation to cell walls and cell contents. Here we test these models using data for leaf and whole-plant functional traits. We use structural equation modelling applied to multiple ecotypes, recombinant inbred lines, near isogenic lines and vascular patterning mutants of Arabidopsis thaliana that express LES trait variation. We show that a wide variation in multiple functional traits recapitulates the LES at the whole-plant scale. The Wright et al. (2004) model and the Blonder et al. (2013) venation network model cannot be rejected by data, while two simple models and the Shipley et al. (2006) allocation model are rejected. Venation networks remain a key hypothesis for the origin of the LES, but simpler explanations also cannot be ruled out.
Published: 2015
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36. Increasing plant group productivity through latent genetic variation for cooperation

Author: Samuel E. Wuest, Nuno D. Pires, Shan Luo, Francois Vasseur, Julie Messier, Ueli Grossniklaus, and Pascal A. Niklaus
Subjects: Biology (General), QH301-705.5
Abstract: Historic yield advances in the major crops have, to a large extent, been achieved by selection for improved productivity of groups of plant individuals such as high-density stands. Research suggests that such improved group productivity depends on “cooperative” traits (e.g., erect leaves, short stems) that—while beneficial to the group—decrease individual fitness under competition. This poses a problem for some traditional breeding approaches, especially when selection occurs at the level of individuals, because “selfish” traits will be selected for and reduce yield in high-density monocultures. One approach, therefore, has been to select individuals based on ideotypes with traits expected to promote group productivity. However, this approach is limited to architectural and physiological traits whose effects on growth and competition are relatively easy to anticipate. Here, we developed a general and simple method for the discovery of alleles promoting cooperation in plant stands. Our method is based on the game-theoretical premise that alleles increasing cooperation benefit the monoculture group but are disadvantageous to the individual when facing noncooperative neighbors. Testing the approach using the model plant Arabidopsis thaliana, we found a major effect locus where the rarer allele was associated with increased cooperation and productivity in high-density stands. The allele likely affects a pleiotropic gene, since we find that it is also associated with reduced root competition but higher resistance against disease. Thus, even though cooperation is considered evolutionarily unstable except under special circumstances, conflicting selective forces acting on a pleiotropic gene might maintain latent genetic variation for cooperation in nature. Such variation, once identified in a crop, could rapidly be leveraged in modern breeding programs and provide efficient routes to increase yields. Some traditional breeding approaches select for “selfish” traits that can reduce yield in high-density monocultures. This paper proposes a simple method to identify plant genotypes that express more cooperative versus more competitive traits, based on how they grow in different social environments, and applies this method to a genetic study with Arabidopsis thaliana.
Published: 2022

37. Gibberellins regulate the transcription of the continuous flowering regulator, RoKSN, a rose TFL1 homologue

Author: Tatiana Thouroude, Marjorie Juchaux, Latifa Hamama, Fabrice Foucher, Marie Randoux, François Vasseur, Julien Jeauffre, Soulaiman Sakr, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, 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), Angers Loire Metropole (France), Université d'Angers (UA)-AGROCAMPUS OUEST, 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Perennial plant, Physiology, Regulator, plant, floral repressor, Plant Science, 01 natural sciences, chemistry.chemical_compound, vernalization, Gene Expression Regulation, Plant, Transcription (biology), lolium-temulentum, Promoter Regions, Genetic, [SDV.SA.HORT]Life Sciences [q-bio]/Agricultural sciences/Horticulture, induction, Florigen, rose, Regulation of gene expression, 0303 health sciences, Microscopy, Confocal, Gene Expression Regulation, Developmental, food and beverages, signals, Vernalization, Plants, Genetically Modified, Up-Regulation, PLANT SCIENCES, RNA, Plant, Gibberellin, Seasons, strawberry, Research Paper, gibberellins, Green Fluorescent Proteins, apple, Flowers, arabidopsis-thaliana, Biology, Genes, Plant, Rosa, Floral initiation, 03 medical and health sciences, Tobacco, Botany, polycarpic plants, gene, 030304 developmental biology, Lolium temulentum, PEBP family, fungi, Sequence Analysis, DNA, biology.organism_classification, chemistry, Agrobacterium tumefaciens, Sequence Alignment, 010606 plant biology & botany
Abstract: International audience; The role of gibberellins (GAs) during floral induction has been widely studied in the annual plant Arabidopsis thaliana. Less is known about this control in perennials. It is thought that GA is a major regulator of flowering in rose. In spring, low GA content may be necessary for floral initiation. GA inhibited flowering in once-flowering roses, whereas GA did not block blooming in continuous-flowering roses. Recently, RoKSN, a homologue of TFL1, was shown to control continuous flowering. The loss of RoKSN function led to continuous flowering behaviour. The objective of this study was to understand the molecular control of flowering by GA and the involvement of RoKSN in this inhibition. In once-flowering rose, the exogenous application of GA(3) in spring inhibited floral initiation. Application of GA(3) during a short period of 1 month, corresponding to the floral transition, was sufficient to inhibit flowering. At the molecular level, RoKSN transcripts were accumulated after GA(3) treatment. In spring, this accumulation is correlated with floral inhibition. Other floral genes such as RoFT, RoSOC1, and RoAP1 were repressed in a RoKSN-dependent pathway, whereas RoLFY and RoFD repression was RoKSN independent. The RoKSN promoter contained GA-responsive cis-elements, whose deletion suppressed the response to GA in a heterologous system. In summer, once-flowering roses did not flower even after exogenous application of a GA synthesis inhibitor that failed to repress RoKSN. A model is presented for the GA inhibition of flowering in spring mediated by the induction of RoKSN. In summer, factors other than GA may control RoKSN.
Published: 2012
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38. A common genetic basis to the origin of the leaf economics spectrum and metabolic scaling allometry

Author: Christine Granier, Cyrille Violle, Brian J. Enquist, Denis Vile, François Vasseur, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Department of Ecology and Evolutionary Biology, University of Arizona, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-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)-Institut de Recherche pour le Développement (IRD [France-Sud]), Santa Fe Institute, Gordon Research Conferences (GRC). USA., and ProdInra, Migration
Subjects: 0106 biological sciences, life history, Arabidopsis thaliana, media_common.quotation_subject, Arabidopsis, Quantitative trait locus, 010603 evolutionary biology, 01 natural sciences, net, Genetic variation, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, metabolic scaling theory, Allele, functional trait, Scaling, Ecology, Evolution, Behavior and Systematics, Selection (genetic algorithm), ComputingMilieux_MISCELLANEOUS, media_common, 2. Zero hunger, biology, Ecology, leaf economics spectrum, Longevity, plant allometry, Genetic Variation, Biodiversity, flowering time, 15. Life on land, Models, Theoretical, biology.organism_classification, Biological Evolution, photosynthetic rate, Plant Leaves, quantitative trait loci, growth rate, Allometry, human activities, 010606 plant biology & botany
Abstract: International audience; Many facets of plant form and function are reflected in general cross-taxa scaling relationships. Metabolic scaling theory (MST) and the leaf economics spectrum (LES) have each proposed unifying frameworks and organisational principles to understand the origin of botanical diversity. Here, we test the evolutionary assumptions of MST and the LES using a cross of two genetic variants of Arabidopsis thaliana. We show that there is enough genetic variation to generate a large fraction of variation in the LES and MST scaling functions. The progeny sharing the parental, naturally occurring, allelic combinations at two pleiotropic genes exhibited the theorised optimum 3/4 allometric scaling of growth rate and intermediate leaf economics. Our findings: (1) imply that a few pleiotropic genes underlie many plant functional traits and life histories; (2) unify MST and LES within a common genetic framework and (3) suggest that observed intermediate size and longevity in natural populations originate from stabilising selection to optimise physiological trade-offs.
Published: 2012
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39. Changes in light intensity reveal a major role for carbon balance in Arabidopsis responses to high temperature

Author: François, Vasseur, Florent, Pantin, and Denis, Vile
Subjects: Chlorophyll, DNA, Complementary, Hot Temperature, Light, Cell Respiration, Arabidopsis, Gene Expression, Plant Transpiration, Genes, Plant, Carbon, Plant Leaves, Phenotype, Gene Expression Regulation, Plant, RNA, Plant, Stress, Physiological, Mutation, Cluster Analysis, Photosynthesis
Abstract: High temperature (HT) is a major limiting factor for plant productivity. Because some responses to HT, notably hyponasty, resemble those encountered in low light (LL), we hypothesized that plant responses to HT are under the control of carbon balance. We analysed the interactive effects of HT and irradiance level on hyponasty and a set of traits related to plant growth in natural accessions of Arabidopsis thaliana and mutants affected in heat dissipation through transpiration (NCED6-OE, ost2) and starch metabolism (pgm). HT induced hyponasty, reduced plant growth and modified leaf structure. LL worsened the effects of HT, while increasing light restored trait values close to levels observed at control temperature. Leaf temperature per se did not play a major role in the observed responses. By contrast, a major role of carbon balance was supported by hyponastic growth of pgm, as well as morphological, physiological (photosynthesis, sugar and starch contents) and transcriptional data. Carbon balance could be a common sensor of HT and LL, leading to responses specific of the shade avoidance syndrome. Hyponasty and associated changes in plant traits could be key traits conditioning plant performance under competition for light, particularly in warm environments.
Published: 2011

40. Quantifying spatial heterogeneity of chlorophyll fluorescence during plant growth and in response to water stress

Author: Denis Vile, Christine Granier, François Vasseur, Garance Koch, Justine Bresson, Myriam Dauzat, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Max Planck Institute for Developmental Biology, and Max-Planck-Gesellschaft
Subjects: 0106 biological sciences, Plant growth, Photosystem II, Arabidopsis thaliana, croissance végétale, Photosynthetic performance, fluorescence chlorophyllienne, Plant Science, Photosynthetic efficiency, Photosynthesis, efficience de la photosynthèse, 01 natural sciences, Modelling, 03 medical and health sciences, Botany, Plant survival, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Chlorophyll fluorescence imaging, photosynthèse, Chlorophyll fluorescence, modélisation, 030304 developmental biology, 2. Zero hunger, Abiotic component, 0303 health sciences, Vegetal Biology, Heterogeneity of Fv/Fm values, biology, Methodology, tolérance à la sécheresse, 15. Life on land, biology.organism_classification, 6. Clean water, Spatial heterogeneity, Pixels distribution, Sensitivity analysis, écophysiologie végétale, stress hydrique, Biologie végétale, 010606 plant biology & botany, Biotechnology
Abstract: Effects of abiotic and biotic stresses on plant photosynthetic performance lead to fitness and yield decrease. The maximum quantum efficiency of photosystem II (F v/F m) is a parameter of chlorophyll fluorescence (ChlF) classically used to track changes in photosynthetic performance. Despite recent technical and methodological advances in ChlF imaging, the spatio-temporal heterogeneity of F v/F m still awaits for standardized and accurate quantification. We developed a method to quantify the dynamics of spatial heterogeneity of photosynthetic efficiency through the distribution-based analysis of F v/F m values. The method was applied to Arabidopsis thaliana grown under well-watered and severe water deficit (survival rate of 40%). First, whole-plant F v/F m shifted from unimodal to bimodal distributions during plant development despite a constant mean F v/F m under well-watered conditions. The establishment of a bimodal distribution of F v/F m reflects the occurrence of two types of leaf regions with contrasted photosynthetic efficiency. The distance between the two modes (called S) quantified the whole-plant photosynthetic heterogeneity. The weighted contribution of the most efficient/healthiest leaf regions to whole-plant performance (called W max) quantified the spatial efficiency of a photosynthetically heterogeneous plant. Plant survival to water deficit was associated to high S values, as well as with strong and fast recovery of W max following soil rewatering. Hence, during stress surviving plants had higher, but more efficient photosynthetic heterogeneity compared to perishing plants. Importantly, S allowed the discrimination between surviving and perishing plants four days earlier than the mean F v/F m. A sensitivity analysis from simulated dynamics of F v/F m showed that parameters indicative of plant tolerance and/or stress intensity caused identifiable changes in S and W max. Finally, an independent comparison of six Arabidopsis accessions grown under well-watered conditions indicated that S and W max are related to the genetic variability of growth. The distribution-based analysis of ChlF provides an efficient tool for quantifying photosynthetic heterogeneity and performance. S and W max are good indicators to estimate plant survival under water stress. Our results suggest that the dynamics of photosynthetic heterogeneity are key components of plant growth and tolerance to stress.
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