PUBLICATIONS

PUBLICATIONS

Fortune telling: metabolic markers of plant performance
Olivier Fernandez, Maria Urrutia, Stéphane Bernillon, Catherine Giauffret, François Tardieu, Jacques Le Gouis, Nicolas Langlade, Alain Charcosset, Annick Moing, Yves Gibon - Metabolomics, 2016
Background: In the last decade, metabolomics has emerged as a powerful diagnostic and predictive tool in many branches of science. Researchers in microbes, animal, food, medical and plant science have generated a large number of targeted or non-targeted metabolic profiles by using a vast array of analytical methods (GC–MS, LC–MS, 1H-NMR….). Comprehensive analysis of such profiles using adapted statistical methods and modeling has opened up the possibility of using single or combinations of metabolites as markers. Metabolic markers have been proposed as proxy, diagnostic or predictors of key traits in a range of model species and accurate predictions of disease outbreak frequency, developmental stages, food sensory<br /> evaluation and crop yield have been obtained. Aim of review (i) To provide a definition of plant performance and metabolic markers, (ii) to highlight recent key applications involving metabolic markers as tools for monitoring or predicting plant performance, and (iii) to propose a workable and cost-efficient pipeline to generate and use metabolic markers with a special focus on plant breeding. Key message Using examples in other models and domains, the review proposes that metabolic markers are tending to complement and possibly replace traditional molecular markers in plant science as efficient estimators of performance. Keywords Breeding: Metabolic marker, Metabolomics, Plant performance, Prediction. DOI: 10.1007/s11306-016-1099-1
CN-Wheat, a functional-structural model of carbon and nitrogen metabolism in wheat culms after anthesis. I. Model description
Romain Barillot, Camille Chambon and Bruno Andrieu - Annals of Botany, 2016
Abstract: Background and Aims Improving crops requires better linking of traits and metabolic processes to whole plant performance. In this paper, we present CN-Wheat, a comprehensive and mechanistic model of carbon (C) and nitrogen (N) metabolism within wheat culms after anthesis. Methods The culm is described by modules that represent the roots, photosynthetic organs and grains. Each of them includes structural, storage and mobile materials. Fluxes of C and N among modules occur through a common pool and through transpiration flow. Metabolite variations are represented by differential equations that depend on the physiological processes occurring in each module. A challenging aspect of CN-Wheat lies in the regulation of these processes by metabolite concentrations and the environment perceived by organs. Key Results CN-Wheat simulates the distribution of C and N into wheat culms in relation to photosynthesis, N-uptake, metabolite turnover, root exudation and tissue death. Regulation of physiological activities by local concentrations of metabolites appears to be a valuable feature for understanding how the behaviour of the whole plant can emerge from local rules. Conclusions The originality of CN-Wheat is that it proposes an integrated view of plant functioning based on a mechanistic approach. The formalization of each process can be further refined in the future as knowledge progresses. This approach is expected to strengthen our capacity to understand plant responses to their environment and investigate plant traits adapted to changes in agronomical practices or environmental conditions. A companion paper will evaluate the model. Key words: Amino acids, carbon, cytokinins, fructans, process-based functional–structural plant model, nitrogen, proteins, plant metabolism and physiology, sink–source relations, sucrose, Triticum aestivum, wheat. DOI: https://doi.org/10.1093/aob/mcw143
CN-Wheat, a functional–structural model of carbon and nitrogen metabolism in wheat culms after anthesis. II. Model evaluation
Romain Barillot, Camille Chambon and Bruno Andrieu - Annals of Botany, 2016
Abstract: Background and Aims Simulating resource allocation in crops requires an integrated view of plant functioning and the formalization of interactions between carbon (C) and nitrogen (N) metabolisms. This study evaluates the functional–structural model CN-Wheat developed for winter wheat after anthesis. Methods In CN-Wheat the acquisition and allocation of resources between photosynthetic organs, roots and grains are emergent properties of sink and source activities and transfers of mobile metabolites. CN-Wheat was calibrated for field plants under three N fertilizations at anthesis. Model parameters were taken from the literature or calibrated on the experimental data. Key Results The model was able to predict the temporal variations and the distribution of resources in the culm. Thus, CN-Wheat accurately predicted the post-anthesis kinetics of dry masses and N content of photosynthetic organs and grains in response to N fertilization. In our simulations, when soil nitrates were non-limiting, N in grains was ultimately determined by availability of C for root activity. Dry matter accumulation in grains was mostly affected by photosynthetic organ lifespan, which was regulated by protein turnover and C-regulated root activity.<br /> Conclusions The present study illustrates that the hypotheses implemented in the model were able to predict realistic dynamics and spatial patterns of C and N. CN-Wheat provided insights into the interplay of C and N metabolism and how the depletion of mobile metabolites due to grain filling ultimately results in the cessation of resource capture. This enabled us to identify processes that limit grain mass and protein content and are potential targets for plant breeding. Key words: Amino acids, carbon, cytokinins, fructans, process-based functional–structural plant model, nitrogen, proteins, plant metabolism and physiology, sink-source relations, sucrose, Triticum aestivum, wheat. DOI: https://doi.org/10.1093/aob/mcw144
Proteomic Approach to Identify Nuclear Proteins in Wheat Grain
Emmanuelle Bancel, Titouan Bonnot, Marlène Davanture, Gérard Branlard, Michel Zivy, and Pierre Martre - Journal of Proteome Research, 2015
Abstract: The nuclear proteome of the grain of the two cultivated wheat species Triticum aestivum (hexaploid wheat; genomes A, B, and D) and T. monococcum (diploid wheat; genome A) was analyzed in two early stages of development using shotgun-based proteomics. A procedure was optimized to purify nuclei, and an improved protein sample preparation was developed to efficiently remove nonprotein substances (starch and nucleic acids). A total of 797 proteins corresponding to 528 unique proteins were identified, 36% of which were classified in functional groups related to DNA and RNA metabolism. A large number (107 proteins) of unknown functions and hypothetical proteins were also found. Some identified proteins may be multifunctional and may present multiple localizations. On the basis of the MS/MS analysis, 368 proteins were present in the two species, and in two stages of development, some qualitative differences between species and stages of development were also found. All of these data illustrate the dynamic function of the grain nucleus in the early stages of development. Keywords: cereal, grain development, bread wheat (Triticum aestivum), einkorn wheat (Triticum monococcum), LC−MS/MS, nuclear proteome. DOI: 10.1021/acs.jproteome.5b00446
Changes in the nuclear proteome of developing wheat (Triticum aestivumL.) grain
Titouan Bonnot, Emmanuelle Bancel, Christophe Chambon, Julie Boudet, Gérard Branlard, and Pierre Martre - Frontiers in Plant Science, 2015
Abstract: Wheat grain end-use value is determined by complex molecular interactions that occur during grain development, including those in the cell nucleus. However, our knowledge of how the nuclear proteome changes during grain development is limited. Here, we analyzed nuclear proteins of developing wheat grains collected during the cellularization, effective grain-filling, and maturation phases of development, respectively. Nuclear proteins were extracted and separated by two-dimensional gel electrophoresis. Image analysis revealed 371 and 299 reproducible spots in gels with first dimension separation along pH 4–7 and pH6–11 isoelectric gradients, respectively. The relative abundance of 464 (67%) protein spots changed during grain development. Abundance profiles of these proteins clustered in six groups associated with the major phases and phase transitions of grain development. Using nano liquid chromatography-tandem mass spectrometry to analyse 387 variant and non-variant protein spots, 114 different proteins were identified that were classified into 16 functional classes. We noted that some proteins involved in the regulation of transcription, like HMG1/2-like protein and histone deacetylase HDAC2, were most abundant before the phase transition from cellularization to grain-filling, suggesting that major transcriptional changes occur during this key developmental phase. The maturation period was characterized by high relative abundance of proteins involved in ribosome biogenesis. Data are available via ProteomeXchange with identifier PXD002999. Keywords: wheat, developing grain, nuclear proteins, 2D gel electrophoresis, LC-MS/MS. DOI: 10.3389/fpls.2015.00905
RulNet: A Web-Oriented Platform for Regulatory Network Inference, Application to Wheat –Omics Data
Jonathan Vincent, Pierre Martre, Benjamin Gouriou, Catherine Ravel, Zhanwu Dai, Jean-Marc Petit, Marie Pailloux - PLOS one, 2015
With the increasing amount of –omics data available, a particular effort has to be made to provide suitable analysis tools. A major challenge is that of unraveling the molecular regulatory networks from massive and heterogeneous datasets. Here we describe RulNet, a weboriented platform dedicated to the inference and analysis of regulatory networks from qualitative and quantitative –omics data by means of rule discovery. Queries for rule discovery can be written in an extended form of the RQL query language, which has a syntax similar to SQL. RulNet also offers users interactive features that progressively adjust and refine the inferred networks. In this paper, we present a functional characterization of RulNet and compare inferred networks with correlation-based approaches. The performance of RulNet has been evaluated using the three benchmark datasets used for the transcriptional network inference challenge DREAM5. Overall, RulNet performed as well as the best methods that participated in this challenge and it was shown to behave more consistently when compared across the three datasets. Finally, we assessed the suitability of RulNet to analyze experimental –omics data and to infer regulatory networks involved in the response to nitrogen and sulfur supply in wheat (Triticum aestivum L.) grains. The results highlight putative actors governing the response to nitrogen and sulfur supply in wheat grains. We evaluate the main characteristics and features of RulNet as an all-in-one solution for RN inference, visualization and editing. Using simple yet powerful RulNet queries allowed RNs involved in the adaptation of wheat grain to N and S supply to be discovered.We demonstrate the effectiveness and suitability of RulNet as a platform for the analysis of RNs involving different types of –omics data. The results are promising since they are consistent with what was previously established by the scientific community. DOI: 10.1371/journal.pone.0127127
Evolution de l'organisation de la recherche et du secteur des semences
Aline Fugeray-Scarbel & Stéphane Lemarie - Le selectionneur français, 2013
Depuis son émergence à la fin du XIXème siècle, le secteur des semences a connu des évolutions importantes conduisant à une réorganisation générale de la recherche en amélioration des plantes. Le premier fait marquant de cette évolution concerne le positionnement relatif de la recherche publique et de la recherche privée. L'effort privé en recherche a augmenté suite aux évolutions réglementaires (DHS, VAT), à la mise en place de droits de propriété (COV) et, dans certains cas, au développement des semences hybrides. La recherche publique s'est alors repositionnée sur les domaines pour lesquels il existait des défaillances du marché (recherche amont, recherche méthodologique, segments orphelins). Le deuxième fait marquant de cette évolution concerne la structure interne du secteur des semences. Bien qu'il soit encore globalement peu concentré, ce secteur a vu progressivement émerger des acteurs majeurs ayant des positions fortes à la fois sur les semences et dans le domaine des biotechnologies, ces positions étant renforcées par le développement de brevets sur le vivant. Cette concentration croissante s'explique également par les coûts (fixes) croissants liés à la recherche, la réglementation, et la gestion de la propriété intellectuelle. Mots clefs: amélioration des plantes, biotechnologie, structure industrielle, recherche publique.