180 results on '"Vincourt, Patrick"'
Search Results
2. Genetic control of plasticity of oil yield for combined abiotic stresses using a joint approach of crop modeling and genome-wide association
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Mangin, Brigitte, Casadebaig, Pierre, Cadic, Eléna, Blanchet, Nicolas, Boniface, Marie-Claude, Carrère, Sébastien, Gouzy, Jérôme, Legrand, Ludovic, Mayjonade, Baptiste, Pouilly, Nicolas, André, Thierry, Coque, Marie, Piquemal, Joël, Laporte, Marion, Vincourt, Patrick, Muños, Stéphane, and Langlade, Nicolas B. more...
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Quantitative Biology - Genomics - Abstract
Understanding the genetic basis of phenotypic plasticity is crucial for predicting and managing climate change effects on wild plants and crops. Here, we combined crop modeling and quantitative genetics to study the genetic control of oil yield plasticity for multiple abiotic stresses in sunflower. First we developed stress indicators to characterize 14 environments for three abiotic stresses (cold, drought and nitrogen) using the SUNFLO crop model and phenotypic variations of three commercial varieties. The computed plant stress indicators better explain yield variation than descriptors at the climatic or crop levels. In those environments, we observed oil yield of 317 sunflower hybrids and regressed it with three selected stress indicators. The slopes of cold stress norm reaction were used as plasticity phenotypes in the following genome-wide association study. Among the 65,534 tested SNP, we identified nine QTL controlling oil yield plasticity to cold stress. Associated SNP are localized in genes previously shown to be involved in cold stress responses: oligopeptide transporters, LTP, cystatin, alternative oxidase, or root development. This novel approach opens new perspectives to identify genomic regions involved in genotype-by-environment interaction of a complex traits to multiple stresses in realistic natural or agronomical conditions., Comment: 12 pages, 5 figures, Plant, Cell and Environment more...
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- 2017
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Catalog
3. Using numerical plant models and phenotypic correlation space to design achievable ideotypes
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Picheny, Victor, Casadebaig, Pierre, Trépos, Ronan, Faivre, Robert, Da Silva, David, Vincourt, Patrick, and Costes, Evelyne
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Quantitative Biology - Quantitative Methods ,Quantitative Biology - Populations and Evolution - Abstract
Numerical plant models can predict the outcome of plant traits modifications resulting from genetic variations, on plant performance, by simulating physiological processes and their interaction with the environment. Optimization methods complement those models to design ideotypes, i.e. ideal values of a set of plant traits resulting in optimal adaptation for given combinations of environment and management, mainly through the maximization of a performance criteria (e.g. yield, light interception). As use of simulation models gains momentum in plant breeding, numerical experiments must be carefully engineered to provide accurate and attainable results, rooting them in biological reality. Here, we propose a multi-objective optimization formulation that includes a metric of performance, returned by the numerical model, and a metric of feasibility, accounting for correlations between traits based on field observations. We applied this approach to two contrasting models: a process-based crop model of sunflower and a functional-structural plant model of apple trees. In both cases, the method successfully characterized key plant traits and identified a continuum of optimal solutions, ranging from the most feasible to the most efficient. The present study thus provides successful proof of concept for this enhanced modeling approach, which identified paths for desirable trait modification, including direction and intensity., Comment: 25 pages, 5 figures, 2017, Plant, Cell and Environment more...
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- 2016
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4. Increased genetic diversity improves crop yield stability under climate variability: a computational study on sunflower
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Casadebaig, Pierre, Trépos, Ronan, Picheny, Victor, Langlade, Nicolas B., Vincourt, Patrick, and Debaeke, Philippe
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Quantitative Biology - Populations and Evolution - Abstract
A crop can be represented as a biotechnical system in which components are either chosen (cultivar, management) or given (soil, climate) and whose combination generates highly variable stress patterns and yield responses. Here, we used modeling and simulation to predict the crop phenotypic plasticity resulting from the interaction of plant traits (G), climatic variability (E) and management actions (M). We designed two in silico experiments that compared existing and virtual sunflower cultivars (Helianthus annuus L.) in a target population of cropping environments by simulating a range of indicators of crop performance. Optimization methods were then used to search for GEM combinations that matched desired crop specifications. Computational experiments showed that the fit of particular cultivars in specific environments is gradually increasing with the knowledge of pedo-climatic conditions. At the regional scale, tuning the choice of cultivar impacted crop performance the same magnitude as the effect of yearly genetic progress made by breeding. When considering virtual genetic material, designed by recombining plant traits, cultivar choice had a greater positive impact on crop performance and stability. Results suggested that breeding for key traits conferring plant plasticity improved cultivar global adaptation capacity whereas increasing genetic diversity allowed to choose cultivars with distinctive traits that were more adapted to specific conditions. Consequently, breeding genetic material that is both plastic and diverse may improve yield stability of agricultural systems exposed to climatic variability. We argue that process-based modeling could help enhancing spatial management of cultivated genetic diversity and could be integrated in functional breeding approaches. more...
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- 2014
5. A biomarker based on gene expression indicates plant water status in controlled and natural environments
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Marchand, Gwenaëlle, Mayjonade, Baptiste, Varès, Didier, Blanchet, Nicolas, Boniface, Marie-Claude, Maury, Pierre, Nambinina, Fety Andrianasolo, Burger, Philippe, Debaeke, Philippe, Casadebaig, Pierre, Vincourt, Patrick, and Langlade, Nicolas B. more...
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Quantitative Biology - Quantitative Methods - Abstract
Plant or soil water status are required in many scientific fields to understand plant responses to drought. Because the transcriptomic response to abiotic conditions, such as water deficit, reflects plant water status, genomic tools could be used to develop a new type of molecular biomarker. Using the sunflower (Helianthus annuus L.) as a model species to study the transcriptomic response to water deficit both in greenhouse and field conditions, we specifically identified three genes that showed an expression pattern highly correlated to plant water status as estimated by the pre-dawn leaf water potential, fraction of transpirable soil water, soil water content or fraction of total soil water in controlled conditions. We developed a generalized linear model to estimate these classical water status indicators from the expression levels of the three selected genes under controlled conditions. This estimation was independent of the four tested genotypes and the stage (pre- or post-flowering) of the plant. We further validated this gene expression biomarker under field conditions for four genotypes in three different trials, over a large range of water status, and we were able to correct their expression values for a large diurnal sampling period., Comment: Plant, Cell & Environment, 2013 more...
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- 2013
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6. Bridging physiological and evolutionary time scales in a gene regulatory network
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Marchand, Gwenaëlle, Huynh-Thu, Vân Anh, Kane, Nolan, Arribat, Sandrine, Varès, Didier, Rengel, David, Balzergue, Sandrine, Rieseberg, Loren, Vincourt, Patrick, Geurts, Pierre, Vignes, Matthieu, and Langlade, Nicolas B. more...
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Quantitative Biology - Molecular Networks - Abstract
Gene regulatory networks (GRN) govern phenotypic adaptations and reflect the trade-offs between physiological responses and evolutionary adaptation that act at different time scales. To identify patterns of molecular function and genetic diversity in GRNs, we studied the drought response of the common sunflower, Helianthus annuus, and how the underlying GRN is related to its evolution. We examined the responses of 32,423 expressed sequences to drought and to abscisic acid and selected 145 co-expressed transcripts. We characterized their regulatory relationships in nine kinetic studies based on different hormones. From this, we inferred a GRN by meta-analyses of a Gaussian graphical model and a random forest algorithm and studied the genetic differentiation among populations (FST) at nodes. We identified two main hubs in the network that transport nitrate in guard cells. This suggests that nitrate transport is a critical aspect of sunflower physiological response to drought. We observed that differentiation of the network genes in elite sunflower cultivars is correlated with their position and connectivity. This systems biology approach combined molecular data at different time scales and identified important physiological processes. At the evolutionary level, we propose that network topology could influence responses to human selection and possibly adaptation to dry environments., Comment: New Phytologist, 2014, in press more...
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- 2013
7. Comparison of GWAS models to identify non-additive genetic control of flowering time in sunflower hybrids
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Bonnafous, Fanny, Fievet, Ghislain, Blanchet, Nicolas, Boniface, Marie-Claude, Carrère, Sébastien, Gouzy, Jérôme, Legrand, Ludovic, Marage, Gwenola, Bret-Mestries, Emmanuelle, Munos, Stéphane, Pouilly, Nicolas, Vincourt, Patrick, Langlade, Nicolas, and Mangin, Brigitte more...
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- 2017
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8. Molecular diversity of sunflower populations maintained as genetic resources is affected by multiplication processes and breeding for major traits
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Mangin, Brigitte, Pouilly, Nicolas, Boniface, Marie-Claude, Langlade, Nicolas B., Vincourt, Patrick, Vear, Felicity, and Muños, Stéphane
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- 2017
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9. New ideotypes of oil & protein crops
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Vincourt Patrick
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Oils, fats, and waxes ,TP670-699 - Published
- 2018
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10. Alternative breeding processes: at which extent Participatory Breeding should modify the concept of ideotypes in plant breeding?
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Vincourt Patrick and Carolo Pierre
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participatory breeding ,ideotype ,G * E interaction ,stakeholders ,bioversity ,Oils, fats, and waxes ,TP670-699 - Abstract
The Participatory Plant Breeding (PPB) concept emerged twenty years ago, particularly with the aim to build alternative organizations of the plant breeding activities in developing countries. It now as well questions the developed countries, in the frame of a more global expectation to make all the stakeholders more involved in the agricultural production, from the farmers to its final clients. We discuss here some of the questions addressed by this trend with regard to the definition of the ideotype: (a) different forms of PPB? (b) changing the paradigm: Client Oriented Breeding? (c) a new way to manage {genotype * environment} interactions? (d) mainly societal concerns at stake? (e) biodiversity and ideotypes. As the same key, technical, limiting factors are involved in both PPB and classical breeding, it is suggested to consider PPB as one of the ways in the frame of a general expectation for diversification, thus eventually resulting in the promotion of alternative ideotypes, rather than an alternative process. more...
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- 2018
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11. Effects of plant morphological traits on phoma black stem in sunflower
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Schwanck, André Aguiar, Savary, Serge, Debaeke, Philippe, Vincourt, Patrick, and Willocquet, Laetitia
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- 2016
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12. Targeted mRNA Oxidation Regulates Sunflower Seed Dormancy Alleviation during Dry After-Ripening
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Bazin, Jérémie, Langlade, Nicolas, Vincourt, Patrick, Arribat, Sandrine, Balzergue, Sandrine, El-Maarouf-Bouteau, Hayat, and Bailly, Christophe
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- 2011
13. Amélioration de la résistance aux stress du tournesol : rôle des ressources génétiques, génomiques et bio-informatiques dans les stratégies de recherche
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Vincourt Patrick
- Subjects
Helianthus annuus ,genetics ,genomics ,abiotic stress ,disease ,Oils, fats, and waxes ,TP670-699 - Abstract
The sunflower crop is occupying an increasing role in the oilseed world production, and particularly within the geographic Europe, for human and industrial purposes. The advantages of the sunflower crop are also increasing due to its environmentally safe status. But there is a need to increase the oil yield per ha in order to improve the competitiveness of farmers and oil industry. This paper is reviewing the genetic, genomic and bioinformatic resources being necessary to handle research programs aiming to provide information for plant breeding as well as more fundamental knowledge. Beside of them, phenotyping tools and modeling approaches appear to be the new frontier for the genetic dissection of traits of interest. more...
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- 2010
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14. Les possibilités de sélection pour le rendement en grains du tournesol par l’étude de caractères morphologiques et architecturaux
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Vear Felicity, Triboi Anne-Marie, Lecoeur Jérémie, Vincourt Patrick, and Debaeke Philippe
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flowering ,hybrid ,inbred line ,inheritance ,leaf area ,prediction ,Oils, fats, and waxes ,TP670-699 - Abstract
In sunflower, the active leaf area during the grain filling period has been shown to be an important character, which can be used to predict seed yield. Total and residual leaf areas of inbred lines and their hybrids are significantly correlated, but there may be some interaction between parents. Strict sense heritability is moderate. The relation between residual leaf area and seed yield has been confirmed using simplified leaf measurements on recombinant inbred lines and estimation of leaf area index with a ceptometer on hybrids. Studies of use of residual leaf area as a character in breeding for seed yield showed that F2 or F3 plants with the smallest leaf areas can be discarded, but, according to genotype, those with medium or largest leaf area give the best seed yields. more...
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- 2010
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15. Genoplante: The 'winter oilseed rape' program
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Vincourt Patrick and Renard Michel
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Oils, fats, and waxes ,TP670-699 - Abstract
The French plant genome initiative GENOPLANTE, associating public research and private companies involved in research for agriculture breeding or agrochemicals , supported several projects in oilseed rape genomics. Some of them intensively used Arabidopsis resources. Beside applied projects including gene cloning or QTL identification, GENOPLANTE succeeded in establishing a set of biological and bioinformatics resources available for the genetic improvement of this crop. more...
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- 2003
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16. Research fields, challenges and opportunities in European oilseed crops breeding
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Vincourt Patrick
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Brassica napus ,Helianthus annuus ,breeding target ,biotic ,abiotic ,Oils, fats, and waxes ,TP670-699 - Abstract
Due to the geographical specialization in oilseed world production, Europe has a major role to play in winter oilseed rape and sunflower breeding. Mainly based on the most recen t results, this review aims to identify the main research and breeding targets for these two crops, as seen through publications, with an attempt to suggest what are opportunities and challenges in these research fields. Growing a healthy and yielding crop remains the key driver for agronomic production. However sustainability and environmental profiles of the cultivar are now entering the field of play: The sustainability concern invested the field of resistance to diseases. Nitrogen use efficiency became an important target for Brassica napus, and crop resilience toward drought stresses is the way chosen in Helianthus annuus breeding for yield improvement. Significant advances are underway for quality traits, but the uncertainty on nutritional and industrial demand may explain why the product diversification remains low. more...
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- 2014
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17. Combined linkage and association mapping of flowering time in Sunflower (Helianthus annuus L.)
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Cadic, Elena, Coque, Marie, Vear, Felicity, Grezes-Besset, Bruno, Pauquet, Jerôme, Piquemal, Joël, Lippi, Yannick, Blanchard, Philippe, Romestant, Michel, Pouilly, Nicolas, Rengel, David, Gouzy, Jerôme, Langlade, Nicolas, Mangin, Brigitte, and Vincourt, Patrick more...
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- 2013
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18. Genetic analysis of phytosterol content in sunflower seeds
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Merah, Othmane, Langlade, Nicolas, Alignan, Marion, Roche, Jane, Pouilly, Nicolas, Lippi, Yannick, Vear, Felicity, Cerny, Muriel, Bouniols, Andrée, Mouloungui, Zephirin, and Vincourt, Patrick
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- 2012
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19. Consensus mapping of major resistance genes and independent QTL for quantitative resistance to sunflower downy mildew
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Vincourt, Patrick, As-sadi, Falah, Bordat, Amandine, Langlade, Nicolas B., Gouzy, Jerome, Pouilly, Nicolas, Lippi, Yannick, Serre, Frédéric, Godiard, Laurence, Tourvieille de Labrouhe, Denis, and Vear, Felicity more...
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- 2012
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20. The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution
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Badouin, Hlne, Gouzy, Jrme, Grassa, Christopher J., Murat, Florent, Staton, S. Evan, Cottret, Ludovic, Lelandais-Brire, Christine, Owens, Gregory L., Carrre, Sbastien, Mayjonade, Baptiste, Legrand, Ludovic, Gill, Navdeep, Kane, Nolan C., Bowers, John E., Hubner, Sariel, Bellec, Arnaud, Brard, Aurlie, Bergs, Hlne, Blanchet, Nicolas, Boniface, Marie-Claude, Brunel, Dominique, Catrice, Olivier, Chaidir, Nadia, Claudel, Clotilde, Donnadieu, Ccile, Faraut, Thomas, Fievet, Ghislain, Helmstetter, Nicolas, King, Matthew, Knapp, Steven J., Lai, Zhao, Le Paslier, Marie-Christine, Lippi, Yannick, Lorenzon, Lolita, Mandel, Jennifer R., Marage, Gwenola, Marchand, Gwenalle, Marquand, Elodie, Bret-Mestries, Emmanuelle, Morien, Evan, Nambeesan, Savithri, Nguyen, Thuy, Pegot-Espagnet, Prune, Pouilly, Nicolas, Raftis, Frances, Sallet, Erika, Schiex, Thomas, Thomas, Justine, Vandecasteele, Cline, Vars, Didier, Vear, Felicity, Vautrin, Sonia, Crespi, Martin, Mangin, Brigitte, Burke, John M., Salse, Jrme, Muos, Stphane, Vincourt, Patrick, Rieseberg, Loren H., and Langlade, Nicolas B. more...
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Plant metabolism -- Genetic aspects ,Sunflowers -- Genetic aspects ,Gene expression -- Observations ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Author(s): Hlne Badouin [1]; Jrme Gouzy [1]; Christopher J. Grassa [1, 2]; Florent Murat [3]; S. Evan Staton [2]; Ludovic Cottret [1]; Christine Lelandais-Brire [4, 5]; Gregory L. Owens [2]; [...]
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- 2017
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21. Optimized cultivar deployment improves the efficiency and stability of sunflower crop production at national scale
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Casadebaig, Pierre, primary, Gauffreteau, Arnaud, additional, Landré, Amélia, additional, Langlade, Nicolas B., additional, Mestries, Emmanuelle, additional, Sarron, Julien, additional, Trépos, Ronan, additional, Vincourt, Patrick, additional, and Debaeke, Philippe, additional more...
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- 2020
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22. Genetic Diversity and Core Collection Constitution for Subsequent Creation of New Sunflower Varieties in Tunisia
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Brunel Dominique, Khoufi Sahari, Pouilly Nicolas, Ben Jeddi Fayçal, Bérard Aurélie, Muños Stéphane, and Vincourt Patrick
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0106 biological sciences ,0301 basic medicine ,Genetic diversity ,Constitution ,media_common.quotation_subject ,Biology ,01 natural sciences ,Sunflower ,03 medical and health sciences ,030104 developmental biology ,Botany ,Core (graph theory) ,Agronomy and Crop Science ,010606 plant biology & botany ,media_common - Abstract
Sunflower (Helianthus annuus L.) is used as “seed snacks”, so called “pipas”, in the Mediterranean countries which may offer an interesting opportunity for agricultural diversification of this crop. The morpho-phenological variability already demonstrated in the Tunisian local populations can be a basis for the creation of new varieties well adapted to climate and soil conditions in that region. The molecular characterization of 59 accessions and reference lines generated 194 alleles from 30 SSR loci (3–10 alleles per locus) and 54 haplotypes, built from 117 SNP detected by NGS sequencing of 7 genes (4–16 haplotypes per gene). These data highlight some uniqueness of the Tunisian material compared to 7 control lines but a low genetic dispersion between accessions. However, a core collection of 8 populations, capturing 88 % of the Tunisian genetic diversity, could be proposed for a future sunflower breeding program. more...
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- 2016
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23. Heliaphen, an Outdoor High-Throughput Phenotyping Platform for Genetic Studies and Crop Modeling
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Gosseau, Florie, primary, Blanchet, Nicolas, additional, Varès, Didier, additional, Burger, Philippe, additional, Campergue, Didier, additional, Colombet, Céline, additional, Gody, Louise, additional, Liévin, Jean-François, additional, Mangin, Brigitte, additional, Tison, Gilles, additional, Vincourt, Patrick, additional, Casadebaig, Pierre, additional, and Langlade, Nicolas, additional more...
- Published
- 2019
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24. Transcriptomic analysis of the interaction between Helianthus annuus and its obligate parasite Plasmopara halstedii shows single nucleotide polymorphisms in CRN sequences
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Gouzy Jérôme, Brunel Dominique, Boniface Marie-Claude, Bordat Amandine, Le Paslier Marie-Christine, Rengel David, Hourlier Thibaut, Gascuel Quentin, Carrere Sébastien, As-sadi Falah, Godiard Laurence, and Vincourt Patrick more...
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Downy mildew in sunflowers (Helianthus annuus L.) is caused by the oomycete Plasmopara halstedii (Farl.) Berlese et de Toni. Despite efforts by the international community to breed mildew-resistant varieties, downy mildew remains a major threat to the sunflower crop. Very few genomic, genetic and molecular resources are currently available to study this pathogen. Using a 454 sequencing method, expressed sequence tags (EST) during the interaction between H. annuus and P. halstedii have been generated and a search was performed for sites in putative effectors to show polymorphisms between the different races of P. halstedii. Results A 454 pyrosequencing run of two infected sunflower samples (inbred lines XRQ and PSC8 infected with race 710 of P. halstedii, which exhibit incompatible and compatible interactions, respectively) generated 113,720 and 172,107 useable reads. From these reads, 44,948 contigs and singletons have been produced. A bioinformatic portal, HP, was specifically created for in-depth analysis of these clusters. Using in silico filtering, 405 clusters were defined as being specific to oomycetes, and 172 were defined as non-specific oomycete clusters. A subset of these two categories was checked using PCR amplification, and 86% of the tested clusters were validated. Twenty putative RXLR and CRN effectors were detected using PSI-BLAST. Using corresponding sequences from four races (100, 304, 703 and 710), 22 SNPs were detected, providing new information on pathogen polymorphisms. Conclusions This study identified a large number of genes that are expressed during H. annuus/P. halstedii compatible or incompatible interactions. It also reveals, for the first time, that an infection mechanism exists in P. halstedii similar to that in other oomycetes associated with the presence of putative RXLR and CRN effectors. SNPs discovered in CRN effector sequences were used to determine the genetic distances between the four races of P. halstedii. This work therefore provides valuable tools for further discoveries regarding the H. annuus/P. halstedii pathosystem. more...
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- 2011
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25. Using numerical plant models and phenotypic correlation space to design achievable ideotypes
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Picheny, Victor, Casadebaig, Pierre, Trepos, Ronan, Faivre, Robert, Da Silva, David, Vincourt, Patrick, Costes, Evelyne, UMR : AGroécologie, Innovations, TeRritoires, Ecole Nationale Supérieure Agronomique de Toulouse, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Architecture et Fonctionnement des Espèces Fruitières [AGAP] (AFEF), 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)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro) more...
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plant architecture ,performance de production ,production functions ,sunflower ,[SDV]Life Sciences [q-bio] ,pommier ,Quantitative Biology - Quantitative Methods ,Models, Biological ,modèle structure fonction ,apple tree ,Quantitative Biology - Populations and Evolution ,Quantitative Methods (q-bio.QM) ,méthode d'optimisation ,Populations and Evolution (q-bio.PE) ,simulation numérique ,Numerical Analysis, Computer-Assisted ,tournesol ,Phenotype ,corrélation phénotypique ,FOS: Biological sciences ,numerical simulation ,Malus ,Feasibility Studies ,Helianthus ,modèle de production ,architecture de la plante - Abstract
Numerical plant models can predict the outcome of plant traits modifications resulting from genetic variations, on plant performance, by simulating physiological processes and their interaction with the environment. Optimization methods complement those models to design ideotypes, i.e. ideal values of a set of plant traits resulting in optimal adaptation for given combinations of environment and management, mainly through the maximization of a performance criteria (e.g. yield, light interception). As use of simulation models gains momentum in plant breeding, numerical experiments must be carefully engineered to provide accurate and attainable results, rooting them in biological reality. Here, we propose a multi-objective optimization formulation that includes a metric of performance, returned by the numerical model, and a metric of feasibility, accounting for correlations between traits based on field observations. We applied this approach to two contrasting models: a process-based crop model of sunflower and a functional-structural plant model of apple trees. In both cases, the method successfully characterized key plant traits and identified a continuum of optimal solutions, ranging from the most feasible to the most efficient. The present study thus provides successful proof of concept for this enhanced modeling approach, which identified paths for desirable trait modification, including direction and intensity., Comment: 25 pages, 5 figures, 2017, Plant, Cell and Environment more...
- Published
- 2017
- Full Text
- View/download PDF
26. Genomic Prediction of Sunflower Hybrids Oil Content
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Mangin, Brigitte, Bonnafous, Fanny, Blanchet, Nicolas, Boniface, Marie-Claude, Bret-Mestries, Emmanuelle, Carrere, Sebastien, Cottret, Ludovic, Legrand, Ludovic, Marage, Gwenola, Pegot - Espagnet, Prune, Munos, Stephane, Pouilly, Nicolas, Vear, Felicity, Vincourt, Patrick, Langlade, Nicolas, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), ANR-11-BTBR-0005,SUNRISE,Ressources génétiques de tournesol pour l'amélioration de la stabilité de production d'huile sous c(2011), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées more...
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[SDV.SA]Life Sciences [q-bio]/Agricultural sciences ,Vegetal Biology ,sunflower ,hybrid ,genomic selection ,factorial design ,oil content ,GBS ,prédiction génétique ,Plant Science ,lcsh:Plant culture ,huile de tournesol ,hybride ,Agricultural sciences ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,lcsh:SB1-1110 ,Biologie végétale ,Sciences agricoles ,Original Research - Abstract
International audience; Prediction of hybrid performance using incomplete factorial mating designs is widely used in breeding programs including different heterotic groups. Based on the general combining ability (GCA) of the parents, predictions are accurate only if the genetic variance resulting from the specific combining ability is small and both parents have phenotyped descendants. Genomic selection (GS) can predict performance using a model trained on both phenotyped and genotyped hybrids that do not necessarily include all hybrid parents. Therefore. GS could overcome the issue of unknown parent GCA. Here, we compared the accuracy of classical GCA-based and genomic predictions for oil content of sunflower seeds using several GS models. Our study involved 452 sunflower hybrids from an incomplete factorial design of 36 female and 36 male lines. Re-sequencing of parental lines allowed to identify 468,194 non-redundant SNPs and to infer the hybrid genotypes. Oil content was observed in a multi-environment trial (MET) over 3 years, leading to nine different environments. We compared GCA-based model to different GS models including female and male genomic kinships with the addition of the female-by-male interaction genomic kinship, the use of functional knowledge as SNPs in genes of oil metabolic pathways, and with epistasis modeling. When both parents have descendants in the training set, the predictive ability was high even for GCA-based prediction, with an average MET value of 0.782. GS performed slightly better (+0.2%). Neither the inclusion of the female-by-male interaction, nor functional knowledge of oil metabolism, nor epistasis modeling improved the GS accuracy. GS greatly improved predictive ability when one or both parents were untested in the training set, increasing GCA-based predictive ability by 10.4% from 0.575 to 0.635 in the MET. In this scenario, performing GS only considering SNPs in oil metabolic pathways did not improve whole genome GS prediction but increased GCA-based prediction ability by 6.4%. Our results show that GS is a major improvement to breeding efficiency compared to the classical GCA modeling when either one or both parents are not well-characterized. This finding could therefore accelerate breeding through reducing phenotyping efforts and more effectively targeting for the most promising crosses. more...
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- 2017
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27. Genetic control of plasticity of oil yield for combined abiotic stresses using a joint approach of crop modeling and genome-wide association
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Casadebaig, Pierre, Cadic, Eléna, Blanchet, Nicolas, Boniface, Marie-Claude, Carrere, Sebastien, Gouzy, Jerome, Legrand, Ludovic, Mayjonade, Baptiste, Pouilly, Nicolas, André, Thierry, Coque, Marie, Piquemal, Joël, Laporte, Marion, Vincourt, Patrick, Munos, Stephane, Mangin, Brigitte, and Langlade, Nicolas more...
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stress abiotique ,Vegetal Biology ,plasticité ,fungi ,food and beverages ,cold ,crop model ,drought ,genetic variation ,multi-stress ,Biologie végétale ,contrôle génétique ,huile végétale ,huile de tournesol - Abstract
Understanding the genetic basis of phenotypic plasticity is crucial for predicting and managing climate change effects on wild plants and crops. Here, we combined crop modeling and quantitative genetics to study the genetic control of oil yield plasticity for multiple abiotic stresses in sunflower. First we developed stress indicators to characterize 14 environments for three abiotic stresses (cold, drought and nitrogen) using the SUNFLO crop model and phenotypic variations of three commercial varieties. The computed plant stress indicators better explain yield variation than descriptors at the climatic or crop levels. In those environments, we observed oil yield of 317 sunflower hybrids and regressed it with three selected stress indicators. The slopes of cold stress norm reaction were used as plasticity phenotypes in the following genome-wide association study. Among the 65,534 tested SNP, we identified nine QTL controlling oil yield plasticity to cold stress. Associated SNP are localized in genes previously shown to be involved in cold stress responses: oligopeptide transporters, LTP, cystatin, alternative oxidase, or root development. This novel approach opens new perspectives to identify genomic regions involved in genotype-by-environment interaction of a complex traits to multiple stresses in realistic natural or agronomical conditions. more...
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- 2017
28. Additional file 4: of Different genetic architectures underlie crop responses to the same pathogen: the {Helianthus annuus * Phoma macdonaldii} interaction case for black stem disease and premature ripening
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Bordat, Amandine, Marchand, Gwenaëlle, Langlade, Nicolas, Pouilly, Nicolas, Muños, Stéphane, Dechamp-Guillaume, Grégory, Vincourt, Patrick, and Bret-Mestries, Emmanuelle
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Genetic architecture of the relationship between morphological and developmental traits, and sunflower resistance traits to Phoma macdonaldii. (DOCX 28 kb)
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- 2017
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29. Heliaphen, an outdoor high-throughput phenotyping platform designed to integrate genetics and crop modeling
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Gosseau, Florie, primary, Blanchet, Nicolas, additional, Varès, Didier, additional, Burger, Philippe, additional, Campergue, Didier, additional, Colombety, Céline, additional, Gody, Louise, additional, Liévin, Jean-François, additional, Mangin, Brigitte, additional, Tison, Gilles, additional, Vincourt, Patrick, additional, Casadebaig, Pierre, additional, and Langlade, Nicolas, additional more...
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- 2018
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30. The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution
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BADOUIN, Hélène, Gouzy, Jerome, GRASSA, Christopher, Murat, Florent, Staton, S Evan, Cottret, Ludovic, Lelandais-briere, Christine, Owens, Gregory L, Carrere, Sebastien, mayjonade, Baptiste, Legrand, Ludovic, Gill, Navdeep, Kane, Nolan C, Bowers, John E, Hubner, Sariel, Bellec, Arnaud, Berard, Aurélie, Berges, Helene, BLANCHET, Nicolas, Boniface, Marie-Claude, Brunel, Dominique, Catrice, Olivier, Chaidir, Nadia, Claudel, Clotilde, Donnadieu, Cecile, Faraut, Thomas, Fievet, Ghislain, Helmstetter, Nicolas, King, Matthew, Knapp, Steven J, Lai, Zhao, Le Paslier, Marie-Christine, Lippi, Yannick, LORENZON, Lolita, Mandel, Jennifer R, Marage, Gwenola, MARCHAND, Gwenaëlle, MARQUAND, Elodie, MESTRIES, Emmanuelle, Morien, Evan, Nambeesan, Savithri, Nguyen, Thuy, Pegot - Espagnet, Prune, Pouilly, Nicolas, Raftis, Frances, Sallet, Erika, Schiex, Thomas, Thomas, Justine, Vandecasteele, Céline, Vares, Didier, Vear, Felicity, Vautrin, Sonia, Crespi, Martin, Mangin, Brigitte, Burke, John M, Salse, Jerome, Munos, Stephane, Vincourt, Patrick, Rieseberg, Loren H, Langlade, Nicolas, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Department of Botany and Biodiversity Research Centre, University of British Columbia (UBC), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Ecology and Evolutionary Biology (Faculty of Biology), University of Science-Vietnam National Universities, Department of Plant Biology, Miller Plant Sciences, University of Georgia [USA], Department of Biotechnology, Tel-Hai Academic College, Galilee Research Institute (Migal), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Etude du Polymorphisme des Génomes Végétaux (EPGV), Dow AgroSciences LLC, Biogemma, GeT PlaGe, Genotoul, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Department of Plant Sciences, University of California, Department of Biology, Northern Arizona University [Flagstaff], Center for Genomics and Bioinformatics, Indiana University [Bloomington], Indiana University System-Indiana University System, Department of Biological Sciences, The Open University [Milton Keynes] (OU), UMR : AGroécologie, Innovations, TeRritoires, Ecole Nationale Supérieure Agronomique de Toulouse, Department of Horticulture, University of Wisconsin-Madison, The Wellcome Trust Sanger Institute [Cambridge], Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), French National Research Agency : SUNYFUEL/ANR-07-GPLA-0022, SUNRISE/ANR-11-BTBR-0005 Midi-Pyrenees Region, European Fund for Regional Development, French Fund for Competitiveness Clusters (FUI), Genoscope SystemSun project, Genome Canada, Genome BC's Applied Genomics Research in Bioproducts or Crops (ABC) Competition, NSF Plant Genome Program : DBI-082045, International Consortium for Sunflower Genomics Resources, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Tel-Hai College, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), ANR-07-GPLA-0022,SUNYFUEL,Improving sunflower yield and quality for biofuel production by genomics and genetics(2007), ANR-11-BTBR-0005,SUNRISE,Ressources génétiques de tournesol pour l'amélioration de la stabilité de production d'huile sous c(2011), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Galilee Research Institute [Israël] (MIGAL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), University of California (UC), Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique ( INRA ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), University of British Columbia ( UBC ), Génétique Diversité et Ecophysiologie des Céréales ( GDEC ), Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ) -Institut National de la Recherche Agronomique ( INRA ), UMR 1403 Institut des Sciences des Plantes de Paris Saclay, Institut National de la Recherche Agronomique ( INRA ) -Université Paris Diderot - Paris 7 ( UPD7 ), Department of Ecology and Evolutionary Biology ( Faculty of Biology ), University of Georgia, Galilee Research Institute ( Migal ), Centre National de Ressources Génomiques Végétales ( CNRGV ), Institut National de la Recherche Agronomique ( INRA ), Etude du Polymorphisme des Génomes Végétaux ( EPGV ), GenPhySE - UMR 1388 ( Génétique Physiologie et Systèmes d'Elevage ), Institut National de la Recherche Agronomique ( INRA ) -École nationale supérieure agronomique de Toulouse [ENSAT]-ENVT, The Open University [Milton Keynes] ( OU ), University of Wisconsin-Madison [Madison], Wellcome Trust Sanger Institute, and Unité de Mathématiques et Informatique Appliquées de Toulouse ( MIAT INRA ) more...
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[ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology ,sunflower ,Acclimatization ,résistance au stress ,génome végétal ,Flowers ,genome evolution ,résilience ,Evolution, Molecular ,Gene Expression Regulation, Plant ,Stress, Physiological ,Gene Duplication ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Plant Oils ,Sunflower Oil ,genome ,food and beverages ,Genetic Variation ,Genomics ,Sequence Analysis, DNA ,tournesol ,genêtic variation ,stress biotique ,diversité génétique ,Helianthus ,Transcriptome ,Genome, Plant - Abstract
The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought. Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives, including numerous extremophile species. Here we report a high-quality reference for the sunflower genome (3.6 gigabases), together with extensive transcriptomic data from vegetative and floral organs. The genome mostly consists of highly similar, related sequences and required single-molecule real-time sequencing technologies for successful assembly. Genome analyses enabled the reconstruction of the evolutionary history of the Asterids, further establishing the existence of a whole-genome triplication at the base of the Asterids II clade and a sunflower-specific whole-genome duplication around 29 million years ago. An integrative approach combining quantitative genetics, expression and diversity data permitted development of comprehensive gene networks for two major breeding traits, flowering time and oil metabolism, and revealed new candidate genes in these networks. We found that the genomic architecture of flowering time has been shaped by the most recent whole-genome duplication, which suggests that ancient paralogues can remain in the same regulatory networks for dozens of millions of years. This genome represents a cornerstone for future research programs aiming to exploit genetic diversity to improve biotic and abiotic stress resistance and oil production, while also considering agricultural constraints and human nutritional needs. more...
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- 2016
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31. HELIAPHEN: a high-throughput phenotyping platform to characterize plant responses to water stress from seedling stage to seed set
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Casadebaig, Pierre, Burger, Philippe, Vares, Didier, Colombet, Céline, Boniface, Marie-Claude, Vincourt, Patrick, Debaeke, Philippe, Langlade, Nicolas, and Blanchet, Nicolas
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robot ,drought ,transpiration ,growth ,imaging - Abstract
Characterization of plant morphological and physiological responses is a limiting step to breed crops adapted to drought-limiting conditions. Automation of plant management on a phenotyping platform overcomes it by allowing large scale experimentation with yet accurate and individual plant monitoring. In response to both genetic and eco-physiological experimentation requirements, we developed the HELIAPHEN platform. This unique outdoor platform can host 1300 plants, such as sunflower, in 15L pots. It allows plant growth in climatic conditions similar to field, as well as a precise and automated monitoring of plant water consumption thanks to a prototype robot. Its primary functions are to move autonomously on the 600m2 platform, and to treat each pot at its location (including weighing and watering up to a targeted weight). Beyond these functions, the robot takes at each handling, plant images from multiple angles with four cameras, to follow the evolution of morphological traits along with the description of the water status. In addition, a ultrasound radar measures automatically plant height and a laser measures stem diameter at the plant basis. These secondary functions are currently improved with new captors such as a light curtain and a 3D laser in order to reconstitute a 3D representation of the plant. To validate the meaning of the HELIAPHEN outputs, we confirmed the impact of drought stress managed with the robot on seed weight, number and thousand kemel weight (TKW). Furthermore, we observed a correlation between field and HELIAPHEN data for TKW and seed number observed on 45 sunflower hybrids. more...
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- 2016
32. Mesurer le niveau de résistance quantitative des variétés de tournesol face au mildiou dans les processus de sélection et d’évaluation variétale : un enjeu fort pour la gestion durable du risque
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Mestries, Emmannelle, Auclert, B., Poisson-Bammé, B., Penaud, Annette, Grimault, Valerie, Perrot, S., Robert, A., Roche, Sylvie, Serre, Frédéric, Tourvieille de Labrouhe, Denis, Vear, Felicity, Boniface, Marie-Claude, Bordat, Amandine, Pouilly, Nicolas, Vincourt, Patrick, Munos, Stephane, Terres Inovia, Station Nationale d’Essais de Semences (SNES), UE 1375 Phénotypage Au Champ des Céréales, Institut National de la Recherche Agronomique (INRA)-Santé des plantes et environnement (S.P.E.)-Biologie et Amélioration des Plantes (BAP)-Phénotypage Au Champ des Céréales (PHACC), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), and Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB) more...
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phenotyping ,quantitative resistance ,résistance quantitative ,conditions contrôlées ,phénotypage ,[SDV]Life Sciences [q-bio] ,Plasmopara halstedii ,controlled conditions - Abstract
La résistance quantitative du tournesol (Helianthus annuus) au mildiou (Plasmopara halstedii), mise en évidence récemment, est difficile à évaluer. Un réseau de onze expérimentations associant la GEVESSNES, deux laboratoires de l’INRA et Terres Inovia a été construit afin de proposer une méthodologie permettant de mieux caractériser et quantifier cette résistance. En plus de lignées témoins, 17 lignées recombinantes obtenues par l’INRA et portant entre 0 et 3 QTL (quantitative trait loci) impliqués dans la résistance quantitative du tournesol au mildiou ont été testées face à 5 pathotypes de mildiou : 710, 704, 714, 304 et 334. Bien que des différences aient été observées entre laboratoires, les résultats ont permis de poser les bases d’un futur protocole utilisable en routine pour valoriser ce type de résistance dès la création variétale jusqu’à l’inscription puis la post-inscription des variétés., A quantitative resistance of sunflower (Helianthus annuus) to downy mildew (Plasmopara halstedii) has been identified a few years ago. An experimental network involving several labs (GEVES-SNES, INRA and Terres Inovia) over several years aimed at describing and quantifying such a quantitative response. It was hoped to propose a methodology useable to improve sustainable resistance. In addition to check varieties and breeding lines, 17 recombinant inbred lines carrying 0 to 3 quantitative trait loci alleles for quantitative resistance were tested with five downy mildew pathotypes (710, 704, 714, 304, 334). While the experimental results revealed some discrepancies between experiments, this study provided a first experimental protocol to evaluate quantitative resistance both for breeding and for variety registration and development more...
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- 2016
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33. Different genetic architectures underlie crop responses to the same pathogen: the {Helianthus annuus * Phoma macdonaldii} interaction case for black stem disease and premature ripening
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Bordat, Amandine, primary, Marchand, Gwenaëlle, additional, Langlade, Nicolas B., additional, Pouilly, Nicolas, additional, Muños, Stéphane, additional, Dechamp-Guillaume, Grégory, additional, Vincourt, Patrick, additional, and Bret-Mestries, Emmanuelle, additional more...
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- 2017
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34. Comparison of GWAS models to identify non-additive genetic control of flowering time in sunflower hybrids
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Bonnafous, Fanny, primary, Fievet, Ghislain, additional, Blanchet, Nicolas, additional, Boniface, Marie-Claude, additional, Carrère, Sébastien, additional, Gouzy, Jérôme, additional, Legrand, Ludovic, additional, Marage, Gwenola, additional, Bret-Mestries, Emmanuelle, additional, Munos, Stéphane, additional, Pouilly, Nicolas, additional, Vincourt, Patrick, additional, Langlade, Nicolas, additional, and Mangin, Brigitte, additional more...
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- 2017
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35. Genetic control of plasticity of oil yield for combined abiotic stresses using a joint approach of crop modelling and genome‐wide association
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Mangin, Brigitte, primary, Casadebaig, Pierre, additional, Cadic, Eléna, additional, Blanchet, Nicolas, additional, Boniface, Marie‐Claude, additional, Carrère, Sébastien, additional, Gouzy, Jérôme, additional, Legrand, Ludovic, additional, Mayjonade, Baptiste, additional, Pouilly, Nicolas, additional, André, Thierry, additional, Coque, Marie, additional, Piquemal, Joël, additional, Laporte, Marion, additional, Vincourt, Patrick, additional, Muños, Stéphane, additional, and Langlade, Nicolas B., additional more...
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- 2017
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36. Genetic characterization of the interaction between sunflower and Orobanche cumana
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Louarn, Johann, Boniface, Marie-Claude, Pouill, Nicolas, Issakoff, Jessica, Velasco Varo, Leonardo, Vincourt, Patrick, Pérez-Vich, Begoña, and Muños, Stéphane
- Abstract
Trabajo presentado en el 13th World Congress on Parasitic Plants (Parasitic plants: the good, the bad, and the mysterious), celebrado en Kunming (China) del 5 al 10 de julio de 2015., Sunflower is an important crop and is mainly used for oil production. Orobanche cumana is a major disease in cultivated areas around the black sea and in Spain. The pathogen spread more recently to several other countries (France, China ...). During the last ten years, several new O. cumana races have emerged but very few efficient methods were available to control their development. Genetic resistance was the more efficient and introgression of major resistance loci was successfully used to produce new resistant sunflower varieties (from races A to E). With the recent emergence of new virulent races (called F and F+), novel resistance loci need to be mapped and characterized. A recombinant inbred line population, derived from the cross between the lines HA89 and LR1, has been developed by INRA. It has been previously characterized for the resistance to the race E of O. cumana. We used this population to map QTLs controlling quantitative resistance to race F. The phenotyping has been conducted on the 107 lines of the population at different stages of the interaction. We evaluated each line for (i) the capacity of their root exudate to induce germination of O. cumana seeds, (ii) their ability to induce incompatible attachment, (iii) the number of broomrape tubercles in growth chamber, and (iv) the number of broomrape emergences in the field. Different response profiles were observed at these 4 stages of development, indicating several resistance mechanisms in sunflower. Interestingly, even if the two parental lines showed a close resistant phenotype, we observed a large diversity of the resistance level in the population. Combined with this detailed phenotyping analysis, we performed the genotyping of the sunflower recombinant inbred lines using an AXIOM array of 586 985 SNPs. QTLs will be mapped for the different traits. more...
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- 2015
37. Sunflower Resistance to Broomrape (Orobanche cumana) Is Controlled by Specific QTLs for Different Parasitism Stages
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Promosol, Louarn, Johann, Boniface, Marie-Claude, Pouill, Nicolas, Velasco Varo, Leonardo, Pérez-Vich, Begoña, Vincourt, Patrick, Muños, Stéphane, Promosol, Louarn, Johann, Boniface, Marie-Claude, Pouill, Nicolas, Velasco Varo, Leonardo, Pérez-Vich, Begoña, Vincourt, Patrick, and Muños, Stéphane more...
- Abstract
Orobanche cumana (sunflower broomrape) is an obligatory and non-photosynthetic root parasitic plant that specifically infects the sunflower. It is located in Europe and in Asia, where it can cause yield losses of over 80%. More aggressive races have evolved, mainly around the Black Sea, and broomrape can rapidly spread to new areas. Breeding for resistance seems to be the most efficient and sustainable approach to control broomrape infestation. In our study, we used a population of 101 recombinant inbred lines (RILs), derived from a cross between the two lines HA89 and LR1 (a line derived from an interspecific cross with Helianthus debilis). Rhizotrons, pots and field experiments were used to characterize all RILs for their resistance to O. cumana race F parasitism at three post vascular connection life stages: (i) early attachment of the parasite to the sunflower roots, (ii) young tubercle and (iii) shoot emergence. In addition, RIL resistance to race G at young tubercle development stage was evaluated in pots. The entire population was genotyped, and QTLs were mapped. Different QTLs were identified for each race (F from Spain and G from Turkey) and for the three stages of broomrape development. The results indicate that there are several quantitative resistance mechanisms controlling the infection by O. cumana that can be used in sunflower breeding. more...
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- 2016
38. Increased genetic diversity improves crop yield stability under climate variability: a computational study on sunflower
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Trépos, Ronan, Picheny, Victor, Langlade, Nicolas, Vincourt, Patrick, Debaeke, Philippe, and Casadebaig, Pierre
- Subjects
phenotypic plasticity ,gene to phenotype ,GxE interaction ,ideotype ,modeling ,simulation ,sunflower crop ,Vegetal Biology ,Biologie végétale - Abstract
A crop can be represented as a biotechnical system in which components are either chosen (cultivar, management) or given (soil, climate) and whose combination generates highly variable stress patterns and yield responses. Here, we used modeling and simulation to predict the crop phenotypic plasticity resulting from the interaction of plant traits (G), climatic variability (E) and management actions (M). We designed two in silico experiments that compared existing and virtual sunflower cultivars ( Helianthus annuus L. ) in a target population of cropping environments by simulating a range of indicators of crop performance. Optimization methods were then used to search for GEM combinations that matched desired crop specifications. Computational experiments showed that the fit of particular cultivars in specific environments is gradually increasing with the knowledge of pedo-climatic conditions. At the regional scale, tuning the choice of cultivar impacted crop performance the same magnitude as the effect of yearly genetic progress made by breeding. When considering virtual genetic material, designed by recombining plant traits, cultivar choice had a greater positive impact on crop performance and stability. Results suggested that breeding for key traits conferring plant plasticity improved cultivar global adaptation capacity whereas increasing genetic diversity allowed to choose cultivars with distinctive traits that were more adapted to specific conditions. Consequently, breeding genetic material that is both plastic and diverse may improve yield stability of agricultural systems exposed to climatic variability. We argue that process-based modeling could help enhancing spatial management of cultivated genetic diversity and could be integrated in functional breeding approaches more...
- Published
- 2014
39. Toward a better understanding of the genetic architecture of sunflower (Helianthus annuus) resistance to the parasitic plant Orobanche cumana
- Author
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Louarn, Johann, Pouill, Nicolas, Boniface, Marie-Claude, Blanchet, Nicolas, Pérez-Vich, Begoña, Vincourt, Patrick, and Promosol
- Subjects
QTL mapping ,race F ,Resistance ,food and beverages ,Helianthus annuus ,Orobanche cumana - Abstract
Trabajo presentado en el Third Internacional Symposium on broomrape (Orobanche spp.) in Sunflower, celebrado en Córdoba (España) del 3 al 6 de junio de 2014., The plant parasite Orobanche cumana is a major threat for the sunflower crop. The emergence of new, virulent “races” during the ten past years reinforced the need to develop new approaches, knowledge and tools in order to control this pest efficiently. Breeding is the most sustainable approach to control broomrape in the field. A RIL population derived from a cross between HA89 and LR1, an inbred line bred from an interspecific cross with Helianthus debilis had been previously characterized for resistance to O. cumana race E, but no data is available for new races. The aim of this study was to characterize the HA89xLR1 RIL population for resistance to race F and to identify QTLs associated with this resistance. The population was phenotyped by counting the number of healthy broomrape tubercles and the rate of tubercle necrosis on young sunflower plants raised in a growth chamber with four biological replications. Differences in l resistance were observed among the RIL population, with some resistant genotypes and some highly susceptible genotypes. The polymorphism of 111 SNP markers previously mapped on a consensus genetic map was used for the QTL detection. Four QTLs were detected on four linkage groups (LG01, LG07, LG15 and LG17), with two QTLs controlling the number of tubercles per plant and two others controlling necrosis. This study suggests that the resistance to O. cumana race F is controlled by several QTLs affecting differently the number of tubercle and the induction of tubercle necrosis., This research was supported by the French Association for the Promotion of Oilseed Crops Breeding (PROMOSOL). more...
- Published
- 2014
40. Identification, variability and in planta recognition of pathogenicity effectors of Plasmopara halstedii, the Oomycete responsible for Downy Mildew in sunflower, Helianthus annuus
- Author
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Gascuel, Quentin, Martinez, Yves, Buendia, Luis, Pouilly, Nicolas, Bordat, Amandine, Marie-Claude Boniface, Blanchet, Nicolas, Vincourt, Patrick, and Godiard, Laurence
- Published
- 2014
- Full Text
- View/download PDF
41. Analyse de risque phytosanitaire Plasmopara halstedii, agent responsable de la maladie du mildiou du tournesol
- Author
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Suffert, Frédéric, Delmotte, François, Délos, Marc, Grimault, Valérie, Labrouhe, Denis Tourvieille De, Vincourt, Patrick, and Wilson, Véronique
- Published
- 2014
- Full Text
- View/download PDF
42. Sunflower Resistance to Broomrape (Orobanche cumana) Is Controlled by Specific QTLs for Different Parasitism Stages
- Author
-
Louarn, Johann, primary, Boniface, Marie-Claude, additional, Pouilly, Nicolas, additional, Velasco, Leonardo, additional, Pérez-Vich, Begoña, additional, Vincourt, Patrick, additional, and Muños, Stéphane, additional more...
- Published
- 2016
- Full Text
- View/download PDF
43. Effector Polymorphisms of the Sunflower Downy Mildew Pathogen Plasmopara halstedii and Their Use to Identify Pathotypes from Field Isolates
- Author
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Gascuel, Quentin, primary, Bordat, Amandine, additional, Sallet, Erika, additional, Pouilly, Nicolas, additional, Carrere, Sébastien, additional, Roux, Fabrice, additional, Vincourt, Patrick, additional, and Godiard, Laurence, additional more...
- Published
- 2016
- Full Text
- View/download PDF
44. Bridging physiological and evolutionary time scales in a gene regulatory network
- Author
-
Marchand, Gwena��lle, Huynh-Thu, V��n Anh, Kane, Nolan, Arribat, Sandrine, Var��s, Didier, Rengel, David, Balzergue, Sandrine, Rieseberg, Loren, Vincourt, Patrick, Geurts, Pierre, Vignes, Matthieu, and Langlade, Nicolas B. more...
- Subjects
Molecular Networks (q-bio.MN) ,FOS: Biological sciences ,food and beverages ,Quantitative Biology - Molecular Networks - Abstract
Gene regulatory networks (GRN) govern phenotypic adaptations and reflect the trade-offs between physiological responses and evolutionary adaptation that act at different time scales. To identify patterns of molecular function and genetic diversity in GRNs, we studied the drought response of the common sunflower, Helianthus annuus, and how the underlying GRN is related to its evolution. We examined the responses of 32,423 expressed sequences to drought and to abscisic acid and selected 145 co-expressed transcripts. We characterized their regulatory relationships in nine kinetic studies based on different hormones. From this, we inferred a GRN by meta-analyses of a Gaussian graphical model and a random forest algorithm and studied the genetic differentiation among populations (FST) at nodes. We identified two main hubs in the network that transport nitrate in guard cells. This suggests that nitrate transport is a critical aspect of sunflower physiological response to drought. We observed that differentiation of the network genes in elite sunflower cultivars is correlated with their position and connectivity. This systems biology approach combined molecular data at different time scales and identified important physiological processes. At the evolutionary level, we propose that network topology could influence responses to human selection and possibly adaptation to dry environments., New Phytologist, 2014, in press more...
- Published
- 2013
45. Comparison of GWAS models to identify non-additive genetic control of flowering time in sunflower hybrids.
- Author
-
Bonnafous, Fanny, Fievet, Ghislain, Blanchet, Nicolas, Boniface, Marie-Claude, Carrère, Sébastien, Gouzy, Jérôme, Legrand, Ludovic, Marage, Gwenola, Bret-Mestries, Emmanuelle, Munos, Stéphane, Pouilly, Nicolas, Vincourt, Patrick, Langlade, Nicolas, and Mangin, Brigitte more...
- Subjects
SUNFLOWER genetics ,FLOWERING time ,SUNFLOWER hybridization ,ALLELES in plants ,HETEROSIS in plants - Abstract
Key message: This study compares five models of GWAS, to show the added value of non-additive modeling of allelic effects to identify genomic regions controlling flowering time of sunflower hybrids. Abstract: Genome-wide association studies are a powerful and widely used tool to decipher the genetic control of complex traits. One of the main challenges for hybrid crops, such as maize or sunflower, is to model the hybrid vigor in the linear mixed models, considering the relatedness between individuals. Here, we compared two additive and three non-additive association models for their ability to identify genomic regions associated with flowering time in sunflower hybrids. A panel of 452 sunflower hybrids, corresponding to incomplete crossing between 36 male lines and 36 female lines, was phenotyped in five environments and genotyped for 2,204,423 SNPs. Intra-locus effects were estimated in multi-locus models to detect genomic regions associated with flowering time using the different models. Thirteen quantitative trait loci were identified in total, two with both model categories and one with only non-additive models. A quantitative trait loci on LG09, detected by both the additive and non-additive models, is located near a GAI homolog and is presented in detail. Overall, this study shows the added value of non-additive modeling of allelic effects for identifying genomic regions that control traits of interest and that could participate in the heterosis observed in hybrids. [ABSTRACT FROM AUTHOR] more...
- Published
- 2018
- Full Text
- View/download PDF
46. La tolérance du tournesol aux maladies
- Author
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Vincourt, Patrick, As Sadi, F., Vear, Felicity, Bordat, Amandine, Tourvieille De Labrouhe, Denis, Godiard, Laurence, Interactions Plantes - Microorganismes, Institut National de la Recherche Agronomique (INRA), UMR 441-2594 INRA-CNRS, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), 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), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS) more...
- Subjects
bioagresseur ,[SDV.SA]Life Sciences [q-bio]/Agricultural sciences ,sclerotinia ,effecteur ,pathogène des semences ,helianthus annuus ,résistance ,phomopsis ,phoma ,pathogénicité ,mildiou du tournesol - Abstract
La culture du tournesol est confrontée aux attaques de différents bioagresseurs. En France, il s’agit essentiellement du mildiou Plasmopara halstedii, du sclérotinia Sclerotinia sclerotiorum, du phomopsis Diaporthe helianthi, et du phoma Phoma macdonaldii dont les attaques au collet entrainent le dessèchement précoce. Les efforts de recherche et de sélection ont permis de conserver à cette culture son statut respectueux de l’environnement. Cependant, les dialogues moléculaires entre la plante et ces différents pathogènes et qui aboutissent à l’immunité ou à la sensibilité, ainsi que sa variabilité génétique, sont encore largement inconnus. Après une revue des principaux résultats récents concernant l’interaction entre le tournesol et ces pathogènes, nous soulevons deux questions d’intérêtpour la poursuite de ces recherches : celle de la répartition des rôles et de la hiérarchisation des questions de recherche d’une part, et d’autre part celle du regard à porter sur les réseaux de gènes que révèle l’analyse du transcriptome grâce aux nouvelles technologies de séquençage., The sunflower crop is subjected to several diseases, among of which Downy Mildew, Sclerotinia, Phomopsis and premature death caused by Phoma macdonaldii are the most important in France today. The research and breeding efforts during the past fifty years have been efficient enough to ensure an “environmentally safe” status to this cultivation. However, little is known about the moleculartalk which leads to immunity or susceptibility between the plant and the pathogens as well as about its genetic variability. After a review of the main recent results on the these sunflower*microorganisms interactions, we are discussing on two questions of interest for the research perspectives: How to establish the research priorities? How to decipher the genes networks revealed by transcriptome analysis with a greater involvement of the genetic variability thanks to the development of the new sequencing technologies? more...
- Published
- 2011
47. Les possibilités de sélection pour le rendement en grains du tournesol par l'étude de caractères morphologiques et architecturaux
- Author
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Vear, Felicity, Triboi, Anne-Marie, Lecoeur, Jérémie, Vincourt, Patrick, Debaeke, Philippe, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Interactions Plantes - Microorganismes, Institut National de la Recherche Agronomique (INRA), Agrosystèmes Cultivés et Herbagers (ARCHE), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Toulouse-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse (ENSAT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP) more...
- Subjects
PREDICTION ,fungi ,[SDV.IDA]Life Sciences [q-bio]/Food engineering ,INBRED LINE ,food and beverages ,FLOWERING ,LEAF AREA ,HYBRID ,INHERITANCE - Abstract
In sunflower, the active leaf area during the grain filling period has been shown to be an important character, which can be used to predict seed yield. Total and residual leaf areas of inbred lines and their hybrids are significantly correlated, but there may be some interaction between parents. Strict sense heritability is moderate. The relation between residual leaf area and seed yield has been confirmed using simplified leaf measurements on recombinant inbred lines and estimation of leaf area index with a ceptometer on hybrids. Studies of use of residual leaf area as a character in breeding for seed yield showed that F2 or F3 plants with the smallest leaf areas can be discarded, but, according to genotype, those with medium or largest leaf area give the best seed yields. more...
- Published
- 2010
- Full Text
- View/download PDF
48. Toward a better understanding of the genetic architecture of sunflower (Helianthus annuus) resistance to the parasitic plant Orobanche cumana
- Author
-
Promosol, Louarn, Johann, Pouill, Nicolas, Boniface, Marie-Claude, Blanchet, Nicolas, Pérez-Vich, Begoña, Vincourt, Patrick, Promosol, Louarn, Johann, Pouill, Nicolas, Boniface, Marie-Claude, Blanchet, Nicolas, Pérez-Vich, Begoña, and Vincourt, Patrick more...
- Abstract
The plant parasite Orobanche cumana is a major threat for the sunflower crop. The emergence of new, virulent “races” during the ten past years reinforced the need to develop new approaches, knowledge and tools in order to control this pest efficiently. Breeding is the most sustainable approach to control broomrape in the field. A RIL population derived from a cross between HA89 and LR1, an inbred line bred from an interspecific cross with Helianthus debilis had been previously characterized for resistance to O. cumana race E, but no data is available for new races. The aim of this study was to characterize the HA89xLR1 RIL population for resistance to race F and to identify QTLs associated with this resistance. The population was phenotyped by counting the number of healthy broomrape tubercles and the rate of tubercle necrosis on young sunflower plants raised in a growth chamber with four biological replications. Differences in l resistance were observed among the RIL population, with some resistant genotypes and some highly susceptible genotypes. The polymorphism of 111 SNP markers previously mapped on a consensus genetic map was used for the QTL detection. Four QTLs were detected on four linkage groups (LG01, LG07, LG15 and LG17), with two QTLs controlling the number of tubercles per plant and two others controlling necrosis. This study suggests that the resistance to O. cumana race F is controlled by several QTLs affecting differently the number of tubercle and the induction of tubercle necrosis. more...
- Published
- 2014
49. Bridging physiological and evolutionary time‐scales in a gene regulatory network
- Author
-
Marchand, Gwenaëlle, primary, Huynh‐Thu, Vân Anh, additional, Kane, Nolan C., additional, Arribat, Sandrine, additional, Varès, Didier, additional, Rengel, David, additional, Balzergue, Sandrine, additional, Rieseberg, Loren H., additional, Vincourt, Patrick, additional, Geurts, Pierre, additional, Vignes, Matthieu, additional, and Langlade, Nicolas B., additional more...
- Published
- 2014
- Full Text
- View/download PDF
50. Effect of recurrent selection on agronomic traits for several sunflower gene pools
- Author
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Griveau, Yves, Kaan, F., Serieys, Herve, Tersac, Michel, VINCOURT, Patrick, Varès, D., Bervillé, A., ProdInra, Migration, Unité de recherches de génétique et amélioration des plantes, and Institut National de la Recherche Agronomique (INRA) more...
- Subjects
[SDV] Life Sciences [q-bio] ,[SDV]Life Sciences [q-bio] ,POOL DE GENES ,GENETIQUE ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 1999
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