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The popularization of sequencing technologies in the past twenty years led to a high increase of the number of sequenced genomes. The diversity of the newly sequenced reference genomes highlighted the biases of using a single reference, which is not enough to access all the diversity within a species. There are many examples of intraspecific variations within plants, including presence / absence and copy number variations. These variations can have a strong effect on plant phenotypes, as exemplified by the African rice in which the presence of the gene Sub1A is linked to drought tolerance. The concept of pangenome appeared to better integrate these variations within genomics approaches. A pangenome can be built from genes only or from any genomic fragments found within a group, and is useful to compare their distributions between multiple individuals. Depending on the presence rate, many categories of elements can be defined; the main ones are the elements present in all the individuals (part of the ‘core’ genome) and these absent in at least one of them (part of the ‘variable’ genome). Pangenomics still lacks tools, especially for visualization. This is particularly true for eukaryotes (including plants) which have larger and more complex genomes than bacteria. Pangenomes were first built for bacteria, but their related tools cannot properly work on bigger genomes. My PhD investigated the creation of novel visual representations and tools for the visualization of plant pangenomes (and eukaryotes in general).Within this dissertation, I introduce the state of the art of pangenome visualization: I distinguish pan-gene from pangenomes, the latter often being represented by pangenome graphs where each sequence is a node and each observed sequence succession forms an edge; I also identify unspecific, qualifying, positioned, structural and composite visualization tools. The first chapter introduce ten principles for creating a genomic visualization tool, for future biology or bioinformatics scientists interested in datavisualization. The second chapter describes my first pangenome visualization, published in the journal Bioinformatics under the name ‘Panache: a Web Browser-Based Viewer for Linearized Pangenomes’. I detail the visual representation used within Panache and the creation of the resulting web application built in JavaScript, enabling the dynamic exploration of pangenomic data. The third and final chapter details the design of a composite visualization tools for pangenomes, called SaVanache, and enabling the navigation between four view scales. There are four of them: one for global diversity, one for structural variations, one for the presence / absence variations, and one for nucleotide variations. I propose a new approach for the annotation and visual representation of structural variations within a pangenome graph, based on a pivot path within the graph used as a reference coordinate system.; La démocratisation des technologies de séquençage lors des vingt dernières années a entraîné une explosion du nombre de génomes séquencés. La diversité des génomes de référence ainsi disponible a mis en évidence les biais induits par l’utilisation d’une unique référence, qui n’est pas suffisante pour donner accès à la diversité au sein d’une espèce. Chez les plantes, de nombreux exemples de variations intraspécifiques ont été recensés, notamment de la variation en présence / absence ou en nombre de copies de gènes. Ces variations peuvent exercer une forte influence sur le phénotype des plantes, par exemple chez le riz où la présence d’un gène Sub1A est associée à une tolérance à l’inondation. Pour une meilleure intégration de ces variations en génomique, le concept de pangénome s’est progressivement développé. Un pangénome peut être construit aussi bien pour recenser des gènes que pour tous types de fragments génomiques présents au sein d’un groupe, et est utile pour comparer la répartition de ces éléments entre plusieurs individus. Plusieurs catégories d’éléments existent selon le taux de présence ; les deux principales recensent les éléments présents chez tous les individus (les éléments ‘core’) et ceux présents seulement chez certains (les éléments ‘variable’). La pangénomique souffre encore d’un manque d’outils, notamment pour sa visualisation. Ce manque est particulièrement vrai pour les eucaryotes (dont les plantes), aux génomes plus gros et complexes que les bactéries, premier domaine d’application des pangénomes et dont les outils existants ne supportent pas facilement le passage à l’échelle vers des génomes plus volumineux. Mes travaux de thèse ont donc porté sur la création de nouvelles représentations visuelles ainsi que la création d’outils de visualisation utilisables pour la visualisation de pangénomes de plantes, et d’eucaryotes en général.Dans ce manuscrit de thèse, je présente l’état de l’art de la pangénomique : j’y fais la distinction entre la notion de pan-gene atlas et de pangénome, le second étant souvent représenté sous la forme d’un graphe où chaque séquence forme un noeud et chaque succession observée de séquence forme des liens entre ces noeuds ; j’identifie également des outils de visualisation non spécifiques, qualitatifs, positionnés, structuraux, et enfin composites. Le premier chapitre recueille dix conseils pour créer un outil de visualisation de données génomiques, à l’attention de futurs chercheu·r·se·s en biologie ou bio-informatique qui s’intéresseraient à la data visualisation. Le second chapitre, décrit mon premier outil de visualisation de pangénome, publié dans le journal Bioinformatics sous le titre « Panache : a Web Browser-Based Viewer for Linearized Pangenomes ». J’y détaille la représentation visuelle utilisée dans Panache, jusqu’à la création d’une application web développée en JavaScript permettant l’exploration dynamique de données pangénomiques. Le troisième et dernier chapitre détaille le travail de conception d’un outil composite de visualisation de pangénomes, appelé SaVanache, permettant la navigation entre plusieurs niveaux d’échelle pangénomique. Quatre vues ont été identifiées : une vue de la diversité globale ; une vue des variations structurales ; une vue dédiée à la variation en présence / absence ; et une dernière vue dédiée au variations nucléotidiques. Je propose une nouvelle approche pour l’annotation et la représentation visuelle de variations structurelles au sein d’un graphe de pangénome, axée autour de la définition d’un chemin pivot servant de système de coordonnées principal.

The evolution of resistance to pesticides is a major economic and environmental burden in agriculture. Resistance management involves maximizing selection pressure heterogeneity, particularly by combining active ingredients (AIs) with different modes of action. Yet, there is still no consensus on the best strategy to delay the emergence and selection of resistance in pathogen populations. Here, we aimed at contributing to this debate while addressing two questions: (i) How can we enhance the performance of anti-resistance strategies and what are the drivers of their optimization? (ii) How the initial status of resistance in populations modulates the performance of strategies? We used Zymoseptoria tritici, the causal agent of the major wheat disease, which is resistant in Europe to most fungicides to varying degrees, to exemplify this debate. We applied an innovative approach for fungi, experimental evolution, to mimic and accelerate, in laboratory-controlled conditions, fungicide resistance usually occurring in the field. In particular, we disentangled the relative impact in reducing resistance selection of multiple drivers of alternation, mixture and dose modulation strategies by submitting a susceptible strain to heterogeneous selection regimes as compared to the single use of the same AIs. In a first experiment, alternation was found a beneficial or neutral strategy to decrease the rate of evolution of resistance, relative to continuous fungicide use, but resulted in higher levels of generalism. We demonstrated that the relative intrinsic resistance risk of AI probably underpinned such trade-off, more than the number of fungicides used or alternation frequency. In a second experiment, we dissected how an efficient-dose mixture, i.e. a mixture with reduced doses of its components but still allowing a disease control similar to that provided by these components used alone, may delay resistance evolution of a naïve population. We concluded that the durability of such mixtures was detrimental to beneficial, strongly depending on its components. Such mixtures possibly favoured generalist or multiple resistance patterns, depending on the combined AIs. Dose reduction in sequence strategies didn’t prevent the selection of highly resistant specialist strains, nor of generalist resistance in some lines. A final experiment was designed to validate the previous findings, while submitting a susceptible isolate and two artificial populations containing low frequencies of single vs. multiple field resistances to selection regimes displaying patterns differing for four possible sources of heterogeneity. Preliminary results concluded that increasing the number of AIs and varying their modes of actions were efficient to delay resistance build-up, either in mixture or alternation regimes, although it facilitated the selection of some generalism in addition to the initially introduced specialist resistances. However, none of these sources of heterogeneity were found efficient at mitigating resistance evolution when multiple resistance was introduced in populations, suggesting that recombination, occurring during sexual reproduction in field populations, should be considered for fungicide sustainability management. At last, fitness cost associated to some resistance alleles shortly delayed resistance evolution and may reshaped population structure in some situations. Experimental evolution has proven to be a powerful tool to enrich the debate on anti-resistance strategies whilst dissecting the interplay between their drivers in realistic biological conditions. These findings open up new possibilities for tailoring resistance management and suggest that the prevention of resistance emergence would be more sustainable than the mitigation of selection.; La résistance aux pesticides impacte économiquement la production agricole et la biodiversité. Sa gestion implique de maximiser l'hétérogénéité des pressions de sélection, notamment en combinant des substances actives (SA) de modes d'action différents. Or, le débat concernant l’efficacité des différentes stratégies pour retarder l'émergence et la sélection de la résistance dans les populations pathogènes reste ouvert. Cette thèse aborde deux questions : (i) Comment améliorer la performance des stratégies anti-résistance et quels sont les facteurs permettant leur optimisation ? (ii) Comment le statut initial de la résistance dans les populations module-t-il la performance des stratégies ? Pour illustrer ce débat, nous avons utilisé Zymoseptoria tritici, agent causal de la principale maladie du blé, résistant à la plupart des fongicides en Europe. Nous avons appliqué une approche innovante pour les champignons, l'évolution expérimentale, qui permet d’imiter et d’accélérer, en conditions contrôlées de laboratoire, la résistance aux fongicides habituellement sélectionnée au champ. En particulier, en soumettant un isolat sensible à des régimes de sélection hétérogènes par comparaison avec l'utilisation en séquence des mêmes SA, nous avons dissocié l'impact relatif de plusieurs facteurs sur la réduction de la sélection au sein de stratégies d'alternance, de mélange et de modulation de dose. Dans une première expérimentation, l'alternance s'est avérée être une stratégie bénéfique ou neutre pour diminuer le taux d'évolution de la résistance par rapport à une utilisation continue, mais a favorisé du généralisme. Nous avons démontré que ce compromis résidait probablement dans le risque de résistance intrinsèque des SA, plutôt que dans le nombre de fongicides utilisés ou le rythme de l'alternance. Dans une deuxième expérimentation, nous avons exploré comment un mélange à dose efficace, c'est-à-dire un mélange avec des doses réduites de ses composants permettant un contrôle de la maladie similaire à celui fourni par ses composants utilisés seuls, peut retarder l'évolution de la résistance d'une population sensible. Nous avons conclu qu’un tel mélange pouvait être, selon ses composants, préjudiciable à bénéfique pour la durabilité. Des résistances généralistes ou multiples ont plus ou moins été favorisées en fonction des combinaisons de SA. La réduction de la dose dans des séquences n'a pas empêché la sélection de souches spécifiques fortement résistantes, ni la résistance généraliste dans certaines lignées. Une dernière expérimentation a été conçue pour valider les résultats précédents en soumettant un isolat sensible et deux populations artificielles, contenant de faibles fréquences de résistances simples ou multiples, à des régimes de sélection contrastés par quatre sources d'hétérogénéité. Les résultats ont conclu que l'augmentation du nombre de SA et la variation des modes d'action étaient efficaces pour retarder la sélection de la résistance, que ce soit en mélange ou alternance. Toutefois cela faciliterait un certain généralisme des isolats sélectionnés, en plus des résistances spécifiques initialement introduites. Aussi, aucune de ces sources d'hétérogénéité ne s'est avérée efficace pour atténuer l'évolution de la résistance lorsque la résistance multiple était présente dans les populations. Cela suggère que la recombinaison, pouvant survenir lors de la reproduction sexuée au champ, est un facteur majeur à considérer. Enfin, la réduction de la valeur sélective associée à certains allèles résistants retarde légèrement leur sélection et peut moduler la structure des populations. L'évolution expérimentale s'avère être un outil puissant pour enrichir le débat sur les stratégies de lutte en analysant les interactions entre ses déterminants. Ces résultats ouvrent de nouvelles perspectives pour optimiser la gestion des résistances et suggèrent que la prévention de l'émergence serait plus durable que de limiter la sélection.

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The objective of the RIFA Ageris® study, realised during 3 years, is to measure the impact of new crops management practices on the risk of pesticides water contamination by run-off and soil‘s erosion in a small bananas watershed in Martinique. The implementation of a hydrologic and water sampling station at the main exit of the watershed gave the opportunity to compare the flow of pesticide‘s activ ingredients used in the field, before and after practices changes. Results show a real benefit of implementation of cover plants between the rows. Herbicides and fungicides water contamination have been decreased. This can be mostly explained by run off decrease rather than erosion‘s decrease in the context of this study.; Le projet Agéris RIFA conduit sur trois années a consisté à mesurer l’impact des changements de pratiques culturales sur les risques d’entraînement de produits phytosanitaires par ruissellement et érosion au sein d’un petit bassin-versant bananier martiniquais. Les mesures présentées ici portent sur l’année de référence et l’année suivant l’implantation de plantes de couverture (petit mouron), sur une partie des deux pentes du bassin versant et l’arrêt quasi total du désherbage à proximité de la ravine. L‘installation d’une station hydrologique et de prélèvement d’échantillons d’eau à l’exutoire du bassin versant a permis de suivre et d’évaluer les teneurs en substances actives présentes dans l’eau brute à l’exutoire et d’ évaluer les flux de substances actives utilisées sur l’exploitation avant et après aménagement et changements de pratiques. Les résultats montrent un réel intérêt des plantes de couverture sur la diminution des pics de pollution et la réduction très nette des transferts vers l’eau de substances actives herbicides sans que ceci ne puisse être lié à la réduction de phénomènes érosifs mais plutôt à une diminution du ruissellement. Pour les fongicides, il a été montré que les plantes de couverture ont fortement contribué à faire baisser les transferts. En effet, le flux exporté a été divisé par 3 alors que la dose de triazoles totale apportée a été multipliée par près de 2 du fait des modifications du programme fongicides consécutif au changement de pratiques (passage d’une organisation aérienne planifiée à des traitements au sol gérés par l’exploitant). Du point de vue économique, il apparaît, dans le contexte de cette exploitation, une surcharge importante, hors coût d’implantation. Elle est principalement liée aux coûts élevés du maintien d’un état satisfaisant de la culture de couverture implantée dans le contexte pédoclimatique de cette exploitation.

International audience; Understanding meiotic crossover (CO) variation in crops like bread wheat (Triticum aestivum L.) is necessary as COs are essential to create new, original and powerful combinations of genes for traits of agronomical interest. We cytogenetically characterized a set of wheat aneuploid lines missing part or all of chromosome 3B to identify the most influential regions for chiasma formation located on this chromosome. We showed that deletion of the short arm did not change the total number of chiasmata genome-wide, whereas this latter was reduced by ~35% while deleting the long arm. Contrary to what was hypothesized in a previous study, deletion of the long arm does not disturb the initiation of the synaptonemal complex (SC) in early meiotic stages. However, progression of the SC is abnormal, and we never observed its completion when the long arm is deleted. By studying six different deletion lines (missing different parts of the long arm), we revealed that at least two genes located in both the proximal (C-3BL2-0.22) and distal (3BL7-0.63-1.00) deletion bins are involved in the control of chiasmata, each deletion reducing the number of chiasmata by ~15%. We combined sequence analyses of deletion bins with RNA-Seq data derived from meiotic tissues and identified a set of genes for which at least the homoeologous copy on chromosome 3B is expressed and which are involved in DNA processing. Among these genes, eight (CAP-E1/E2, DUO1, MLH1, MPK4, MUS81, RTEL1, SYN4, ZIP4) are known to be involved in the recombination pathway.

International audience; In their natural environment, plants are exposed to biotic or abiotic stresses that occur sequentially or simultaneously. Plant responses to these stresses have been studied widely and have been well characterised in simplified systems involving single plant species facing individual stress. Temperature elevation is a major abiotic driver of climate change and scenarios have predicted an increase in the number and severity of epidemics. In this context, here we review the available data on the effect of heat stress on plant-pathogen interactions. Considering 45 studies performed on model or crop species, we discuss the possible implications of the optimum growth temperature of plant hosts and pathogens, mode of stress application and temperature variation on resistance modulations. Alarmingly, most identified resistances are altered under temperature elevation, regardless of the plant and pathogen species. Therefore, we have listed current knowledge on heat-dependent plant immune mechanisms and pathogen thermosensory processes, mainly studied in animals and human pathogens, that could help to understand the outcome of plant-pathogen interactions under elevated temperatures. Based on a general overview of the mechanisms involved in plant responses to pathogens, and integrating multiple interactions with the biotic environment, we provide recommendations to optimise plant disease resistance under heat stress and to identify thermotolerant resistance mechanisms.

Comparative genomics is the analysis of genomic relationships among different species and serves as a significant base for evolutionary and functional genomic studies. GreenPhylDB (https://www.greenphyl.org) is a database designed to facilitate the exploration of gene families and homologous relationships among plant genomes, including staple crops critically important for global food security. GreenPhylDB is available since 2007, after the release of the Arabidopsis thaliana and Oryza sativa genomes and has undergone multiple releases. With the number of plant genomes currently available, it becomes challenging to select a single reference for comparative genomics studies but there is still a lack of databases taking advantage several genomes by species for orthology detection. GreenPhylDBv5 introduces the concept of comparative pangenomics by harnessing multiple genome sequences by species. We created 19 pangenes and processed them with other species still relying on one genome. In total, 46 plant species were considered to build gene families and predict their homologous relationships through phylogenetic-based analyses. In addition, since the previous publication, we rejuvenated the website and included a new set of original tools including protein-domain combination, tree topologies searches and a section for users to store their own results in order to support community curation efforts.

International audience; Pesticide resistance poses a critical threat to agriculture, human health and biodiversity. Mixtures of fungicides are recommended and widely used in resistance management strategies. However, the components of the efficiency of such mixtures remain unclear. We performed an experimental evolutionary study on the fungal pathogen Z. tritici to determine how mixtures managed resistance. We compared the effect of the continuous use of single active ingredients to that of mixtures, at the minimal dose providing full control of the disease, which we refer to as the “efficient” dose. We found that the performance of efficient-dose mixtures against an initially susceptible population depended strongly on the components of the mixture. Such mixtures were either as durable as the best mixture component used alone, or worse than all components used alone. Moreover, efficient dose mixture regimes probably select for generalist resistance profiles as a result of the combination of selection pressures exerted by the various components and their lower doses. Our results indicate that mixtures should not be considered a universal strategy. Experimental evaluations of specificities for the pathogens targeted, their interactions with fungicides and the interactions between fungicides are crucial for the design of sustainable resistance management strategies.

Simple Summary To meet the challenge of feeding almost 10 billion people by 2050, wheat yield has to double by 2050. However, over the past 20 years, yield increase has slowed down and even stagnated in the main producing countries. Similar to what has been observed in maize, hybrids have been suggested as a solution to overcome yield stagnation in wheat. However, wheat heterosis, i.e., the fact that a progeny surpasses the performances of its parents, is still limited and poorly understood. To better characterize this phenomenon, we developed and phenotyped for physiological and agronomic traits 91 hybrids and their nineteen female and sixteen male parents. We showed that hybrids had a longer grain filling phase that led to bigger grains and an increased thousand kernel weight. This resulted in a better yield for 86% of hybrids compared to the average yield of their parents. In addition, hybrids appeared to be less affected by the negative correlation between protein content and yield compared to pure lines. These results shed light on the physiological bases underlying yield heterosis in wheat, paving new ways to breed for better wheat hybrids that can help to meet agriculture’s challenges. Abstract To meet the challenge of feeding almost 10 billion people by 2050, wheat yield has to double by 2050. However, over the past 20 years, yield increase has slowed down and even stagnated in the main producing countries. Following the example of maize, hybrids have been suggested as a solution to overcome yield stagnation in wheat. However, wheat heterosis is still limited and poorly understood. Gaining a better understanding of hybrid vigor holds the key to breed for better varieties. To this aim, we have developed and phenotyped for physiological and agronomic traits an incomplete factorial design consisting of 91 hybrids and their nineteen female and sixteen male parents. Monitoring the plant development with normalized difference vegetation index revealed that 89% of the hybrids including the five higher yielding hybrids had a longer grain filling phase with a delayed senescence that results in larger grain size. This average increase of 7.7% in thousand kernel weight translated to a positive mid-parent heterosis for grain yield for 86% of hybrids. In addition, hybrids displayed a positive grain protein deviation leading to a +4.7% heterosis in protein yield. These results shed light on the physiological bases underlying yield heterosis in wheat, paving new ways to breed for better wheat hybrids.

International audience; Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a "protracted period" of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available.

Tocochromanols constitute the different forms of vitamin E (VTE), essential components of the human diet, and display a high membrane protectant activity. By combining interval mapping and genome-wide association studies (GWAS), we unveiled the genetic determinants of tocochromanol accumulation in tomato (Solanum lycopersicum) fruits. To enhance the nutritional value of this highly consumed vegetable, we dissected the natural intraspecific variability of tocochromanols in tomato fruits and genetically engineered their biosynthetic pathway. These analyses allowed the identification of a total of 25 quantitative trait loci interspersed across the genome pinpointing the chorismate–tyrosine pathway as a regulatory hub controlling the supply of the aromatic head group for tocochromanol biosynthesis. To validate the link between the chorismate–tyrosine pathway and VTE, we engineered tomato plants to bypass the pathway at the arogenate branch point. Transgenic tomatoes showed moderate increments in tocopherols (up to approximately 20%) and a massive accumulation of tocotrienols (up to approximately 3400%). Gene expression analyses of these plants reveal a trade-off between VTE and natural variation in chorismate metabolism explained by transcriptional reprogramming of specific structural genes of the pathway. By restoring the accumulation of alpha-tocotrienols (α-t3) in fruits, the plants produced here are of high pharmacological and nutritional interest. Fil: Burgos, Estanislao. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: de Luca, Maria Belén. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Diouf, Isidore. Centre Nouvelle - Aquitaine Bordeaux ; Instituto National de Recherches Agronomiques, Alimetation Et Environnement; Fil: de Haro, Luis Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Albert, Elise. Michigan State University; Estados Unidos. Centre Nouvelle - Aquitaine Bordeaux ; Instituto National de Recherches Agronomiques, Alimetation Et Environnement; Fil: Sauvage, Christopher. Centre Nouvelle - Aquitaine Bordeaux ; Instituto National de Recherches Agronomiques, Alimetation Et Environnement; . Syngenta France SAS; Francia Fil: Tao, Zhao J.. Centre Nouvelle - Aquitaine Bordeaux ; Instituto National de Recherches Agronomiques, Alimetation Et Environnement; Fil: Bermudez Salazar, Luisa Fernanda. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina. Universidad de Buenos Aires. Facultad de Agronomía; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Asís, Ramon. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; Argentina Fil: Nesi, Adriano N.. Universidade Federal de Viçosa.; Brasil Fil: Matringe, Michel. Universite Joseph Fourier; Francia. Centre Nouvelle - Aquitaine Bordeaux ; Instituto National de Recherches Agronomiques, Alimetation Et Environnement; Fil: Bréhélin, Claire. Universite Joseph Fourier; Francia. Centre Nouvelle - Aquitaine Bordeaux ; Instituto National de Recherches Agronomiques, Alimetation Et Environnement; Fil: Guiraud, Thomas. Universite de Bordeaux; Francia. Centre Nouvelle - Aquitaine Bordeaux ; Instituto National de Recherches Agronomiques, Alimetation Et Environnement; Fil: Ferrand, Carine. Universite de Bordeaux; Francia. Centre Nouvelle - Aquitaine Bordeaux ; Instituto National de Recherches Agronomiques, Alimetation Et Environnement; Fil: Atienza, Isabelle. Universite de Bordeaux; Francia. Centre Nouvelle - Aquitaine Bordeaux ; Instituto National de Recherches Agronomiques, Alimetation Et Environnement; Fil: Jorly, Joana. Universite de Bordeaux; Francia. Centre Nouvelle - Aquitaine Bordeaux ; Instituto National de Recherches Agronomiques, Alimetation Et Environnement; Fil: Mauxion, Jean P.. Universite de Bordeaux; Francia. Centre Nouvelle - Aquitaine Bordeaux ; Instituto National de Recherches Agronomiques, Alimetation Et Environnement; Fil: Baldet, Pierre. Centre Nouvelle - Aquitaine Bordeaux ; Instituto National de Recherches Agronomiques, Alimetation Et Environnement; . Universite de Bordeaux; Francia Fil: Fernie, Alisdair R.. Institut Max Planck fur Molekulare Physiologie; Alemania Fil: Quadrana, Leandro. Inserm; Francia. Centre National de la Recherche Scientifique; Francia Fil: Rothan, Christophe. Universite de Bordeaux; Francia. Centre Nouvelle - Aquitaine Bordeaux ; Instituto National de Recherches Agronomiques, Alimetation Et Environnement; Fil: Causse, Mathilde. Centre Nouvelle - Aquitaine Bordeaux ; Instituto National de Recherches Agronomiques, Alimetation Et Environnement; Fil: Carrari, Fernando Oscar. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina. Universidad de Buenos Aires; Argentina

International audience; Three viruses transmitted by aphids (non-persistent transmission) are responsible of strong yield losses on squash crops in France and around the world: Cucumber mosaic virus (CMV), Zucchini yellow mosaic virus (ZYMV) and Watermelon mosaic virus (WMV). For each virus, different biological, serological and molecular groups were described. The resistance is polygenic for CMV, ZYMV and with a major gene for WMV but always with an intermediate resistance.The evaluation of squash resistance to viruses and the assessment of symptoms are complex due to the partial and not complete resistance and the quantitative results observed. It is important to describe the different levels of virulence of virus strains and to identify the different levels of resistance of squash varieties. There are currently no harmonized protocols to define the levels of partial resistance of squash to these viruses.The aim of this project, in collaboration between GEVES, INRAE and breeding companies (HMClause, Gautier, Monsanto, Rijk Zwaan, Sakata, Syngenta) was to acquire a better knowledge of levels of squash resistance and to define robust resistance tests to these viruses. Based on the INRAE’s characterized collection of strains of viruses, three strains per virus (with different virulences and from different groups) were selected. These strains and different protocols from INRAE and partners (stage of inoculation, optimal conditions of test, notation scale) were compared, on a panel of commercial varieties with different levels of resistance, to define for each virus a robust resistance test.One strain per virus, making it possible to differentiate the different levels of resistance of varieties, was selected. For each virus, a resistance test and reference materials (strain and controls) were validated. The reference collection of GEVES was characterized for the three viruses. These new protocols, used for CTPS registration, will be proposed to CPVO and UPOV for a harmonized use.; Trois virus transmis par les pucerons selon le mode non-persistant sont responsables d’importantes pertes de récolte dans les cultures de courgette en France et dans le monde : les Cucumber mosaic virus (CMV), Zucchini yellow mosaic virus (ZYMV) et Watermelon mosaic virus (WMV)L’évaluation de la résistance de la courgette aux virus est complexe du fait du caractère partiel (ou non complet) de la résistance et des résultats quantitatifs observés. Il est important d’identifier les différents niveaux de résistance des variétés de courgette à ces virus, et de décrire les niveaux d’agressivité des souches permettant de mieux différencier les variétés. Actuellement, il n’existe pas de protocole harmonisé pour définir les différents niveaux de résistance partielle de la courgette à ces virus.Le but de ce projet collaboratif entre le GEVES, l’INRAE et des sociétés semencières (HMClause, Gautier, Monsanto, Rijk Zwaan, Sakata, Syngenta) était d’acquérir de meilleures connaissances des niveaux de résistance de la courgette et de définir un protocole de test robuste pour ces virus. Basée sur la collection de souches de virus caractérisée par INRAE, trois souches par virus (avec différentes agressivités et appartenant à différents groupes) ont été sélectionnées. Ces souches et les différents protocoles de INRAE et des partenaires (stade d’inoculation, conditions optimales de test, échelle de notation) ont été comparées sur un panel composé de variétés commerciales avec différents niveaux de résistance afin de définir pour chaque virus un test de résistance robuste.Une souche, permettant de différencier les différents niveaux de résistance des variétés, a été sélectionnée par virus. Pour chaque virus, un test de résistance et le matériel de référence (souches et témoins) ont été validés. La collection de référence du GEVES a été caractérisée pour les trois virus. Ces nouveaux protocoles, utilisés pour les

Il est important d’étudier la sécrétion nectarifère des plantes entomophiles, c’est-à-dire pollinisées par les insectes, car plus une culture sécrète de nectar floral, plus elle est visitée par les insectes pollinisateurs. C’est le cas du tournesol de consommation, pour lequel il faut la visite, en moyenne, d’une abeille pour cinq capitules pour atteindre le potentiel maximum de rendement. Ces cultures doivent donc être suffisamment attractives pour attirer assez d’insectes afin que les rendements ne soient pas limités par un déficit de pollinisation.Cultivé pour la production d’huile alimentaire ou de diester, le tournesol est aussi très recherché par les apiculteurs comme plante mellifère. Différents facteurs sont avancés pour expliquer la tendance à la baisse de production de miel de tournesol observée en France depuis trente ans : une baisse des surfaces en tournesol, qui ont été divisées par près de deux entre les années 1980-1990 et 2000, des conditions climatiques défavorables à la nectarification et au butinage des insectes, mais aussi une faible attractivité des variétés récentes. La profession apicole suspecte en effet les nouvelles variétés de tournesol de produire moins de nectar que celles plus anciennes. Malheureusement, aucune donnée officielle n’est disponible pour étayer ces observations. C’est pourquoi cette étude a examiné les effets variétaux et météorologiques, en mesurant la sécrétion nectarifère de trente-quatre variétés actuelles de tournesol.

The sunflower crop provides an important honey flow for beekeepers. In France, beekeepers observed a decrease in honey yield from this crop these past years compared to the 1980s–1990s. They suspect the new cultivars to be less productive in nectar compared to the older ones, but no data is available to support this, and it is known that climate conditions have a strong impact on nectar secretion. This study aimed to explore the effect of abiotic environmental conditions on nectar secretion in sunflower, as well the range of variation of this secretion in a sample of current cultivars. Thirty-four current sunflower hybrid cultivars were sampled in test plots for their nectar secretion under varying conditions of temperature, air humidity and soil moisture. Air humidity controlled the sugar concentration of nectar, and thus its volume. To study nectar secretion independently from this effect, analyses subsequently focused on nectar sugar mass per floret. The nectar sugar mass increased with temperature up to an optimum of 32 °C, while the variation range of soil water tension was not sufficient to detect an effect on nectar sugar mass. This varied by up to 100% among the 34 cultivars (from 101 to 216 mg sugar per staminate floret in average), with a similar range to those reported in the literature for older cultivars. Likewise, oleic cultivars, a new type introduced since the early 2000s, were found to secrete the same amounts of nectar as linoleic cultivars, an older conventional type. The more self-fertile cultivars also showed no reduction in nectar secretion. Finally, we tested the method that measures the nectar gross secretion rate in one hybrid, and we observed that this hybrid secreted in average 28 mg sugar per hour per staminate floret. The potential benefits of this method were discussed.; Le tournesol constitue une miellée importante pour les apiculteurs. En France, les apiculteurs ont constaté des baisses de miellées sur cette culture ces dernières années par rapport aux années 1980–1990. Ils suspectent les nouvelles variétés d’être moins nectarifères que les plus anciennes, mais aucune donnée ne permet de l’établir, et l’on sait que les conditions climatiques ont un fort impact sur la sécrétion de nectar. Cette étude avait pour objectif d’explorer l’effet des conditions environnementales abiotiques sur la sécrétion de nectar chez le tournesol, ainsi que la gamme de variation de cette sécrétion sur un échantillon de variétés courantes. Trente-quatre variétés hybrides actuelles de tournesol ont été échantillonnées dans des micro-parcelles pour leur sécrétion nectarifère dans des conditions variables de température et d’humidité de l’air et du sol. L’humidité de l’air contrôlait la concentration du nectar et donc son volume. Pour s’affranchir de cet effet, l’analyse a porté ensuite sur la masse de sucres sécrétée par fleuron. Cette masse de sucres a augmenté avec la température jusqu’à un optimum de 32 °C, tandis que la gamme de variation de la tension hydrique du sol n’a pas été suffisamment importante pour observer une diminution de la masse de sucres par fleuron. Cette masse de sucres a varié du simple au double parmi lestrente-quatre variétés étudiées (de 101 à 216 mg de sucres par fleuron staminé en moyenne), mais la gamme de variation observée n’était pas différente de celles rapportées dans la littérature pour des variétés plus anciennes. De même, les variétés oléiques, type nouveau introduit depuis le début des années 2000, ne se sont pas révélées moins nectarifères que le type linoléique conventionnel, plus ancien. Les variétés plus auto-fertiles n’étaient pas non plus moins nectarifères. Enfin, nous avons testé la méthode qui mesure le taux de sécrétion brut du nectar sur un hybride, et nous avons observé que cet hybride sécrétait en moyenne 28 mg de sucres par heure par fleuron staminé. Les potentiels avantages de cette méthode ont été discutés.

Plant metabolites are important to world food security due to their roles in crop yield and nutritional quality. Here we report the metabolic profile of 300 tomato accessions (Solanum lycopersicum and related wild species) by quantifying 60 primary and secondary metabolites, including volatile organic compounds, over a period of 2 yr. Metabolite content and genetic inheritance of metabolites varied broadly, both within and between different genetic groups. Using genotype information gained from 10 000 single nucleotide polymorphism markers, we performed a metabolite genome-wide association mapping (GWAS) study. We identified 79 associations influencing 13 primary and 19 secondary metabolites with large effects at high resolution. Four genome regions were detected, highlighting clusters of associations controlling the variation of several metabolites. Local linkage disequilibrium analysis and allele mining identified possible candidate genes which may modulate the content of metabolites that are of significant importance for human diet and fruit consumption. We precisely characterized two associations involved in fruit acidity and phenylpropanoid volatile production. Taken together, this study reveals complex and distinct metabolite regulation in tomato subspecies and demonstrates that GWAS is a powerful tool for gene-metabolite annotation and identification, pathways elucidation, and further crop improvement.

National audience

National audience; Contexte - La pollinisation entomophile est régulièrement citée comme un facteur contribuant au rendement et à la qualité des graines du tournesol. Mais si l'apport des abeilles mellifères a été estimé comme essentiel en tournesol semences, son impact sur le rendement du tournesol de consommation est considéré comme modeste et variable. Etude - Un projet multipartenaire, mené conjointement par Syngenta, Agrosolutions, l'INRA et Arterris Innovation, permet de dresser un bilan de deux années d'expérimentation en conditions agriculteurs pour mesurer l'impact des insectes pollinisateurs sur les composantes du rendement de cette culture. Résultats - Les expérimentations illustrent l'intérêt économique de la pollinisation entomophile sur le tournesol de consommation. Dans la majorité des parcelles, le potentiel de rendement (nombre et masse de graines) est atteint dès 0.25 insectes par capitules, un seuil généralement dépassé naturellement. En deça de ce seuil, il peut être intéressant de réaliser des apports dans les parcelles qui ne sont pas 100% autofertiles.

Orobanche cumana (sunflower broomrape) is an obligate parasitic plant that infects sunflower roots, causing yield losses. Here, by using a map-based cloning strategy, we identified HaOr7—a gene that confers resistance to O. cumana race F—which was found to encode a leucine-rich repeat receptor-like kinase. The complete HAOR7 protein is present in resistant lines of sunflower and prevents O. cumana from connecting to the vascular system of sunflower roots, whereas susceptible lines encode a truncated protein that lacks transmembrane and kinase domains., This work was supported by INRA, Syngenta seeds and the French Laboratory of Excellence project TULIP (ANR-10-LABX-41; ANR-11-IDEX-0002-02).

The sunflower crop provides an important honey flow for beekeepers. In France, beekeepers observed a decrease in honey yield from this crop these past years compared to the 1980s–1990s. They suspect the new cultivars to be less productive in nectar compared to the older ones, but no data is available to support this, and it is known that climate conditions have a strong impact on nectar secretion. This study aimed to explore the effect of abiotic environmental conditions on nectar secretion in sunflower, as well the range of variation of this secretion in a sample of current cultivars. Thirty-four current sunflower hybrid cultivars were sampled in test plots for their nectar secretion under varying conditions of temperature, air humidity and soil moisture. Air humidity controlled the sugar concentration of nectar, and thus its volume. To study nectar secretion independently from this effect, analyses subsequently focused on nectar sugar mass per floret. The nectar sugar mass increased with temperature up to an optimum of 32 °C, while the variation range of soil water tension was not sufficient to detect an effect on nectar sugar mass. This varied by up to 100% among the 34 cultivars (from 101 to 216 mg sugar per staminate floret in average), with a similar range to those reported in the literature for older cultivars. Likewise, oleic cultivars, a new type introduced since the early 2000s, were found to secrete the same amounts of nectar as linoleic cultivars, an older conventional type. The more self-fertile cultivars also showed no reduction in nectar secretion. Finally, we tested the method that measures the nectar gross secretion rate in one hybrid, and we observed that this hybrid secreted in average 28 mg sugar per hour per staminate floret. The potential benefits of this method were discussed.; Le tournesol constitue une miellée importante pour les apiculteurs. En France, les apiculteurs ont constaté des baisses de miellées sur cette culture ces dernières années par rapport aux années 1980–1990. Ils suspectent les nouvelles variétés d’être moins nectarifères que les plus anciennes, mais aucune donnée ne permet de l’établir, et l’on sait que les conditions climatiques ont un fort impact sur la sécrétion de nectar. Cette étude avait pour objectif d’explorer l’effet des conditions environnementales abiotiques sur la sécrétion de nectar chez le tournesol, ainsi que la gamme de variation de cette sécrétion sur un échantillon de variétés courantes. Trente-quatre variétés hybrides actuelles de tournesol ont été échantillonnées dans des micro-parcelles pour leur sécrétion nectarifère dans des conditions variables de température et d’humidité de l’air et du sol. L’humidité de l’air contrôlait la concentration du nectar et donc son volume. Pour s’affranchir de cet effet, l’analyse a porté ensuite sur la masse de sucres sécrétée par fleuron. Cette masse de sucres a augmenté avec la température jusqu’à un optimum de 32 °C, tandis que la gamme de variation de la tension hydrique du sol n’a pas été suffisamment importante pour observer une diminution de la masse de sucres par fleuron. Cette masse de sucres a varié du simple au double parmi lestrente-quatre variétés étudiées (de 101 à 216 mg de sucres par fleuron staminé en moyenne), mais la gamme de variation observée n’était pas différente de celles rapportées dans la littérature pour des variétés plus anciennes. De même, les variétés oléiques, type nouveau introduit depuis le début des années 2000, ne se sont pas révélées moins nectarifères que le type linoléique conventionnel, plus ancien. Les variétés plus auto-fertiles n’étaient pas non plus moins nectarifères. Enfin, nous avons testé la méthode qui mesure le taux de sécrétion brut du nectar sur un hybride, et nous avons observé que cet hybride sécrétait en moyenne 28 mg de sucres par heure par fleuron staminé. Les potentiels avantages de cette méthode ont été discutés.

Multiparental designs combined with dense genotyping of parents have been proposed as a way to increase the diversity and resolution of quantitative trait loci (QTL) mapping studies, using methods combining linkage disequilibrium information with linkage analysis (LDLA). Two new nested association mapping designs adapted to European conditions were derived from the complementary dent and flint heterotic groups of maize (Zea mays L.). Ten biparental dent families (N = 841) and 11 biparental flint families (N = 811) were genotyped with 56,110 single nucleotide polymorphism markers and evaluated as test crosses with the central line of the reciprocal design for biomass yield, plant height, and precocity. Alleles at candidate QTL were defined as (i) parental alleles, (ii) haplotypic identity by descent, and (iii) single-marker groupings. Between five and 16 QTL were detected depending on the model, trait, and genetic group considered. In the flint design, a major QTL (R2 = 27%) with pleiotropic effects was detected on chromosome 10, whereas other QTL displayed milder effects (R2 < 10%). On average, the LDLA models detected more QTL but generally explained lower percentages of variance, consistent with the fact that most QTL display complex allelic series. Only 15% of the QTL were common to the two designs. A joint analysis of the two designs detected between 15 and 21 QTL for the five traits. Of these, between 27 for silking date and 41% for tasseling date were significant in both groups. Favorable allelic effects detected in both groups open perspectives for improving biomass production.

Key message We enhance power and accuracy of QTL mapping in multiple related families, by clustering the founders of the families on their local genomic similarity. Abstract MCQTL is a linkage mapping software application that allows the joint QTL mapping of multiple related families. In its current implementation, QTLs are modeled with one or two parameters for each parent that is a founder of the multi-cross design. The higher the number of parents, the higher the number of model parameters which can impact the power and the accuracy of the mapping. We propose to make use of the availability of denser and denser genotyping information on the founders to lessen the number of MCQTL parameters and thus boost the QTL discovery. We developed clusthaplo, an R package (http://cran.r-project.org/web/packages/clusthaplo/index.html), which aims to cluster haplotypes using a genomic similarity that reflects the probability of sharing the same ancestral allele. Computed in a sliding window along the genome and followed by a clustering method, the genomic similarity allows the local clustering of the parent haplotypes. Our assumption is that the haplotypes belonging to the same class transmit the same ancestral allele. So their putative QTL allelic effects can be modeled with the same parameter, leading to a parsimonious model, that is plugged in MCQTL. Intensive simulations using three maize data sets showed the significant gain in power and in accuracy of the QTL mapping with the ancestral allele model compared to the classical MCQTL model. MCQTL_LD (clusthaplo outputs plug in MCQTL) is a versatile and powerful tool for QTL mapping in multiple related families that makes use of linkage and linkage disequilibrium (web site http://carlit.toulouse.inra.fr/MCQTL/). Electronic supplementary material The online version of this article (doi:10.1007/s00122-014-2267-1) contains supplementary material, which is available to authorized users.

Tospovirus is the only member of the Bunyavirus family which infects plants (the other members infecting animals and humans). Tomato spotted wilt virus (TSWV), the most famous tospovirus, is a major pathogen for tomato and pepper cultures. Because there is no chemical treatment against viruses, the only way to fight them is to develop genetic resistance. Genetic resistances to tospoviruses are available, but are largely overcome. Therefore, there is an urgent need to characterize new sources of resistance. The aim of my PhD is to find new genetic resistances based on susceptibility factors, which are proteins required by the virus to accomplish its cycle and infect the plant. As a first step, I will develop a 3D model of the TSWV RNA-dependent RNA polymerase (RdRp), a key viral protein for its infectious cycle. Based on this model, a part of the RdRp protein will be selected as bait in order to identify plant protein interactors by yeast-two hybrid screening. Finally, I will search for new tomato alleles encoding variant forms of those tomato susceptibility factors. If those variants impair the interaction between the plant factor and the viral protein, those alleles are very likely to be associated with the crop resistance to the pathogen.

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., 12 pages, 5 figures, Plant, Cell and Environment

Honeybees (Apis mellifera) are constantly subjected to many biotic stressors including parasites. This study examined honeybees infected with Nosema ceranae (N. ceranae). N. = ceranae infection increases the bees energy requirements and may contribute to their decreased survival. RNA-seq was used to investigate gene expression at days 5, 10 and 15 Post Infection (P. I) with N. ceranae. The expression levels of genes, isoforms, alternative transcription start sites (TSS) and differential promoter usage revealed a complex pattern of transcriptional and post-transcriptional gene regulation suggesting that bees use a range of tactics to cope with the stress of N. ceranae infection. N. ceranae infection may cause reduced immune function in the bees by: (i) disturbing the host amino acids metabolism (ii) down-regulating expression of antimicrobial peptides (iii) down-regulation of cuticle coatings and (iv) down-regulation of odorant binding proteins.

Hybridization technology has proven valuable in enhancing yields in many crops, but was only recently adopted in the small grain cereals. Hybrid varieties in barley (Hordeum vulgare) rely on the cytoplasmic male sterility (CMS) system msm1 derived from Hordeum vulgare ssp. spontaneum. The major restorer gene described for the msm1 system is known as Rfm1 and maps to the top of chromosome 6H. To gain further insight into mechanisms underlying male fertility restoration in barley, we used a map-based cloning approach to identify the nuclear gene involved in the restoration mechanism of this hybridization system. Taking advantage of the available genomic resources in barley in combination with a custom-made non-gridded BAC library developed from a restorer line, we cloned and sequenced the Rfm1 restorer locus. The characterization and annotation of the nucleotide sequence for the Rfm1 restorer allele allowed for the identification of the candidate gene for Rfm1. The Rfm1 locus carries a tandem repeat of a gene encoding a pentatricopeptide repeat (PPR) protein. Surprisingly, Rfm1 belongs to the PLS-DYW subfamily of PPR genes known for their involvement in RNA editing in plants organelles, but that to date have not been identified as restorer genes.

National audience; La pollinisation entomophile du tournesol est souvent mentionnée comme un facteur contribuant au rendement et à la qualité de cette culture. Alors que les rendements stagnent depuis une trentaine d’années en France, l’amélioration de la pollinisation des tournesols de consommation constitue une piste pour les relancer en conditions agricoles. Notre étude visait à évaluer l’impact d’un front d’insectes pollinisateurs (colonies d’abeilles domestiques installées dans une bande fleurie disposée sur une bordure de parcelles agricoles longue de plus de 550m de long). Cet impact a été mesuré à différentes distances de ce front d’insectes pollinisateurs sur la fréquentation des capitules par les insectes floricoles, la charge en pollen des stigmates, le rendement et la teneur en huile des graines. Nous avons bien observé un gradient négatif d’activité des abeilles domestiques en fonction de l’éloignement au front de colonies et aussi une diminution du rendement et de la teneur en huile chez le tournesol. Nous présentons la méthodologie originale utilisée ainsi que les premiers résultats obtenus.

A panel of 300 tomato accessions including breeding materials was built and characterized with >11,000 SNP. A population structure in six subgroups was identified. Strong heterogeneity in linkage disequilibrium and recombination landscape among groups and chromosomes was shown. GWAS identified several associations for fruit weight, earliness and plant growth. Genome-wide association studies (GWAS) have become a method of choice in quantitative trait dissection. First limited to highly polymorphic and outcrossing species, it is now applied in horticultural crops, notably in tomato. Until now GWAS in tomato has been performed on panels of heirloom and wild accessions. Using modern breeding materials would be of direct interest for breeding purpose. To implement GWAS on a large panel of 300 tomato accessions including 168 breeding lines, this study assessed the genetic diversity and linkage disequilibrium decay and revealed the population structure and performed GWA experiment. Genetic diversity and population structure analyses were based on molecular markers (>11,000 SNP) covering the whole genome. Six genetic subgroups were revealed and associated to traits of agronomical interest, such as fruit weight and disease resistance. Estimates of linkage disequilibrium highlighted the heterogeneity of its decay among genetic subgroups. Haplotype definition allowed a fine characterization of the groups and their recombination landscape revealing the patterns of admixture along the genome. Selection footprints showed results in congruence with introgressions. Taken together, all these elements refined our knowledge of the genetic material included in this panel and allowed the identification of several associations for fruit weight, plant growth and earliness, deciphering the genetic architecture of these complex traits and identifying several new loci useful for tomato breeding.

International audience; In the context of climate change, an increased variability is expected in timing and amount of water available for crop production. For sunflower crop, yield losses of 10 to 30 % have been predicted at 2030 horizon in Europe. During the past 10 years, genetic progress was lower than expected to improve yield, which imposes to the sunflower community to re-invest current breeding resources and methodologies. To reach high and stable yields across a wide range of environments a French project of 8 years, named 'SUNRISE' (SUNflower Resources to Improve yield Stability in a changing Environment) and supported by the French National Research Agency, is gathering 9 public and 7 private partners since 2012. It associates several approaches: (i) the sequencing and genotyping of the genetic diversity among cultivated and wild sunflowers, (ii) the development of appropriate and high-throughput phenotyping strategies to characterize the molecular, physiological and agronomical responses to variation of the abiotic environment, (iii) the discovery through genome-wide association, linkage mapping and genomic selection of the genetic factors involved in those responses, (iv) the integration of this genetic knowledge into a crop mode! (SUNFLO) to test in silico G by E interactions and design promising ideotypes in future environments, and finally (v) the evaluation of the outputs for the breeding sector and the transfer ofknowledge to agriculture. This partnership will ensure that the developed knowledge, resources and methods will be translated into products and varieties supporting the adaptation of the agriculture to societal and ecological challenges.

It is generally admitted that durum wheat pasta quality is greatly influenced by both protein content and composition. Durum wheat crops need high nitrogen inputs to produce grains with protein content required by manufacturers. With increasing fertilizer price and facing new environmental constraints, farmers have to modify their practises. Modifying practices is not always sufficient to maintain a high yield level with acceptable protein content so the need to create cultivars with better nitrogen use efficiency becomes necessary. The objective of breeders is now to create new durum wheat cultivars able to grow up with limited nitrogen intake and to remobilize efficiently nitrogen from vegetative organs of the crop to grains during filling with the need to fulfil quality criteria required by pasta making industries. In this context a study was undertaken by French breeders in association with public research, development organizations and pasta manufacturers in order to define minimal requirements in terms of protein quantity and quality to produce pasta able to satisfy consumers. Eight cultivars were grown during two years in the south of France with nitrogen intakes varying from 0 to 360 units. At harvest, grain characteristics (thousand kernel weight, specific weight, yellow berry…) were determined. Protein content and composition measured by size exclusion-chromatography were also evaluated along with gluten index, SDS sedimentation test. Semolina were produced and used to make spaghetti and dough discs. Pasta quality was evaluated through different measurements (texture, color, smoothness and appearance, cooking losses…) before and after cooking. A statistical analysis was then performed and shown that it is possible to reduce nitrogen fertilization to some extent without affecting dramatically pasta quality. Data also provide useful information to reconsider tests used during breeding programs to predict the end use quality of durum wheats.

International audience; Transposable elements (TEs) account for more than 80% of the wheat genome. Although they represent a major obstacle for genomic studies, TEs are also a source of polymorphism and consequently of molecular markers such as insertion site-based polymorphism (ISBP) markers. Insertion site-based polymorphisms have been found to be a great source of genome-specific single-nucleotide polymorphism (SNPs) in the hexaploid wheat (Triticum aestivum L.) genome. Here, we report on the development of a high-throughput SNP discovery approach based on sequence capture of ISBP markers. By applying this approach to the reference sequence of chromosome 3B from hexaploid wheat, we designed 39,077 SNPs that are evenly distributed along the chromosome. We demonstrate that these SNPs can be efficiently scored with the KASPar (Kompetitive allele-specific polymerase chain reaction) genotyping technology. Finally, through genetic diversity and genome-wide association studies, we also demonstrate that ISBP-derived SNPs can be used in marker-assisted breeding programs.

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; International audience; Fruit firmness in tomato (Solanum lycopersicum) is determined by a number of factors including cell wall structure, turgor, and cuticle properties. Firmness is a complex polygenic trait involving the coregulation of many genes and has proved especially challenging to unravel. In this study, a quantitative trait locus (QTL) for fruit firmness was mapped to tomato chromosome 2 using the Zamir Solanum pennellii interspecific introgression lines (ILs) and fine-mapped in a population consisting of 7,500 F2 and F3 lines from IL 2-3 and IL 2-4. This firmness QTL contained five distinct subpeaks, Fir(s.p.)QTL2.1 to Fir(s.p.)QTL2.5, and an effect on a distal region of IL 2-4 that was nonoverlapping with IL 2-3. All these effects were located within an 8.6-Mb region. Using genetic markers, each subpeak within this combinatorial locus was mapped to a physical location within the genome, and an ethylene response factor (ERF) underlying Fir(s.p.)QTL2.2 and a region containing three pectin methylesterase (PME) genes underlying Fir(s.p.)QTL2.5 were nominated as QTL candidate genes. Statistical models used to explain the observed variability between lines indicated that these candidates and the nonoverlapping portion of IL 2-4 were sufficient to account for the majority of the fruit firmness effects. Quantitative reverse transcription-polymerase chain reaction was used to quantify the expression of each candidate gene. ERF showed increased expression associated with soft fruit texture in the mapping population. In contrast, PME expression was tightly linked with firm fruit texture. Analysis of a range of recombinant lines revealed evidence for an epistatic interaction that was associated with this combinatorial locus.

SPEEAGESTADAGROSUP; Membres du comité d’organisation scientifique et logistique. 23. Conférence du COLUMA - Journées Internationales sur la Lutte contre les Mauvaises Herbes

Caractérisation de génotypes maintenant une haute qualité technologique sous fertilisation réduite. Séminaire scientifique CTPS

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International audience

Environmental rules and fertilizer price increase have pushed farmers to reduce nitrogen fertilization applied to the durum wheat crops. In order to optimize nitrogen application, cultivation practices such as splitting were promoted. These practices are not always sufficient to maintain elevated yield and grain quality required by milling and pasta making processes. The need to create cultivars with better nitrogen use efficiency is essential. Currently, for cultivar registration in the French national list, varieties are not tested under reduced fertilization conditions and it appears difficult to detect those which have the capacity to better use nitrogen. The objective of breeders is now to create new durum wheat cultivars able to grow up with limited nitrogen intake and to remobilize efficiently nitrogen from vegetative organs of the crop to grains during filling with the need to fulfil quality criteria required by pasta making industries. To achieve this goal a study was carried by French breeders associated with public research, development organizations and industrials in order to define minimal requirements in terms of protein quantity and quality to produce pasta able to satisfy consumers. Eight cultivars were grown during two years in the south of France with nitrogen intakes varying from 0 to 360 units. At harvest, grain characteristics (thousand kernel weight, specific weight, yellow berry…) were recorded and milling value was assessed with a micromill. Protein composition measured by chromatography and content were also evaluated along with gluten index, SDS sedimentation, tenacity. Semolina were produced and used to make pasta on a pilot plant. Pasta quality was appraised by different tests before and after cooking. A statistical analysis was then performed and shown that it is possible to reduce nitrogen fertilization to some extent without affecting dramatically pasta quality. Data also provide information useful to reconsider registration tests.

[EN] Background: Domestication modifies the genomic variation of species. Quantifying this variation provides insights into the domestication process, facilitates the management of resources used by breeders and germplasm centers, and enables the design of experiments to associate traits with genes. We described and analyzed the genetic diversity of 1,008 tomato accessions including Solanum lycopersicum var. lycopersicum (SLL), S. lycopersicum var. cerasiforme (SLC), and S. pimpinellifolium (SP) that were genotyped using 7,720 SNPs. Additionally, we explored the allelic frequency of six loci affecting fruit weight and shape to infer patterns of selection. Results: Our results revealed a pattern of variation that strongly supported a two-step domestication process, occasional hybridization in the wild, and differentiation through human selection. These interpretations were consistent with the observed allele frequencies for the six loci affecting fruit weight and shape. Fruit weight was strongly selected in SLC in the Andean region of Ecuador and Northern Peru prior to the domestication of tomato in Mesoamerica. Alleles affecting fruit shape were differentially selected among SLL genetic subgroups. Our results also clarified the biological status of SLC. True SLC was phylogenetically positioned between SP and SLL and its fruit morphology was diverse. SLC and “cherry tomato” are not synonymous terms. The morphologically-based term “cherry tomato” included some SLC, contemporary varieties, as well as many admixtures between SP and SLL. Contemporary SLL showed a moderate increase in nucleotide diversity, when compared with vintage groups. Conclusions: This study presents a broad and detailed representation of the genomic variation in tomato. Tomato domestication seems to have followed a two step-process; a first domestication in South America and a second step in Mesoamerica. The distribution of fruit weight and shape alleles supports that domestication of SLC occurred in the Andean region. Our results also clarify the biological status of SLC as true phylogenetic group within tomato. We detect Ecuadorian and Peruvian accessions that may represent a pool of unexplored variation that could be of interest for crop improvement., We are grateful to the gene banks for their collections that made this study possible. We thank Syngenta Seeds for providing genotyping data for 42 accessions. We would like to thank the Supercomputing and Bioinnovation Center (Universidad de Malaga, Spain) for providing computational resources to process the SNAPP phylogenetic tree. This research was supported in part by the USDA/NIFA funded SolCAP project under contract number to DF and USDA AFRI 2013-67013-21229 to EvdK and DF.

National audience

National audience

Pairwise distance data for maize (Zea mays L.) inbred lines generated using sets of single nucleotide polymorphisms (SNPs) selected from a 50k Infinium array were compared with pairwise distances generated using a set of 163 simple sequence repeat (SSR) loci previously identified to help determine essentially derived variety (EDV) status (UPOV, 1991). Final comparisons were made using 26,874 SNPs after discarding SNPs with insufficient data quality or vulnerability to ascertainment bias. Inbred lines developed in the United States or in western Europe that had been previously published to establish SSR-based thresholds provided the means to determine equivalent SNP-based protocols. Use of 3072 SNPs selected to provide even genomic coverage according to genetic and physical maps provided robust, precise, high discrimination among inbred lines with consistent zonal classification with up to 20% missing data. Comparisons of intercepts and slopes for SSR and SNP inbred pairwise distance data translated the 82% SSR green-orange similarity threshold to 91% using SNPs and the 90% SSR orange-red threshold to 95% using SNPs. Information required to conduct analyses using these 3072 SNPS is presented.

National audience

International audience

National audience; Une pépinière comprenant 184 variétés et lignées issues des ressources génétiques françaises, Européennes, Nord-Africaines, et CIMMYT/ICARDA a été phénotypée pour sa résistance dans des essais au champ avec inoculation contrôlée (un seul pathotype par essai) de rouille brune, dans 4 lieux en France et deux lieux au Mexique, en 2009 et 2010. De plus, ces 184 lignées et variétés ont été phénotypées pour leur résistance en serre à 9 pathotypes de rouille brune. Les gènes Lr27+31 et Lr3 sont efficaces en France, mais vu qu'ils sont déjà contournés au Mexique, il est peu probable qu'ils constituent une source de résistance durable en France. Les gènes Lr61, LrCamayo, Lr19 et Lr47 sont efficaces en France et au Mexique, et peuvent constituer des sources de résistance intéressantes. Certaines lignées ont montré un niveau très élevé de résistance dans tous les lieux, probablement du à un gène majeur de résistance non identifié. Quatre variétés françaises, ainsi que plusieurs lignées "slow rusting" du CIMMYT ont montré un niveau intéressant de résistance partielle dans tous les environnement testés. Une analyse de génétique d'association, conduite à l'aide de 1300 marqueurs DArT et 34 variables de phénotypage, a mis en évidence deux QTLs et un locus correspondant à un gène majeur : i) un QTL sur le chromosome 2B, associé à wPt-1064, wPt-6477 and wPt-0408 ii) un QTL sur le chromosome 6B, associé à wPt-8059 et wPt-7065 iii) un gène majeur sur le chromosome 7B, associé à wPt-0465, wPt- 3700 et wPt-9515, qui correspond au gène Lr14a. Ce gène est surmonté en France, mais il reste efficace au Mexique.

National audience

The efficiency of marker-assisted prediction of phenotypes has been studied intensively for different types of plant breeding populations. However, one remaining question is how to incorporate and counterbalance information from biparental and multiparental populations into model training for genome-wide prediction. To address this question, we evaluated testcross performance of 1652 doubled-haploid maize (Zea mays L.) lines that were genotyped with 56,110 single nucleotide polymorphism markers and phenotyped for five agronomic traits in four to six European environments. The lines are arranged in two diverse half-sib panels representing two major European heterotic germplasm pools. The data set contains 10 related biparental dent families and 11 related biparental flint families generated from crosses of maize lines important for European maize breeding. With this new data set we analyzed genome-based best linear unbiased prediction in different validation schemes and compositions of estimation and test sets. Further, we theoretically and empirically investigated marker linkage phases across multiparental populations. In general, predictive abilities similar to or higher than those within biparental families could be achieved by combining several half-sib families in the estimation set. For the majority of families, 375 half-sib lines in the estimation set were sufficient to reach the same predictive performance of biomass yield as an estimation set of 50 full-sib lines. In contrast, prediction across heterotic pools was not possible for most cases. Our findings are important for experimental design in genome-based prediction as they provide guidelines for the genetic structure and required sample size of data sets used for model training.