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Plant omics data is often not published, or dispersed among multiple repositories and, owing to poor annotation of submissions with descriptive metadata, effectively not FAIR (i.e. Findable, Accessible, Interoperable and Re-usable). In this work package, our goal is to make plant -omics data FAIR, and the first part of this work has involved the development of standards for the annotation of data sets, and their exemplary application to diverse data from diverse species. Finally, the annotated data has been made available in the public repositories. In developing these standards, we have built from previous work in the field, most notably the development of the Minimal Information about a Plant Phenotyping experiment (MIAPPE) standard (http://www.miappe.org). We have taken MIAPPE as our starting point, and extended and revised it according to the characteristics of our exemplar data. Because a proposed standard becomes a real one through its adoption, we have actively participated in the wider community developing MIAPPE, with the goal of incorporating our developments within the official MIAPPE specification. A particularly important issue is the identification of material used in an experiment. Materials used within and between experiments may be related to each other (by time, space, condition or genealogy), and multiple assays may be taken from the same material; moreover, what is often of interest is to connect experimental data to the physical material assayed (or at least, related physical material, such as a stock held in a germplasm repository). We have taken special care in aligning the MIAPPE standards with the FAO Multi Crop Passport Descriptor Data standard used by the gene banks and used the BioSamples database (http://www.ebi.ac.uk/biosamples) as an integrative layer to allow us to capture the relationships between samples and the measurements that have been made upon them. This work was presented as Deliverable D7.1 of the ELIXIR-EXCELERATE project.ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559.

Compléter la rubrique "Rapport" (n° contrat, date signature...) Ajouter MC Préciser mail correspondant; BRCs need to manage their collections using effective information technology, based on open-access web technologies, adapted to their diverse management needs. For several years, various pragmatic initiatives have been developed independently by BRCs or groups of BRCs, in order to develop their tools. One of the pre-existing tools has been used for fifteen collections. It is currently being adapted, using this generic and consensual model. The work was led by four computer scientists, including a fixed-term contract, and by a group of collections managers and other IT professionals. With the aim of sharing and improving performance, a working group was formed in November 2014 at the request of BAP department of INRA, for examining the situation, and for devising a joint development strategy shared by the BRCs in charge of plant genetic resources in France, overseas and mainland (INRA, Cirad, IRD). The group's conclusions are that it is necessary to come to a limited number of tools (ideally a single one) that are generic at all levels, configurable by the user according to his BRCs’ specificity, with a collaborative maintenance and improvement Three partners have already worked on this common concept and a conceptual data model has been validated by this group of BRCs. The object of the present proposal is to go beyond that stage of "good will” and to develop an information systeme (Coll-GATE-IS) with the core functionalities for the BRCs who need it. This will be done through the improvement of one of the existing tools. Along with the local needs of collection management, this tool will take into account the needs of interoperability at the national level (link with GnpIS-Siregal, the RGScope, Florilège and other future portals), as well as at the European and international level (link with EURISCO, GBIF, ...). For this purpose, the project will contribute to the improvement of the use of international metadata standards and ontologies in the BRCs of the network by developing an online “cookbook” of good practices that will be in turn implemented in the . Beyond the technical achievement, this project will allow us to continue the momentum of dialogue and networking we undertook, in order to gain relevance in our choice of tools, and finally to strengthen our international visibility.

BRCs need to manage their collections using effective information technology, based on open-access web technologies, adapted to their diverse management needs. For several years, various pragmatic initiatives have been developed independently by BRCs or groups of BRCs, in order to develop their tools. One of the pre-existing tools has been used for fifteen collections. It is currently being adapted, using this generic and consensual model. The work was led by four computer scientists, including a fixed-term contract, and by a group of collections managers and other IT professionals. With the aim of sharing and improving performance, a working group was formed in November 2014 at the request of BAP department of INRA, for examining the situation, and for devising a joint development strategy shared by the BRCs in charge of plant genetic resources in France, overseas and mainland (INRA, Cirad, IRD). The group's conclusions are that it is necessary to come to a limited number of tools (ideally a single one) that are generic at all levels, configurable by the user according to his BRCs’ specificity, with a collaborative maintenance and improvement Three partners have already worked on this common concept and a conceptual data model has been validated by this group of BRCs. The object of the present proposal is to go beyond that stage of "good will” and to develop an information systeme (Coll-GATE-IS) with the core functionalities for the BRCs who need it. This will be done through the improvement of one of the existing tools. Along with the local needs of collection management, this tool will take into account the needs of interoperability at the national level (link with GnpIS-Siregal, the RGScope, Florilège and other future portals), as well as at the European and international level (link with EURISCO, GBIF, ...). For this purpose, the project will contribute to the improvement of the use of international metadata standards and ontologies in the BRCs of the network by developing an online “cookbook” of good practices that will be in turn implemented in the . Beyond the technical achievement, this project will allow us to continue the momentum of dialogue and networking we undertook, in order to gain relevance in our choice of tools, and finally to strengthen our international visibility.

Trabajo presentado en la Plant and Animal Genome XXII Conference, celebrada en San Diego del 11 al 15 de enero de 2014., A major breakthrough in grapevine genomics was achieved in 2007 with the sequencing of the Vitis vinifera cv. PN40024 genome. Subsequently, invaluable data related to the structural and functional characterization of the genes accumulated exponentially. Unfortunately, part of this data is episodic by nature or was acquired prior to the genome release. Furthermore, because of heterogeneous sources these data were greatly under-exploited with issues like incompatibility of data but also decentralized storage making retrieval more difficult. Classically, a large amount of useful data describing gene functions only appears in printed articles that describe the experiments carried out to answer the initial question of the publishing research team without being deposited in a common database, then remaining inaccessible for automatic data mining. High throughput “omics” data are typically stored in public repositories, but generally remain confined to their initial aim. With the objective of providing a high quality and highly accessible annotation of the grapevine genes, the International Grapevine Genome Project (IGGP) commissioned an international Supernomenclature Committee for Grape Gene Annotation to coordinate the expert-annotation effort of the grapevine genes. The goal of the committee is to provide a standard nomenclature for locus identifiers and to define the convention for the gene naming system. This system will be implemented on a new version of grapevine annotation that is being developed on an improved version of the grapevine genome chromosome assembly., Acknowledgements: GRCN NSF program, Grant Plant-KBBE-2008-GrapeReSeq, EU COST FA 1106.

Póster presentado en la 2nd Annual ConferenceFleshy Fruit Development & Ripening (COST Action FA1106 QualityFruit), celebrada en Chania (Grecia) del 22 al 25 de septiembre de 2013., A major breakthrough in grapevine genomics was achi eved in 2007 with the sequencing of the Vitis vinifera cv. PN40024 genome. Subsequently, invaluable data relat ed to the structural and functional characterization of the g enes accumulated exponentially. Unfortunately, data that were acquired prior to the genome release are largely under- exploited. Furthermore, because of heterogeneous so urces these data remain often incompatible but also decentralized storage is maki ng retrieval more difficult. Classically, a large amount of useful data describing gene functio ns only appeared in printed articles describing experiments carried out to answer specif ic questions. These data remain inaccessible for automatic text mining. High throug hput “omics” data are typically stored in public repositories, but generally are confined to their initial aim. With the objective of providing a high quality and highly accessible anno tation of grapevine genes, the International Grapevine Genome Project (IGGP) commi ssioned an international Super- nomenclature Committee for Grape Gene Annotation to coordinate the expert-annotation effort of the grapevine genes. The goal of the comm ittee is to provide a standard nomenclature for locus identifiers and to define co nventions for a gene naming system. Using previous experience acquired on similar initi atives for other plant species such as Arabidopsis , rice and tomato, a versatile system was implement ed anticipating on future developments and issues. Specific emphasis has focu sed on directions for the expert annotators by: (i) providing a clearly-identified c ommon annotation platform that also enables community-based gene curation (ii) emphasiz ing a gene naming scheme reflecting the biological features of gene products, (iii) and using a genetic ontology consistent with other organisms to facilitate evolutionary comparis on of genes.

With the release of the grapevine genome sequence and with the increasing affordability of high throughput analysis tools, an ever increasing wealth of grapevine bioinformatics resources have been developed over the last decade in highly diverse biological fields. The grapevine community can now access extensive databases containing information relative to molecular markers, genetic maps, the genome sequence and its annotation, gene expression, proteins and metabolites. The present paper presents how to access these resources and provides some review of their contents and use. The next challenge is the further development of systems biology for grapevine; regarding this aspect, we discuss the different tools currently available for the integration of different types of data.

Le déterminisme génétique d'une source de résistance au mildiou de la vigne (Plasmopara viticola) ayant pour origine Muscadinia rotundifolia a été étudié sur une population ségrégante RV2 produite par une hybridation suivie de deux recroisements par Vitis vinifera. Après inoculation des feuilles sur plante entière par une suspension contrôlée de sporanges, le niveau de résistance des individus RV2 ainsi que des parents résistant et sensible a été évalué à l'aide d'une échelle notation visuelle comprise entre 1 (très sensible) et 9 (très résistant). Le niveau de résistance des individus RV2 couvrent toute la gamme de notation et montre une distribution bimodale. le niveau moyen des parents sensible et résistant étant respectivement de 3,7 et 6,9. L'héritabilité du caractère a été estimée à 0,88. Une stratégie bsa a été utilisée pour rechercher des marqueurs liés à la résistance parmi ceux générés par 151 amorces RAPD, 13 amorces ISSR et 208 locus SSR en testant leur polymorphisme entre deux lots d'ADN regroupant respectivement les six individus les plus sensibles et les six individus les plus résistants. In fine, après analyse sur la totalité de la population RV2, 1 RAPD, 4 ISSR et 8 SSR ont montré un effet significatif sur le niveau de résistance. Ces marqueurs ont tous été cartographiés sur le même groupe de liaison et couvrent une région de 45 cM. La présence d'un QTL de résistance a été confirmé par interval mapping. Ce QTL explique 73% de la variation totale observée, soit 83% de la variance génétique. Il peut être considéré comme un gène majeur que nous avons appelé Rpv1. La ségrégation de la population RV2 pour sa résistance à l'oïdium a également été analysée. Un gène de résistance à l'oïdium, correspondant putativement au gène Run1 déjà décrit, a été colocalisé sur le même groupe de liaison que Rpv1. (Texte intégral)

High-throughput “omics” technologies are widely used and increasingly important to support plant biology research and breeding of diverse plant species for production of food, feed, fibre and other biomaterials, and bio-energy. Significant advances in plant science can be obtained from the integration of available genomic and genotyping data with diverse types of phenotyping data, including field or greenhouse experimental data, molecular, -omics and image data. Although most -omics data, and especially phenomic data, are being generated in increasing scale, either from public or private research institutes, the dispersion of datasets and metadata among multiple repositories and their often poor description and annotation, make their use and exploitation still challenging or even unapproachable. To help unlock the full potential of a multi-omics approach to plant science, the overarching goal of this work package is to make plant data reusable and interoperable in accordance with the FAIR principles (i.e. Findable, Accessible, Interoperable and Re-usable). Hence, several standards have been built these past years for the annotation of data sets, and the ELIXIR plant community is co-authoring most of them. Their use has been demonstrated by exemplary application to data from diverse species published in public repositories (Deliverable 7.1). They are also the foundation of the ELIXIR Plant Data Search Service, FAIDARE, that gives access to distributed and standardized datasets. This service uses the Breeding API (BrAPI1), an API for accessing data relevant for plant breeding developed by the international plant community (Deliverable 7.2). It is based on a federation of plant phenotyping/genotyping data repositories, accessible through a single data discovery webportal2, that connects not only ELIXIR data repositories, but also any other Breeding API compatible database. This work represents a major step towards plant FAIR data and a significant tool for the international plant community focused on plant breeding, either of crops or forest trees. Furthermore, with this deliverable we reach the main goal of WP7, to provide a distributedinfrastructure to allow plant genotype-phenotype analysis based on the widest available public datasets, and we give an important contribution to address goal one of the ELIXIR-EXCELERATE project: Deliver world-leading data services for academia and industry.

High-throughput “omics” technologies are widely used and increasingly important to support plant biology research and breeding of diverse plant species for production of food, feed, fibre and other biomaterials, and bio-energy. Significant advances in plant science can be obtained from the integration of available genomic and genotyping data with diverse types of phenotyping data, including field or greenhouse experimental data, molecular, -omics and image data. Although most -omics data, and especially phenomic data, are being generated in increasing scale, either from public or private research institutes, the dispersion of datasets and metadata among multiple repositories and their often poor description and annotation, make their use and exploitation still challenging or even unapproachable. To help unlock the full potential of a multi-omics approach to plant science, the overarching goal of this work package is to make plant data reusable and interoperable in accordance with the FAIR principles (i.e. Findable, Accessible, Interoperable and Re-usable). Hence, several standards have been built these past years for the annotation of data sets, and the ELIXIR plant community is co-authoring most of them. Their use has been demonstrated by exemplary application to data from diverse species published in public repositories (Deliverable 7.1). They are also the foundation of the ELIXIR Plant Data Search Service, FAIDARE, that gives access to distributed and standardized datasets. This service uses the Breeding API (BrAPI1), an API for accessing data relevant for plant breeding developed by the international plant community (Deliverable 7.2). It is based on a federation of plant phenotyping/genotyping data repositories, accessible through a single data discovery webportal2, that connects not only ELIXIR data repositories, but also any other Breeding API compatible database. This work represents a major step towards plant FAIR data and a significant tool for the international plant community focused on plant breeding, either of crops or forest trees. Furthermore, with this deliverable we reach the main goal of WP7, to provide a distributed infrastructure to allow plant genotype-phenotype analysis based on the widest available public datasets, and we give an important contribution to address goal one of the ELIXIR-EXCELERATE project: Deliver world-leading data services for academia and industry.

The grapevine reference genome was published by Jaillon et al. [1]. The sequence for the first version of the genome, called the 8X version, was obtained using a whole genome shotgun strategy and the Sanger sequencing technology and was assembled from reads representing 8X coverage. Soon after, the assembly was improved through the addition of 4X of additional coverage, including more Bacterial Artificial Chromosome end sequences that greatly improved the scaffolding of the sequence contigs [2], [3]. The corresponding scaffolds and raw sequences were deposited in European Molecular Biology Laboratory (EMBL) archives (FN594950-FN597014, 2065 entries, release 102). A new chromosome assembly was also developed, based on an improved version of the maps used for the 8X genome version [2], [3], [4], [5] and was also archived at EMBL (FN597015-FN597047, 33 entries, release 102): it is referenced in the grapevine community as the 12X.v0 version of the grapevine reference genome. The chromosome sequence scaffolding of this version still necessitated improvements as around 9% of the sequence was not anchored to chromosomes (with the corresponding scaffolds stacked in the “Unknown” chromosome) and 3.5% of the sequence could be assigned to a chromosome but without certain placement and orientation within the chromosome (stacked in additional “random” chromosomes)., This work was supported by the French National Institute for Agriculture (INRA, France), the University of Udine and the Institute of Applied Genomics (Italy), the Vlaams Institut voor Biotechnologie and the University of Ghent (Belgium), the Istituto de Ciencas de la Vid et del Vino (Logroño, Spain) and several grants: ANR-Plant-KBBE-2008- GrapeReSeq and ANR-2008-Muscares funded by the French National Research Agency (ANR), Valorizzazione dei Principali Vitigni Autoctoni Italiani e dei loro Terroir (Vigneto, no. COSVIR27129) funded by the Italian Ministry of Agriculture and the COST action FA1106 funded under the European FP7 Research Program

Chez les espèces fruitières, la floraison est un évènement majeur qui influencera fortement la fructification. Ce processus, finement régulé par de nombreux facteurs génétiques et environnementaux, est encore peu connu. Chez le cerisier doux (Prunus avium), les fleurs ne s’épanouissent qu’après avoir satisfait des besoins en froid et en chaud. Les effets du changement climatique sur la floraison sont déjà notables et pourraient induire d’importantes pertes économiques. La compréhension des déterminants génétiques et moléculaires impliqués dans la floraison permettra l’amélioration des programmes de sélection variétale visant l’obtention d’arbres adaptés aux futures conditions climatiques. L’objectif de cette thèse est d’accroître les connaissances sur ces déterminants et d’identifier les gènes contrôlant la floraison chez le cerisier. En étudiant les deux familles intra spécifiques ‘Regina’ × ‘Lapins’ et ‘Regina’ × ‘Garnet’, la détection de nombreux quantitative trait loci (QTL) sur l’ensemble des groupes de liaisons (GL) a permis de confirmer la forte implication des besoins en froid dans la floraison ainsi que la complexité de ces caractères. Un QTL à effet majeur a été localisé sur le GL4. Dans les régions couvertes par les QTL contrôlant la date de floraison, une centaine de gènes candidats (GC) pour ce caractère a été identifiée. Un sous ensemble de ces GC a ensuite été étudié pour leur expression au cours du développement des bourgeons par PCR quantitative (qPCR). A terme, ces travaux serviront de bases pour l’identification et la sélection de gènes qui permettront l’obtention de génotypes adaptés aux futures conditions climatiques., In fruit species, the flowering is a major event which strongly influences fructification. This process tiny controlled by many genetic and environmental factors is still little known. In sweet cherry (Prunus avium), flowers open out only after having satisfied chill and heat requirements. The effects of climate change on the flowering are already notable and could induce important economic losses. Identification of genetic and molecular determinants involved in the flowering will allow the improvement of varietal selection programs to obtain trees adapted to future climate conditions. Objective of this thesis is to increase the knowledge of these determinants and identify genes involved in flowering in sweet cherry. By studying two intraspecific progenies ‘Regina’ × ‘Lapins’ and ‘Regina’ × ‘Garnet’, detection of many quantitative trait loci (QTL) on all linkage groups (LG) has enabled us to confirm the strong involvement of chill requirements in the flowering as well as the complexity of these traits. QTL with major effect was localized on the LG4. In regions covered by all the QTLs controlling flowering date, a hundred candidate genes (CG) for this trait was identified. A subset of these GC was then studied for their expression during development of buds by quantitative PCR (qPCR). In the long term, this work will serve as a basis for the identification and selection of genes that allow obtaining genotypes adapted to future climate conditions.

L’esca est une maladie de dépérissement du bois de la vigne conduisant à la mort des ceps. Actuellement le vignoble mondial est atteint, et au niveau français, cette maladie ne cesse de progresser. Ainsi, 8% des ceps dans le Jura et 4,5% dans la région de Bordeaux manifestent des symptômes d’esca, selon les parcelles des chiffres beaucoup plus élevés sont obtenus, certains cépages sont aussi beaucoup plus sensibles que d’autres. Plusieurs champignons seraient impliqués dans l’esca mais leur rôle ainsi que la détermination de la microflore responsable de cette maladie est encore sujette à interrogation. Dans ce contexte, l’objectif de cette thèse a été de caractériser et de comparer les microflores fongiques et bactériennes colonisant le bois de ceps de vigne ayant exprimé ou non des symptômes foliaires d’esca. Dans un premier temps, nous avons prélevé des ceps (cultivar Cabernet Sauvignon) relativement jeunes (10 ans d’âge) car ils présentaient l’intérêt d’être peu dégradés au niveau du bois du tronc, les symptômes foliaires étant associés à la présence d’amadou (une nécrose typique de l’esca) uniquement dans les bras. Une grande diversité dans les communautés fongiques (674 OTUs) et bactériennes (222 OTUs) colonisant le bois a été observée. Cette diversité est plus importante dans le bois sain de la vigne que dans celui partiellement ou totalement nécrosé. Les techniques utilisées, i.e. isolement/séquençage de souches, empreinte moléculaire (Single Strand Conformation Polymorphism, SSCP) et pyroséquençage 454, ont montré que les communautés bactériennes ou fongiques étaient différentes dans les tissus dégradés comparés à ceux qui ne l’étaient pas. Des changements de microflores en fonction du temps (expérimentation durant 1 année) ont aussi été observés. D’une façon générale, les espèces de champignons impliquées dans l’esca sont déjà présentes dans le bois apparemment sain de ceps esca-foliaires symptomatiques mais aussi des asymptomatiques. Il n’a pas été possible de différencier ces 2 types de microflores au niveau du bois sain des plants, cette différentiation se faisant au niveau des nécroses, qui sont plus abondantes dans les ceps esca-symptomatiques. Pour la première fois nous avons montré que des communautés bactériennes spécifiques étaient associées à l’esca, leurs aptitudes trophiques étant différentes selon les tissus où elles étaient prélevées. Les espèces isolées suggèrent que certaines pourraient avoir un rôle dans la protection du végétal, d’autres dans la dégradation des structures du bois, e.g. de la lignine, préparant ainsi le terrain aux champignons dégradateurs des tissus ligneux, déjà présents à l’intérieur des ceps. Nous avons aussi étudiés des ceps plus âgés (cultivar Baco blanc), de 42 et 58 ans, qui avaient un rendement acceptable et n’avaient pas manifesté de symptômes d’esca ou eutypiose (une autre maladie du bois) l’année du prélèvement. Au niveau des tissus fonctionnels du bois, les communautés fongiques étaient caractéristiques de plants atteints par l’eutypiose (ceps de 42 ans) ou de l’esca (ceux de 58 ans). La non expression par les ceps de ces 2 maladies pourrait cependant être associée à la forte présence de champignons mycoparasites et protecteur du végétal, comme Trichoderma spp., dans ces tissus fonctionnels. Les interactions au sein des communautés fongiques créant un équilibre où le pathogène ne se développerait pas de façon extensive. Les caractéristiques du Baco blanc, un hybride, moins sensible à certaines maladies de la vigne, pourrait aussi expliquer ce résultat. Ainsi la présence d’une microflore bénéfique naturellement présente dans le bois des ceps associée à des plants ayant une tolérance à ces maladies pourrait ouvrir de nouvelles perspectives pour lutter l’esca, voire l’eutypiose, pour lesquelles aucun moyen de protection n’existe aujourd’hui., Esca is a Grapevine Trunk Disease (GTD) that induces a decline in grapevine vigour that generally leads up with the death of the plants. Nowadays, vineyards worldwide are attacked by esca and, in France this disease increases steadily. In the Jura, 8% of the grapevines are esca-foliar symptomatic and approximately 4.5% in the Bordeaux region. However, some vineyards are more severely attacked by esca, and certain cultivars are more susceptible than others. Although several pathogenic fungi are associated with esca, their individual roles and their interaction with other microorganisms for the esca have still to be determined. In this context, the objective of the present PhD study is to characterize and compare the bacterial and fungal microflora that colonize the wood tissues of esca-foliar symptomatic and asymptomatic grapevines. First, we sampled young (10 year-old) grapevines (Cabernet Sauvignon cultivar) because they had only few necroses in the trunk and white-rot (also called amadou) was only present in the cordons of symptomatic plants. Great diversity in the fungal (674 OTUs) and bacterial (222 OTUs) communities was observed. This diversity was higher in the apparently healthy wood than in the partially or totally necrotic wood tissues. The methods used isolation/sequencing of microbial strains, a molecular fingerprinting method (Single Strand Conformation Polymorphism, SSCP) and 454 pyrosequencing showed that the fungal and bacterial communities of the necrotic and healthy wood tissues were different. Changes in the microflora over time (over a one-year period) have been observed. Fungal species involved in esca are already present in the apparently healthy wood of esca-foliar symptomatic plants but also in the asymptomatic ones. It was not possible to differentiate these 2 microflora. Only microflora from the necroses differed from those of the healthy wood with these necroses being more developed in the esca-foliar symptomatic grapevines. For the first time, we were able to determine that specific bacterial communities are associated with esca. Depending on the wood tissues, different types of bacteria were isolated, with different trophic behaviour. Two roles could be assigned to the species isolated from the various wood tissues: (i) a positive role, due to the biocontrol potential that many species have; (ii) a negative one, by predisposing the wood of grapevines to fungal attacks. We also studied, old (42 and 58 year-old) grapevines of the cultivar, Baco blanc, that produced regular harvests. The plants had no expressed foliar symptoms of esca or eutypa dieback during the sampling year. Many plant pathogens colonized the functional wood tissues, but in 58 year-old plants they were associated with esca, and in 42 year-old plants, with eutypa dieback. The absence of GTDs expression could be linked to the numerous plant protectant mycoparasites, such as Trichoderma spp., that colonized the functional wood tissues. Interactions between species within the fungal communities may create a balance that is unfavourable to the development of the pathogens. The use of Baco blanc, a hybrid less susceptible to certain grapevine diseases could also explain this result. So, because no means of protection are currently available, the combination of beneficial microflora within the garpevine wood tissues with plants that are tolerant to esca, or even eutypa dieback, could be helpful to control those diseases.