Caractérisation phénotypique et moléculaire de la collection nationale de ressources génétiques de blé tendre

The bread wheat national collection, gathering 1783 French accessions, was evaluated during threeyears for ten agro-morphological traits in a multisite network of private breeders. Furthermore, the wholecollection was genotyped for a set of 42 microsatellite loci. Field evaluation results show a wide diversityfor all observed traits. ANOVA performed on heading date, plant height, spike density and lodgingsusceptibility indicates both high significant genotype and year effect, without interaction. The use ofempiric selection index on disease traits (yellow and brown rusts, septoria, fusarium and powderymildew) makes it possible to define different panels of accessions showing high level of resistance foreach specific pathogen.Molecular analysis also reveals a large diversity at neutral level. From genotyping data, clusteringanalysis of the whole collection exhibits the importance of registration year effect on structure of thewhole collection. A first approach of association genetics between markers and traits indicates a total of130 significant associations (p<0.001).The national collection was declared as French contribution to the TIRPAA (international treaty ongenetic resources for food and agriculture). Seeds from this collection are freely available in order to beused in breeding programsThe whole passport and evaluation dataset of this collection is currently transferred on the nationaldatabase SIReGaL and will be soon accessible on internetLa collection nationale blé tendre, regroupant 1783 accessions françaises, a été évaluée sur trois anspour dix caractères agro-morphologiques (précocité, hauteur, compacité et aristation de l’épi, sensibilitéà la verse, sensibilité aux rouilles jaunes, rouilles brunes, fusarioses, oïdium et septorioses) dans leréseau multilocal des sites de sélection des partenaires privés membres de l’UFS. Par ailleurs, lacollection a été génotypée pour 42 locus microsatellites répartis sur l’ensemble du génome.Les résultats d’évaluations agronomiques mettent en évidence une large variabilité pour l’ensemble descaractères observés. Une analyse de variance menée sur la précocité, la hauteur, la compacité,l’arisation et la sensibilité à la verse révèle de forts effets principaux du génotype et de l’année pour laplupart de ces variables, tandis que leurs interactions sont négligeables. L’application d’un indexempirique de sélection sur les caractères de sensibilités aux maladies a permis de définir différentspanels d’accessions montrant de bons niveaux de résistances aux cinq pathogènes étudiés.L’analyse au niveau moléculaire révèle également une grande diversité au niveau du polymorphismeneutre. A partir de ces données, une analyse de la structure de la collection a confirmé l’importance dela date d’inscription des variétés comme facteur structurant fortement la collection. Par la suite, unepremière approche de génétique d’association a permis de révéler 130 associations statistiquementsignificatives entre phénotypes et génotypes aux marqueurs étudiés.La collection nationale a été déclarée comme contribution française auprès de la FAO dans le cadre dutraité international sur les ressources phytogénétiques. Elle est à ce titre largement diffusée sous formede semences auprès de la communauté internationale.L’ensemble des données d’évaluations du projet est en cours de transfert sur la base de donnéesinformatisées SIReGaL et sera bientôt publiquement accessible sur le ne

The PGR Networks in France: Collaboration of users and the genetic resources centre on small grain cereals

Plant genetic resources (PGR) have been used in breeding programs for many decades to produce modern varieties by introducing genes of interest, in particular, resistance genes. Nevertheless, these resources remain underestimated if we focus on abiotic stress tolerance or new agricultural techniques, which consider productivity with regard to the environment. In recent years, new users, such as scientists and farmers, have discovered diverse sources of interest for screening and exploiting natural diversity conserved in PGR collections.In the case of the French cereals PGR Network, a share of the responsibility, based on the knowledge and ability of network members, has been decided in order to better promote the use of PGR. The main species of Triticum (wheat), Hordeum (barley), Secale (rye), ×Triticosecale (triticale), Avena (oat) genera and their wild relatives are held in the collection. By combining phenotypic and genotypic data, the whole genetic resource collection has been structured into smaller functional groups of accessions, in order to facilitate the access and meet the increasing number of different requirements for the distribution of adapted samples of accessions.New panels are being processed to give breeders and scientists new useful tools to study, for instance, stress resistance or to develop association studies. All these data obtained from the French small grain cereal Network will be progressively available through the INRA Genetic Resource Website (http://urgi.versailles.inra.fr/siregal/siregal/welcome.do)

Une plateforme pour l'acquisition, la maintenance et la validation de ressources lexicales

International audienceNous présentons une plateforme de développement de lexique offrant une base lexicale accompagnée d'un certain nombre d'outils de maintenance et d'utilisation. Cette base, qui comporte aujourd'hui 440.000 formes du Français contemporain, est destinée à être diffusée et remise à jour régulièrement. Nous exposons d'abord les outils et les techniques employées pour sa constitution et son enrichissement, notamment la technique de calcul des fréquences lexicales par catégorie morphosyntaxique. Nous décrivons ensuite différentes approches pour constituer un sous-lexique de taille réduite, dont la particularité est de couvrir plus de 90% de l'usage. Un tel lexique noyau offre en outre la possibilité d'être réellement complété manuellement avec des informations sémantiques, de valence, pragmatiques etc

Étude des complémentarités entre gestion dynamique à la ferme et gestion statique en collection: Cas de la variété de blé Rouge de Bordeaux

National audienceWhile on-farm conservation was considered minor in the development of the National Charter on Genetic Resources in 1998, there is increasing recognition of its important role in the conservation of genetic diversity. In addition to amateur gardening associations that save and exchange seeds, farmers in France have formed networks around systems of shared seed conservation and exchanges, with the goal of protecting the diversity of cultivated species. Parallel to this, the contribution of farmers to the dynamic management of agricultural biodiversity has been recognized by many scientific studies and in international treaties. These developments led us to examine the complementary nature of on-farm and gene-bank conservation efforts in terms of the management of genetic resources. This study, which combines ethnobotanical and genetic approaches, was conducted on bread wheat, for which France has a national collection of 10 000 accessions. There is also an active network of farmers who cultivate historic varieties and landraces, including the Rouge de Bordeaux, which was chosen for a detailed study. By conducting individual interviews with farmers, we were able to understand better their management practices, seed exchanges with other farmers and with the national collection, and strategies for maintaining and selecting this variety on their own farms. We characterized the genetic diversity conserved by several farmers and in the samples preserved in the national collection for Rouge de Bordeaux by using a comparative genetic analysis of samples obtained from farmers and from the collection, in light of the management practices and exchange networks that exist among farmers and between farmers and the national collection. Our results demonstrate that the diversity of these populations is far from being redundant. While certain samples are quite homogeneous and similar to samples from the national collection, others are highly heterogeneous. There is also a high degree of genetic differentiation among populations, with clear groupings of populations identified. The structure of the diversity may be explained by the structure of exchanges and the development of local adaptation within the populations to environmental conditions and management practices, and by differing strategies of selection and conservation. Further analysis will help us understand more precisely what defines a variety and what type of genetic diversity or phenotypic traits are conserved with different management strategies. Our results also support a greater degree of seed circulation between farmers' fields and the national collection, to conserve the adaptive potential and a broader range of genetic diversity for each variety.Considérée comme mineure lors de la rédaction de la Charte nationale des ressources génétiques en 1998, la gestion à la ferme a depuis gagné en importance et en reconnaissance. En effet, après les associations de jardiniers amateurs, des réseaux d'agriculteurs se sont fédérés en France autour de systèmes mutualistes de sélection/conservation de la diversité cultivée. Parallèlement, la contribution des paysans à la gestion dynamique de l'agrobiodiversité a été scientifiquement et institutionnellement reconnue. Ces éléments nous ont conduit à examiner les complémentarités dans la gestion des ressources génétiques à la ferme et en collection. Cette étude, qui croise des approches ethnobotanique et génétique, a été menée sur le blé tendre pour lequel il existe en France une collection nationale de 10 000 accessions et un réseau actif d'agriculteurs-collectionneurs de variétés. Pour la variété Rouge de Bordeaux, nous avons tenté de caractériser la diversité dans les champs et en collection, en procédant à une analyse génétique d'échantillons obtenus auprès d'agriculteurs et auprès de la collection. Nos résultats montrent que les ressources génétiques conservées dans les deux compartiments sont loin d'être redondantes. La structuration de la diversité s'explique par les réseaux d'échanges de semences (entre paysans, et entre les paysans et la collection), par l'adaptation locale des populations aux conditions du milieu et aux pratiques de culture, et par les pratiques de sélection/conservation. Ces résultats appellent des analyses complémentaires pour comprendre précisément ce qui est conservé/cultivé sous un nom variétal donné, et plaident en faveur d'une circulation accrue des semences entre champs et collection

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Introduction: Wheat (Triticum aestivum L.) is the most widely cultivated crop on Earth, contributing about a fifth of the total calories consumed by humans. Consequently, wheat yields and production affect the global economy, and failed harvests can lead to social unrest. Breeders continuously strive to develop improved varieties by fine-tuning genetically complex yield and end-use quality parameters while maintaining stable yields and adapting the crop to regionally specific biotic and abiotic stresses. Rationale: Breeding efforts are limited by insufficient knowledge and understanding of wheat biology and the molecular basis of central agronomic traits. To meet the demands of human population growth, there is an urgent need for wheat research and breeding to accelerate genetic gain as well as to increase and protect wheat yield and quality traits. In other plant and animal species, access to a fully annotated and ordered genome sequence, including regulatory sequences and genome-diversity information, has promoted the development of systematic and more time-efficient approaches for the selection and understanding of important traits. Wheat has lagged behind, primarily owing to the challenges of assembling a genome that is more than five times as large as the human genome, polyploid, and complex, containing more than 85% repetitive DNA. To provide a foundation for improvement through molecular breeding, in 2005, the International Wheat Genome Sequencing Consortium set out to deliver a high-quality annotated reference genome sequence of bread wheat. Results: An annotated reference sequence representing the hexaploid bread wheat genome in the form of 21 chromosome-like sequence assemblies has now been delivered, giving access to 107,891 high-confidence genes, including their genomic context of regulatory sequences. This assembly enabled the discovery of tissue- and developmental stage–related gene coexpression networks using a transcriptome atlas representing all stages of wheat development. The dynamics of change in complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. Aspects of the future value of the annotated assembly for molecular breeding and research were exemplarily illustrated by resolving the genetic basis of a quantitative trait locus conferring resistance to abiotic stress and insect damage as well as by serving as the basis for genome editing of the flowering-time trait. Conclusion: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. Importantly, the bioinformatics capacity developed for model-organism genomes will facilitate a better understanding of the wheat genome as a result of the high-quality chromosome-based genome assembly. By necessity, breeders work with the genome at the whole chromosome level, as each new cross involves the modification of genome-wide gene networks that control the expression of complex traits such as yield. With the annotated and ordered reference genome sequence in place, researchers and breeders can now easily access sequence-level information to precisely define the necessary changes in the genomes for breeding programs. This will be realized through the implementation of new DNA marker platforms and targeted breeding technologies, including genome editing

Impact de la sélection sur la diversité des blés tendres français et conséquences sur la gestion des collections.

National audienc

Ray grass anglais: etude de la variabilite genetique et creation de populations ameliorees.

National audienc

Histoire et diversité des blés cultivés du Néolithique à nos jours

Histoire et diversité des blés cultivés du Néolithique à nos jours. Colloque jeunes chercheurs unité BI