Microsatellite diversity and broad scale geographic structure in a model legume: building a set of nested core collection for studying naturally occurring variation in Medicago truncatula

BACKGROUND: Exploiting genetic diversity requires previous knowledge of the extent and structure of the variation occurring in a species. Such knowledge can in turn be used to build a core-collection, i.e. a subset of accessions that aim at representing the genetic diversity of this species with a minimum of repetitiveness. We investigate the patterns of genetic diversity and population structure in a collection of 346 inbred lines representing the breadth of naturally occurring diversity in the Legume plant model Medicago truncatula using 13 microsatellite loci distributed throughout the genome. RESULTS: We confirm the uniqueness of all these genotypes and reveal a large amount of genetic diversity and allelic variation within this autogamous species. Spatial genetic correlation was found only for individuals originating from the same population and between neighbouring populations. Using a model-based clustering algorithm, we identified four main genetic clusters in the set of individuals analyzed. This stratification matches broad geographic regions. We also identified a set of "admixed" individuals that do not fit with this population structure scheme. CONCLUSION: The stratification inferred is discussed considering potential historical events like expansion, refuge history and admixture between neighbouring groups. Information on the allelic richness and the inferred population structure are used to build a nested core-collection. The set of inbred lines and the core collections are publicly available and will help coordinating efforts for the study of naturally occurring variation in the growing Medicago truncatula community

The molecular genetic linkage map of the model legume Medicago truncatula: an essential tool for comparative legume genomics and the isolation of agronomically important genes

BACKGROUND: The legume Medicago truncatula has emerged as a model plant for the molecular and genetic dissection of various plant processes involved in rhizobial, mycorrhizal and pathogenic plant-microbe interactions. Aiming to develop essential tools for such genetic approaches, we have established the first genetic map of this species. Two parental homozygous lines were selected from the cultivar Jemalong and from the Algerian natural population (DZA315) on the basis of their molecular and phenotypic polymorphism. RESULTS: An F2 segregating population of 124 individuals between these two lines was obtained using an efficient manual crossing technique established for M. truncatula and was used to construct a genetic map. This map spans 1225 cM (average 470 kb/cM) and comprises 289 markers including RAPD, AFLP, known genes and isoenzymes arranged in 8 linkage groups (2n = 16). Markers are uniformly distributed throughout the map and segregation distortion is limited to only 3 linkage groups. By mapping a number of common markers, the eight linkage groups are shown to be homologous to those of diploid alfalfa (M. sativa), implying a good level of macrosynteny between the two genomes. Using this M. truncatula map and the derived F3 populations, we were able to map the Mtsym6 symbiotic gene on linkage group 8 and the SPC gene, responsible for the direction of pod coiling, on linkage group 7. CONCLUSIONS: These results demonstrate that Medicago truncatula is amenable to diploid genetic analysis and they open the way to map-based cloning of symbiotic or other agronomically-important genes using this model plant

Biodiversity Informatics: An interactive computer- aided identification and knowledge base on tree species of Lao PDR

International audienceObjectives • To enrich the existing knowledge base (BIOTIK project*) on a major "hot spot" of biodiversity: the rain forests of Annamite Mountain range of Lao PDR, in the framework of the Inventory of biodiversity of forest canopies conducted in 2012 in Lao PDR under F. Hallé scientific direction, and also to participate to broader initiatives such as Pl@ntNet project**. • To translate the identification tool in the Lao language in order to contribute to the capacity-building in plant taxonomy in the country. • To transfer the identification system to touch pads, enabling plant identification and entering data directly in the field

Les collections de ressources génétiques : un enjeu pour l’adaptation des espèces cultivées

National audienc

ARCAD : une nouvelle plateforme dédiée à la caractérisation des semences et à l'analyse de leur qualité germinative

National audienc

La conservation des ressources génétiques des plantes fourragères : quelle diversité génétique au sein des collections ?

National audienceThe establishment of collections (ex situ conservation of the genetic diversity) is a means of studying the structuration of this diversity, and gives the breeders access to sources of genetic variability which they may use in programmes of cultivar breeding. In the case of the pasture species and the related wild species, actions should be undertaken for the preservation of the natural sites themselves, whether under cultivation or not (in situ conservation). The management of the genetic resources in forage species and lawn species is part of a national policy of genetic resources, undertaken at the request of the 'Bureau of Genetic Resources'. A national collection has been constituted ; other collections are managed by INRA and/or by private breeders. The long-term conservation of large collections raises technical difficulties. It is possible to reduce the number of entries by conserving only a limited number of them (core collection) or by grouping them into pools ; in both cases it is necessary to have the best representation of the diversity present in the initial collection by studying its structuration beforehand.La caractérisation et l’étude de la structuration de la diversité génétique des espèces végétales imposent le recours à des expérimentations planifiées. Afin de mener à bien de telles investigations, il est nécessaire de constituer des collections de ressources génétiques et d’organiser leur conservation (conservation ex situ de la diversité génétique). La mise en place de collections est aussi pour les sélectionneurs le moyen de disposer de "réservoirs" de variabilité génétique pour les programmes de création variétale. Le maintien de collections ne doit cependant pas être considéré comme le seul moyen efficace de conservation à long terme de la diversité génétique. Dans le cas des espèces prairiales et des espèces sauvages apparentées, le développement d’actions de préservation des sites naturels, exploités ou non, où ces espèces sont spontanées (conservation in situ), ainsi que des programmes de gestion dynamique de la variabilité doivent être envisagés. La gestion des ressources génétiques des espèces fourragères et à gazon s’inscrit dans le cadre d’une politique nationale des ressources génétiques, mise en place sous l’impulsion du Bureau des Ressources Génétiques. Une Collection nationale a été constituée ; elle rassemble des variétés radiées des catalogues français, d’anciennes variétés de pays et des populations naturelles issues de prospections sur le territoire français. D’autres collections plus vastes font l’objet d’une gestion commune entre l’INRA et les obtenteurs privés, ou bien sont détenues par l’INRA. La conservation des accessions d’une collection doit s’accompagner de l’enregistrement de données de passeport (origine, taxinomie, informations géographiques et écologiques), ces informations étant le plus souvent complétées de données d’évaluation phénotypique, voire de données de marquage génétique. Durant la décennie passée, des actions importantes ont été entreprises par l’INRA pour la prospection et l’étude de populations naturelles françaises de ray-grass anglais et de populations spontanées espagnoles de luzerne pérenne. Ces études ont permis d’analyser la structuration de la diversité génétique collectionnée, de préciser les relations entre compartiment cultivé et sauvage dans le cas de la luzerne, et d’initier des actions de conservation et de sélection. La conservation à long terme de collections d’effectif important peut se heurter à des difficultés techniques, qui rendent souhaitable une réduction du nombre d’entités à conserver. Ceci peut se réaliser en ne conservant qu’un nombre limité d’accessions (‘core collection’), ou bien en regroupant les accessions sous forme de pools ; dans les deux cas, il est nécessaire de représenter au mieux la diversité de la collection initiale en s’appuyant sur une étude préalable de sa structuration

ARCAD: Challenges faced by a new platform for preserving, characterizing and distributing tropical and Mediterranean crop genetic resources for research

National audienc

Potential Implications of Climate Change on Aegilops Species Distribution: Sympatry of These Crop Wild Relatives with the Major European Crop Triticum aestivum and Conservation Issues.

Gene flow from crop to wild relatives is a common phenomenon which can lead to reduced adaptation of the wild relatives to natural ecosystems and/or increased adaptation to agrosystems (weediness). With global warming, wild relative distributions will likely change, thus modifying the width and/or location of co-occurrence zones where crop-wild hybridization events could occur (sympatry). This study investigates current and 2050 projected changes in sympatry levels between cultivated wheat and six of the most common Aegilops species in Europe. Projections were generated using MaxEnt on presence-only data, bioclimatic variables, and considering two migration hypotheses and two 2050 climate scenarios (RCP4.5 and RCP8.5). Overall, a general decline in suitable climatic conditions for Aegilops species outside the European zone and a parallel increase in Europe were predicted. If no migration could occur, the decline was predicted to be more acute outside than within the European zone. The potential sympatry level in Europe by 2050 was predicted to increase at a higher rate than species richness, and most expansions were predicted to occur in three countries, which are currently among the top four wheat producers in Europe: Russia, France and Ukraine. The results are also discussed with regard to conservation issues of these crop wild relatives

ARCAD: Florilege, the access portal to French collections of plant genetic resources.

National audienc