High-quality SNPs from genic regions highlight introgression patterns among European white oaks (Quercus petraea and Q. robur)

International audienceIn the post-genomics era, non-model species like most Fagaceae still lack operational diversity resources for population genomics studies. Sequence data were produced from over 800 gene fragments covering ~530 kb across the genic partition of European oaks, in a discovery panel of 25 individuals from western and central Europe (11 Quercus petraea, 13 Q. robur, one Q. ilex as an outgroup). Regions targeted represented broad functional categories potentially involved in species ecological preferences, and a random set of genes. Using a high-quality dedicated pipeline, we provide a detailed characterization of these genic regions, which included over 14500 polymorphisms, with ~12500 SNPs −218 being triallelic-, over 1500 insertion-deletions, and ~200 novel di- and tri-nucleotide SSR loci. This catalog also provides various summary statistics within and among species, gene ontology information, and standard formats to assist loci choice for genotyping projects. The distribution of nucleotide diversity (θπ) and differentiation (FST) across genic regions are also described for the first time in those species, with a mean n θπ close to ~0.0049 in Q. petraea and to ~0.0045 in Q. robur across random regions, and a mean FST ~0.13 across SNPs. The magnitude of diversity across genes is within the range estimated for long-term perennial outcrossers, and can be considered relatively high in the plant kingdom, with an estimate across the genome of 41 to 51 million SNPs expected in both species. Individuals with typical species morphology were more easily assigned to their corresponding genetic cluster for Q. robur than for Q. petraea, revealing higher or more recent introgression in Q. petraea and a stronger species integration in Q. robur in this particular discovery panel. We also observed robust patterns of a slightly but significantly higher diversity in Q. petraea, across a random gene set and in the abiotic stress functional category, and a heterogeneous landscape of both diversity and differentiation. To explain these patterns, we discuss an alternative and non-exclusive hypothesis of stronger selective constraints in Q. robur, the most pioneering species in oak forest stand dynamics, additionally to the recognized and documented introgression history in both species despite their strong reproductive barriers. The quality of the data provided here and their representativity in terms of species genomic diversity make them useful for possible applications in medium-scale landscape and molecular ecology projects. Moreover, they can serve as reference resources for validation purposes in larger-scale resequencing projects. This type of project is preferentially recommended in oaks in contrast to SNP array development, given the large nucleotide variation and the low levels of linkage disequilibrium revealed

Quercus portal

Quercus portail donne accès à diverses bases de données concernant les ressources génétiques et génomiques et d'information. Il comprend également une interface utilisateur dynamique permettant la soumission des requêtes complexes dans toutes les bases de données (recherche globale). En outre, une section statique du portail est consacrée à l'information générale du genre Quercus.Quercus Portal provides access to various databases regarding genetic and genomic resources and information. It includes also a dynamic user interface allowing the submission of complex queries across all data bases (Global Search). Additionally a static section of the portal is devoted to general information of the genus Quercus

Quercus portal

Quercus portail donne accès à diverses bases de données concernant les ressources génétiques et génomiques et d'information. Il comprend également une interface utilisateur dynamique permettant la soumission des requêtes complexes dans toutes les bases de données (recherche globale). En outre, une section statique du portail est consacrée à l'information générale du genre Quercus.Quercus Portal provides access to various databases regarding genetic and genomic resources and information. It includes also a dynamic user interface allowing the submission of complex queries across all data bases (Global Search). Additionally a static section of the portal is devoted to general information of the genus Quercus

SUMATECS : Gestion durable des sols contaminés par les éléments traces : état de l'art et besoins de recherche

National audienceLe développement des technologies de remédiation in situ dites "douces" comme la phytoremédiation ou la stabilisation in situ, fait l'objet de recherches intenses depuis plusieurs dizaines d'années (Fig 1). D'importants progrès ont été réalisés au niveau expérimental mais l'application de ces technologies en pratique n'en est qu'à ses débuts. Le projet européen SUMATECS a pour objectif de faire un état de l'art à partir de la littérature et des projets disponibles, y compris les projets nationaux et les procédures locales, pour identifier le statut actuel de la recherche et des applications en Europe. Ce projet a également pour objectif de proposer des scénarios de remédiation incluant les impacts potentiels sur l'environnement local et de définir les futurs besoins de recherche. Plus particulièrement, le projet s'est attaché à (a) réaliser un état de l'art de la recherche et de la mise en pratique des technologies douces de remédiation, (b) réaliser un état de l'art des aspects environnementaux et socio-économiques associées à ces technologies, (c) de rassembler et d'évaluer les méthodes existantes pour déterminer les fractions d'éléments traces (métaux et non-métaux) pertinentes pour leur écotoxicologie (c'est à dire la fraction biodisponible), et (d) de réaliser un état de l'art des outils d'aide à la décision existants. En plus de l'approche bibliographique, des essais en laboratoire ayant pour objectif la valorisation de la biomasse contaminée ont été conduits. Une synthèse des résultats obtenus ainsi que les besoins de recherche identifiés seront présentés lors du colloque

SUMATECS : Gestion durable des sols contaminés par les éléments traces : état de l'art et besoins de recherche

Le développement des technologies de remédiation in situ dites "douces" comme la phytoremédiation ou la stabilisation in situ, fait l'objet de recherches intenses depuis plusieurs dizaines d'années (Fig 1). D'importants progrès ont été réalisés au niveau expérimental mais l'application de ces technologies en pratique n'en est qu'à ses débuts. Le projet européen SUMATECS a pour objectif de faire un état de l'art à partir de la littérature et des projets disponibles, y compris les projets nationaux et les procédures locales, pour identifier le statut actuel de la recherche et des applications en Europe. Ce projet a également pour objectif de proposer des scénarios de remédiation incluant les impacts potentiels sur l'environnement local et de définir les futurs besoins de recherche. Plus particulièrement, le projet s'est attaché à (a) réaliser un état de l'art de la recherche et de la mise en pratique des technologies douces de remédiation, (b) réaliser un état de l'art des aspects environnementaux et socio-économiques associées à ces technologies, (c) de rassembler et d'évaluer les méthodes existantes pour déterminer les fractions d'éléments traces (métaux et non-métaux) pertinentes pour leur écotoxicologie (c'est à dire la fraction biodisponible), et (d) de réaliser un état de l'art des outils d'aide à la décision existants. En plus de l'approche bibliographique, des essais en laboratoire ayant pour objectif la valorisation de la biomasse contaminée ont été conduits. Une synthèse des résultats obtenus ainsi que les besoins de recherche identifiés seront présentés lors du colloque

Sustainable management of trace element contaminated soils – Development of a decision tool system and its evaluation for practical application (SUMATECS) - Final Research Report

The development of “gentle”, in-situ remediation technologies (i.e. phytoremediation, in situ immobilisation, etc.) has been under intensive research over the last few decades. A great deal of progress has been achieved at the experimental level, but the application of these technologies as practical solutions is still at its early stage. First; methods for determination of the trace element (metals and non-metals) fractions relevant for their ecotoxicology (i.e., the bioavailable fraction) still have their limitations since they may insufficiently reflect the potential risks. Second, a number of gentle in-situ remediation options are available and thus a decision tool system has to be developed allowing to choose the most suitable technique. Third, the application of gentle remediation options may have significant implications for the environment and the socio-economic situation of the local population. TECS (trace element contaminated soils) management moved into a new century where environmental decisions must be ‘socially-robust’ within a context of sustainable development and is a part of the conceptual framework “Risk-based land management”. All efforts need to ensure management and/or remediation is affordable, feasible, effective and sustainable. The aim of this project was to summarise the current state of the art using data from literature (SCI journals, project reports) and from a questionaire that has been sent to all kind of experts involved in remeddiation of trace element contaminated soils (scientists, stakeholders, policy makers, etc.). All collected information was used to identify the current status of research and application in Europe and to (i) derive decision tool systems, remediation scenarios including the potential impacts on the local environment and (ii) define further research needs

Sustainable management of trace element contaminated soils – Development of a decision tool system and its evaluation for practical application (SUMATECS) - Final Research Report

The development of “gentle”, in-situ remediation technologies (i.e. phytoremediation, in situ immobilisation, etc.) has been under intensive research over the last few decades. A great deal of progress has been achieved at the experimental level, but the application of these technologies as practical solutions is still at its early stage. First; methods for determination of the trace element (metals and non-metals) fractions relevant for their ecotoxicology (i.e., the bioavailable fraction) still have their limitations since they may insufficiently reflect the potential risks. Second, a number of gentle in-situ remediation options are available and thus a decision tool system has to be developed allowing to choose the most suitable technique. Third, the application of gentle remediation options may have significant implications for the environment and the socio-economic situation of the local population. TECS (trace element contaminated soils) management moved into a new century where environmental decisions must be ‘socially-robust’ within a context of sustainable development and is a part of the conceptual framework “Risk-based land management”. All efforts need to ensure management and/or remediation is affordable, feasible, effective and sustainable. The aim of this project was to summarise the current state of the art using data from literature (SCI journals, project reports) and from a questionaire that has been sent to all kind of experts involved in remeddiation of trace element contaminated soils (scientists, stakeholders, policy makers, etc.). All collected information was used to identify the current status of research and application in Europe and to (i) derive decision tool systems, remediation scenarios including the potential impacts on the local environment and (ii) define further research needs