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In marine systems, coastal environments are viewed as discontinuous and made up of a mosaic of diversified seascapes, leading to highly fragmented species distributions. Coastal marine species are thus structured in networks of populations that are connected to each other through larval dispersal. Understanding functioning and connectivity patterns between populations of a given species is essential to adapt conservation strategies. The fan mussel, Pinna nobilis, endemic to the Mediterranean Sea, is facing today a major crisis threatening its survival. Starting in October 2016, mass mortalities caused by the protozoan parasite Haplosporidium pinnae have been reported through the entire Mediterranean Sea. This is an unprecedented situation for which neither the mortality rates (around 100%) nor the speed of propagation have ever been recorded for a marine species, and it could lead to the potential extinction of P. nobilis. By focusing on the Occitan coast, this work provides knowledge on the biology and ecology of the species but also on the processes which allow the replenishment of its populations in order to suggest priorities for conservation. We highlighted the wide diversity of habitats colonized by the species and the importance of lagoons as they shelter 90 % of fan mussels recorded on the Occitan coast, and seem to provide natural refuge as only the lagoon populations remain unaffected by H. pinnae. Using newly developed microsatellite markers, we highlighted a very homogeneous genetic structure over the entire coast, which implies some connectivity and suggests that most of the genetic diversity of the species remains preserved in the lagoons. By focusing on the population of Peyrefite Bay, in the Marine Protected Area of Cerbère-Banyuls, through parentage analysis, we provided knowledge on the demographic dynamics and the repopulation processes of the species. Based on the present work, we defined recommendations that will help to design adapted conservation measures that will be essential for the survival of the species., Les systèmes marins côtiers sont généralement discontinus et constitués d’une mosaïque de paysages sous-marins différents, créant ainsi des distributions parfois très fragmentées chez les espèces qui les colonisent. Les espèces marines côtières sont donc structurées en réseaux de populations connectées entre elles via la dispersion larvaire. Comprendre le fonctionnement et la connectivité entre les populations d’une espèce est indispensable pour adapter les stratégies de conservation. La grande nacre, Pinna nobilis, est une espèce endémique de la mer Méditerranée qui fait aujourd’hui face à une crise majeure qui menace sa survie. Depuis Octobre 2016, des mortalités de masse sont signalées sur ses populations, à travers toutes la mer Méditerranée, causées par un protozoaire parasite, Haplosporidium pinnae. Il s’agit d’un évènement sans précédent, que ce soit par le taux de mortalité (près de 100 %) ou la vitesse de propagation, et qui pourrait conduire à l’extinction de l’espèce. En se focalisant sur le littoral Occitan, cette thèse apporte des connaissances sur la biologie et l’écologie de l’espèce mais aussi sur son fonctionnement et les processus qui permettent le maintien de ses populations afin de proposer des priorités de conservation. Ainsi, nous avons mis en évidence la diversité d’habitats colonisés par l’espèce ainsi que l’importance des lagunes car elles abritent près de 90 % des grandes nacres, sur le littoral Occitan, et semblent servir d’habitat refuge à l’espèce en limitant l’infestation par le parasite. A l’aide de marqueurs microsatellites nouvellement développés, nous avons montré une structure génétique très homogène sur toute la côte, ce qui implique un certain niveau de connectivité et laisse penser qu’une grande partie de la diversité génétique de l’espèce reste préservée dans les lagunes. En se focalisant sur la population de la baie de Peyrefite, dans la Réserve Naturelle Marine de Cerbère-Banyuls, et grâce à une analyse de parenté, nous avons apporté des connaissances sur la dynamique démographique et les processus de repeuplement de l’espèce. L’ensemble de cette thèse permet de définir des recommandations qui seront utiles à la mise en place de mesures de conservation adaptées, indispensables pour la survie de l’espèce.

Marine ecosystems formed by kelp forests are severely threatened by global change and local coastline disturbances in many regions. In order to take appropriate conservation, mitigation, and restoration actions, it is crucial to identify the most diverse populations which could serve as a “reservoir” of genetic diversity. This requires the development of specifc tools, such as microsatellite markers to investigate the level and spatial distribution of genetic diversity. Here, we tested new polymorphic microsatellite loci from the genome of the kelp, Laminaria digitata, and tested them for cross-amplifcation and polymorphism in four closely related congeneric species (Laminaria hyperborea, Laminaria ochroleuca, Laminaria rodriguezii, and Laminaria pallida). Adding these 20 new microsatellite loci to the ten L. digitata loci previously developed by Billot et al. (Mol Ecol 7:1778-1780, 1998) and Brenan et al. (J R Soc Interface 11:1-12, 2014) and to the ten L. ochroleuca loci previ ously developed by Coelho et al. (Conserv Genet Resource 6:949-950, 2014), we retained a total of 30 polymorphic loci for L. digitata, 21 for L. hyperborea, 16 for L ochroleuca, 18 for L. rodriguezii, and 12 for L. pallida. These markers have been tested for the frst time in the last two species. As predicted, the proportion of markers that cross-amplifed between species decreased with increasing genetic distance. In addition, as problems of species identifcation were reported in this family, mainly between L. digitata and Hedophyllum nigripes, but also between L. digitata, L. hyperborea, and L. ochroleuca in areas where their range distributions overlap, we report a rapid PCR identifcation method based on species-specifc COI mitochondrial primers that allows these four species of kelp to be rapidly distinguished. info:eu-repo/semantics/publishedVersion

The genotyping of European fruit tree collections has helped to identify synonyms, determine parentage, reveal key specimens in the collections and provide information on the development of modern cultivars from one or several progenitors. However, studies on European plum Prunus domestica L. accessions have been lagging behind, mainly because of the hexaploid chromosome number. In this co-operative study, 104 accessions conserved by 14 partners across Europe were phenotyped for 20 descriptors, and genotyped for 8 SSR loci together with 8 reference cultivars. Based on the descriptors and additional information supplied by the partners, as well as the scientific and horticultural literature, each accession was assigned to one of six pomological groups; (1) egg plums sensu lato (E), (2) prunes of the French d’Agen type (P/A), (3) prunes of the Central-Southeast European Zwetschen type (P/Z), (4) greengages (G), (5) mirabelles (M) and (6) bullaces, damsons and var. pomariorum (D/B). A MANOVA conducted on descriptor data revealed significant differentiation among the pomological groups as well as a geographic impact on the differentiation of local plum accessions in Europe. SSR data showed that two trios and seven pairs of genotypes had very similar allele profiles and possibly are genetically identical in spite of different accession names. An AMOVA indicated sparse genetic differentiation when accessions were grouped according to geographic origin whereas significant differences were obtained among pomological groups. A Bayesian analysis of genetic structure, as well as a discriminant analysis of principal components (DAPC), further revealed levels of similarity among and within the different pomological groups, suggesting that egg plums sensu lato (E) and greengages (G) can be referred to subsp. domestica while damsons and bullaces (D/B) but also Central-Southeast European prunes (P/Z) show more affinity to subsp. insititia. The small and possibly heterogeneous groups with mirabelles (M) and prunes of the d’Agen type (P/A) take an intermediate position suggesting a hybridogenic origin.

International audience; Crop diversity is shaped by biological and social processes interacting at different spatiotemporal scales. Here we combined population genetics and ethnobotany to investigate date palm (Phoenix dactylifera L.) diversity in Siwa Oasis, Egypt. Based on interviews with farmers and observation of practices in the field, we collected 149 date palms from Siwa Oasis and 27 uncultivated date palms from abandoned oases in the surrounding desert. Using genotyping data from 18 nuclear and plastid microsatellite loci, we confirmed that some named types each constitute a clonal line, i.e. a true-to-type cultivar. We also found that others are collections of clonal lines, i.e. ethnovarieties, or even unrelated samples, i.e. local categories. This alters current assessments of agrobiodiversity, which are visibly underestimated, and uncovers the impact of low-intensity, but highly effective, farming practices on biodiversity. These hardly observable practices, hypothesized by ethnographic survey and confirmed by genetic analysis, are enabled by the way Isiwans conceive and classify living beings in their oasis, which do not quite match the way biologists do: a classic disparity of etic vs. emic categorizations. In addition, we established that Siwa date palms represent a unique and highly diverse genetic cluster, rather than a subset of North African and Middle Eastern palm diversity. As previously shown, North African date palms display evidence of introgression by the wild relative Phoenix theophrasti Greuter, and we found that the uncultivated date palms from the abandoned oases share even more alleles with this species than cultivated palms in this region. The study of Siwa date palms could hence be a key to the understanding of date palm diversification in North Africa. Integration of ethnography and population genetics promoted the understanding of the interplay between diversity management in the oasis (short-time scale), and the origins and dynamic of diversity through domestication and diversification (long-time scale).; La diversité des plantes cultivées est façonnée par des processus biologiques et sociaux qui interagissent à différentes échelles spatiotemporelles. Nous avons ici combiné la génétique des populations et l’ethnobotanique pour étudier la diversité du palmier-dattier (Phoenix dactylifera L.) dans l’oasis de Siwa, en Égypte. Sur la base d’entretiens avec des agriculteurs et de l’observation des pratiques sur le terrain, nous avons collecté 149 palmiers dattiers de l’oasis de Siwa et 27 palmiers dattiers non cultivés provenant d’oasis abandonnées dans le désert environnant. En utilisant les données de génotypage de 18 loci microsatellites nucléaires et plastidiques, nous avons confirmé que certains types nommés constituent chacun une ligne clonale, c’est-à-dire un « cultivar vrai » (true-to-type). Nous avons également constaté que d’autres sont des collections de lignes clonales, c’est-à-dire des « ethnovariétés », voire même des échantillons non apparentés, c’est-à-dire des « catégories locales ». Cela modifie les évaluations existantes de l’agrobiodiversité, qui sont visiblement sous-estimées, et révèle l’impact des pratiques agricoles de faible intensité, mais très efficaces, sur la biodiversité. Ces pratiques difficilement observables, supposées par l’enquête ethnographique et confirmées par l’analyse génétique, sont rendues possibles par la façon dont les Isiwans conçoivent et classifient les êtres vivants dans leur oasis, qui ne correspond pas tout à fait à la façon dont les biologistes le font : une disparité classique des catégorisations étiques vs. émiques. En outre, nous avons établi que les palmiers dattiers de Siwa représentent un groupe génétique unique et très diversifié, plutôt qu’un sous-ensemble de la diversité des palmiers d’Afrique du Nord et du Moyen-Orient. Comme nous l’avons montré précédemment, les palmiers dattiers d’Afrique du Nord présentent des signes d’introgression par le parent sauvage Phoenix theophrasti Greuter, et nous avons constaté que les palmiers dattiers non cultivés des oasis abandonnées partagent encore plus d’allèles avec cette espèce que les palmiers cultivés de cette région. L’étude des palmiers dattiers de Siwa pourrait donc être une clé pour la compréhension de la diversification des palmiers dattiers en Afrique du Nord. L’intégration de l’ethnographie et de la génétique des populations a permis de comprendre l’interaction entre la gestion de la diversité dans l’oasis (l’échelle du court terme) et les origines et la dynamique de la diversité au travers de la domestication et de la diversification (l’échelle du long terme).

International audience; AbstractKey messageA moderate genetic diversity, the absence of a significant genetic differentiation between wild and cultivated stands and a highly admixed genetic structure of sweet chestnut with two main clusters were observed in France using two different data sets with 10 and 18 microsatellites.ContextRenewed interest in European chestnut in France is focused on finding locally adapted populations partially resistant to ink disease and identifying local landraces.AimsWe genotyped trees to assess (i) the genetic diversity of wild and cultivated chestnut across most of its range in France, (ii) their genetic structure, notably in relation with the sampled regions, and (iii) to a lesser extent the relations between French chestnuts with 10 cultivated chestnuts from the Northwest of Spain that were previously classified in the Iberian or Italian groups.MethodsA total of 693 trees in 16 sampling regions in France were genotyped at 24 SSRs and 1401 trees in 17 sampling regions at 13 SSRs.ResultsGenetic diversity was moderate in most sampling regions, with redundancy between them. No significant differentiation was found between wild and cultivated chestnut. A genetic structure analysis with no a priori information found a low yet significant structure and identified two clusters at 18 SSRs. One cluster gathers trees from south-east France and Corsica (RPP1), and another cluster gathers trees from all other sampled regions (RPP2). A substructure was detected at 10 SSRs suggesting differentiation within both RPP1 and RPP2. RPP1 was split between south-east France and Corsica. RPP2 was split between northwest France, Aveyron, Pyrenees, and a last cluster gathering individuals from several other regions.ConclusionThe genetic structure within and between our sampling regions is likely the result of natural events (recolonization after the last glaciation) and human activities (migration and exchanges). These advances on our knowledge of chestnut genetic diversity and structure will benefit conservation and help our local partners’ valorization efforts.

International audience; Evidence of strong gene flow among French populations of the carrot cyst nematode [i]Heterodera carotae[/i]

Forest fragmentation may affect mating and pollen dispersal patterns through conversion of continuous forests into small, spatially isolated remnant patches and individual trees in an anthropogenic landscape. We investigated reproductive investment and success, pollen dispersal, mating system, and genetic diversity and spatial structure of Qualea grandiflora trees in two environmental contexts: a continuous natural Cerrado area and isolated individuals on roadsides. Roadside trees produced more flowers and more fruit than Cerrado trees. Pollen dispersal kernels were fat-tailed in both contexts, indicating long-distance dispersal, but in Cerrado the mean pollen dispersal distance (524.7 m) and the effective number of pollen donors per mother-tree (Nep = 12.7) were higher than for roadside trees (60.9 m, Nep = 4.6). The levels and structure of genetic diversity, outcrossing rates ( $$t_{m}$$ > 0.98), and mating among relatives ( $$t_{m} - t_{s}$$ < 0.1) were similar in both environmental contexts. Allelic richness and number of private alleles were similar between the two environments. The fixation index was significantly lower in adults (minimum of 0.08) than in offspring (minimum of 0.23) in both contexts, suggesting selection against inbred individuals between offspring and adult stage. Our results indicate that the spatial isolation of roadside trees, by increasing the number of flowers produced, decreased pollinator movements, thereby reducing effective pollen flow and the number of pollen donors. All these results suggest that roadside trees can be used for harvesting seeds for recovery plans, and that these trees are a biological legacy, and reservoir of Q. grandiflora genetic diversity, from the original Cerrado forest.

High population of the whitefly, Bemisia tabaci Gennadius, a cryptic species complex had been associated with the vectoring and spread of viruses causing two diseases of cassava in East Africa: the cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). Among the B. tabaci species, sub-Saharan Africa 2 (SSA2) was the vector associated with an epidemic of CMD since the 1990s in Uganda. However, this species is now replaced by the SSA1 and led to development of another epidemic by CBSD since the mid 2000s. The spread of both diseases toward South and West Africa is feared with this new supposed invader. In my thesis I have used ecological data and molecular approaches (mitochondrial and nuclear markers) to better understand the factors driving the presence of the superabundant whitefly populations on cassava in East Africa. We have analyzed: i) species abundance, diversity and distribution (geographic and host plants) along a transect survey over three East African countries: Uganda, Tanzania, Malawi, ii) the genetic diversity and structure of current populations of B. tabaci species, and iii) comparing genetic changes between the old and new populations collected in 1997 and 2017, respectively.This study involving large number of samples provided insights of a more complex picture than expected. SSA1 was found to be the source of the some observed outbreaks although other species, notably IO and sub-group 3 of SSA1 (SSA1-SG3) have also shown this capability. The observed outbreaks are therefore not just related to a single species in East Africa. In addition, we showed that the species community and its genetic diversity differ from one country to another, involving different epidemiological situations, without any clear pattern of invasion detected between the countries. Analysis of old samples did not show the involvement of a new species or the emergence of a new population in 20 years, although the dynamics within the whitefly genetic groups was observed over time. Our results contributed new knowledge on the super abundant populations on cassava in Eastern Africa and help develop targeted control measures for the local populations., Des pullulations d’aleurodes du complexe d'espèces cryptiques de Bemisia tabaci ont été associées à la propagation de deux maladies frappant le manioc en Afrique orientale: la maladie de la mosaïque du manioc (CMD) et, plus récemment (2000), la maladie de la striure brune du manioc (CBSD). Parmi les espèces d’aleurodes de ce complexe, l’espèce SSA2 a été associée à la première épidémie de CMD au cours des années 1990 en Ouganda. Cependant, SSA2 aurait été remplacée par SSA1 dans les années 2000, provoquant une recrudescence de CMD et de CBSD, participant à leur propagation dans plusieurs pays voisins. L’hypothèse défendue à ce jour expliquant la propagation de ces maladies vers le sud et l'ouest de l'Afrique incrimine cette nouvelle espèce considérée comme émergente dans certains de ces pays. Dans ma thèse, j’ai utilisé des données écologiques et des approches moléculaires afin de mieux comprendre les facteurs à l'origine des pullulations de vecteurs en Afrique de l'Est. Nous avons ainsi analysé : i) l’abondance, la diversité et la répartition des espèces sur un transect comprenant : Ouganda, Tanzanie et Malawi, ii) la diversité génétique et la structure des populations actuelles des espèces de B. tabaci, iii) des échantillons des années 90 comparés aux populations actuelles (2017). Cette étude nous a permis d’avoir une image d’une situation plus complexe qu’attendue, en effet, l’espèce SSA1 a été détectée comme à l’origine dans certaines des pullulations observées mais également d’autres espèces, notamment IO et SSA1-SG3 ont aussi montrées cette capacité. Les pullulations observées ne sont donc pas uniquement liées à une seule espèce en Afrique de l’Est. En outre, nous avons pu montrer que la communauté d'espèces et sa diversité génétique diffère d'un pays à l'autre, impliquant des situations épidémiologiques différentes, sans aucun schéma d'invasion détecté entre pays. En outre, l’analyse des anciens échantillons n’a pas montré l’implication d’une nouvelle espèce ou population en 20 ans, toutefois, nous avons observé un changement de dynamique au sein des groupes génétiques représentés au cours du temps.

International audience; Effective population sizes have rarely been estimated in ticks despite the importance of this parameter for evaluating the evolutionary and adaptive potential of tick populations. The present study was aimed at evaluating the effective population sizes of Amblyomma variegatum, the tropical bont tick, in three villages in Burkina Faso. For this purpose, microsatellites markers were developed. Eight out of 19 assessed markers provided good amplification results with 4 to 24 alleles recorded per marker on 216 genotyped ticks. The within-samples polymorphism was congruent with Hardy-Weinberg expectations at four markers while sex linkage and/or null alleles were observed at the others. As sampling involved two tick generations, effective population sizes were independently estimated by two methods insensitive to heterozygosity: the first one is based on linkage dis-equilibrium analysis within a single cohort while the second uses the changes in allele frequencies across generations. Both methods estimated the number of reproducing ticks ranging from two to a few tens reproductive adults per village and cohort. Such small estimates are congruent with the rarity of records of acaricide resistance in A. variegatum.

The primary aim of this work was to study the risk of resistance evolution to acetolactate synthase (ALS) inhibiting herbicides in mugwort (Ambrosia artemisiifolia L.) through four points: (i) selection pressure (study of the efficacy of a range of ALS-inhibiting herbicides), (ii) the adaptive response capacity of the weed (determination of the variation in sensitivity to ALS inhibitors between plants and implementation of a recurrent selection programme), (iii) a field study (search for resistance to ALS inhibitors in the field in France), (iv) the study of resistance mechanisms (target-linked - TLR - and non-target-linked - NLR - by a transcriptomics approach). The second objective was to study the connectivity of A. artemisiifolia populations in agricultural landscapes using microsatellite markers developed during this work in order to determine the factors that could facilitate the dispersal of this species and of resistance at the agricultural landscape scale.With regard to herbicide resistance:The response of A. artemisiifolia to ALS inhibiting herbicides is highly variable between substances.Plants surviving the maximum permitted dose and higher doses of metsulfuron were selected to start a recurrent selection programme. After two cycles of selection, there was an intensification of metsulfuron resistance and an emergence of imazamox and tribenuron resistance.Three cases of imazamox resistance were identified in the field, including two cases of pure RNLC and one case of RLC - RNLC coexistence.A transcriptome of A. artemisiifolia was generated using the PacBio sequencing technique to search for genes involved in RNLC mechanisms (RNAseq approach). 62 candidate genes were identified, including ABC transporters, cytochromes P450 and glutathione-S-transferases known to be involved in herbicide degradation.For the study of population connectivity :26 microsatellite markers were developed and revealed high genetic variability. Genetic structuring was studied on a large scale for A. artemisiifolia populations in Europe (invasion area) and North America (area of origin). At a finer scale (agricultural landscape), the genetic structure of populations is still influenced by colonisation events. The migration events that have been identified between areas of ragweed presence suggest moderate gene flow (pollen/seed) and connectivity at the scale of an agricultural territory. In agricultural environments, dispersal of herbicide resistance alleles could easily occur from close to home via pollen flows, and also at longer distances via seed dispersal. Anthropogenic activities play a major role in seed dispersal (agricultural machinery, contaminated seed lots...).Analysis of the reproductive system confirmed that this species is allogamous, which leads to significant intra- and inter-population gene flow.The knowledge acquired in the course of this work could help to develop better adapted control strategies to efficiently fight against A. artemisiifolia in order to limit its expansion, such asDiversified weed control strategies: combination of mechanical (including false seeding) and chemical control (diversification of herbicide modes of action).Extending and diversifying crop rotations by favouring winter crops and/or covering and competitive crops. This knowledge could also be used to combat another weed of the Ambrosia genus, Ambrosia trifida., Ce travail a eu pour but premier d’étudier le risque d’évolution de la résistance aux herbicides inhibiteurs de l’acétolactate synthase (ALS) chez l’ambroisie à feuilles d’armoise (Ambrosia artemisiifolia L.) à travers quatre points : (i) la pression de sélection (étude de l’efficacité d’une gamme d'herbicides inhibiteurs de l’ALS), (ii) la capacité de réponse adaptative de l’adventice (détermination de la variation de la sensibilité aux inhibiteurs de l’ALS entre plantes et mise en place d’un programme de sélection récurrente), (iii) une étude de terrain (recherche de résistance aux inhibiteurs de l’ALS au champ en France), (iv) l’étude des mécanismes de résistance (liée à la cible – RLC – et non liée à la cible – RNLC – par une approche de transcriptomique). Le second objectif fut d’étudier la connectivité des populations d’A. artemisiifolia dans des paysages agricoles à l’aide de marqueurs microsatellites développés lors de ce travail afin de déterminer les facteurs qui pourraient faciliter la dispersion de cette espèce et de la résistance à l’échelle du paysage agricole.En ce qui concerne la résistance aux herbicides : La réponse de d’A. artemisiifolia aux herbicides inhibiteurs de l’ALS est très variable entre substances. Des plantes ayant survécu à la dose maximale autorisée et à des doses supérieures de metsulfuron ont été sélectionnées pour débuter un programme de sélection récurrente. Après deux cycles de sélection, on observe une intensification de la résistance au metsulfuron et une émergence de la résistance à l’imazamox et au tribénuron. Trois cas de résistance à l’imazamox ont été identifiés au champ dont deux cas de pure RNLC et un cas de coexistence RLC – RNLC. Un transcriptome d’A. artemisiifolia a été généré grâce à la technique de séquençage PacBio pour rechercher des gènes impliqués dans les mécanismes de RNLC (approche RNAseq). 62 gènes candidats ont été identifiés dont des transporteurs ABC, des cytochromes P450 ainsi que des glutathione-S-transférases connus pour être impliqués dans la dégradation des herbicides.Pour l’étude de la connectivité des populations : 26 marqueurs microsatellites ont été développés et ont révélé une forte variabilité génétique. La structuration génétique a été étudiée à grande échelle pour des populations d’A. artemisiifolia d’Europe (aire d’invasion) et d’Amérique du Nord (aire d’origine).  À une échelle plus fine (paysage agricole), la structure génétique des populations reste influencée par les évènements de colonisation. Les événements de migration qui ont été identifiés entre zones de présence de l’ambroisie suggèrent des flux de gènes (pollen/semences) et une connectivité modérés à l’échelle d’un territoire agricole. Dans les environnements agricoles, la dispersion des allèles de résistance aux herbicides pourrait se faire facilement de proche en proche via les flux de pollen, et également à plus longue distance via des dispersions de graines. Les activités anthropiques jouent un rôle majeur dans la dispersion des semences (machineries agricoles, lots de semences contaminés…). L’analyse du système de reproduction a confirmé que cette espèce est allogame ce qui entraine des flux de gènes intra- et inter-populations importants.Les connaissances acquises au cours de ce travail pourront aider à développer des stratégies de contrôle mieux adaptées, pour lutter efficacement contre A. artemisiifolia afin de limiter son expansion, telles que : Des stratégies de désherbage diversifiées : combinaison de lutte mécanique (dont faux semis) et chimique (diversification des modes d’action herbicides). Un allongement et une diversification des rotations de cultures en favorisant des cultures d’hiver et/ou des cultures couvrantes et compétitrices. Ces connaissances pourront aussi être utilisées dans la lutte contre une autre espèce adventice du genre Ambrosia, Ambrosia trifida.

White mould can affect the production of a wide range of economically important crops worldwide. The symptoms may be caused by several species, including Sclerotinia subarctica, a species mostly occurring in northern latitudes in sympatry with S. sclerotiorum. Although the two species are morphologically indistinguishable, S. subarctica was reported to have different climatic requirements for mycelial growth and production of apothecia. These differences may affect the precision of white mould risk prediction models that are based on the production of ascospores by S. sclerotiorum. To assess the presence of S. subarctica in France, we adapted a rapid PCR-based test to distinguish S. subarctica from other commonly found species of Sclerotinia. This test was used to characterize a collection of 969 Sclerotinia sp. isolates originating from various plants (bean, canola, carrot, lettuce, melon and witloof chicory), air and soil samples in different regions of France. One single isolate, collected from witloof chicory in northern France, was identified as S. subarctica. When genotyped with five microsatellite markers designed for S. sclerotiorum, this isolate had a haplotypic profile that was clearly distinct from the other isolates. The ITS sequence of this isolate was identical to those of isolates collected in northern Europe and Alaska. Koch’s postulates were verified. When inoculated on witloof chicory, the isolate identified as S. subarctica induced white mould symptoms. This study is the first to report the presence of S. subarctica south of the 51st parallel north and on witloof chicory., La pourriture blanche affecte la production d’un vaste panel de cultures économiquement importantes partout dans le monde. Les symptômes peuvent être causés par plusieurs espèces, dont S. subarctica, une espèce principalement présente sous les latitudes septentrionales en sympatrie avec S. sclerotiorum. Bien que les deux espèces ne puissent être distinguées sur la base de critères morphologiques, S. subarctica semble avoir besoin de conditions climatiques différentes pour sa croissance mycélienne et sa production d’apothécies. Ces différences peuvent affecter la précision des modèles de prédiction de risque de pourriture blanche qui sont basés sur la production d’ascospores par S. sclerotiorum. Pour évaluer la présence de S. subarctica en France, nous avons adapté un test PCR rapide pour distinguer S. subarctica des autres espèces de Sclerotinia communément rencontrées. Ce test a été utilisé pour caractériser une collection de 969 isolats de Sclerotinia sp. provenant de plantes (haricot, colza, carotte, laitue, melon, endive), d’air et de sol dans différentes régions de France. Un seul isolat, prélevé sur endive au nord de la France, a été identifié comme S. subarctica. Lorsque cet isolat a été genotypé avec 5 marqueurs microsatellites spécifiques de S. sclerotiorum, son profil haplotypique était clairement distinct de celui des autres isolats. La séquence ITS de cet isolat était identique à celle des isolats prélevés en Europe du Nord et en Alaska. Les postulats de Koch ont été vérifiés. L’isolat identifié comme S. subarctica a produit les symptômes de pourriture blanche lorsqu’il a été inoculé sur endive. Cette étude est la première à signaler la présence de S. subarctica au sud du 51e parallèle nord et sur endive.

International audience; We evaluate date palm (Phoenix dactylifera L.) agrobiodiversity of Siwa oasis, Egypt, located at the crossroads of ancient Trans-Saharan routes, focusing on diversity both as expressed and maintained by the folk categorization system of Siwa inhabitants (through an ethnographic analysis) and as described by genetic sciences and a morpho- metric tool based on size and geometry of seeds. We verified that some named types are true cultivars, sharing not only a formal identity, important for Isiwan people, but also a genetic identity. However, we also confirm the existence of "ethnovarieties," i.e. voluntary collections of multiple clones sharing phenotypic characteristics with the same local name, suggesting the genetic richness is higher than the apparent agrobiodiversity estimated by a superficial ethnobotanical approach. Finally, our research offers new insights on the relative importance of feral and cultivated date palms.; L'agrobiodiversité de l'oasis de Siwa (Égypte), située au carrefour d'anciennes routes transsahariennes, est évaluée dans cet article en se centrant sur le palmier dattier (Phoenix dactylifera L.), l'espèce "ingénieur écosystémique" de l'oasis. Cette évaluation confronte différentes ontologies: la diversité telle qu'exprimée et maintenue par le système de catégorisation local des habitants de Siwa (à travers les résultats d'une analyse ethnographique) et la diversité décrite par les sciences génétiques et un outil morphométrique basé sur la taille et la géométrie des graines. Au-delà de la simple instrumentalisation d'une discipline par une autre, cette étude offre un espace interdisciplinaire d'enrichissement mutuel et des résultats qui auraient autrement été inaccessibles. L'étude a vérifié que certains types nommés sont de "véritables cultivars", partageant non seulement une identité formelle, ce qui importe aux Isiwans, mais aussi une identité génétique. Cependant, elle corrobore également l'existence d'"ethnovariétés", c'est-à-dire de collections volontaires de multiples clones partageant des caractéristiques phénotypiques sous un même nom donné local, suggérant que la richesse génétique est supérieure à l'apparente agrobiodiversité estimée par une approche ethnobotanique superficielle. Enfin, cette étude offre de nouvelles perspectives sur l'importance relative des palmiers dattiers féraux et cultivés.

WOS:000431009400014; International audience; Selective breeding strategies require pedigree information over generations, but many species produced in aquaculture are too small to be physically tagged at early stages. Consequently, maintaining a sufficient number of separate families is often needed but costly and logistically difficult. Alternatively, parentage assignment can be obtained using DNA markers. We developed a panel of single nucleotide polymorphism (SNP) markers for the European abalone Haliotis tuberculata using an existing transcriptomic resource. An initial set of 2,176,887 SNPs was filtered to select 500 for high throughput genotyping. Of these, 298 SNPs were amplified in at least 90% of our H. tuberculata samples, consisting of a mixed family cohort (945 offspring) generated by crossing 40 abalones, and 5 full-sib training families (70 offspring). Based on amplification success among parents, minimum allele frequency and checks carried out against the training families, a subset of 123 markers was used to carry out parentage assignment in our mixed family cohorts. Maximum likelihood and exclusion-based methods of parentage assignment yielded consistent results, allowing parentage to be assigned in 98.9% of the studied progeny. Optimization of markers suggests that the 60 most informative SNPs may be sufficient for 95% assignment success in these progeny. The panel was also used to estimate effective population size, and revealed a low N-e due to high variance of reproductive success between parents. Our panel could be used to estimate genetic parameters of traits in mixed family cohorts, an essential stage to initiate selective breeding in H. tuberculata. It could also be useful tool in the context of monitoring stock enhancement and population genetics studies.

International audience; We evaluate date palm (Phoenix dactylifera L.) agrobiodiversity of Siwa oasis, Egypt, located at the crossroads of ancient Trans-Saharan routes, focusing on diversity both as expressed and maintained by the folk categorization system of Siwa inhabitants (through an ethnographic analysis) and as described by genetic sciences and a morpho- metric tool based on size and geometry of seeds. We verified that some named types are true cultivars, sharing not only a formal identity, important for Isiwan people, but also a genetic identity. However, we also confirm the existence of "ethnovarieties," i.e. voluntary collections of multiple clones sharing phenotypic characteristics with the same local name, suggesting the genetic richness is higher than the apparent agrobiodiversity estimated by a superficial ethnobotanical approach. Finally, our research offers new insights on the relative importance of feral and cultivated date palms.; L'agrobiodiversité de l'oasis de Siwa (Égypte), située au carrefour d'anciennes routes transsahariennes, est évaluée dans cet article en se centrant sur le palmier dattier (Phoenix dactylifera L.), l'espèce "ingénieur écosystémique" de l'oasis. Cette évaluation confronte différentes ontologies: la diversité telle qu'exprimée et maintenue par le système de catégorisation local des habitants de Siwa (à travers les résultats d'une analyse ethnographique) et la diversité décrite par les sciences génétiques et un outil morphométrique basé sur la taille et la géométrie des graines. Au-delà de la simple instrumentalisation d'une discipline par une autre, cette étude offre un espace interdisciplinaire d'enrichissement mutuel et des résultats qui auraient autrement été inaccessibles. L'étude a vérifié que certains types nommés sont de "véritables cultivars", partageant non seulement une identité formelle, ce qui importe aux Isiwans, mais aussi une identité génétique. Cependant, elle corrobore également l'existence d'"ethnovariétés", c'est-à-dire de collections volontaires de multiples clones partageant des caractéristiques phénotypiques sous un même nom donné local, suggérant que la richesse génétique est supérieure à l'apparente agrobiodiversité estimée par une approche ethnobotanique superficielle. Enfin, cette étude offre de nouvelles perspectives sur l'importance relative des palmiers dattiers féraux et cultivés.

International audience; Date palm (Phoenix dactylifera L.) is mainly cultivated for its edible fruit and is of great socio-economic importance for the populations of arid zones. Analysis of the date palm genetic diversity in the Old World had revealed a strong genetic structure with the existence of two gene pools, one Eastern comprising Asia and Djibouti, and one Western, consisting of North African accessions. So far, mainly date palm populations from countries within the Maghreb and the Middle East were characterized, but no information from the Sahel was included. Here, we present the genetic diversity of date palms from Southeastern Niger. The DNA of 113 date palm accessions were analyzed and compared with a database containing the genetic information of 248 accessions from the Old World. The diversity generated from microsatellite markers was compared to that of the same loci of both the Eastern and Western genetic pools. Our results show that date palms from Southeastern Niger constitute a unique group with a high level of genetic diversity. Moreover, even though this group is included in the Western genetic pool, it shows a specific originality which differentiates it from other Western populations. It also shows one of the lowest admixture levels of the Western pool. Global analysis showed a secondary genetic structure within the Western pool highlighting a new genetic group located in Southeastern Niger that distinguishes itself from the North African group.

International audience; Defining the pattern of genetic diversity of Toxoplasma gondii is important to understand its worldwide distribution. During the last decades, a large number of studies have been published on Toxoplasma genotypes circulating in Europe, in North and South America. Two continents are still largely unexplored, Africa and, to a less extent, Asia. In this last continent, an increasing number of publications reported genotypes circulating in diverse provinces of China, but very few data are available for other Asian countries. After a systematic database search, 47 papers related to T. gondii genotypes in Asia were analyzed. Genetic characterization of DNA was performed by microsatellite markers, or more usually by a multiplex PCR using 11 PCR-RFLP markers, allowing data comparison to draw a first global picture of the population structure of this parasite throughout Asia. Overall, 390 isolates or DNA extracts were completely typed by PCR-RFLP and/or microsatellite marker methods, revealing 36 different PCR-RFLP or equivalent microsatellite genotypes: 15 genotypes identified by a ToxoDB number and 21 atypical or unique genotypes. The most common genotype found in Asia is the genotype ToxoDB#9 (Chinese 1). The clonal types I, II and II variant, and III were also commonly found in Asia. The geographical distribution of these genotypes across Asia may reflect either a continuum with Europe for the western part of Asia (presence of Type II), or the circulation of strains through animal migration or human activities between Africa and the Southwestern part of Asia (Africa 1 genotype in Turkey or ToxoDB#20 both I Sri-Lanka and in Ethiopia or Egypt). Although there are some indications of a genetic population structure in Southeast Asian countries different from the rest of Asia, more studies in this tropical part of Asia will be necessary for a region which represent as well as Africa one of the missing links of the T. gondii genetic diversity.

Background Consumption of undercooked or insufficiently cured meat is a major risk factor for human infection with Toxoplasma gondii. Although horsemeat is typically consumed rare or undercooked, information on the risk of T. gondii from infected horse meat to humans is scarce. Here, we present the results of a study to determine the presence of T. gondii infection in slaughter horses in Serbia, and to attempt to isolate viable parasites. Methods The study included horses from all regions of Serbia slaughtered at two abattoirs between June 2013 and June 2015. Blood sera were tested for the presence of specific IgG T. gondii antibodies by the modified agglutination test (MAT), and samples of trypsin-digested heart tissue were bioassayed in mice. Cyst-positive mouse brain homogenates were subjected to DNA extraction and T. gondii strains were genotyped using 15 microsatellite markers (MS). Results A total of 105 slaughter horses were sampled. At the 1:6 cut-off 48.6% of the examined horses were seropositive, with the highest titre being 1:400. Viable parasites were isolated from two grade type mares; both parasite isolates (RS-Eq39 and RS-Eq40) were T. gondii type III, and both displayed an increased lethality for mice with successive passages. These are the first cases of isolation of T. gondii from horses in Serbia. When compared with a worldwide collection of 61 type III and type III-like strains, isolate RS-Eq39 showed a combination of MS lengths similar to a strain isolated from a duck in Iran, and isolate RS-Eq40 was identical in all markers to three strains isolated from a goat from Gabon, a sheep from France and a pig from Portugal. Interestingly, the source horses were one seronegative and one weakly seropositive. Conclusions The isolation of viable T. gondii parasites from slaughter horses points to horsemeat as a potential source of human infection, but the fact that viable parasites were isolated from horses with only a serological trace of T. gondii infection presents further evidence that serology may not be adequate to assess the risk of toxoplasmosis from horsemeat consumption. Presence of T. gondii type III in Serbia sheds more light into the potential origin of this archetypal lineage in Europe. Electronic supplementary material The online version of this article (doi:10.1186/s13071-017-2104-x) contains supplementary material, which is available to authorized users.

Peach palm (Bactris gasipaes Kunth) is a Neotropical palm domesticated by Native Americans. Its domestication resulted in a set of landraces (var. gasipaes), some with very starchy fruit used for fermentation, others with an equilibrium of starch and oil used as snacks. Which of the three wild types (var. chichagui) was involved and where the domestication process began are unclear, with three hypotheses under discussion: an origin in southwestern Amazonia; or in northwestern South America; or multiple origins. We reevaluate one of the wild types, defining it as the incipient domesticate, and then evaluate these hypotheses using the Brazilian peach palm Core Collection and selected herbaria samples to: (1) model the potential distributions of wild and domesticated populations; (2) identify the probable origin of domestication with a phylogeographic analysis of chloroplast DNA sequences; and (3) determine the dispersal routes after domestication using spatial analysis of genetic diversity based on 17 nuclear microsatellite loci. The two very small-fruited wild types have distinct distributions in the northern Andes region and across southern Amazonia, both under moderately humid climates, while the incipient domesticate, partly sympatric with the southern wild type, is also found along the Equatorial Andes, in a more humid climatic envelope, more similar to that of the domesticated landraces. Two distribution models for Last Glacial Maximum conditions (CCSM4, MIROC) also suggest distinct distributions for the two wild populations. The chloroplast DNA phylogeographic network confirms the area of sympatry of the incipient domesticate and the southern wild type in southwestern Amazonia as the origin of domestication. The spatial patterns of genetic diversity confirm the proposal of two dispersals, one along the Ucayali River, into western Amazonia, northwestern South America and finally Central America; the other along the Madeira River into central and then eastern Amazonia. The first dispersal resulted in very starchy fruit for fermentation, while the second may have been later and resulted in snack fruits. Further explorations of southwestern Amazonia are essential for more precise identification of the earliest events, both with new archeological methods and genetic analyses with larger samples. © 2017 Clement, Cristo-Araújo, Coppens d'Eeckenbrugge, Reis, Lehnebach and Picanço-Rodrigues.

North Africa enclosed original apricot genetic resources with the cohabitation of grafting and seed-propagated accessions. In this study, we assessed the genetic diversity and population structure of 183 apricot accessions using 24 microsatellite markers distributed evenly in thePrunusgenome. A total of 192 alleles and a high level of gene diversity (0.593) were detected among the whole panel. Genetic structure analysis revealed the presence of four genetic clusters. We also found that both geographical origin and mode of propagation are important factors structuring genetic diversity in apricot species. Results confirmed the presence of gene exchange between the northern and southern countries of the Mediterranean Basin. Subsequently, a core collection of 98 accessions based on M (maximization) strategy showing 99.47% of allele retention ratio was constructed. No significant differences for Shannon's information index and Nei's diversity index were observed between the core and entire collections. Our results provide an effective aid for future germplasm preservation and conservation strategies as well as genetic association studies development in relation to phenotypic data.

Sex determination is ruled by haplodiploidy in Hymenoptera, with haploid males arising from unfertilized eggs and diploid females from fertilized eggs. However, diploid males with null fitness are produced under Complementary Sex Determination (CSD), whenindividuals are homozygous for this locus. Diploid males are expected to be more frequent in genetically eroded populations (such as islands and captive populations), as genetic diversity at the csd locus should be low. However, only a few studies have focused on the relation between population size, genetic diversity and the proportion of diploid males in the field. Here, we developed new microsatellites markers in order to assess and compare genetic diversity and diploid male proportion in populations from three distinct habitat types (mainland, island or captive), in the parasitoid waspVenturia canescens. Eroded genetic diversity and higher diploid male proportion were found in island and captive populations, and habitat type had large effect on genetic diversity. Therefore, diploid male proportion reflects the decreasing genetic diversity in small and isolated populations. Thus, Hymenopteran populations can be at high extinction risk due to habitat destruction or fragmentation.

Assessing the process that gives rise to hybrid pathogens is central to understanding the evolution of emerging plant diseases. Phytophthora ×alni , a pathogen of alder, results from the homoploid hybridization of two related species, Phytophthora uniformis and Phytophthora × multiformis . Describing the genetic characteristics of P . × alni should help us understand how reproductive mechanisms and historical processes shaped the population structure of this emerging hybrid pathogen. The population genetic structure of P . × alni and the relationship with its parental species were investigated using 12 microsatellites and one mitochondrial DNA (mtDNA) marker on a European collection of 379 isolates. Populations of P . × alni were dominated by one multilocus genotype (MLG). The frequency of this dominant MLG increased after the disease emergence together with a decline in diversity, suggesting that it was favored by a genetic mechanism such as drift or selection. Combined microsatellite and mtDNA results confirmed that P . × alni originated from multiple hybridization events that involved different genotypes of the progenitors. Our detailed analyses point to a geographic structure that mirrors that observed for P. uniformis in Europe. The study provides more insights on the contribution of P. uniformis , an invasive species in Europe, to the emergence of Phytophthora -induced alder decline. IMPORTANCE Our study describes an original approach to assess the population genetics of polyploid organisms using microsatellite markers. By studying the parental subgenomes present in the interspecific hybrid P. ×alni , we were able to assess the geographical and temporal structure of European populations of the hybrid, shedding new light on the evolution of an emerging plant pathogen. In turn, the study of the parental subgenomes permitted us to assess some genetic characteristics of the parental species of P. ×alni , P. uniformis , and P . × multiformis , which are seldom sampled in nature. The subgenomes found in P. ×alni represent a picture of the “fossilized” diversity of the parental species.

International audience; Background and Aims: The pseudometallophyte Noccaea caerulescens is an excellent model to study evolutionary processes, as it grows both on normal and on heavy-metal-rich, toxic soils. The evolution and demography of populations are critically impacted by mating system and, yet, information about the N. caerulescens mating system is limited.Methods: Mean selfing rates were assessed using microsatellite loci and a robust estimation method (RMES) in five metallicolous and five non-metallicolous populations of N. caerulescens in Southern France, and this measure was replicated for two successive reproductive seasons. As a part of the study, the patterns of gene flow among populations were analysed. The mating system was then characterized at a fine spatial scale in three populations using the MLTR method on progeny arrays.Key Results: The results confirm that N. caerulescens has a mixed mating system, with selfing rates ranging from 0Á2 to 0Á5. Selfing rates did not vary much among populations within ecotypes, but were lower in the metallicolous than in the non-metallicolous ecotype, in both seasons. Effective population size was also lower in non-metallicolous populations. Biparental inbreeding was null to moderate. Differentiation among populations was generally high, but neither ecotype nor isolation by distance explained it.Conclusions: The consequences of higher selfing rates on adaptation are expected to be weak to moderate in non-metallicolous populations and they are expected to suffer less from inbreeding depression, compared to metal-licolous populations.

Considered as a sister species of Saccharomyces cerevisiae, S. uvarum is, to a lesser extent, an interesting species for fundamental and applied research studies. Despite its potential interest as a new gene pool for fermenting agents, the intraspecific molecular genetic diversity of this species is still poorly investigated. In this study, we report the use of nine microsatellite markers to describe S. uvarum genetic diversity and population structure among 108 isolates from various geographical and substrate origins (wine, cider and natural sources). Our combined microsatellite markers set allowed differentiating 89 genotypes. In contrast to S. cerevisiae genetic diversity, wild and human origin isolates were intertwined. A total of 75% of strains were proven to be homozygotes and estimated heterozygosity suggests a selfing rate above 0.95 for the different population tested here. From this point of view, the S. uvarum life cycle appears to be more closely related to S. paradoxus or S. cerevisiae of natural resources than S. cerevisiae wine isolates. Population structure could not be correlated to distinct geographic or technological origins, suggesting lower differentiation that may result from a large exchange between human and natural populations mediated by insects or human activities.

Clonal lines are a powerful scientific tool for improved genetic characterization of organisms used in research. Inbred fish lines can be produced in only two generations using uniparental reproduction techniques. Androgenesis, achieved with variable success in several freshwater species, has been attempted in the European sea bass (Dicentrarchus labrax L), a marine fish of commercial and scientific interest. The low yields of progenies inheriting only the paternal genome after UV-irradiation of eggs led to considerations on the occurrence of UV screening compounds in pelagic eggs. Mycosporine-like amino acids and gadusol were found in many marine and freshwater organisms, but their occurrence in fish eggs was not clearly related to a behavioral pattern and while gadusol appeared in higher proportions in pelagic marine eggs compared to benthic species, this statement did not apply in freshwater, and moreover the kind of compounds was related to phylogeny. Further studies on DNA photorepair could enlighten hypotheses to understand the mechanisms underlying the disparate results obtained in inducing androgenesis in different fish species. Gynogenesis was reported successful to produce clonal founders in the sea bass, but high numbers of meiotic individuals contaminating fully homozygous progenies highlighted the need for efficient DNA markers to distinguish mitotic gynogenetic individuals. Furthermore, gonad development was highly delayed in gynogenetic progenies enhancing the difficulties to produce clonal lines. A high variability between individuals in the success of uniparental reproduction brought out gamete characterization and quality as a prerequisite., Les lignees clonales sont un outil puissant pour une meilleure caracterisation genetique des organismes utilises en recherche. En utilisant les techniques de reproduction uniparentale, de telles lignees peuvent etre developpees chez les poissons en seulement deux generations. L.androgenese avait deja ete realisee chez plusieurs especes d.eau douce et a ete tentee chez le loup, une espece d.interet economique et scientifique. Le faible nombre d.individus contenant effectivement uniquement le patrimoine genetique du pere, apres irradiation des oeufs aux UV, a souleve des questions quant a la presence de composes photoprotecteurs dans les oeufs pelagiques. Les acides amines de type mycosporines et le gadusol ont ete recenses dans de nombreux organismes marins et d.eau douce, mais leur presence n.a pu etre reliee au comportement flottant ou coulant des oeufs. Tandis que le gadusol apparaissait en plus grande quantite dans les oeufs marins flottants, ce resultat etait beaucoup moins clair en eau douce et le type de compose photoprotecteur semble lie a la phylogenie. D.autres etudes sur les mecanismes de photoreparation de l.ADN pourraient eclairer les resultats obtenus dans les experiences d.androgenese. La gynogenese avait deja ete reportee chez le loup mais le grand nombre d.individus meiotiques contaminant les descendances homozygotes produites a conduit a valider des marqueurs de l.ADN efficaces a distinguer les individus mitotiques. De plus, un retard de developpement des gonades a ete observe, augmentant les difficultes a obtenir les lignees clonales. La grande variabilite observee entre les individus quant au succes des reproductions uniparentales a montre que la caracterisation et la qualite des gametes sont un prealable indispensable.

Tsetse flies are the cyclical vectors of deadly human and animal trypanosomes in sub-Saharan Africa. Tsetse control is a key component for the integrated management of both plagues, but local eradication successes have been limited to less than 2% of the infested area. This is attributed to either resurgence of residual populations that were omitted from the eradication campaign or reinvasion from neighboring infested areas. Here we focused on Glossina palpalis gambiensis, a riverine tsetse species representing the main vector of trypanosomoses in West Africa. We mapped landscape resistance to tsetse genetic flow, hereafter referred to as friction, to identify natural barriers that isolate tsetse populations. For this purpose, we fitted a statistical model of the genetic distance between 37 tsetse populations sampled in the region, using a set of remotely sensed environmental data as predictors. The least-cost path between these populations was then estimated using the predicted friction map. The method enabled us to avoid the subjectivity inherent in the expert-based weighting of environmental parameters. Finally, we identified potentially isolated clusters of G. p. gambiensis habitat based on a species distribution model and ranked them according to their predicted genetic distance to the main tsetse population. The methodology presented here will inform the choice on the most appropriate intervention strategies to be implemented against tsetse flies in different parts of Africa. It can also be used to control other pests and to support conservation of endangered species.

International audience; Identifying the invasion routes and determining the origin of new outbreaks of invasive species are of crucial importance if we are to understand the invasion process, improve or establish regulatory measures and, potentially, limit the damage. We focused here on the invasion of Europe by the pinewood nematode (PWN), Bursaphelenchus xylophilus (Steiner & Buhrer, 1934; Nickle 1970; Nematoda: Aphelenchoididae), a major pest of forest ecosystems, native to North America and already invasive in Asia since the beginning of the twentieth century. We evaluated the genetic diversity and structure of worldwide field PWN samples by classical and Bayesian population genetics methods to determine the source of the European invasive populations and the number of introduction events in Europe. We found (1) a very strong spatial genetic structure in native PWN populations, (2) a very low level of polymorphism in each of the invaded areas and (3) contrasted results concerning the origin of European invasive populations. Our findings provide evidence for: (1) a large effect of genetic drift on the biological cycle of the PWN, due to intense demographic bottlenecks during tree infections, not compensated for by effective dispersal of its vector; (2) a single introduction event for each of the invaded areas in Japan and Europe and a small effective size for the introduced populations and (3) a mainland Portuguese origin for PWN populations from Madeira. However, more sophisticated methods of invasion route inference and broader sampling are required to conclusively determine the origin of the European outbreak.

International audience; This study tested the hypothesis that B. cinerea shows host specialization on tomato and lettuce, using phenotypic and genotypic tools. Strains were isolated from tomato and lettuce grown together in a same greenhouse. Forty-four lettuce strains and forty-two tomato strains were investigated for their genetic diversity and their aggressiveness. Both gene diversity and allelic richness were significantly higher in lettuce strains than in tomato strains (P=0.01). Cluster analysis revealed a clear structure of the strains under study in two clusters. However, this structure did not separate the strains according to their host of origin. Tomato strains were significantly more aggressive than lettuce strains when inoculated on tomatoes (P=0.001). But no significant differences in aggressiveness were observed when the strains were inoculated on lettuce (P=0.17) or on apple (P=0.87). Our results suggest an absence of clear host specialization of B. cinerea on tomato and lettuce.

Recent global changes affect the physiology, distribution and phenology of species, also they impact population dynamic and interactions among species. Plantpollinators interactions are particularly threated by global changes and perturbations of these interactions may lead to important changes in plant mating system. In this context of globalchanges, we determined the pollinator assemblages of Rhododendron ferrugineum and howthe variability of their efficiencies affects the mating system. We also studied thebiogeographic history of R. ferrugineum and how it responds to past climatic changes.We have shown that R. ferrugineum is visited by a large variety of insects. Visitorassemblages efficiency varied along environmental gradients but did not seem to impact themating system of R. ferrugineum. This species presents a mixed mating system, indeed it isable to self-fecundate but high levels of inbreeding depression are limiting the development of self-fecundate descendants. High levels of inbreeding depression maintain high genetic diversity in the Pyrenees. Also, it did not allow the evolution of selfing and maintain a mixed mating system. The ability to self-fecundate may favor the colonization of new habitats.During the last glaciation, R. ferrugineum survived in large lowland refugia and in nunataks at high altitude. Some marginal populations present a high level of selfing (FIS> 0) and low genetic diversity. This genetic pattern is consistent with foundation events and loss of genetic diversity and heterozygosity along colonization rods. Our data suggest that inbreeding depression in these populations should have been low and the reproductive assurance played akey role in the establishment of these populations.; Les changements globaux récents affectent la physiologie, la distribution et la phénologie des espèces, ainsi que la dynamique des populations et les interactions entre espèces. Les interactions plantes-pollinisateurs sont particulièrement menacées par les changements globaux et la perturbation de ces interactions peut avoir des conséquences importantes sur le système de reproduction des espèces végétales. Dans ce contexte des changements globaux, nous avons déterminé les cortèges de visiteurs de Rhododendron ferrugineum le long de gradients environnementaux et étudié comment la variabilité de leur efficacité affectait le système de reproduction de cette espèce. Nous nous sommes également intéressés à l’histoire biogéographique de cette espèce et comment elle a répondu à des changements passés tels que les dernières glaciations. Nous avons mis en évidence que R. ferrugineum est visité par une large diversité d’espèces d’insectes. L’efficacité des cortèges de visiteurs varie le long de gradients environnementaux mais ne semble pas avoir un impact sur le système de R. ferrugineum. Cette espèce présente un système mixte de reproduction, avec une capacité à l’autofécondation mais les taux élevés de dépression de consanguinité limitent le développement des individus issus d’autofécondation. Cette forte dépression de consanguinité a permis un maintien relativement élevé de la diversité génétique dans les Pyrénées. Un tel niveau de dépression de consanguinité ne permet pas l’évolution de l’autofécondation et maintient ainsi le système mixte de reproduction chez R. ferrugineum. La capacité d’autofécondation de R. ferrugineum pourrait lui permettre de coloniser de nouveaux milieux ou de survivre aux changements globaux. Durant les dernières glaciations, R. ferrugineum a survécu dans de grands refuges de basse altitude ainsi que dans des nunataks (refuges de haute altitude). Quelques populations marginales présentent un taux significatifs de consanguinité (FIS> 0) et des niveaux de diversité génétique particulièrement faibles. Ce patron génétique est consistant avec des évènements de fondation accompagnés de perte de diversité génétique et d’hétérozygotie durant les périodes d’expansion de l’aire de répartition de l’espèce. Ces données suggèrent que la dépression de consanguinité dans ces populations devait être faible et que l’assurance reproductive a joué un rôle fondamental dans l’établissement de ces populations.

National audience; A new Task Force within the COST-SMARTER has recently been created. This group is composed of population genetics experts from five European countries in charge of focusing on “Genetics on Ambrosia” (Austria, France, Germany, Hungary, Sweden). Their mission was to review molecular methods used in published genetics studies on common ragweed and to discuss about future projects. Two different types of molecular markers are generally used in the literature to investigate the genetic structure within and between introduced and/or native populations of common ragweed: microsatellite markers and amplified fragment length polymorphism (AFLP). These methods permit the researchers to trace-back the common ragweed invasion history and its worldwide spread as well as to identify certain evolutionary processes like selection, adaptation or genetic bottleneck due to introduction. One common conclusion is the presence of two main genetic clusters within Europe coming from two different regions of the native range. However, this conclusion is based on a limited number of microsatellite markers used (12 nuclear + 4 plastid). New methods using haplotype analysis or selected markers present on functional parts of the genome (i.e., related to herbicide-resistance) should be more investigated in order to increase the knowledge on common ragweed. Transcriptomic analyses are starting to be employed in USA to observe gene expression related to adaptations and identify the genes of the “invasiveness”. These new methods will now be promoted within the different European projects in order to open the way of whole-genome sequencing of Ambrosia artemisiifolia in the future.

International audience; Phelipanche ramosa is a parasitic plant that infects numerous crops worldwide. In Western Europe it recently expanded to a new host crop, oilseed rape, in which it can cause severe yield losses. We developed 13 microsatellite markers for P. ramosa using next-generation 454 sequencing data. The polymorphism at each locus was assessed in a sample of 96 individuals collected in France within 6 fields cultivated with tobacco, hemp or oilseed rape. Two loci were monomorphic. At the other 11 loci, the number of alleles and the expected heterozygosity ranged from 3 to 6 and from 0.31 to 0.60, respectively. Genetic diversity within each cultivated field was very low. The host crop from which individuals were collected was the key factor structuring genetic variation. Individuals collected on oilseed rape were strongly differentiated from individuals collected on hemp or tobacco, which suggests that P. ramosa infecting oilseed rape forms a genetically diverged race. The microsatellites we developed will be useful for population genetics studies and for elucidating host-associated genetic divergence in P. ramosa.

Truffles are ectomycorrhizal Ascomycota fungi belonging to the Tuberaceae family and more specifically to the Tuber genus. More than thirty Tuber species are currently described in Europe. In this thesis, we specifically focused on the Tuber aestivum-uncinatum model. This truffle is commonly called "Burgundy Truffle" and has a gastronomic and cultural interest.The first part of this thesis focused on the taxonomic status of the Burgundy truffle (Tuber uncinatum). For this, we used a multi-marker approach combining several genetic markers commonly used at the interspecific scale. Our analyses showed that the two taxa, Tuber aestivum (summer truffle) and Tuber uncinatum are conspecific.In the second part, we addressed the genetic diversity of Tuber aestivum. To do this, we firstly developed specific microsatellite markers by "direct shotgun pyrosequencing". This method has allowed the development of 15 polymorphic microsatellite markers. Then, we used those markers to genotype individuals from different European locations. We have identified four differentiated subpopulations that not correspond, for the majority, to a geographical distribution. However, one cluster differs from the others by its location (south of France) and its genetic characteristics (presence of rare alleles). These preliminary results may indicate the existence of a particular ecotype attached to a southern ecology: Tuber aestivum sensu stricto.We were then interested, in the third part of this thesis, to the aromatic diversity of Tuber aestivum at a local scale. Our results highlight the existence of a moderate differentiation between individuals from a natural truffle orchard and individuals from planted orchard. From one season to another, genotypic stability was observed. Only C8 volatile organic compounds seem to be related to the genotypes.In the last part, we analyzed harvesting data, over more than thirty years, from an hazelnut truffle orchard initially inoculated by Tuber melanosporum. Through simple statistical analyzes, we noted changes in both quantity and weight of truffles harvested according to the seasons and hazelnut trees. It appears that Tuber aestivum rapidly replaced Tuber melanosporum (in three years). The disappearance of Tuber melanosporum can probably be explained by the canopy closure; Tuber melanosporum not appreciating excessive shading.; Les Truffes sont des champignons ascomycètes ectomycorhiziens appartenant à la famille des Tuberaceae et plus précisément au genre Tuber. On dénombre à ce jour plus d’une trentaine d’espèces de Tuber en Europe. Lors de ce travail de thèse, nous nous sommes plus précisément focalisés sur le modèle Tuber aestivum-uncinatum. Cette truffe communément appelée « Truffe de Bourgogne » présente un intérêt à la fois gastronomique et culturel.La première partie de ce travail de thèse a porté sur la clarification du statut taxonomique de la truffe de Bourgogne (Tuber uncinatum). Pour cela, nous avons utilisé une approche multi-marqueurs combinant des marqueurs génétiques couramment utilisés à l’échelle interspécifique. Nos analyses ont montré que les deux taxons Tuber aestivum (la truffe d’été) et Tuber uncinatum sont conspécifiques. Durant la deuxième partie, nous nous sommes intéressés à la diversité génétique de Tuber aestivum. Pour cela, nous avons tout d’abord développé des marqueurs microsatellites spécifiques par une approche de « direct shotgun pyrosequencing ». Cette méthode a permis le développement de 15 marqueurs microsatellites polymorphes. Nous les avons ensuite utilisés pour génotyper des individus provenant de différentes localisations en Europe. Nous avons pu identifier quatre sous populations différenciées qui ne correspondent pas, pour la majorité, à une répartition géographique. Cependant, un des clusters se différencie des autres à la fois par sa situation géographique (sud de la France) et ses caractéristiques génétiques (présence d’allèles rares). Ces résultats préliminaires pourraient indiquer l’existence d’un écotype particulier attaché à une écologie méridionale, Tuber aestivum sensu stricto.Nous nous sommes ensuite intéressés, dans la troisième partie de ce travail de thèse à la diversité aromatique de Tuber aestivum à l’échelle locale. Les résultats obtenus permettent de mettre en évidence l’existence d’une différenciation modérée entre les individus issus d’une truffière naturelle et les individus issus d’une truffière plantée. D’une saison de récolte à l’autre, une stabilité génotypique a été observée. Au niveau aromatique, seuls les composés C8 semblent être liés aux génotypes.Dans la dernière partie, nous nous sommes intéressés à l’analyse de données de récolte sur plus de trente ans au sein d’une truffière plantée de noisetiers inoculés initialement par Tuber melanosporum. Grâce à des analyses statistiques simples, nous avons pu noter les fluctuations tant en quantité qu’en poids des truffes récoltées suivant les saisons et les arbres truffiers. Il apparait que le remplacement de Tuber melanosporum par Tuber aestivum s’est fait de manière très rapide (trois ans). La disparition de Tuber melanosporum peut probablement être expliquée par la fermeture de la canopée des noisetiers, Tuber melanosporum n’appréciant pas un ombrage excessif

Background Adaptation, which induces differentiation between populations in relation to environmental conditions, can initiate divergence. The balance between gene flow and selection determines the maintenance of such a structure in sympatry. Studying these two antagonistic forces in plant pathogens is made possible because of the high ability of pathogens to disperse and of the strong selective pressures exerted by their hosts. In this article, we analysed the genetic structure of the population of the apple scab fungus, Venturia inaequalis, in a heterogeneous environment composed of various Malus species. Inferences were drawn from microsatellite and AFLP data obtained from 114 strains sampled in a single orchard on nine different Malus species to determine the forces that shape the genetic structure of the pathogen. Results Using clustering methods, we first identified two specialist subpopulations: (i) a virulent subpopulation sampled on Malus trees carrying the Rvi6 resistance gene; and (ii) a subpopulation infecting only Malus trees that did not carry this resistance gene. A genome scan of loci on these two subpopulations did not detect any locus under selection. Additionally, we did not detect any other particular substructure linked to different hosts. However, an isolation-by-distance (IBD) pattern at the orchard scale revealed free gene flow within each subpopulation. Conclusions Our work shows a rare example of a very strong effect of a resistance gene on pathogen populations. Despite the high diversity of Malus hosts, the presence of Rvi6 seems sufficient to explain the observed genetic structure. Moreover, detection of an IBD pattern at the orchard scale revealed a very low average dispersal distance that is particularly significant for epidemiologists and landscape managers for the design of scab control strategies

10 pages; International audience; Understanding how fitness is related to genetic variation is of crucial importance in both evolutionary ecology and conservation biology. We report a study of heterozygosity-fitness correlations in a wild, noninbred population of Zenaida Doves, Zenaida aurita, based on a sample comprising 489 individuals (382 adults and 107 juveniles) typed at 13 microsatellite loci, resulting in a data set comprising 5793 genotypes. In both adults and juveniles, and irrespective of sex, no evidence was found for an effect of either multilocus or single-locus heterozygosity on traits potentially related to fitness such as foraging tactic, competitive ability, and fluctuating asymmetry. In contrast, a significant negative correlation between body condition and multilocus heterozygosity, indicative of outbreeding depression, was found in juveniles, whereas no such trend was observed in adults. However, the frequency distribution of heterozygosity did not differ between the two age classes, suggesting compensatory growth by heterozygous juveniles. We discuss our results in relation to some practical limitations associated with studies of heterozygosity-fitness correlations, and suggest that tropical bird species with allopatric divergence between island populations may provide a good biological model for the detection of outbreeding depression.

Truffles are ectomycorrhizal Ascomycota fungi belonging to the Tuberaceae family and more specifically to the Tuber genus. More than thirty Tuber species are currently described in Europe. In this thesis, we specifically focused on the Tuber aestivum-uncinatum model. This truffle is commonly called "Burgundy Truffle" and has a gastronomic and cultural interest.The first part of this thesis focused on the taxonomic status of the Burgundy truffle (Tuber uncinatum). For this, we used a multi-marker approach combining several genetic markers commonly used at the interspecific scale. Our analyses showed that the two taxa, Tuber aestivum (summer truffle) and Tuber uncinatum are conspecific.In the second part, we addressed the genetic diversity of Tuber aestivum. To do this, we firstly developed specific microsatellite markers by "direct shotgun pyrosequencing". This method has allowed the development of 15 polymorphic microsatellite markers. Then, we used those markers to genotype individuals from different European locations. We have identified four differentiated subpopulations that not correspond, for the majority, to a geographical distribution. However, one cluster differs from the others by its location (south of France) and its genetic characteristics (presence of rare alleles). These preliminary results may indicate the existence of a particular ecotype attached to a southern ecology: Tuber aestivum sensu stricto.We were then interested, in the third part of this thesis, to the aromatic diversity of Tuber aestivum at a local scale. Our results highlight the existence of a moderate differentiation between individuals from a natural truffle orchard and individuals from planted orchard. From one season to another, genotypic stability was observed. Only C8 volatile organic compounds seem to be related to the genotypes.In the last part, we analyzed harvesting data, over more than thirty years, from an hazelnut truffle orchard initially inoculated by Tuber melanosporum. Through simple statistical analyzes, we noted changes in both quantity and weight of truffles harvested according to the seasons and hazelnut trees. It appears that Tuber aestivum rapidly replaced Tuber melanosporum (in three years). The disappearance of Tuber melanosporum can probably be explained by the canopy closure; Tuber melanosporum not appreciating excessive shading., Les Truffes sont des champignons ascomycètes ectomycorhiziens appartenant à la famille des Tuberaceae et plus précisément au genre Tuber. On dénombre à ce jour plus d’une trentaine d’espèces de Tuber en Europe. Lors de ce travail de thèse, nous nous sommes plus précisément focalisés sur le modèle Tuber aestivum-uncinatum. Cette truffe communément appelée « Truffe de Bourgogne » présente un intérêt à la fois gastronomique et culturel.La première partie de ce travail de thèse a porté sur la clarification du statut taxonomique de la truffe de Bourgogne (Tuber uncinatum). Pour cela, nous avons utilisé une approche multi-marqueurs combinant des marqueurs génétiques couramment utilisés à l’échelle interspécifique. Nos analyses ont montré que les deux taxons Tuber aestivum (la truffe d’été) et Tuber uncinatum sont conspécifiques. Durant la deuxième partie, nous nous sommes intéressés à la diversité génétique de Tuber aestivum. Pour cela, nous avons tout d’abord développé des marqueurs microsatellites spécifiques par une approche de « direct shotgun pyrosequencing ». Cette méthode a permis le développement de 15 marqueurs microsatellites polymorphes. Nous les avons ensuite utilisés pour génotyper des individus provenant de différentes localisations en Europe. Nous avons pu identifier quatre sous populations différenciées qui ne correspondent pas, pour la majorité, à une répartition géographique. Cependant, un des clusters se différencie des autres à la fois par sa situation géographique (sud de la France) et ses caractéristiques génétiques (présence d’allèles rares). Ces résultats préliminaires pourraient indiquer l’existence d’un écotype particulier attaché à une écologie méridionale, Tuber aestivum sensu stricto.Nous nous sommes ensuite intéressés, dans la troisième partie de ce travail de thèse à la diversité aromatique de Tuber aestivum à l’échelle locale. Les résultats obtenus permettent de mettre en évidence l’existence d’une différenciation modérée entre les individus issus d’une truffière naturelle et les individus issus d’une truffière plantée. D’une saison de récolte à l’autre, une stabilité génotypique a été observée. Au niveau aromatique, seuls les composés C8 semblent être liés aux génotypes.Dans la dernière partie, nous nous sommes intéressés à l’analyse de données de récolte sur plus de trente ans au sein d’une truffière plantée de noisetiers inoculés initialement par Tuber melanosporum. Grâce à des analyses statistiques simples, nous avons pu noter les fluctuations tant en quantité qu’en poids des truffes récoltées suivant les saisons et les arbres truffiers. Il apparait que le remplacement de Tuber melanosporum par Tuber aestivum s’est fait de manière très rapide (trois ans). La disparition de Tuber melanosporum peut probablement être expliquée par la fermeture de la canopée des noisetiers, Tuber melanosporum n’appréciant pas un ombrage excessif

Understanding the way in which the climatic oscillations of the Quaternary Period have shaped the distribution and genetic structure of extant tree species provides insight into the processes driving species diversification, distribution and survival. Deciphering the genetic consequences of past climatic change is also critical for the conservation and sustainable management of forest and tree genetic resources, a timely endeavour as the Earth heads into a period of fast climate change. We used a combination of genetic data and ecological niche models to investigate the historical patterns of biogeographic range expansion of a wild fruit tree, the European crabapple (Malus sylvestris), a wild contributor to the domesticated apple. Both climatic predictions for the last glacial maximum and analyses of microsatellite variation indicated that M. sylvestris experienced range contraction and fragmentation. Bayesian clustering analyses revealed a clear pattern of genetic structure, with one genetic cluster spanning a large area in Western Europe and two other genetic clusters with a more limited distribution range in Eastern Europe, one around the Carpathian Mountains and the other restricted to the Balkan Peninsula. Approximate Bayesian computation appeared to be a powerful technique for inferring the history of these clusters, supporting a scenario of simultaneous differentiation of three separate glacial refugia. Admixture between these three populations was found in their suture zones. A weak isolation by distance pattern was detected within each population, indicating a high extent of historical gene flow for the European crabapple.

International audience; The golden cyst nematode (Globodera rostochiensis), native to South America, has been introduced in many parts of the world, including Europe and North America. Recently, it was found for the first time in the province of Quebec, Canada in the locality of St. Amable near Montreal. To date, very few studies have examined the population genetics of this pest. Consequently, there is a lack of knowledge about the genetic structure and evolution of this nematode. In this study, twelve new microsatellite markers were developed in order to explore these questions. These markers were used to genotype fifteen populations originating from different regions of the world, including five from Canada. Within populations, the highest genetic diversity was consistently observed in the populations from Bolivia, the postulated region of origin of the golden nematode, and the lowest in populations from British Columbia (Canada) and New York (USA). The two Quebec populations were very similar to each other and to the population found in Newfoundland, but surprisingly, they were significantly different from three other North American populations including those from New York and British Columbia. Based on our results, we conclude that the golden cyst nematode has been introduced in North America at least twice from distinct regions of the world. Crown Copyright (C) 2013 Published by Elsevier Inc. All rights reserved.

International audience; A major challenge in population ecology of long-lived plants is to disentangle the intricate effects of seed dispersal and seedlings mortality on spatial and genetic structure of recruited seedlings. A common way to address this issue is to compare dispersal patterns among seeds (i.e. basic dispersal) and established seedlings (i.e. effective dispersal). High density-dependent mortality near adults is expected to shift the mode of the effective dispersal distance away from the mother-plant relative to the mode of the basic dispersal distance. Here, we proposed a new approach to address this issue by using seedlings cohorts of different age and by combining parentage analyses to retrieve effective seed dispersal and Spatially Explicit Mating Models (SEMM) to estimate basic seed dispersal. We applied this approach in two seedling cohorts at each of two plots of Fagus sylvatica L., relying on adult and seedling genotypes at 10 microsatellite loci. Basic seed dispersal was primarily local, with mean distances of 12-25 m (young cohort) and 22-25 m (old cohort). The effective seed dispersal distance increased between young and old cohorts from 33 m to 48 m at site I and from 23 m to 33 m at site 2. The hypothesis of density-dependent mortality was supported at site 2 but not at site 1 possibly because of different ecological conditions among sites. Our results shed light on the interplay between seed dispersal and density-dependent mortality in F. sylvatica. Moreover, the new approach proposed here alleviates general problems associated to synchronic studies comparing spatial patterns across different-age cohorts at a single point in time.

Whether sex chromosomes are differentiated is an important aspect of our knowledge of dioecious plants, such as date palm (Phoenix dactylifera). In this crop plant, the female individuals produce dates, and are thus the more valuable sex. However, there is no way to identify the sex of date palm plants before reproductive age, and the sex-determining mechanism is still unclear. To identify sex-linked microsatellite markers, we surveyed a set of 52 male and 55 female genotypes representing the geographical diversity of the species. We found three genetically linked loci that are heterozygous only in males. Male-specific alleles allowed us to identify the gender in 100% of individuals. These results confirm the existence of an XY chromosomal system with a nonrecombining XY-like region in the date palm genome. The distribution of Y haplotypes in western and eastern haplogroups allowed us to trace two male ancestral paternal lineages that account for all known Y diversity in date palm. The very low diversity associated with Y haplotypes is consistent with clonal paternal transmission of a nonrecombining male-determining region. Our results establish the date palm as a biological model with one of the most ancient sex chromosomes in flowering plants.

Eighteen novel microsatellite markers were developed in Rhododendron ferrugineum using pyrosequencing technology. They were tested on populations in the Alps, Jura and Pyrenees to study genetic diversity at the species range margins. Protection of populations at margins is important for conserving the genetic diversity of species. We found 2–7 alleles per locus. The expected and observed heterozygosity ranged from 0.07 to 0.79 and from 0.05 to 0.85, respectively. These loci were successfully amplified in 22 other Rhododendron species and four Ericaceae species. These markers will be useful for investigating the genetic structure of R. ferrugineum and related species at their distribution margins.

Phenotypic characterisation of germplasm collections is a decisive step towards association mapping analyses, but it is particularly expensive and tedious for woody perennial plant species. Characterisation could be more efficient if focused on a reasonably sized subset of accessions, or so-called core collection (CC), reflecting the geographic origin and variability of the germplasm. The questions that arise concern the sample size to use and genetic parameters that should be optimized in a core collection to make it suitable for association mapping. Here we investigated these questions in olive (Olea europaea L.), a perennial fruit species. By testing different sampling methods and sizes in a worldwide olive germplasm bank (OWGB Marrakech, Morocco) containing 502 unique genotypes characterized by nuclear and plastid loci, a two-step sampling method was proposed. The Shannon-Weaver diversity index was found to be the best criterion to be maximized in the first step using the CORE HUNTER program. A primary core collection of 50 entries (CC 50) was defined that captured more than 80% of the diversity. This latter was subsequently used as a kernel with the MSTRAT program to capture the remaining diversity. 200 core collections of 94 entries (CC 94) were thus built for flexibility in the choice of varieties to be studied. Most entries of both core collections (CC50 and CC 94) were revealed to be unrelated due to the low kinship coefficient, whereas a genetic structure spanning the eastern and western/central Mediterranean regions was noted. Linkage disequilibrium was observed in CC 94 which was mainly explained by a genetic structure effect as noted for OWGB Marrakech. Since they reflect the geographic origin and diversity of olive germplasm and are of reasonable size, both core collections will be of major interest to develop long-term association studies and thus enhance genomic selection in olive species.

National audience

Quantitative resistance is postulated to be more durable than qualitative (R-gene mediated) resistance, which is usually quickly overcome by the pathogen population. Despite its wide use for nearly 10 years in France, the French bread wheat cultivar Apache remains resistant to stripe rust. Here, we investigated the genetic architecture of cv. Apache resistance to examine whether its durability could be explained by quantitative characteristics. We identified quantitative trait loci (QTL) by composite interval mapping of disease progress data recorded throughout 4 years of field assays. These assays included inoculation with three different pathotypes on a segregating population originating from a cross between cv. Apache and cv. Taldor, a French cultivar susceptible to stripe rust. Three QTLs derived from Apache, QYr.inra-2AS, QYr.inra-2BL and QYr.inra-4B, were detected. Each of these QTLs contributed between approximately 15 and 69 % of the phenotypic variance and corresponds to a race-specific resistance gene. We showed that QYr.inra-2AS and QYr.inra-2BS map to the positions of Yr17 and Yr7, respectively, whereas QYr.inra-4B corresponds to an adult plant resistance gene. Our results demonstrate that a combination of two or more race-specific resistance genes can confer durable resistance provided that it is properly managed at a continental level. Race-specific resistance genes should not be removed from breeding programs provided that they are properly managed.

Various international initiatives have emerged to develop new sets of biodiversity indicators for wild biodiversity but little progress has been made for crop diversity. This study proposes a new methodology to assess the diversity of cultivated species. We developed a new integrative indicator H-T* that takes account of varietal richness, spatial evenness, between-variety genetic diversity, and within-variety genetic diversity. This index is compared to existing indexes using a comprehensive historical dataset from a French territory. The study reveals that more varieties (the varietal richness factor) can mean less diversity when (i) their genetic structure is more similar (the effect of between-variety genetic diversity), or (ii) when more diverse landraces are replaced by many homogeneous lines (the effect of within-variety genetic diversity) or (iii) when one or a few varieties become hegemonic in the landscape (the spatial evenness effect). Furthermore, an increased evenness in variety distribution (varietal evenness) can also mean less diversity when varieties are genetically related. This is why indicators which do not take into account the full range of factors (varietal richness, between-variety genetic diversity, spatial evenness and within-variety genetic diversity) may provide a misleading assessment of the state and trend of crop biodiversity. New integrative indicators such as HT. are critically needed. We discuss potential further development such as the use of this indicator for monitoring and the perspective of a broader indicator to assess genetic diversity at the multi-species scale and landscape level. In the future, this indicator could be used to guide managerial decisions to prevent the erosion of crop genetic diversity in agricultural landscapes. (c) 2012 Elsevier Ltd. All rights reserved.

The study of the dispersal capability of a species can provide essential information for the management and conservation of its genetic variability. Comparison of gene flow rates among populations characterized by different management and evolutionary histories allows one to decipher the role of factors such as isolation and tree density on gene movements. We used two paternity analysis approaches and different strategies to handle the possible presence of genotyping errors to obtain robust estimates of pollen flow in four European beech (Fagus sylvatica L.) populations from Austria and France. In each country one of the two plots is located in an unmanaged forest; the other plots are managed with a shelterwood system and inside a colonization area (in Austria and France, respectively). The two paternity analysis approaches provided almost identical estimates of gene flow. In general, we found high pollen immigration (~75% of pollen from outside), with the exception of the plot from a highly isolated forest remnant (~50%). In the two unmanaged plots, the average within-population pollen dispersal distances (from 80 to 184 m) were higher than previously estimated for beech. From the comparison between the Austrian managed and unmanaged plots, that are only 500 m apart, we found no evidence that either gene flow or reproductive success distributions were significantly altered by forest management. The investigated phenotypic traits (crown area, height, diameter and flowering phenology) were not significantly related with male reproductive success. Shelterwood seems to have an effect on the distribution of within-population pollen dispersal distances. In the managed plot, pollen dispersal distances were shorter, possibly because adult tree density is three-fold (163 versus 57 trees per hectare) with respect to the unmanaged one. © 2012 Macmillan Publishers Limited All rights reserved.

Theobroma cacao is an economically important tree of several tropical countries. Its genetic improvement is essential to provide protection against major diseases and improve chocolate quality. We discovered and mapped new expressed sequence tag-single nucleotide polymorphism (EST-SNP) and simple sequence repeat (SSR) markers and constructed a high-density genetic map. By screening 149 650 ESTs, 5246 SNPs were detected in silico, of which 1536 corresponded to genes with a putative function, while 851 had a clear polymorphic pattern across a collection of genetic resources. In addition, 409 new SSR markers were detected on the Criollo genome. Lastly, 681 new EST-SNPs and 163 new SSRs were added to the pre-existing 418 co-dominant markers to construct a large consensus genetic map. This high-density map and the set of new genetic markers identified in this study are a milestone in cocoa genomics and for marker-assisted breeding. The data are available at http://tropgenedb.cirad.fr.

In this study, we characterize and compare the genetic structure of aboveground and belowground populations of the ectomycorrhizal fungus Laccaria amethystina in an unmanaged mixed beech forest. Fruiting bodies and mycorrhizas of L.similar to amethystina were mapped and collected in four plots in the Swietokrzyskie Mountains (Poland). A total of 563 fruiting bodies and 394 mycorrhizas were successfully genotyped using the rDNA IGS1 (intergenic spacer) and seven simple sequence repeat markers. We identified two different genetic clusters of L.similar to amethystina in all of the plots, suggesting that a process of sympatric isolation may be occurring at a local scale. The proportion of individuals belonging to each cluster was similar among plots aboveground while it significantly differed belowground. Predominance of a given cluster could be explained by distinct host preferences or by priority effects and competition among genets. Both aboveground and belowground populations consisted of many intermingling small genets. Consequently, host trees were simultaneously colonized by many L.similar to amethystina genets that may show different ecophysiological abilities. Our data showed that several genets may last for at least 1 year belowground and sustain into the next season. Ectomycorrhizal species reproducing by means of spores can form highly diverse and persistent belowground genets that may provide the host tree with higher resilience in a changing environment and enhance ecosystem performance.

International audience; Only few studies are available dealing with the relation between winter host density and spatial distribution and spring colonization of winter cereals by the host-alternating cereal aphid species Rhopalosiphum padi and Metopolophium dirhodum. Large-scale studies in climatically different agroecosystems in Germany from 2004 to 2006 revealed for R.padi and M.dirhodum larger spring/summer populations in landscapes with higher densities of winter hosts. A small-scale study was performed in winter wheat fields adjacent to a large hedge with several typical winter hosts plants, bird cherry (Prunus padus) and wild rose species (Rosa spp.) to indentify distance effects (08, 824 and 2460 m). Weekly measurements of aphid density between May to July showed significantly higher densities of R.padi compared with those of other aphids. Statistical analysis (TukeyKramer test and regression analyses) revealed significant gradients from the hedge to the field centre for R.padi and M.dirhodum. In comparative studies, winged R.padi from winter and adjacent summer hosts were genotyped using four microsatellite markers. The results showed that individuals from a certain winter host were not genetically similar with individuals from neighbouring summer hosts; it, therefore, seems that winter host clones did not significantly contribute to population built-up in cereal fields over short distances. It could be concluded that on a regional scale, the density of sources for early migrants of R.padi is important for colonization intensity of surrounding summer hosts, but that the high local movement intensity and the relative small proportion of aphids that could be analysed in such tracking studies are blurring close spatial relations within short time periods.

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; Codling moth Cydia pomonella L. (Lepidoptera: Tortricidae) is the most important insect pest of apple production in Europe. Despite the economic importance of this pest, there is not information about the genetic structure of its population in Greece and the patterns of gene-flow which might affect the success of control programs. In this study, we analysed nine samples from apple, pear and walnut from various regions of mainland Greece using 11 microsatellite loci. Six samples from the aforementioned hosts from southern France were also examined for comparison. Bayesian clustering and genetic distance analyses separated the codling moth samples in two genetic clusters. The first cluster consisted mainly of the individuals from Greece, and the second of those from France, although admixture and missclassified individuals were also observed. The low genetic differentiation among samples within each country was also revealed by FST statistics (0.009 among Greek samples and 0.0150 among French samples compared to 0.050 global value among all samples and 0.032 the mean of the pair-wise values between the two countries). These F-ST values suggest little structuring at large geographical scales in agreement with previous published studies. The host species and local factors (climatic conditions, topography, pest control programs) did not affect the genetic structure of codling moth populations within each country. The results are discussed in relation to human-made activities that promote gene-floweven at large geographic distances. Possible factors for the genetic differentiation between the two genetic clusters are also discussed.

Background The abscisic acid (ABA) pathway plays an important role in the plants’ reaction to drought stress and ABA-stress response (Asr) genes are important in controlling this process. In this sense, we accessed nucleotide diversity at two candidate genes for drought tolerance (Asr1 and Asr2), involved in an ABA signaling pathway, in the reference collection of cultivated common bean (Phaseolus vulgaris L.) and a core collection of wild common bean accessions. Results Our wild population samples covered a range of mesic (semi-arid) to very dry (desert) habitats, while our cultivated samples presented a wide spectrum of drought tolerance. Both genes showed very different patterns of nucleotide variation. Asr1 exhibited very low nucleotide diversity relative to the neutral reference loci that were previously surveyed in these populations. This suggests that strong purifying selection has been acting on this gene. In contrast, Asr2 exhibited higher levels of nucleotide diversity, which is indicative of adaptive selection. These patterns were more notable in wild beans than in cultivated common beans indicting that natural selection has played a role over long time periods compared to farmer selection since domestication. Conclusions Together these results suggested the importance of Asr1 in the context of drought tolerance, and constitute the first steps towards an association study between genetic polymorphism of this gene family and variation in drought tolerance traits. Furthermore, one of our major successes was to find that wild common bean is a reservoir of genetic variation and selection signatures at Asr genes, which may be useful for breeding drought tolerance in cultivated common bean.

Biogeographical patterns and large-scale genetic structure have been little studied in ectomycorrhizal (EM) fungi, despite the ecological and economic importance of EM symbioses. We coupled population genetics and phylogenetic approaches to understand spatial structure in fungal populations on a continental scale. Using nine microsatellite markers, we characterized gene flow among 16 populations of the widespread EM basidiomycete Laccaria amethystina over Europe (i.e. over 2900 km). We also widened our scope to two additional populations from Japan (104 km away) and compared them with European populations through microsatellite markers and multilocus phylogenies, using three nuclear genes (NAR, G6PD and ribosomal DNA) and two mitochondrial ribosomal genes. European L. amethystina populations displayed limited differentiation (average FST = 0.041) and very weak isolation by distance (IBD). This panmictic European pattern may result from effective aerial dispersal of spores, high genetic diversity in populations and mutualistic interactions with multiple hosts that all facilitate migration. The multilocus phylogeny based on nuclear genes confirmed that Japanese and European specimens were closely related but clustered on a geographical basis. By using microsatellite markers, we found that Japanese populations were strongly differentiated from the European populations (FST = 0.416), more than expected by extrapolating the European pattern of IBD. Population structure analyses clearly separated the populations into two clusters, i.e. European and Japanese clusters. We discuss the possibility of IBD in a continuous population (considering some evidence for a ring species over the Northern Hemisphere) vs. an allopatric speciation over Eurasia, making L. amethystina a promising model of intercontinental species for future studies.