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Analysis of major histocompatibility complex class II gene in water voles using capillary electrophoresis-single stranded conformation polymorphism Inra
Bryja, J.; Galan, M.; Charbonnel, N.; Cosson, J.-F..
Analysis of a single strand conformation polymorphism (SSCP) using capillary electrophoresis (CE) is a novel method to study polymorphism of DNA sequences in large scale population studies. We optimized CE-SSCP analysis to study the major histocompatibility complex (MHC) class II alpha gene (DQA) polymorphism. Short-chain linear polyacrylamide (6%) as sieving matrix, TrisCl (pH 8.5) as buffer for sample dilution, and 27 ° C, 9 kV as electrophoresis parameters were suitable for sufficient resolution of all alleles. We found that almost 25% of clones contained a PCR (polymerase chain reaction) artefact and strict criteria have to be applied when using cloning and sequencing to analyse the allelic diversity of MHC genes
Tipo: Journal Article Palavras-chave: MAJOR HISTOCOMPATIBILITY COMPLEX; MEGABACE; POPULATION GENETICS; QUISCA; RT1.BA; CAPILLARY ELECTROPHORESIS SINGLE STRANDED CONFORMATION POLYMORPHISM.
Ano: 2005 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD200792a93ff8&uri=/notices/prodinra1/2007/08/
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Bread, beer and wine: Saccharomyces cerevisiae diversity reflects human history Inra
Legras, J.L.; Merdinoglu, D.; Cornuet, J.M.; Karst, F..
Fermented beverages and foods have played a significant role in most societies worldwide for millennia. To better understand how the yeast species Saccharomyces cerevisiae , the main fermenting agent, evolved along this historical and expansion process, we analysed the genetic diversity among 651 strains from 56 different geographical origins, worldwide. Their genotyping at 12 microsatellite loci revealed 575 distinct genotypes organized in subgroups of yeast types, i.e. bread, beer, wine, sake. Some of these groups presented unexpected relatedness: Bread strains displayed a combination of alleles intermediate between beer and wine strains, and strains used for rice wine and sake were most closely related to beer and bread strains. However, up to 28% of...
Tipo: Journal Article Palavras-chave: BIERE; INFERENCE BAYESIENNE DOMESTICATION; MICROSATELLITE; POPULATION GENETICS; SACCHAROMYCES CEREVISIAE; BAYESIAN INFERENCE.
Ano: 2007 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD20083bedc889&uri=/notices/prodinra1/2008/08/
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Cameraria ohridella Deschka & Dimic 1986 Inra
Lees, D. C.; Lopez Vaamonde, C.; Augustin, S.; National History Museum, Biodiversity Heritage Library (GBR); Field Museum (USA); Harvard University, Museum of Comparative Zoology (USA); MacArthur Foundation (USA); MBL, Marine Biological Laboratory (USA); Missouri Botanical Garden (USA); Alfred P. Sloan Foundation (USA); NMNH, Smithsonian Institution National Museum of Natural History (USA).
Tipo: Book Chapter Palavras-chave: LEPIDOPTERA; GRACILLARIIDAE; CAMERARIA OHRIDELLA; MINEUSE DU MARRONNIER D'INDE; ESPECE EXOTIQUE INVASIVE; DESCRIPTION; DISPERSION; PHYLOGENETIQUE; PHYLOGEOGRAPHIE HORSE CHESTNUT LEAFMINER; PEST INSECT; INVASIVE ALIEN SPECIES; LIFE CYCLE; DISPERSAL; PHYLOGENETIC; PHYLOGEOGRAPHY; POPULATION GENETICS; HOST-PARASITE RELATIONSHIP.
Ano: 2009 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD201094dccb4a&uri=/notices/prodinra1/2011/01/
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Characterization and PCR multiplexing of polymorphic microsatellite loci in the whipworm Trichuris arvicolae, parasite of arvicoline rodents and their cross-species utilization in T. muris, parasite of murines Inra
Deter, J.; Galan, M.; Charbonnel, N.; Cosson, J.F..
Trichuris arvicolae and T. muris are gastro-intestinal nematodes of respectively arvicoline and murine rodents. We aim to investigate the ecology of these Trichuris species using population genetics. We sampled nematodes from rodents trapped in the East of France. After confirming the species identification of the nematodes using ITS1-5.8S-ITS2 ribosomal DNA sequences, we isolated and characterized twelve dinucleotide microsatellite loci in T. arvicolae. A multiplex panel was developed. Application to a set of 30 individuals allowed clear and easy characterization of allele sizes. The number of alleles ranged from 2 to 6 per locus with observed heterozygosities ranging from 0 to 0.93. A test on eleven T. muris revealed that eight loci among twelve...
Tipo: Journal Article Palavras-chave: MICROSATELLITE MICROSATELLITE BANK; MULTIPLEX PCR; PARASITIC NEMATODE; POPULATION GENETICS.
Ano: 2009 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD20103758e5d0&uri=/notices/prodinra1/2010/12/
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Comparison of genetic and virulence diversity of Melampsora larici-populina populations on wild and cultivated poplar and influence of the alternate host Inra
Gérard, P.R.; Husson, C.; Pinon; Frey, P..
The aims of this study were, first, to compare the genetic and virulence diversity between populations of the rust fungus Melanipsora larici-populina on wild and cultivated poplar stands and, second, to investigate the influence of the presence of the alternate host of the pathogen, larch, on which its sexual reproduction occurs, on these diversities. Nine French M. larici-populina populations collected from poplar trees in autumn and four. populations collected from larch trees during the following spring were analyzed using both virulence factors and neutral markers. In all, 30 pathotypes were identified within the 13 populations studied. The pathotypic structure clearly distinguished the cultivated stands with high richness and complexity from the wild...
Tipo: Journal Article Palavras-chave: GENETIQUE DES POPULATIONS; ROUILLE; MALADIE DES PLANTES; POUVOIR PATHOGENE; DIVERSITE GENETIQUE; PATHOTYPE; HOTE ALTERNATIF; EPIDEMIOLOGIE BLACK POPLAR; DOMINANT MARKERS; POPULATION GENETICS; RUST EPIDEMICS.
Ano: 2006 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2007e8ace244&uri=/notices/prodinra1/2007/03/
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Genetic diversity of the west European honey bee (Apis mellifera mellifera and A. m. iberia). II.Microsatellite loci Inra
Garnery, L.; Franck, P.; Baudry, E.; Vautrin, D.; Cornuet, J.M.; Solignac, M..
La variabilité génétique et la différenciation entre populations a été étudiée pour 11 locus microsatellites dans 15 populations de l’abeille ouest européenne. Les deux sous-espèces qui constituent ce rameau (Apis mellifera mellifera et A. m. iberica) ont une variabilité génétique plus réduite que la plupart des autres populations étudiées avec les mêmes outils moléculaires et plusieurs tests statistiques sont révélateurs d’une réduction récente de leur effectif. De plus, les profils génétiques des populations sont très comparables, du sud de l’Espagne à la Scandinavie, Les populations françaises sont plus ou moins introgressées (de quelques pourcentages jusqu’à 57 %) par des gènes de la lignée nordméditerranéenne, les races ligustica et carnica...
Tipo: Journal Article Palavras-chave: ABEILLE HONEY BEE; MICROSATELLITES; POPULATION GENETICS; INTROGRESSION; CONSERVATION.
Ano: 1998 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2007f04ca494&uri=/notices/prodinra1/2011/02/
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Genetic structure of the grapevine fungal pathogen Phaeomoniella chlamydospora in southeastern Australia and southern France Inra
Smetham, G.M.; Ades, P.K.; Peros, J.P.; Ford, R..
In this study, 18 microsatellite loci were used to examine the genetic structure and mode of reproduction of Phaeomoniella chlamydospora, the fungus that causes Petri disease of grapevine and is involved in another grapevine disease, esca. A total of 60 southeastern Australian isolates were tested and compared with 64 isolates from southern France. The French population possessed relatively high genotypic diversity (G = 29Æ2) whilst the Australian population showed low genotypic diversity (G = 11Æ1), consistent with a limited founder population. Haplotypes from four different grapevine cultivars were not significantly differentiated (Fpt values effectively zero). Likewise, genetic differentiation of haplotypes from different regions within each country was...
Tipo: Journal Article Palavras-chave: MICROSATELLITE; ESCA; MALADIE CRYPTOGAMIQUE CLONAL POPULATION; ESCA DISEASE; MICROSATELLITE MARKERS; PETRI DISEASE; POPULATION GENETICS.
Ano: 2010 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD20104d696814&uri=/notices/prodinra1/2010/12/
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Genome-wide survey and analysis of microsatellites in nematodes, with a focus on the plant-parasitic species Meloidogyne incognita Inra
Castagnone, P.; Danchin, E.; Deleury, E.; Guillemaud, T.; Malausa, T.; Abad, P..
Background.Microsatellites are the most popular source of molecular markers for studying population genetic variation in eukaryotes. However, few data are currently available about their genomic distribution and abundance across the phylum Nematoda. The recent completion of the genomes of several nematode species, including Meloidogyne incognita, a major agricultural pest worldwide, now opens the way for a comparative survey and analysis of microsatellites in these organisms.Results.Using MsatFinder, the total numbers of 1-6 bp perfect microsatellites detected in the complete genomes of five nematode species (Brugia malayi, Caenorhabditis elegans, M. hapla, M. incognita, Pristionchus pacificus) ranged from 2,842 to 61,547, and covered from 0.09 to 1.20% of...
Tipo: Journal Article Palavras-chave: DIVERSITE GENETIQUE GENETIC DIVERSITY; POPULATION GENETICS; MICROSATELLITE MARKERS.
Ano: 2010 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2010b0148310&uri=/notices/prodinra1/2010/11/
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Infering population history with DIYABC: a user-friendly approach to Approximate Bayesian Computation Inra
Cornuet, J.M.; Santos, F.; Beaumont, M.A.; Robert, C.P.; Marin, J.M.; Balding, D.J.; Guillemaud, T.; Estoup, A..
Genetic data obtained on population samples convey information about their evolutionary history. Inference methods can extract this information (at least partially) but they require sophisticated statistical techniques that have been made available to the biologist community (through computer programs) only for simple and standard situations typically involving a small number of samples. We propose here a computer program (DIYABC) for inference based on Approximate Bayesian Computation (ABC), in which scenarios can be customized by the user to fit many complex situations involving any number of populations and samples. Such scenarios involve any combination of population divergences, admixtures and stepwise population size changes. DIYABC can be used to...
Tipo: Journal Article Palavras-chave: INFERENCE; HISTORY; POPULATION DYNAMICS; POPULATION GENETICS; STATISTICS; MATHEMATICAL PROGRAMMING.
Ano: 2008 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2009bea71fa3&uri=/notices/prodinra1/2011/04/
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Invasive patterns of an exotic seed chalcid, Megastigmus schimitscheki Novitzky, in the cedar plantations of southern France Inra
Auger-Rozenberg, M.A.; Roques, L.; Boivin, S.; Chalon, A.; Fabre, J.P.; Roques, A..
Tipo: Meeting Paper Palavras-chave: HYMENOPTERA; TORYMIDAE; MEGASTIGMUS SCHIMITSCHEKI; MEGASTIGMUS PINSAPINIS; MEGASTIGMUS SUSPECTUS; CHALCIDIEN; ESPECE EXOTIQUE INVASIVE CHALCID; INVASIVE ALIEN SPECIES; PEST INSECT; SEED INSECT; HOST-PARASITE RELATIONSHIP; POPULATION GENETICS.
Ano: 2003 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2009206df3c&uri=/notices/prodinra1/2011/05/
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Micropterix of Cyprus and the Middle East (Micropterigidae) Inra
Zeller-Lukashort, C.H.; Kurz, M.A.; Lees, D.C.; Schwartz-Tzachor, R..
All known species of the genus Micropterix Hübner, 1825 (Micropterigidae) from Cyprus(Micropterix cypriensis Heath, 1985) and the Middle East (Israel, Lebanon: Micropterix berytella de Joannis, 1886, Micropterix elegans Stainton, 1867 and Micropterix islamella Amsel, 1935) are treated. The male genitalia of Micropterix islamella Amsel, 1935 are illustrated for the fi rst time. The association of two Micropterix species with Cyclamen persicum Mill. (Myrsinaceae) is detailed. Adults and male genitalia of all species are illustrated, showing the habitus of all species in their natural environment.
Tipo: Journal Article Palavras-chave: LEPIDOPTERA; MICROPTERIGIDAE; MICROPTERIX CYPRIENSIS; MICROPTERIX BERYTELLA; MICROPTERIX ELEGANS; MICROPTERIX ISLAMELLA; DISTRIBUTION SPATIALE INSECT; MICROPTERIX OF CYPRUS; POPULATION BIOLOGY; POPULATION GENETICS; TAXONOMY; SPATIAL DISTRIBUTION; POPULATION BIOLOGY; POPULATION GENETICS; CYPRUS; MIDDLE EAST; MEDITERRANEAN COUNTRIES.
Ano: 2009 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2010c95ab6a4&uri=/notices/prodinra1/2011/01/
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Permanent Genetic Resources added to the Molecular Ecology Resources Database 1 February 2010–31 March 2010 Inra
Aurelle, D.; Baker, A.J.; Bottin, L.; Brouat, C.; Caccone, A.; Chaix, A.; Dhakal, P.; Ding, Y.; Duplantier, J.M.; Fiedler, W.; Fietz, J.; Fong, Y.; Forcioli, D.; Freitas, T.R.O.; Gunnarsson, G.H.; Haddrath, O.; Hadziabdic, D.; Hauksdottir, S.; Havill, N.P.; Heinrich, M.; Heinz, T.; Hjorleifs-Dottir, S.; Hong, Y.; Hreggvidsson, G.O.; Huchette, S.; Hurst, J.; Kane, N.C.; Kawakami, T.; Ke, W.; Keith, R.A.; Klauke, N.; Klein, J.L.; Kun, J.F.J.; Li, C.; Li, G.Q.; Li, J.J.; Loiseau, A.; Lu, L.Z.; Lucas, M.; Martins-Ferreira, C.; Mokhtar-Jamaï, K.; Olafsson, K.; Pampoulie, C.; Pan, L.; Pooler, M.R.; Ren, J.D.; Rinehart, T.A.; Roussel, V.; Santos, M.O.; Schaefer, H.M.; Scheffler, B.E.; Schmidt, A.; Segelbacher, G.; Shen, J.D.; Skirnisdottir, S.; Sommer, S.; Tao, Z.R.; Taubert, R.; Tian, Y.; Tomiuk, J.; Trigiano, R.N.; Ungerer, M.C.; van Wormhoudt, A.; Wadl, P.A.; Wang, P.A.; Weis-Dootz, T.; Xia, Q.; Yuan, Q.Y.; Molecular Ecology Resources Primer Development Consortium, Aix-Marseille Universite (FRA).
This article documents the addition of 228microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Anser cygnoides, Apodemus flavicollis, Athene noctua, Cercis canadensis, Glis glis, Gubernatrix cristata, Haliotis tuberculata, Helianthus maximiliani, Laricobius nigrinus, Laricobius rubidus, Neoheligmonella granjoni, Nephrops norvegicus, Oenanthe javanica, Paramuricea clavata, Pyrrhura orcesi and Samanea saman. These loci were cross-tested on the following species: Apodemus sylvaticus, Laricobius laticollis and Laricobius osakensis (a proposed new species currently being described)
Tipo: Journal Article Palavras-chave: CATALOGUE; REFERENCEMENT; GENBANK; MOLECULAR MARKERS; ECOLOGY; POPULATION GENETICS; INSECTS; PHYLOGENY; TAXONOMY.
Ano: 2010 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD201132e67fca&uri=/notices/prodinra1/2011/06/
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Probability distribution of haplotype frequencies under the two-locus Wright-Fisher model by diffusion approximation Inra
Boitard, S.; Loisel, P..
The probability distribution of haplotype frequencies in a population, and the way it is influenced by genetical forces such as recombination, selection, random drift y is a question of fundamental interest in population genetics. For large populations, the distribution of haplotype frequencies for two linked loci under the classical Wright–Fisher model is almost impossible to compute because of numerical reasons. However the Wright–Fisher process can in such cases be approximated by a diffusion process and the transition density can then be deduced from the Kolmogorov equations. As no exact solution has been found for these equations, we developed a numerical method based on finite differences to solve them. It applies to transient states and models...
Tipo: Journal Article Palavras-chave: POPULATION GENETICS; PROBABILITE; METHODE MONTE CARLO; METHODE DES DIFFERENCES FINIES WRIGHT–FISHER MODEL; DIFFUSION PROCESSES; KOLMOGOROV FORWARD EQUATION; FINITE DIFFERENCE SCHEME.
Ano: 2007 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2010e741cfd3&uri=/notices/prodinra1/2011/01/
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The role of topography in structuring the demographic history of the pine processionary moth Thaumetopoea pityocampa (Lepidoptera: Notodontidae) Inra
Rousselet, J.; Zhao, R.; Argal, D.; Simonato, M.; Battisti, A.; Roques, A.; Kerdelhue, C..
Aim: We investigated the Quaternary history of the pine processionary moth, Thaumetopoea pityocampa, an oligophagous insect currently expanding its range. We tested the potential role played by mountain ranges during the post-glacial recolonization of western Europe.Location: Western Europe, with a focus on the Pyrenees, Massif Central and western Alps.Methods: Maternal genetic structure was investigated using a fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. We analysed 412 individuals from 61 locations and we performed maximum-likelihood and maximum parsimony phylogenetic analyses, hierarchical analysis of molecular variance, and investigated signs of past expansion.Results: A strong phylogeographic pattern was found, with two...
Tipo: Journal Article Palavras-chave: LEPIDOPTERA; THAUMETOPOEA PITYOCAMPA; PROCESSIONNAIRE DU PIN ; EXPANSION DE l'AIRE DE REPARTITION; MIGRATION VERTICALE; REFUGE GLACIAIRE; BIOGEOGRAPHIE; ADN MITOCHONDRIAL; BASSIN MEDITERRANEEN PROCESSIONARY MOTH ; PEST INSECT; LATITUDINAL SHIFT; RANGE EXPANSION; GLACIATION REFUGE; MITOCHONDRIAL DNA; CLIMATE CHANGE; POPULATION GENETICS; DNA; MEDITERRANEAN BASIN.
Ano: 2010 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD201086242aeb&uri=/notices/prodinra1/2011/05/
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Use of chloroplast microsatellites to differentiate oak populations Inra
Deguilloux, M. F.; Pemonge, M. H.; Petit, R.J..
Nous avons cherché à comparer l'efficacité de deux types de marqueurs chloroplastiques, les marqueurs microsatellites (cpSSR) et marqueurs PCR-RFLP (cpRFLP), à différencier des populations de chênes sessiles et pédonculés, deux espèces d'arbres forestiers économiquement importantes. Le niveau et la structuration de la diversité inter et intra-spécifique ont été mesurés au sein de 48 populations françaises au travers de l'analyse de 24 microsatellites chloroplastiques. Une faible diversité intra-population, ainsi qu'une forte différenciation des populations de chênes ont pu être mesurées à l'aide des deux types de marqueurs, du fait d'une redondance quasi-complète des haplotypes identifiés par les deux techniques. Nos résultats indiquent donc que les...
Tipo: Journal Article Palavras-chave: DIVERSITE HAPLOTYPIQUE MICROSATELLITE; CPSSR; PCR-RFLP; HAPLOTYPIC DIVERSITY; POPULATION GENETICS.
Ano: 2004 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2007c93e442f&uri=/notices/prodinra1/2009/11/
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