A low-cost open-source SNP genotyping platform for association mapping applications

Association mapping aimed at identifying DNA polymorphisms that contribute to variation in complex traits entails genotyping a large number of single-nucleotide polymorphisms (SNPs) in a very large panel of individuals. Few technologies, however, provide inexpensive high-throughput genotyping. Here, we present an efficient approach developed specifically for genotyping large fixed panels of diploid individuals. The cost-effective, open-source nature of our methodology may make it particularly attractive to those working in nonmodel systems

Sex-Specific Expression of Alternative Transcripts in \u3ci\u3eDrosophila\u3c/i\u3e

Background: Many genes produce multiple transcripts due to alternative splicing or utilization of alternative transcription initiation/termination sites. This \u27transcriptome expansion\u27 is thought to increase phenotypic complexity by allowing a single locus to produce several functionally distinct proteins. However, sex, genetic and developmental variation in the representation of alternative transcripts has never been examined systematically. Here, we describe a genome-wide analysis of sex-specific expression of alternative transcripts in Drosophila melanogaster. Results: We compared transcript profiles in males and females from eight Drosophila lines (OregonR and 2b, and 6 RIL) using a newly designed 60-mer oligonucleotide microarray that allows us to distinguish a large proportion of alternative transcripts. The new microarray incorporates 7,207 oligonucleotides, satisfying stringent binding and specificity criteria that target both the common and the unique regions of 2,768 multi-transcript genes, as well as 12,912 oligonucleotides that target genes with a single known transcript. We estimate that up to 22% of genes that produce multiple transcripts show a sex-specific bias in the representation of alternative transcripts. Sexual dimorphism in overall transcript abundance was evident for 53% of genes. The X chromosome contains a significantly higher proportion of genes with female-biased transcription than the autosomes. However, genes on the X chromosome are no more likely to have a sexual bias in alternative transcript representation than autosomal genes. Conclusion: Widespread sex-specific expression of alternative transcripts in Drosophila suggests that a new level of sexual dimorphism at the molecular level exists

Sex-specific expression of alternative transcripts in Drosophila

BACKGROUND: Many genes produce multiple transcripts due to alternative splicing or utilization of alternative transcription initiation/termination sites. This 'transcriptome expansion' is thought to increase phenotypic complexity by allowing a single locus to produce several functionally distinct proteins. However, sex, genetic and developmental variation in the representation of alternative transcripts has never been examined systematically. Here, we describe a genome-wide analysis of sex-specific expression of alternative transcripts in Drosophila melanogaster. RESULTS: We compared transcript profiles in males and females from eight Drosophila lines (OregonR and 2b, and 6 RIL) using a newly designed 60-mer oligonucleotide microarray that allows us to distinguish a large proportion of alternative transcripts. The new microarray incorporates 7,207 oligonucleotides, satisfying stringent binding and specificity criteria that target both the common and the unique regions of 2,768 multi-transcript genes, as well as 12,912 oligonucleotides that target genes with a single known transcript. We estimate that up to 22% of genes that produce multiple transcripts show a sex-specific bias in the representation of alternative transcripts. Sexual dimorphism in overall transcript abundance was evident for 53% of genes. The X chromosome contains a significantly higher proportion of genes with female-biased transcription than the autosomes. However, genes on the X chromosome are no more likely to have a sexual bias in alternative transcript representation than autosomal genes. CONCLUSION: Widespread sex-specific expression of alternative transcripts in Drosophila suggests that a new level of sexual dimorphism at the molecular level exists

A thousand-genome panel retraces the global spread and adaptation of a major fungal crop pathogen

Human activity impacts the evolutionary trajectories of many species worldwide. Global trade of agricultural goods contributes to the dispersal of pathogens reshaping their genetic makeup and providing opportunities for virulence gains. Understanding how pathogens surmount control strategies and cope with new climates is crucial to predicting the future impact of crop pathogens. Here, we address this by assembling a global thousand-genome panel of Zymoseptoria tritici, a major fungal pathogen of wheat reported in all production areas worldwide. We identify the global invasion routes and ongoing genetic exchange of the pathogen among wheat-growing regions. We find that the global expansion was accompanied by increased activity of transposable elements and weakened genomic defenses. Finally, we find significant standing variation for adaptation to new climates encountered during the global spread. Our work shows how large population genomic panels enable deep insights into the evolutionary trajectory of a major crop pathogen

Course aux armements entre plantes transgéniques et insectes (estimation des risques d'évolution de la résistance des populations de Chrysomela tremulae aux toxines de Bacillus thuringiensis produites par les peupliers transgéniques)

The leaf beetle chrysomela tremulae, a phytophagous insect which is an important pest species on young poplar plantations, is a good model for risk assessment of the evolution of resistance to bacillus thuringiensis toxins produced by transgenic plants. An hybrid clone populus tremula x P. Tremuloides has been genetically engineered via Agrobacterium with a synthetic cry3A gene. This gene encodes a toxin homologous to the one encoded by the native Bacillus thuringiensis ssp tenebrionis gene. Upon molecular characterisation of transgenic plants, consumption tests of transgenic lines expressing cry3A were performed. Toxin production by the transgenic lines was sufficient to induce a complete mortality of all development stages of chrysomela tremulae. An estimation of resistance alleles frequencies was performed using the F2 screen method. One isofemale line (among 64) gave some resistant offspring to transgenic poplar foliage in her F2 progeny. These results indicate that resistance allele frequencies are not necessarily rare in C. Tremulae populations. This line was subsequently selected in order to obtain a resistant strain to the cry3A toxin. This later allowed a preliminary study on the genetic characteristics of the resistance. The genetic structure of C. Tremulae populations was determined by sampling 15 sites in France and 1 in Belgium. The genetic diversity was investigated by analysing the allelic frequencies of seven allozymic polymorphic markers. This study gave the following conclusions (i) the genotypic frequencies did not differ from those expected from Hardy-Weinberg equilibrium, suggesting a panmictic reproduction within populations (ii) a very low level of genetic differentiation was observed whatever the geographic scaled concidered indicating a high level of gene flow between population. This work emphasises that the study of biological parameters (such as the migration, the resistance alleles frequencies, and the genetics of resistance) of polyphagous species is a prerequisite before the introduction of transgenic plants producing a toxin against their pest species. In the case of poplar - chrysomela system, the pest may rapidly lead the race.La chrysomèle du tremble, chrysomela tremulae (coléoptère, chrysomelidae), phytophage du peuplier capable de provoquer des dégâts très importants sur de jeunes plantations, constitue un bon modèle d'étude pour estimer les risques d'evolution de la résistance des insectes aux transformations génétiques des plantes. un clone de peuplier hybride Populus tremula x populus tremuloides a été génétiquement transformé via Agrobacterium avec un gène synthétique cry3A. Ce gène code une toxine insecticide, homologue à celle produite par le gène natif issu de Bacillus thuringiensis ssp tenebrionis. Après caractérisation moléculaire des plants transgéniques, des tests de consommation des lignéees exprimant cry3A ont été effectués. La production de toxines par ces lignées est suffisante pour engendrer la mort de tous les stades de développement de C. Tremulae. Une estimation des fréquences des allèles conférant une résistance à la toxine Cry3A a été effectuée selon la méthode du F2 screen. Une lignée isofemelle (parmi 64) a présenté des individus résistants au feuillage de peuplier transgénique. Ces résultats indiquent que les fréquences des allèles conférant la résistance aux toxines de Bt ne sont pas nécessairement rares dans les populations de C. tremulae. La lignée isofemelle résistante a permis de sélectionner une souche résistante à la toxine cry3A, permettant une étude préliminaire du déterminisme génétique de la résistance. Une étude de la structuration génétique des populations de c. tremulae a été effectuée en France (15 sites) et en Belgique (1 site d'échantillonnage), à l'aide de 7 marqueurs allozymiques polymorphes. Elle a mis en évidence (i) que les populations étaient à l'équilibre de Hardy-Weinberg, suggérant une reproduction panmictique au sein des populations (ii) une faible différenciation génétique entre les sites échantillonnés, indiquant d'intenses flux de gènes entre les populations de chrysomèles, quelque soit l'échelle géographique considérée. Ce travail met en évidence l'indispensable étude des paramètres biologiques (migration, fréquence des allèles de résistance, génétique de cette résistance) des insectes avant la culture des plantes transgéniques produisant des toxines actives contre leurs ravageurs. Dans le cas du système peuplier - Chrysomèle du tremble, cette dernière a toutes les chances de gagner rapidement la course aux armements.TOURS-BU Sciences Pharmacie (372612104) / SudocSudocFranceF

Prise en charge de l'allaitement maternel à la maternité

ANGERS-BU Médecine-Pharmacie (490072105) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

Population genetics of Chrysomela tremulae: a first step towards management of transgenic Bacillus thuringiensis poplars Populus tremula x P. tremuloides

40 ref.International audienc

Insecticide resistance and dominance levels

International audienc

Evolution and Plasticity of the Transcriptome Under Temperature Fluctuations in the Fungal Plant Pathogen Zymoseptoria tritici

International audienceMost species live in a variable environment in nature. Yet understanding the evolutionary processes underlying molecular adaptation to fluctuations remains a challenge. In this study we investigate the transcriptome of the fungal wheat pathogenZymoseptoria triticiafter experimental evolution under stable or fluctuating temperature, by comparing ancestral and evolved populations simultaneously. We found that temperature regimes could have a large and pervasive effect on the transcriptome evolution, with as much as 38% of the genes being differentially expressed between selection regimes. Although evolved lineages showed different changes of gene expression based on ancestral genotypes, we identified a set of genes responding specifically to fluctuation. We found that transcriptome evolution in fluctuating conditions was repeatable between parallel lineages initiated from the same genotype for about 60% of the differentially expressed genes. Further, we detected several hotspots of significantly differentially expressed genes in the genome, in regions known to be enriched in repetitive elements, including accessory chromosomes. Our findings also evidenced gene expression evolution toward a gain of robustness (loss of phenotypic plasticity) associated with the fluctuating regime, suggesting robustness is adaptive in changing environment. This work provides valuable insight into the role of transcriptional rewiring for rapid adaptation to abiotic changes in filamentous plant pathogens