59 research outputs found
BMC Plant Biol
Combining innovation in vineyard management andgenetic diversity for a sustainable European viticultur
Focal Conic Stacking in Smectic A Liquid Crystals: Smectic Flower and Apollonius Tiling
We investigate two different textures of smectic A liquid crystals. These textures are particularly symmetric when they are observed at crossed polars optical microscopy. For both textures, a model has been made in order to examine the link between the defective macroscopic texture and the microscopic disposition of the layers. We present in particular in the case of some hexagonal tiling of circles (similar to the Apollonius tiling) some numeric simulation in order to visualize the smectic layers. We discuss of the nature of the smectic layers, which permit to assure their continuity from one focal conic domain to another adjacent one
Light management in scintillator crystals: a multi-scale computational study (Conference Presentation)
International audienc
New generation sequencer to rapidly genotype grape diversity
New generation sequencer (NGS) allows to obtain within only one run hundreds of billions bases in order to study SNP diversity. The first step of this work we develop lab protocols adapted for NGS to test them for grape. In this context we have firstly developed a nuclear DNA extraction protocol to limit the level of cytoplasmic DNA, and secondly with have analyzed three runs of 454 GS-FLX. Our protocol allows the limitation of cytoplasmic DNA at BAC libraries similar level (4%) whereas a classical DNA extraction contains around 12%. Our data sets from the 454 have been aligned on the grape reference genome PN40024 (12X) with a compilation of different software: Mosaik-assembler, Repeat-Masker. Sixty-six percent of the reads obtained from each 454 runs aligned at a unique locus (30% coverage of the grape genome of reference). The quantity of reads aligned is proportional of the length of chromosomes. Compare to the PN40024 genome, we obtained a similar GC percentage, coding and non coding ratio, element mobile ratio. Nerveless, we observed that some genomic regions are more easily accessed by these types of methodologies. The chromosome structure, centromeres and histones localizations could be responsible for this observation. Such protocol would be a great asset for sequencing project as GrapeReseq
Comparaison de modÚles univariés et multivariés pour la sélection de marqueurs et la prédiction génomique
International audienc
Etude des nouvelles composantes de l'agressivité du pathogÚne Eutypa lata cryptogame vasculaire responsable de l'eutypiose
National audienceEÌtude de nouvelles composantes de lâagressiviteÌ du pathogeÌne Eutypa lata, cryptogame vasculaire responsable de lâeutypiose 1 Luc P.R. Bidel, 2 LoiÌc Le Cunff, 3 Anne CleÌment-Vidal, 1 Philippe Chatelet et 1Jean-Pierre PeÌros 1 INRA, UMR AGAP, Equipe DAAV (DiversiteÌâAdaptation et AmeÌlioration de la Vigne), 2 place Viala, F-34060, Montpellier. 2 IFV, UMT GeÌno-Vigne, INRA-Montpellier SupAgro, 2 Place Viala, F-34060, Montpellier. 3 CIRAD, UMR AGAP, avenue dâAgropolis, F-34398, Montpellier. Contact : [email protected] Lâeutypiose est une maladie de deÌpeÌrissement causeÌe par le champignon ascomyceÌte Eutypa lata. Les ceps atteints preÌsentent au printemps des rameaux rabougris portant des feuilles neÌcroseÌes. Dans le bois, la maladie se caracteÌrise par une neÌcrose sectorielle qui progresse dâanneÌe en anneÌe jusquâaÌ la mort de la plante. E. lata sâattaque aÌ de nombreux ligneux et preÌsente un fort impact eÌconomique en viticulture. Des ceÌpages treÌs reÌpandus comme Ugni Blanc et Cabernet Sauvignon sont particulieÌrement sensibles aÌ la maladie. Aucune meÌthode curative nâexiste contre le pathogeÌne qui colonise ses hoÌtes apreÌs la contamination des plaies de taille par les ascospores. Les travaux dâOctave (2006) ont montreÌ que des fractions glycoproteÌiques exsudeÌs par E. lata en culture pure eÌtaient plus phytotoxiques que lâeutypine, principale toxine jusquâalors identifieÌe. Ces fractions nâavaient pas encore eÌteÌ caracteÌriseÌes en proteÌomique. Afin dâidentifier les peptides et les proteÌines toxiques pour la vigne, nous avons fractionneÌ par chromatographie les exsudats proteÌiques de souches dâE. lata dont lâagressiviteÌ avait eÌteÌ caracteÌriseÌe sur boutures (PeÌros et Berger 1994), et nous avons mesureÌ leur phytotoxiciteÌ sur pastilles foliaires. Plusieurs fractions proteÌiques induisent des neÌcroses, suggeÌrant effectivement lâexistence de diffeÌrents composants toxiques. La taille de ces neÌcroses sâaveÌre aussi correÌleÌe avec la quantiteÌ de proteÌines preÌsentes dans la fraction. De plus, lorsquâune meÌme fraction phytotoxique est appliqueÌe sur une gamme de ceÌpages de peu sensibles aÌ treÌs sensibles aÌ la maladie, nous observons une correÌlation entre les symptoÌmes observeÌs et la sensibiliteÌ estimeÌe au vignoble (Grosman et Doublet 2012). Les travaux se poursuivent pour identifier au sein des fractions phytotoxiques les mycotoxines peptidiques et leurs cibles proteÌiques chez la vigne. Lâensemble de ces recherches a pour but de mieux comprendre lâinteraction entre le pathogeÌne et la plante afin de deÌvelopper des outils performants pour identifier des sources de toleÌrance aÌ utiliser dans de nouveaux projets dâameÌlioration varieÌtale. Grosman J., B. Doublet, 2012. Maladies du bois de la vigne. SyntheÌse des dispositifs dâobservation au vignoble, de lâobservatoire 2003-2008 au reÌseau dâeÌpideÌmio-surveillance actuel. Phytoma â La DeÌfense des VeÌgeÌtaux 651, 31-35. Octave S., Roblin G., Vachaud M, Fleurat-Lessard P., 2006. Polypeptidic metabolites secreted by the fungal pathogen Eutypa lata participate in Vitis vinifera L. cell structure damage observed in Eutypa dieback. Functional Plant Biology 33:297-307. PeÌros J-P., Berger G. 1994. A rapid method to assess the aggressiveness of Eutypa lata isolates and the susceptibility of grapevine cultivars to Eutypa dieback. Agronomie 14: 515-523
Multivariate statistical modelling for QTL detection and marker selection in a bi-parental grapevine population
Genetic selection in grapevine and many similar species is a challenge due to their perennial status and outbred nature. Marker-assisted selection and genomic selection can hence be useful methods to ease and speed up breeding. In Coupel-Ledru et al (2014), a 191 progeny of Syrah x Grenache was phenotyped in two successive years for several ecophysiological traits under two conditions, well-watered and water deficit, on a high-throughput phenotyping platform coupled to a controlledâenvironment chamber. As offsprings were previously genotyped at 153 SSR markers, several QTLs were found for each trait separately, differing across years and conditions.But do these differences reflect biological processes or contrasted power between conditions? And how accurately do they allow predicting phenotypes depending on the conditions? To answer such questions, our aim is to explore the ability of sparse and regularized multivariate regression models and algorithms to select QTLs based on their predictive properties. In the present study, we perform variable selection with various flavours of the LASSO method (group Lasso, fused Lasso) adapted for multiple responses, extending the model and algorithm from Chiquet et al. (2017). We apply these methods on simulated data and on real data fromCoupel-Ledru et al. (2014)
Finding regulators of grape flavonoid biosynthesis via eQTL mapping
International audienceExpression QTL (eQTL) mapping consists in applying QTL analysis method on transcript abundance in a segregating population. eQTL studies allow the identification of candidate regions and therefore candidate genes involved in regulation of transcript abundance. We describe here the first eQTL study in grapevine. We used a pseudo-F1 population of 191 progenies (SxG) derived from a reciprocal cross of Syrah and Grenache. Expression of target genes was recorded by RT-qPCR. Our interest pathway is the proanthocyanidin (PA) branch of the flavonoid biosynthesis. Indeed, PA are the most abundant secondary metabolites in grape berry and are responsible of astringency, a major quality trait of wine. We first validated the feasibility of eQTL approach by mapping expression of VvUFGT, a well known gene of anthocyanin synthesis, another branch of the flavonoid pathway. A cis- and a trans-eQTL were detected for VvUFGT, and the trans-eQTL colocalized with the major transcription factor cluster of anthocyanin synthesis. For PA branch, we measured the expression of specific PA synthetic genes (VvANR, VvLAR1, VvLAR2) and two genes of the flavonoid synthesis, VvDFR and VvLDOX, common to both PA and anthocyanin synthesis. One trans- and two cis-eQTL were detected for three of the five investigated genes. Our results show the interest to use eQTL approach to understand genomic regulation of grapevine quality traits and provide perspectives to extend grapevine eQTL analysis to a genome-wide extent
CrĂ©er les cĂ©pages de demain avec les outils dâaujourdâhui
Ce volume rassemble l'ensemble des travaux de recherche conduits dans le cadre des appels Ă projets soutenus par le plan Ecophyto, et prĂ©sentĂ©s Ă l'occasion du colloque Ecophyto Recherche des 13 et 14 octobre 2015National audienceViticulture is one of the crops with the largest use of pesticides. Moreover viticulture is also impacted by climate change. Among the possible answers to these challenges, the development of new varieties is a possible way. Nowadays, the selection assisted by molecular markers (SAM) presents a great potential in plant breeding programs. In grapevine, SAM is only used to select simple traits (monogenic) as resistance to downy and powdery mildew, Muscat aroma or seedless. However many targeted traits as quality of berries show a complex inheritance (oligogenic or polygenic). In the project, we designed a strategy to speed up grapevine selection of complex traits including new methodologies and scientific knowledge.La viticulture est aujourdâhui une des espĂšces les plus fortes utilisatrices de produits phytosanitaires en Europe. Par ailleurs, les Ă©volutions du climat pourraient engendrer de profondes modifications et notamment dans la zone mĂ©diterranĂ©enne. La crĂ©ation variĂ©tale peut-ĂȘtre une des solutions possibles pour rĂ©pondre Ă ces dĂ©fis LâamĂ©lioration variĂ©tale est aujourdâhui assistĂ©e de plus en plus par des donnĂ©es molĂ©culaires. Chez la vigne, les marqueurs utilisĂ©s actuellement sont liĂ©s Ă des caractĂšres monogĂ©niques comme la rĂ©sistance au mildiou et Ă lâoĂŻdium, lâapyrĂ©nie et le gout muscat. Les marqueurs sont connus et leur utilisation en routine est maintenant actĂ©e. Ce projet sâaxe sur lâĂ©tude de mĂ©thodologies ou dâoutils permettant i) la sĂ©lection de caractĂšres complexes gĂ©nĂ©ralement contrĂŽlĂ©s par plusieurs gĂšnes ii) lâaccĂ©lĂ©ration du cycle de gĂ©nĂ©ration pour faciliter lâobtention de gĂ©niteurs Ă©lites. Ce projet permet la dĂ©finition de plusieurs stratĂ©gies pour dĂ©velopper la crĂ©ation variĂ©tale chez la vigne
- âŠ