14 research outputs found

    Du gĂšne au phĂ©notype : contrĂŽle gĂ©nĂ©tique et modĂ©lisation du mĂ©tabolisme des sucres chez la pĂȘche

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    Fruit quality is a multi-criteria character with frequent antagonistic relationships. The perceptionof the fruit quality is highly dependent on the balance between the levels of sugars and acids. Among thethree so-called major sugars in fruit that are sucrose, glucose and fructose, fructose is the sweetest and itsconcentration is the factor that most affects the fruit sweetness. The objective of the present thesis is toanalyze the sugar metabolism in peach fruit from metabolic, enzymatic and genetic aspects and integrateinto a mathematical model all information obtained. This work focuses on the identification of the effect of alow fructose concentration on the whole sugar metabolism and the understanding of the mechanismsresponsible of this phenotype called ‘low-fructose-to-glucose-ratio’. A nearly exhaustive biochemicalcharacterization of sugar metabolism was conducted along peach fruit development. For this, 6 metabolitesand 12 enzyme capacities were assayed in 106 genotypes of a population derived from an interspecific cross.This study revealed a high stability of the enzyme capacities despite large variations of metabolites. Based ondata from 10 genotypes, a kinetic metabolic model that simulates the sugar accumulation in fruit wasdeveloped and validated. This model simulates contrasting phenotypes and helps in understanding theunderlying mechanisms of the ‘low-fructose-to-glucose-ratio’ phenotype. The biochemical characterizationof the population gave the opportunity to perform a QTL research. It highlighted the instability of the effectof certain loci along fruit development and QTL collocations of metabolites, enzyme capacities and candidategenes. It also confirmed the genomic region responsible for the ‘low-fructose-to-glucose-ratio’ phenotypewithin which a functional candidate gene was identified. It is a gene homologous to fructose vacuolartransporter (SWEET17) recently discovered in Arabidopsis. An analysis of this gene was engaged to validateits function and its responsibility in the ‘low-fructose-to-glucose-ratio’ phenotype. In the future, theintegration of the genetic control into the metabolic model will allow simulating virtual genotypes withdifferent combinations of alleles and predict their sugar content. Optimizing allele combinations to increasesugar concentrations in peach fruit will undoubtedly give new breeding opportunities.La qualitĂ© du fruit est un caractĂšre multicritĂšre avec des relations antagonistes frĂ©quentes. La perception de la qualitĂ© du fruit dĂ©pend fortement de l’équilibre entre les teneurs en sucres et acides. Parmi les 3 sucres dits majeurs dans les fruits que sont le saccharose, le glucose et le fructose, le fructose prĂ©sente un pouvoir sucrant plus important et sa concentration est le facteur qui affecte le plus le goĂ»t sucrĂ© du fruit.L’objectif de cette thĂšse est d’analyser le mĂ©tabolisme des sucres chez la pĂȘche d’un point de vue mĂ©tabolique, enzymatique et gĂ©nĂ©tique et d’intĂ©grer dans un modĂšle mathĂ©matique l’ensemble des informations obtenues. Ce travail porte plus particuliĂšrement sur la mise en Ă©vidence de l’effet d’une perturbation de la teneur en fructose sur l’ensemble du mĂ©tabolisme des sucres ainsi que sur la comprĂ©hension des mĂ©canismes Ă  l’origine de ce phĂ©notype appelĂ© ‘peu de fructose’. Une caractĂ©risation biochimique quasi-exhaustive du mĂ©tabolisme des sucres a Ă©tĂ© rĂ©alisĂ©e au cours du dĂ©veloppement du fruit.Pour cela 6 mĂ©tabolites et 12 capacitĂ©s enzymatiques ont Ă©tĂ© mesurĂ©s chez 106 gĂ©notypes d’une population issue d’un croisement interspĂ©cifique. Cette Ă©tude a rĂ©vĂ©lĂ© une grande stabilitĂ© des capacitĂ©s enzymatiques malgrĂ© l’importante variation des mĂ©tabolites. Sur la base des donnĂ©es de 10 des gĂ©notypes, un modĂšle mĂ©tabolique dynamique permettant de simuler l’accumulation des sucres au cours du dĂ©veloppement du fruit a Ă©tĂ© dĂ©veloppĂ© et validĂ©. Ce modĂšle permet de simuler des phĂ©notypes contrastĂ©s et aide ainsi Ă  l'exploration des mĂ©canismes sous-jacents au phĂ©notype ‘peu de fructose’. La caractĂ©risation biochimique de la population a Ă©galement fait l’objet d’une recherche de QTL. Cette Ă©tude a mis en exergue l’inconstance de l’effet de certains loci au cours du dĂ©veloppement du fruit ainsi que des co-localisations de QTL de mĂ©tabolites et capacitĂ©s enzymatiques et de gĂšnes candidats. Cette recherche a Ă©galement confirmĂ© la rĂ©gion gĂ©nomique responsable du phĂ©notype ‘peu de fructose’ au sein de laquelle un gĂšne candidat fonctionnel a Ă©tĂ© mis en Ă©vidence. Il s’agit d’un gĂšne homologue au transporteur vacuolaire exportateur de fructose (SWEET17) dĂ©couvert rĂ©cemment chez Arabidopsis. Une analyse de ce gĂšne a Ă©tĂ© engagĂ©e afin de valider sa fonction et son implication dans le phĂ©notype ‘peu de fructose’. GrĂące Ă  l’intĂ©gration des informations obtenues sur le contrĂŽle gĂ©nĂ©tique du mĂ©tabolisme des sucres dans le modĂšle mĂ©tabolique,une perspective de cette thĂšse sera de simuler les concentrations en sucres de gĂ©notypes virtuels ayant diffĂ©rentes combinaisons d’allĂšles. On pourra alors optimiser les combinaisons d’allĂšles pour augmenter les concentrations en sucres dans la pĂȘche, ce qui donnera sans doute de nouvelles pistes Ă  l’innovation variĂ©tale

    From gene to phenotype : Genetic control and modeling of sugar metabolism in peach

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    La qualitĂ© du fruit est un caractĂšre multicritĂšre avec des relations antagonistes frĂ©quentes. La perception de la qualitĂ© du fruit dĂ©pend fortement de l’équilibre entre les teneurs en sucres et acides. Parmi les 3 sucres dits majeurs dans les fruits que sont le saccharose, le glucose et le fructose, le fructose prĂ©sente un pouvoir sucrant plus important et sa concentration est le facteur qui affecte le plus le goĂ»t sucrĂ© du fruit.L’objectif de cette thĂšse est d’analyser le mĂ©tabolisme des sucres chez la pĂȘche d’un point de vue mĂ©tabolique, enzymatique et gĂ©nĂ©tique et d’intĂ©grer dans un modĂšle mathĂ©matique l’ensemble des informations obtenues. Ce travail porte plus particuliĂšrement sur la mise en Ă©vidence de l’effet d’une perturbation de la teneur en fructose sur l’ensemble du mĂ©tabolisme des sucres ainsi que sur la comprĂ©hension des mĂ©canismes Ă  l’origine de ce phĂ©notype appelĂ© ‘peu de fructose’. Une caractĂ©risation biochimique quasi-exhaustive du mĂ©tabolisme des sucres a Ă©tĂ© rĂ©alisĂ©e au cours du dĂ©veloppement du fruit.Pour cela 6 mĂ©tabolites et 12 capacitĂ©s enzymatiques ont Ă©tĂ© mesurĂ©s chez 106 gĂ©notypes d’une population issue d’un croisement interspĂ©cifique. Cette Ă©tude a rĂ©vĂ©lĂ© une grande stabilitĂ© des capacitĂ©s enzymatiques malgrĂ© l’importante variation des mĂ©tabolites. Sur la base des donnĂ©es de 10 des gĂ©notypes, un modĂšle mĂ©tabolique dynamique permettant de simuler l’accumulation des sucres au cours du dĂ©veloppement du fruit a Ă©tĂ© dĂ©veloppĂ© et validĂ©. Ce modĂšle permet de simuler des phĂ©notypes contrastĂ©s et aide ainsi Ă  l'exploration des mĂ©canismes sous-jacents au phĂ©notype ‘peu de fructose’. La caractĂ©risation biochimique de la population a Ă©galement fait l’objet d’une recherche de QTL. Cette Ă©tude a mis en exergue l’inconstance de l’effet de certains loci au cours du dĂ©veloppement du fruit ainsi que des co-localisations de QTL de mĂ©tabolites et capacitĂ©s enzymatiques et de gĂšnes candidats. Cette recherche a Ă©galement confirmĂ© la rĂ©gion gĂ©nomique responsable du phĂ©notype ‘peu de fructose’ au sein de laquelle un gĂšne candidat fonctionnel a Ă©tĂ© mis en Ă©vidence. Il s’agit d’un gĂšne homologue au transporteur vacuolaire exportateur de fructose (SWEET17) dĂ©couvert rĂ©cemment chez Arabidopsis. Une analyse de ce gĂšne a Ă©tĂ© engagĂ©e afin de valider sa fonction et son implication dans le phĂ©notype ‘peu de fructose’. GrĂące Ă  l’intĂ©gration des informations obtenues sur le contrĂŽle gĂ©nĂ©tique du mĂ©tabolisme des sucres dans le modĂšle mĂ©tabolique,une perspective de cette thĂšse sera de simuler les concentrations en sucres de gĂ©notypes virtuels ayant diffĂ©rentes combinaisons d’allĂšles. On pourra alors optimiser les combinaisons d’allĂšles pour augmenter les concentrations en sucres dans la pĂȘche, ce qui donnera sans doute de nouvelles pistes Ă  l’innovation variĂ©tale.Fruit quality is a multi-criteria character with frequent antagonistic relationships. The perceptionof the fruit quality is highly dependent on the balance between the levels of sugars and acids. Among thethree so-called major sugars in fruit that are sucrose, glucose and fructose, fructose is the sweetest and itsconcentration is the factor that most affects the fruit sweetness. The objective of the present thesis is toanalyze the sugar metabolism in peach fruit from metabolic, enzymatic and genetic aspects and integrateinto a mathematical model all information obtained. This work focuses on the identification of the effect of alow fructose concentration on the whole sugar metabolism and the understanding of the mechanismsresponsible of this phenotype called ‘low-fructose-to-glucose-ratio’. A nearly exhaustive biochemicalcharacterization of sugar metabolism was conducted along peach fruit development. For this, 6 metabolitesand 12 enzyme capacities were assayed in 106 genotypes of a population derived from an interspecific cross.This study revealed a high stability of the enzyme capacities despite large variations of metabolites. Based ondata from 10 genotypes, a kinetic metabolic model that simulates the sugar accumulation in fruit wasdeveloped and validated. This model simulates contrasting phenotypes and helps in understanding theunderlying mechanisms of the ‘low-fructose-to-glucose-ratio’ phenotype. The biochemical characterizationof the population gave the opportunity to perform a QTL research. It highlighted the instability of the effectof certain loci along fruit development and QTL collocations of metabolites, enzyme capacities and candidategenes. It also confirmed the genomic region responsible for the ‘low-fructose-to-glucose-ratio’ phenotypewithin which a functional candidate gene was identified. It is a gene homologous to fructose vacuolartransporter (SWEET17) recently discovered in Arabidopsis. An analysis of this gene was engaged to validateits function and its responsibility in the ‘low-fructose-to-glucose-ratio’ phenotype. In the future, theintegration of the genetic control into the metabolic model will allow simulating virtual genotypes withdifferent combinations of alleles and predict their sugar content. Optimizing allele combinations to increasesugar concentrations in peach fruit will undoubtedly give new breeding opportunities

    Comment rationaliser le stockage d’échantillons dans les congĂ©lateurs - 80°C ?

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    Avant 2011, Ă  l’UGAFL (UnitĂ© de GĂ©nĂ©tique et AmĂ©lioration des fruits et lĂ©gumes, INRA), l’utilisation dĂ©mesurĂ©e de la place dans les congĂ©lateurs - 80°C pĂ©nalisait les futures expĂ©rimentations. La rĂ©flexion menĂ©e dans l’UnitĂ© pour gĂ©rer le stockage d’échantillons dans les congĂ©lateurs -80°C, a permis de sensibiliser les utilisateurs Ă  anticiper le volume d’échantillons Ă  stocker lors de leurs expĂ©rimentations. Cette rĂ©flexion avait plusieurs objectifs : gĂ©rer au mieux l’espace dans ces appareils, faciliter la traçabilitĂ© des Ă©chantillons, diminuer l’utilisation de consommables et Ă©conomiser le temps passĂ© Ă  la prĂ©paration des Ă©chantillons. La validation de cette procĂ©dure de stockage s’est faite sur deux annĂ©es consĂ©cutives, dans le contexte d’une thĂšse au laboratoire pour doser des mĂ©tabolites et des activitĂ©s enzymatiques sur la plateforme mĂ©tabolomique et fluxomique de Bordeaux. ConcrĂštement, nous avons gagnĂ© 50% de place dans les congĂ©lateurs, tout en conservant un pot d’échantillon de rĂ©serve. La traçabilitĂ© des Ă©chantillons a Ă©tĂ© facilitĂ©e. L’économie de temps passĂ© Ă  la prĂ©paration des Ă©chantillons a permis d’aborder les campagnes fruitiĂšres avec plus de sĂ©rĂ©nitĂ©. Aujourd’hui, cette procĂ©dure est utilisĂ©e par d’autres Ă©quipes de l’UnitĂ© de recherche pour l’ensemble des congĂ©lateur

    A kinetic model of sugar metabolism in peach fruit allows the exploration of genetic variability

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    International audienceThe organoleptic properties of peach, as fruit in general, largely depend on the accumulated sugars and acids. From sucrose, glucose and fructose, main sugars found in peach, fructose is the sweetest one. While commercial peach has equivalent fructose and glucose concentration, some wild or ornamental accessions display an imbalanced fructose-to-glucose ratio with a very low fructose concentration. In addition to genetic control, sugar metabolism is driven by fruit development and environment. The relative role of biochemical strengths and gene regulation in the elaboration of fruit sugar content at maturity is not well known. As the complex interplay between synthesis, degradation, transport and storage held in the cell is difficult to formulate, mathematical modelling appears to be an effective tool to challenge the issue. Thus, on the basis of profiling data, we developed a kinetic model of sugar metabolism in peach fruit. It simulates the evolution of sucrose, glucose, fructose and sorbitol concentrations during fruit development. A particular attention has been given to represent cellular compartmentation (cytosol and vacuole) in order to modulate the availability of the metabolites for the enzymatic reactions. The model was parameterized for different peach genotypes including a particular phenotype with low fructose-to-glucose ratio. It described well genetic variability. It was then used to further explore the system including the mechanisms driving genotypic differences

    The relative roles of local climate adaptation and phylogeny in determining leaf-out timing of temperate tree species

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    Background Leaf out times of temperate forest trees are a prominent determinant of global carbon dynamics throughout the year. Abiotic cues of leaf emergence are well studied but investigation of the relative roles of shared evolutionary history (phylogeny) and local adaptation to climate in determining the species-level responses to these cues is needed to better apprehend the effect of global change on leaf emergence. We explored the relative importance of phylogeny and climate in determining the innate leaf out phenology across the temperate biome. Methods We used an extensive dataset of leaf-out dates of 1126 temperate woody species grown in eight Northern Hemisphere common gardens. For these species, information on the native climate and phylogenetic position was collected. Using linear regression analyses, we examine the relative effect of climate variables and phylogeny on leaf out variation among species. Results Climate variables explained twice as much variation in leaf out timing as phylogenetic information, a process that was driven primarily by the complex interactive effects of multiple climate variables. Although the primary climate factors explaining species-level variation in leaf-out timing varied drastically across different families, our analyses reveal that local adaptation plays a stronger role than common evolutionary history in determining tree phenology across the temperate biome. Conclusions In the long-term, the direct effects of physiological adaptation to abiotic effects of climate change on forest phenology are likely to outweigh the indirect effects mediated through changes in tree species composition

    Profiling sugar metabolism during fruit development in a peach progeny with different fructose-to-glucose ratios.

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    BackgroundFruit taste is largely affected by the concentration of soluble sugars and organic acids and non-negligibly by fructose concentration, which is the sweetest-tasting sugar. To date, many studies investigating the sugars in fruit have focused on a specific sugar or enzyme and often on a single variety, but only a few detailed studies addressing sugar metabolism both as a whole and dynamic system are available. In commercial peach fruit, sucrose is the main sugar, followed by fructose and glucose, which have similar levels. Interestingly, low fructose-to-glucose ratios have been observed in wild peach accessions. A cross between wild peach and commercial varieties offers an outstanding possibility to study fruit sugar metabolism.ResultsThis work provides a large dataset of sugar composition and the capacities of enzymes that are involved in sugar metabolism during peach fruit development and its genetic diversity. A large fraction of the metabolites and enzymes involved in peach sugar metabolism were assayed within a peach progeny of 106 genotypes, of which one quarter displayed a low fructose-to-glucose ratio. This profiling was performed at six stages of growth using high throughput methods. Our results permit drawing a quasi-exhaustive scheme of sugar metabolism in peach. The use of a large number of genotypes revealed a remarkable robustness of enzymatic capacities across genotypes and years, despite strong variations in sugar composition, in particular the fructose-to-glucose ratio, within the progeny. A poor correlation was also found between the enzymatic capacities and the accumulation rates of metabolites.ConclusionsThese results invalidate the hypothesis of the straightforward enzymatic control of sugar concentration in peach fruit. Alternative hypotheses concerning the regulation of fructose concentration are discussed based on experimental data. This work lays the foundation for a comprehensive study of the mechanisms involved in sugar metabolism in developing fruit
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