La vigne (Vitis vinifera) possède un métabolisme secondaire particulièrement riche donnant naissance à une large palette de molécules dont certaines sont impliquées dans les défenses contre les pathogènes et d'autres dans la grande diversité d’arômes qui fait la renommée des vins. L’analyse de la séquence de référence du génome de la vigne a permis de mettre en évidence une remarquable expansion de certaines familles de gènes liés au métabolisme secondaire par rapport aux autres plantes. Dans ce travail, j'ai étudié les familles gènes codant pour les cytochromes P450, dont certains sont impliqués dans la production d’arômes, les gènes codant pour les stilbènes synthases (STS), les endo-β-1,3-glucanases et les gènes de résistance de type NBS impliqués dans les défenses de la vigne. Ma thèse vise à proposer des hypothèses expliquant l’organisation structurale de ces familles de gènes et ainsi à mieux comprendre pourquoi certaines familles présentent une amplification dans le génome de la vigne. Des approches bioinformatiques ont été utilisées afin d’étudier ces différentes familles de gènes. Les gènes cytochromes P450 et gènes R de type NBS ont tout d'abord été annotés de manière manuelle dans le génome de référence de la vigne. L’expression des gènes endo-β-1,3- glucanases, STS et cytochromes P450 a été analysée en utilisant une approche transcriptomique à grande échelle. Pour ce faire, un outil a été développé durant cette thèse pour estimer le niveau d’expression des gènes à partir de données RNA-Seq disponibles dans les banques de données publiques. Parallèlement, des données de reséquençage d’ADN de 56 cépages et espèces de vigne ont été analysées, afin de déterminer les variations structurales de type CNV au sein des familles de gènes à domaine NBS et de gènes STS. Ces différents travaux ont permis de montrer que l’amplification des familles de gènes étudiées n’est pas spécifique du génome de référence mais est retrouvée dans l'ensemble du genre Vitis, mais également de mettre en évidence des variations structurales au sein des différents génomes étudiés. L'analyse de la famille STS a montré que ces gènes sont organisés en blocs de duplication, et que les gènes plus conservés sont aussi les plus exprimés. Nous avons également montré que les gènes à domaine NBS sont organisés en cluster, dont certains sont particulièrement soumis à variation. Ces travaux contribuent à une meilleure connaissance de facteurs de défense efficaces et durables ainsi que des gènes impliqués dans la synthèse d’arômes dans la vigne. Ces connaissances pourront bénéficier aux programmes de création variétale mis en œuvre à l’INRA de Colmar. / Grapevine (Vitis vinifera) has a particularly rich secondary metabolism, giving rise to a wide range of molecules, some of which are involved in defences against pathogens and others in the great diversity of aromas that make wines famous. Analysis of grapevine reference genome has shown a remarkable expansion of certain families of genes linked to secondary metabolism in comparison with the other plants. In this work, I have analysed gene families coding for cytochromes P450, some of them being involved in the production of aromas, genes coding for stilbene synthases (STS), endo-β-1,3-glucanases and NBS type resistance genes involved in grapevine defences. My thesis intends to propose hypothesis to explain the structural organisation of these families and therefore better understand why some of these families are amplified in the grapevine genome. Bioinformatic approaches have been used to study these different genes families. The cytochromes P450 and R genes of NBS type were manually annotated to improve the knowledge of these families of genes. The expression of endo-β-1,3-glucanases, STS and cytochromes P450 genes has been quantified using a large-scale transcriptomic approach. To this purpose, a tool has been developed during this thesis to estimate the level of genes expression from RNA- Seq data available in public databases. In the meantime, DNA resequencing data from 56 cultivars and grapevine species have been analysed to identify structural variations of CNV types within the genes with a NBS domain and the STS genes. These works showed that the amplification of the gene families of interest was not specific to the reference genome but occurred at the scale of the Vitis genus, but also to highlighted structural variations in different genomes. Regarding the STS genes, blocks of duplication and more conserved and expressed genes were identified. For the genes with NBS domain, a clustered organisation has been highlighted with some clusters varying more than others in the studied genotypes. These works contribute to a better knowledge of gene families for efficient and durable defence against pathogens and optimal aromas synthesis in grapevine. This knowledge will benefit to breeding programs currently in progress at INRA Colmar.

Reactive oxygen species are formed internally through cellular metabolism and through external sources including radiation and pollutants. They play an important role in physiologic functions; however, when reactive oxygen species exceed our body’s antioxidant defense system, oxidative stress can occur. Oxidative stress has been implicated in aging and aging-related diseases including cancer and cardiovascular disease. Numerous oxidative stress genes produce antioxidative enzymes to mitigate the effects of reactive oxygen species. Single nucleotide polymorphisms within these genes may impact the functionality of antioxidant enzymes produced leaving the body more susceptible to damage from oxidative stress. The Iowa 65+ Rural Health Study was one of the four study populations in the Established Population for Epidemiologic Studies of the Elderly (EPESE) project initiated by the intramural Epidemiology, Demography and Biometry Program of the National Institute on Aging in 1980. The Iowa cohort was comprised of Iowa county and Washington county residents aged 65 and older at the time of the baseline interview in 1982. Participants completed three in-person interviews and five telephone interviews over eight years which collected data on habits, lifestyle and disease. During the in-person Year 06 interview participants were asked to donate a blood sample. The DNA extracted from the samples was used in each of the three aims of this project. The first aim evaluated single nucleotide polymorphisms in selected oxidative stress genes and their association with lifespan while controlling for aging-associated risk factors such as body mass index, comorbidity, alcohol consumption, smoking, and physical activity. Multivariable linear regression models were fit in the framework of the co-dominant genetic model. The oxidative stress genes selected for this project included the sirtuin family of genes (SIRT1-7), two of the forkhead box genes (FOXO1 and FOXO3), superoxide dismutase 2 and 3 (SOD2 and SOD3), glutathione peroxidase (GPX1), AKT, TP53, and CAMK4. A model was fitted with the risk factors before assessing the impact of each single nucleotide polymorphism. The q-value was used to control for the multiple hypothesis tests. Significant associations were detected between human lifespan and SNPs in genes SIRT3, SIRT5, SIRT6, FOXO3, and SOD3; gender modified the effect of SNPs in SIRT3, SIRT5, and AKT1. The second aim of this project evaluated single nucleotide polymorphisms in selected oxidative stress genes and their association with blood pressure measures while controlling for known risk factors including body mass index, alcohol consumption, smoking, and physical activity. Blood pressure was measured at the baseline and Year 06 interviews. Systolic pressure and diastolic pressure were used to calculate mean arterial pressure and pulse pressure at baseline and Year 06. Multivariable linear regression was used within the co-dominant genetic framework to determine if single nucleotide polymorphisms in SIRT1-7, FOXO1, FOXO3, SOD2-3, GPX1, AKT, TP53, and CAMK4 were associated with systolic, diastolic, mean arterial, or pulse pressure at baseline or Year 06. To examine longitudinal effects, the difference between each measure (i.e., Year 06 systolic – baseline systolic) was calculated for each individual and used to evaluate if any of the single polymorphisms was associated with change in blood pressure measures over time. Significant associations were detected between SIRT1 and SIRT3 and for males in SIRT1 and various blood pressure measures for females. Gender modified the effect of SIRT1, SIRT3, SIRT6, and FOXO1 variants. The third aim of this project evaluated if these genetic variants were associated with incident stroke while controlling for known risk factors including blood pressure, diabetes, body mass index, alcohol consumption, smoking, and physical activity. Multivariable logistic regression within the framework of the co-dominant genetic model was used. Individuals with the GPX1 genotype TT had 2.76 times the risk of an incident stroke compared to the CC genotype. This project identified several associations between single nucleotide polymorphisms within oxidative stress genes and lifespan, blood pressure measures, and incident stroke. Gender modified the association of several single nucleotide polymorphisms and lifespan as well as blood pressure measures. These results suggest genetic variation within oxidative stress genes may play a role in aging, blood pressure and incident stroke.