La canalisation génétique est définie comme la capacité d’un organisme à avoir un développement constant en dépit des mutations qui l’affectent. A l’heure actuelle, trois hypothèses majoritaires cherchent à expliquer l’apparition de ce processus : évolutive, congruente et intrinsèque. Pour tester ces hypothèses, j’ai choisi d’étudier les réseaux de régulation. Pour cela, j’ai réutilisé un modèle théorique pour simuler in silico l’évolution des architectures génétiques, et les analyser par les outils de la génétique quantitative. J’ai d’abord étudié les comportements évolutifs de notre modèle et sa capacité de réponse à la sélection stabilisante. Outre l’analyse de l’impact des paramètres du modèle, j’ai mis en évidence l’absence d’équilibre mutation – sélection – dérive après des milliers de générations du fait de l’augmentation progressive de la canalisation. J’ai ensuite montré que les réseaux soumis à des mutations fréquentes et fortes, sélectionnés vers des optimums phénotypiques extrêmes, et dans lesquels certains gènes sont laissés libres d’évoluer sont plus aptes à faire évoluer de la canalisation génétique. Ces résultats nous ont amenés à proposer un double mécanisme impliqué dans l’évolution de la canalisation dans les réseaux de régulation : la réduction de la cible mutationnelle et la redondance de la régulation génique. Je termine ce manuscrit en présentant quelques pistes d’études complémentaires, portant notamment sur l’étude de la canalisation contre les perturbations environnementales et l’utilisation de modèles alternatifs. / Genetic canalization is defined as the capacity of an organism to undergo a normal development even when the genome is altered by mutations. Currently, three main hypotheses are prone to explain the apparition of such a process: evolutionary, congruent and intrinsic. To test these hypotheses, I chose to study gene regulatory networks. To this end, I used a theoretical model, ran in silico simulations, and analyzed the genetic architecture by using quantitative genetics tools. I first studied the evolutionary behavior of the model, and its capacity to respond to stabilizing selection. In addition to the sensitivity analysis to model parameters, I evidenced the absence of mutation-selection-drift equilibrium after several thousand generations, which reveals the evolution of canalization. I also showed that networks submitted to frequent and large mutations, and/or selected toward extreme phenotypic optima are more prone to evolve genetic canalization. This result leads us to propose a two-fold mechanism able to explain the evolution of canalization in gene regulatory networks: shrinkage of mutational targets and redundancy in genetic regulation. At the end of this manuscript, I propose some possible future studies, such as the study of canalization towards environmental perturbations, and use of alternative models.

La variabilité phénotypique existante au sein d’une population est d’une importance cruciale ; elle permet l’adaptation à de nouvelles conditions par la sélection naturelle de traits bénéfiques. La variabilité phénotypique est le résultat du polymorphisme génétique de chaque individu, couplé à l’influence de divers facteurs environnementaux. Ces travaux ont pour objectif d’élucider quels sont les facteurs génétiques responsables de la variabilité phénotypique de chaque individu afin de comprendre comment celle-ci évolue de génération en génération et peut s’accentuer au-delà des prédispositions parentales. Finalement, les résultats obtenus seront utilisés pour prédire un phénotype à partir d’un génotype inconnu. Nous avons utilisé des techniques de phénomique et de génomique de haut débit pour décomposer avec une précision inédite la variabilité phénotypique d’une large population de souches diploïdes de Saccharomyces cerevisiae. Le génotype exact de plus de 7000 souches uniques a ainsi été obtenu via le croisement et le séquençage de souches haploïdes distinctes. Nous avons mesuré la capacité de croissance de ces souches et identifié les composants génétiques influant sur ce trait. De plus, nous avons identifié des « loci de caractères quantitatifs » additifs et non-additifs, et étudié la fréquence du phénomène d’hétérosis et ses mécanismes. Enfin, en utilisant les données phénotypiques et génotypiques de la même population de levures, nous avons pu prédire les traits de chaque individu avec une presque parfaite exactitude. Ces travaux ont ainsi permis d’identifier avec précision les facteurs génétiques modulant la variation phénotypique d’une population diploïde, et de prédire un trait à partir du génotype et de l’ensemble des données phénotypiques. En plus de ce projet, nous travaillons aussi sur l’identification des bases génétiques à l’origine de la non-viabilité des gamètes, ainsi que sur la compréhension des caractères complexes chez des souches hybrides intra-espèce. De par l’étude de 9000 gamètes séquencés issus de six hybrides différents, nous avons pour objectif de caractériser leur profil de recombinaison et d’observer quelle est l’influence du fond génétique sur ce dernier. De plus, nous avons caractérisé la capacité de croissance de ces gamètes dans neuf conditions environnementales différentes et nous prévoyons de disséquer l’architecture génétique de ces traits dans différents fonds génétiques. / The phenotypic variation between individuals in a population is of crucial importance. It allows populations to evolve to novel conditions by the natural selection of beneficial traits. Variation in traits can be caused by genetic or environmental factors. This work endeavors to study the genetic factors that underlie phenotypic variation in order to understand how variation can be created from one generation to the next; to know what genetic mechanisms are most prominent; to learn how variation can extend beyond the parents; and finally, to use this in order to predict phenotypes of unknown genetic constellations. We used large scale phenomics and genomics to give an unprecedented decomposition of the phenotypic variation in a large population of diploid Saccharomyces cerevisiae strains. Constructing phased outbred lines by large scale crosses of sequenced haploid strains allowed us to infer the genetic makeup of more than 7,000 colonies. We measured the growth of these strains and decomposed the phenotypic variation into its genetic components. In addition, we mapped additive and nonadditive quantitative trait loci, we investigated the occurrence of heterosis and its genetic basis, and using the same populations we used phenotypic and genetic data to predict traits with near perfect accuracy. By using the phased outbred line approach, we succeeded in giving a conclusive account of what genetic factors define phenotypic variation in a diploid population, and in accurately predicting phenotypes from genetic and phenotypic data. Beyond the phased outbred line project, I am currently investigating the genetic basis of gamete inviability and complex traits in intraspecies yeast hybrids. Using 9,000 sequenced gametes from six different hybrids we aim to characterize their recombination landscape and how the genetic background influences it. Furthermore, we have phenotyped these gametes in nine conditions and will dissect the genetic architecture of these traits across multiple genomic backgrounds.

No description available.

In the last years, Genome-Wide Associations Studies (GWAS) found many variants associated with complex diseases. However, the biological and molecular links between these variants and phenotypes are still mostly unknown. Also, even if sample sizes are constantly increasing, the associated variants do not explain all the heritability estimated for many traits. Many hypotheses have been proposed to explain the problem: from variant-variant interactions, the effect of rare and ultra-rare coding variants and also technical biases related to sequencing or statistic on sexual chromosomes. In this thesis, we mainly explore the hypothesis of variant-variant interaction and, briefly, the rare coding variants hypothesis while also considering possible molecular effects like allele-specific expression and the effects of variants on protein interfaces. Some parts of the thesis are also devoted to explore the implementation of efficient computational tools to explore these effects and to perform scalable genotyping of germline single nucleotide polymorphisms (SNPs) in huge datasets. The main part of the thesis regards the development of a new resource to identify putative variant-variant interactions. In particular, we integrated ChIP-seq data from ENCODE, transcription factor binding motifs from several resources and genotype and transcript level data from GTeX and TCGA. This new dataset allows us to formalize new models, to make hypothesis and to find putative novel associations and interactions between (mainly non-coding) germline variants and phenotypes, like cancer-specific phenotypes. In particular, we focused on the characterization of breast cancer and Alzheimer’s Disease GWAS risk variants, looking for putative variants’ interactions. Recently, the study of rare variants has become feasible thanks to the biobanks that made available genotypes and clinical data of thousands of patients. We characterize and explore the possible effects of rare coding inherited polymorphisms on protein interfaces in the UKBioBank trying to understand if the change in structure of protein can be one of the causes of complex diseases. Another part of the thesis explores variants as causal molecular effect for allele-specific expression. In particular, we describe UTRs variants that can alter the post-transcriptional regulation in mRNA leading to a phenomenon where an allele is more expressed than the other. Finally, we show those variants can have prognostic significance in breast cancer. This thesis work introduces results and computational tools that can be useful to a broad community of researcher studying human polymorphisms effects.

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Em estudos recentes, a epistasia tem sido detectada no controle genético de caracteres quantitativos em diversas espécies. Dado o grande número de locos controlando um único caráter, é evidente que ocorram interações inter-alélicas, além de pleiotropia, que resulta do controle de mais de um caráter por um mesmo loco. Também tem sido reportada a presença de epistasia pleiotrópica em animais, que basicamente resulta do efeito da epistasia sobre locos pleiotrópicos ou sobre múltiplos caracteres, afetando a correlação genética entre esses. Desse modo, o objetivo desta pesquisa foi a análise genética de diversos caracteres de importância econômica e agronômica em milho, incluindo estimativas de componentes de variância genética e presença de efeitos epistáticos em ambientes com e sem estresse hídrico; e estimativas de epistasia pleiotrópica. Para isso foi utilizado o delineamento triple test cross (TTC), obtendo-se 300 progênies de retrocruzamentos que foram avaliadas em oito ambientes nos anos agrícolas de 2008/2009 e 2009/2010, na cidade de Piracicaba, São Paulo, Brasil. Ao longo da condução dos experimentos observou-se a ocorrência de déficit hídrico, de modo que os ambientes foram divididos em dois grupos (sem estresse - SE e com estresse - CE). Avaliou-se os caracteres da planta: dias para os florescimentos masculino (FM) e feminino (FF), intervalo entre florescimentos (IF), altura da planta (AP) e espiga (AE), posição relativa da espiga (PRE), acamamento e quebramento de plantas (ACQ), stay green (SG); produção de grãos (PG) e seus componentes de produção: número de fileiras (NF), número de grãos por fileira (NGF), peso de 300 grãos (P300), comprimento de grãos (CG) e prolificidade (PRO). Foram realizadas análises de variâncias individuais para cada ambiente; análises conjuntas de ambientes; e análises conjuntas de grupos, das quais estimaram-se as variâncias aditiva, de dominância, epistática e suas respectivas interações com ambiente; o grau médio de dominância, coeficientes de herdabilidade em nível de médias de progênies e em nível de parcelas e também os efeitos epistáticos em plantas F2. Também foram feitas análises de covariâncias considerando todos os caracteres combinados dois a dois, tendo sido estimados os coeficientes de correlações. A epistasia foi detectada para a maioria dos caracteres nos dois grupos, exceto ACQ, IF, SG e CG, no grupo SE; e ACQ, CG e PRO, no grupo CE. Porém não foi detectada interação epistasia x ambiente em nenhum dos grupos e a interação epistasia x grupos só foi detectada para IF. Os efeitos epistáticos em plantas F2 para PG variaram de -3,03 t ha-1 a 5,13 t ha-1 no grupo SE e -1,94 t ha-1 a 2,87 t ha-1 no grupo CE, mas não foram detectadas altas magnitudes dos coeficientes de correlações entre esses efeitos e as médias gerais dos retrocruzamentos. Foram detectados coeficientes de correlações epistáticas para 29,67% das combinações, indicando a presença de epistasia pleiotrópica entre caracteres. Observou-se a formação de agrupamentos entre caracteres relacionados. Em vista desses resultados, a epistasia se constituiu num componente importante no controle dos caracteres analisados, sugerindo ainda que a epistasia pleiotrópica possa ser responsável pelas interações complexas no genoma. / In recent studies, epistasis has been considered in genetic control of quantitative traits in several species. Due to a large number of loci controlling a single trait, it is evident that inter allele interactions occur in addition to pleiotropy, which results in the control of more than one trait by the same locus. Besides, the presence of pleiotropy, epistasis has been reported in animals, which basically result from the effect of epistasis on pleiotropic loci or on multiple traits, affecting the genetic correlation between them. Thus, the objective of this research was to do genetic analysis of several traits of economic and agronomic importance in maize, including estimates of genetic variance components and the presence of epistatic effects in environments with and without water stress; and estimates of pleiotropic epistasis. For this, the triple test cross (TTC) design was used to obtain 300 backcrosses progenies, which were evaluated in eight environments in the 2008/2009 and 2009/2010 agricultural seasons, in Piracicaba, Sao Paulo State, Brazil. During the conduction of the experiments, the occurrence of water deficit was observed, so that the environments were divided into two groups (without stress - WS and with stress - SS). The traits evaluated were: days to anthesis (DA), days to silking (DS), anthesis-silking interval (ASI), plant height (PH), ear height (EH), ear placement (EP), root and stalk lodging (PL) and stay green (SG), grain yield (GY), kernel rows (KR), kernels per row (KPR), 300-grain weight (300W), kernel depth (KD) and prolificacy (PRO). Individual analysis of variances were performed for each environment; joint analysis of environments; and joint analysis of groups, from which additive, dominance and epistatic variances and their respective interactions with the environment were estimated; besides average degree of dominance, heritability coefficients at level of half-sib progenies and at plots level; also epistatic effects in F2 plants were estimated. Covariance analyses were also performed considering all pairs of traits, two by two, and the correlation coefficients were estimated. Epistasis was detected for most traits in both groups except to PL, ASI, SG and KD, in WS group; and PL, KD, and PRO, in SS group. However, no epistasis x environment interaction was detected in any group and epistasis x group interaction was detected only to ASI. Epistatic effects on F2 plants were detected to GY, oscillating from -3.03 t/ha to 5.13 t/ha in WS group and from -1.94 t/ha to 2.87 t/ha in SS group. However, high magnitudes of correlation coefficients between these F2 epistatic effects and averages of backcrosses were not detected. Epistatic correlation coefficients were detected for 29.67% of pairs of traits, indicating the presence of pleiotropic epistasis. The formation of clusters was observed between related traits. In view of these results, epistasis was considered an important component in the control of traits analyzed, furthermore suggesting that pleiotropic epistasis may be responsible for complex interactions in the genome.

Em estudos recentes, a epistasia tem sido detectada no controle genético de caracteres quantitativos em diversas espécies. Dado o grande número de locos controlando um único caráter, é evidente que ocorram interações inter-alélicas, além de pleiotropia, que resulta do controle de mais de um caráter por um mesmo loco. Também tem sido reportada a presença de epistasia pleiotrópica em animais, que basicamente resulta do efeito da epistasia sobre locos pleiotrópicos ou sobre múltiplos caracteres, afetando a correlação genética entre esses. Desse modo, o objetivo desta pesquisa foi a análise genética de diversos caracteres de importância econômica e agronômica em milho, incluindo estimativas de componentes de variância genética e presença de efeitos epistáticos em ambientes com e sem estresse hídrico; e estimativas de epistasia pleiotrópica. Para isso foi utilizado o delineamento triple test cross (TTC), obtendo-se 300 progênies de retrocruzamentos que foram avaliadas em oito ambientes nos anos agrícolas de 2008/2009 e 2009/2010, na cidade de Piracicaba, São Paulo, Brasil. Ao longo da condução dos experimentos observou-se a ocorrência de déficit hídrico, de modo que os ambientes foram divididos em dois grupos (sem estresse - SE e com estresse - CE). Avaliou-se os caracteres da planta: dias para os florescimentos masculino (FM) e feminino (FF), intervalo entre florescimentos (IF), altura da planta (AP) e espiga (AE), posição relativa da espiga (PRE), acamamento e quebramento de plantas (ACQ), stay green (SG); produção de grãos (PG) e seus componentes de produção: número de fileiras (NF), número de grãos por fileira (NGF), peso de 300 grãos (P300), comprimento de grãos (CG) e prolificidade (PRO). Foram realizadas análises de variâncias individuais para cada ambiente; análises conjuntas de ambientes; e análises conjuntas de grupos, das quais estimaram-se as variâncias aditiva, de dominância, epistática e suas respectivas interações com ambiente; o grau médio de dominância, coeficientes de herdabilidade em nível de médias de progênies e em nível de parcelas e também os efeitos epistáticos em plantas F2. Também foram feitas análises de covariâncias considerando todos os caracteres combinados dois a dois, tendo sido estimados os coeficientes de correlações. A epistasia foi detectada para a maioria dos caracteres nos dois grupos, exceto ACQ, IF, SG e CG, no grupo SE; e ACQ, CG e PRO, no grupo CE. Porém não foi detectada interação epistasia x ambiente em nenhum dos grupos e a interação epistasia x grupos só foi detectada para IF. Os efeitos epistáticos em plantas F2 para PG variaram de -3,03 t ha-1 a 5,13 t ha-1 no grupo SE e -1,94 t ha-1 a 2,87 t ha-1 no grupo CE, mas não foram detectadas altas magnitudes dos coeficientes de correlações entre esses efeitos e as médias gerais dos retrocruzamentos. Foram detectados coeficientes de correlações epistáticas para 29,67% das combinações, indicando a presença de epistasia pleiotrópica entre caracteres. Observou-se a formação de agrupamentos entre caracteres relacionados. Em vista desses resultados, a epistasia se constituiu num componente importante no controle dos caracteres analisados, sugerindo ainda que a epistasia pleiotrópica possa ser responsável pelas interações complexas no genoma. / In recent studies, epistasis has been considered in genetic control of quantitative traits in several species. Due to a large number of loci controlling a single trait, it is evident that inter allele interactions occur in addition to pleiotropy, which results in the control of more than one trait by the same locus. Besides, the presence of pleiotropy, epistasis has been reported in animals, which basically result from the effect of epistasis on pleiotropic loci or on multiple traits, affecting the genetic correlation between them. Thus, the objective of this research was to do genetic analysis of several traits of economic and agronomic importance in maize, including estimates of genetic variance components and the presence of epistatic effects in environments with and without water stress; and estimates of pleiotropic epistasis. For this, the triple test cross (TTC) design was used to obtain 300 backcrosses progenies, which were evaluated in eight environments in the 2008/2009 and 2009/2010 agricultural seasons, in Piracicaba, Sao Paulo State, Brazil. During the conduction of the experiments, the occurrence of water deficit was observed, so that the environments were divided into two groups (without stress - WS and with stress - SS). The traits evaluated were: days to anthesis (DA), days to silking (DS), anthesis-silking interval (ASI), plant height (PH), ear height (EH), ear placement (EP), root and stalk lodging (PL) and stay green (SG), grain yield (GY), kernel rows (KR), kernels per row (KPR), 300-grain weight (300W), kernel depth (KD) and prolificacy (PRO). Individual analysis of variances were performed for each environment; joint analysis of environments; and joint analysis of groups, from which additive, dominance and epistatic variances and their respective interactions with the environment were estimated; besides average degree of dominance, heritability coefficients at level of half-sib progenies and at plots level; also epistatic effects in F2 plants were estimated. Covariance analyses were also performed considering all pairs of traits, two by two, and the correlation coefficients were estimated. Epistasis was detected for most traits in both groups except to PL, ASI, SG and KD, in WS group; and PL, KD, and PRO, in SS group. However, no epistasis x environment interaction was detected in any group and epistasis x group interaction was detected only to ASI. Epistatic effects on F2 plants were detected to GY, oscillating from -3.03 t/ha to 5.13 t/ha in WS group and from -1.94 t/ha to 2.87 t/ha in SS group. However, high magnitudes of correlation coefficients between these F2 epistatic effects and averages of backcrosses were not detected. Epistatic correlation coefficients were detected for 29.67% of pairs of traits, indicating the presence of pleiotropic epistasis. The formation of clusters was observed between related traits. In view of these results, epistasis was considered an important component in the control of traits analyzed, furthermore suggesting that pleiotropic epistasis may be responsible for complex interactions in the genome.