Hybrids and polyploids are very common in plants and some animals. Although hybrid vigor or heterosis has been widely adopted in agricultural practices, the underlying mechanisms are poorly understood partly because of their multigenic nature and the lack of a good model system for the study. Allotetraploidy is an emerging model system for investigating molecular mechanisms of hybrid vigor. An allotetraploid is formed by interspecific hybridization followed by chromosome doubling or hybridization between two autotetraploid parents and is genetically stable. A previous study showed nonadditive expression (different from the mid-parent value) of over 5% of genes in the allotetraploids, suggesting altered transcriptional and post-transcriptional regulation. Here oligo-gene microarray analysis of mRNA stability in allotetraploids was carried out to investigate how nonadditive gene regulation upon allopolyploidization is achieved at the posttranscriptional level. Approximately 1% of annotated genes were identified as unstable transcripts, and their estimated half-life is less than 60 minutes. The unstable transcripts in Arabidopsis allotetraploids are associated with nonadditive gene expression and with stress and environmental responses. The nonadditively expressed genes identified in the previous study include those encoding proteins involved in energy and metabolic pathways, which are putative targets of circadian clock regulators. To test how circadian clock genes affect downstream genes and pathways, expression of CIRCADIAN CLOCK ASSOCIATED1 (CCA1) was up- or down-regulated by overexpressing CCA1 or cca1(RNAi) driven by the promoter of TIMING OF CAB EXPRESSION 1 (TOC1). Upregulation of CCA1 was associated with repression of downstream genes in chlorophyll biosynthesis and starch metabolism, whereas down-regulation of CCA1 correlated with upregulation of these downstream genes. As a result, chlorophyll and starch content was ~10% higher in the TOC1::cca1(RNAi) transgenic plants than the controls, while the growth vigor is lower in the TOC1::CCA1 transgenic plants. To further test the effects of clock genes in growth vigor, CCA1 expression was examined in reciprocal hybrids of A. thaliana ecotypes. The maternal effect on starch content was observed in several combinations of hybrids, which was correlated with preferential expression of maternal CCA1 during early stages of seed development. Although the cause of parent-of-origin effects is still unclear, the data have clearly documented parent-of-origin effects on circadian clock gene expression and starch metabolism in hybrids. / text

Dados de peso ao nascimento, ao desmame, aos 390 dias, o ganho de peso do desmame aos 390 dias, o perímetro escrotal e a musculosidade aos 390 dias de uma população, composta por vários tipos biológicos e envolvida na formação do composto Montana Tropical® foram analisados, segundo três modelos diferentes, com os objetivos de: i) analisar a influência dos efeitos genéticos e de ambiente; ii) estimar os fatores de ajuste para esses efeitos; iii) avaliar a contribuição genética aditiva direta e materna, os efeitos genéticos aditivos e não aditivos; iv) estimar parâmetros genéticos e v) quantificar os efeitos dos modelos sobre as DEPs de peso ao desmame. Os três modelos estudados foram: Modelo RM - modelo que incluiu os efeitos fixos de grupo de contemporâneos (GC), a classe de idade da mãe ao parto (CIMP) e as covariáveis associadas aos efeitos genéticos aditivos diretos e maternos, além das covariáveis associadas aos efeitos genéticos não aditivos das heterozigoses, tanto para efeitos diretos, quanto para efeitos maternos; Modelo R - considerou os mesmos efeitos do modelo RM à exceção dos efeitos aditivos de raça materna e o Modelo H, que considerou os efeitos incluídos no modelo R, à exceção dos efeitos aditivos de raças. As estimativas de componentes de (co) variâncias e parâmetros genéticos foram obtidas pela metodologia REML, sob um modelo animal. O efeito de GC foi o principal responsável por parte das somas de quadrados total nas diferentes características. Os efeitos das CIMPs sobre as características estudadas foram importantes, alcançando magnitudes de ajustes de até 30 kg, relativos às diferenças entre fêmeas jovens (CIMP = 1) e fêmeas adultas (CIMP = 4). Os efeitos aditivos diretos e maternos e as heterozigoses, de um modo geral, foram significativos (P<0,05) para todas as características. O modelo RM parece fornecer estimativas de melhor qualidade que os modelos R e H, o que é confirmado junto ao processo de predição do desempenho por parte destes modelos. Em termos gerais, o modelo RM foi capaz de predizer com boa capacidade as combinações genéticas mais freqüentes dentro desta população composta. Os parâmetros genéticos estimados para as características estudadas foram em geral de médias a altas magnitudes e podem servir como apoio para a realização de análises e estimação de valores genéticos. O tipo biológico N contribuiu para a geração de vacas que promovem maiores pesos ao desmame e aos 390 dias, sobretudo, em relação aos tipos biológicos adaptado e britânico. É possível concluir que: i) os efeitos de GC e de CIMP devem ser incorporados no processo de modelagem; ii) Modelos de estimação que sejam capazes de quantificar e segregar os efeitos aditivos de raça diretos e maternos daqueles efeitos das heterozigoses, como o modelo RM, devem ser eleitos; iii) como, em geral, existe a relação linear entre as heterozigoses e as heteroses e deve ser considerada nas avaliações genéticas; iv) os resultados evidenciam a contribuição genética da heterose nos sistemas de produção e v) são necessárias avaliações suplementares com modelos mais complexos. / Data of weights at birth, weaning, 390 days, weight gain from weaning to 390 days, scrotal circumference and muscling scores at 390 days of age of a population used in the formation of the Montana Tropical® beef composite, raised under tropical conditions, were analyzed under three different models to: i) determine genetic and environment effects ii) determine the adjustment factors those effects; iii) study genetic contribution of additive direct and maternal breed effects and non additive genetic effects; iv) estimate genetic parameters and v) quantify the effects of those models on estimation of expected progeny differences. Three models studied were: Model RM - included the effect of group of contemporaries (GC), the class of age of the cow to the calving (CIMP), the covariates associated to the genetic additive maternal and direct breed effect and the covariates associated to the non additive genetic effect of heterozygosis; Model R considered the effects of model RM, except the maternal additive breed effect and Model H, that considered effects of model R, except the additive direct breed effect. The estimates of (co)variance components and genetic parameters were obtained by the REML methodology under an animal model. The GC effect was the main effect in the different characteristics. The effect of the CIMP was also very important and differences up to 30 kg were observed in weaning weights of young heifers (CIMP = 1) when compared to adult cows (CIMP = 4). Additive direct and maternal breed effects and heterozygosis, in a general, had been significant (P<0.05) for all the traits. Model RM seems to supply better estimates than models R and H, what it is confirmed in the process of prediction of the performance on the part of these models. The estimated genetics parameters were from average to the high magnitudes. It can be conclude that CIMP and GC effect must be incorporated in the modeling process. Models of estimation that are able to segregate and quantify the additive maternal and direct breeds effects and also the effect of heterozygosis, as model RM, must be elect. In general terms, model RM was able to predict the performance of the more frequent genetic combinations of this composite population. The variance components and heritability estimated can support selection programs. Biological type N contributed for the generation of cows that promote higher weaning and 390 days weights as compared to the biological types Adapted and British. In general the linear relation between heterozigoses and heterosis and must be considered in the genetic evaluations. The results evidence the genetic contribution of heterosis in the production systems and further and more complex models are needed to elucidate the composite populations (co)variance components estimation.

Dados de peso ao nascimento, ao desmame, aos 390 dias, o ganho de peso do desmame aos 390 dias, o perímetro escrotal e a musculosidade aos 390 dias de uma população, composta por vários tipos biológicos e envolvida na formação do composto Montana Tropical® foram analisados, segundo três modelos diferentes, com os objetivos de: i) analisar a influência dos efeitos genéticos e de ambiente; ii) estimar os fatores de ajuste para esses efeitos; iii) avaliar a contribuição genética aditiva direta e materna, os efeitos genéticos aditivos e não aditivos; iv) estimar parâmetros genéticos e v) quantificar os efeitos dos modelos sobre as DEPs de peso ao desmame. Os três modelos estudados foram: Modelo RM - modelo que incluiu os efeitos fixos de grupo de contemporâneos (GC), a classe de idade da mãe ao parto (CIMP) e as covariáveis associadas aos efeitos genéticos aditivos diretos e maternos, além das covariáveis associadas aos efeitos genéticos não aditivos das heterozigoses, tanto para efeitos diretos, quanto para efeitos maternos; Modelo R - considerou os mesmos efeitos do modelo RM à exceção dos efeitos aditivos de raça materna e o Modelo H, que considerou os efeitos incluídos no modelo R, à exceção dos efeitos aditivos de raças. As estimativas de componentes de (co) variâncias e parâmetros genéticos foram obtidas pela metodologia REML, sob um modelo animal. O efeito de GC foi o principal responsável por parte das somas de quadrados total nas diferentes características. Os efeitos das CIMPs sobre as características estudadas foram importantes, alcançando magnitudes de ajustes de até 30 kg, relativos às diferenças entre fêmeas jovens (CIMP = 1) e fêmeas adultas (CIMP = 4). Os efeitos aditivos diretos e maternos e as heterozigoses, de um modo geral, foram significativos (P<0,05) para todas as características. O modelo RM parece fornecer estimativas de melhor qualidade que os modelos R e H, o que é confirmado junto ao processo de predição do desempenho por parte destes modelos. Em termos gerais, o modelo RM foi capaz de predizer com boa capacidade as combinações genéticas mais freqüentes dentro desta população composta. Os parâmetros genéticos estimados para as características estudadas foram em geral de médias a altas magnitudes e podem servir como apoio para a realização de análises e estimação de valores genéticos. O tipo biológico N contribuiu para a geração de vacas que promovem maiores pesos ao desmame e aos 390 dias, sobretudo, em relação aos tipos biológicos adaptado e britânico. É possível concluir que: i) os efeitos de GC e de CIMP devem ser incorporados no processo de modelagem; ii) Modelos de estimação que sejam capazes de quantificar e segregar os efeitos aditivos de raça diretos e maternos daqueles efeitos das heterozigoses, como o modelo RM, devem ser eleitos; iii) como, em geral, existe a relação linear entre as heterozigoses e as heteroses e deve ser considerada nas avaliações genéticas; iv) os resultados evidenciam a contribuição genética da heterose nos sistemas de produção e v) são necessárias avaliações suplementares com modelos mais complexos. / Data of weights at birth, weaning, 390 days, weight gain from weaning to 390 days, scrotal circumference and muscling scores at 390 days of age of a population used in the formation of the Montana Tropical® beef composite, raised under tropical conditions, were analyzed under three different models to: i) determine genetic and environment effects ii) determine the adjustment factors those effects; iii) study genetic contribution of additive direct and maternal breed effects and non additive genetic effects; iv) estimate genetic parameters and v) quantify the effects of those models on estimation of expected progeny differences. Three models studied were: Model RM - included the effect of group of contemporaries (GC), the class of age of the cow to the calving (CIMP), the covariates associated to the genetic additive maternal and direct breed effect and the covariates associated to the non additive genetic effect of heterozygosis; Model R considered the effects of model RM, except the maternal additive breed effect and Model H, that considered effects of model R, except the additive direct breed effect. The estimates of (co)variance components and genetic parameters were obtained by the REML methodology under an animal model. The GC effect was the main effect in the different characteristics. The effect of the CIMP was also very important and differences up to 30 kg were observed in weaning weights of young heifers (CIMP = 1) when compared to adult cows (CIMP = 4). Additive direct and maternal breed effects and heterozygosis, in a general, had been significant (P<0.05) for all the traits. Model RM seems to supply better estimates than models R and H, what it is confirmed in the process of prediction of the performance on the part of these models. The estimated genetics parameters were from average to the high magnitudes. It can be conclude that CIMP and GC effect must be incorporated in the modeling process. Models of estimation that are able to segregate and quantify the additive maternal and direct breeds effects and also the effect of heterozygosis, as model RM, must be elect. In general terms, model RM was able to predict the performance of the more frequent genetic combinations of this composite population. The variance components and heritability estimated can support selection programs. Biological type N contributed for the generation of cows that promote higher weaning and 390 days weights as compared to the biological types Adapted and British. In general the linear relation between heterozigoses and heterosis and must be considered in the genetic evaluations. The results evidence the genetic contribution of heterosis in the production systems and further and more complex models are needed to elucidate the composite populations (co)variance components estimation.

Heterosis, or hybrid vigor, refers to the superiority of F₁hybrid performance over the mean of its parents (mid-parent heterosis) theoretically, or the performance of better parents. It has been discovered in many species of plants and animals as well as in humans, and played an important role in enhanced agricultural production, especially in maize, rice and sorghum although the mechanism have not been elucidated. We studied the molecular basis of heterosis with a combined genomics and systems biology approach using model organism maize. We profiled the expression of 39 genes that were most differentially expressed (DG) between the mid-parents and their F1 hybrid (Mo17 x B73) in the 13V-satged, developed whole ear shoots of 13 inbred lines and their 22 F1 hybrids grown in the field trails and phenotyped their 13 traits significant for grain yield. The results showed that gene expression varies significantly among inbreds, among hybrids and in heterosis. The gene clustering heat map and gene action networks in inbreds and hybrids were constructed respectively based on their gene expression profile. According to these pattern analyses, we find dramatically difference between inbreds and their hybrids, although the differential expression varies across different hybrids. Our results also suggest that gene networks are altered from inbreds to hybrids, including their gene contents and wire structures. Last but not least, we have determined the genetic variation correlations between the gene expression and trait performance and constructed the gene networks for the development of 12 of the 13 traits that varied significantly among genotypes. This has led to identification of genes significantly contributing to the performances of the traits, with 1 – 16 genes per trait. These results have indicated that heterosis results not only from altered expression level of corresponding genes between inbreds and their hybrids, importantly, also from the altered gene action networks and expression patterns. These alternations could be derived from gene actions in a manner of additivity, dominance, over dominance, pseudo-overdominance, epistasis and/or their combinations. Therefore, our findings provide a better understanding of the underlying molecular basis of heterosis. The genes identified for the traits will provide tools for advanced studies of the trait heterosis and could be used as tools for their heterosis breeding in maize. The strategy developed in this study will provide an effective tool for studies of other complicated, quantitative traits in maize and other species.

Les changements globaux ont en partie pour effet de modifier les aires de répartition géographique des espèces. Les interactions nouvelles entre espèces n’ayant jamais été en contact peuvent potentiellement mener à des cas atypiques de reproduction, notamment l’hybridation. Ce phénomène peut avoir des implications épidémiologiques fortes car il peut conduire à la genèse de pathogènes hybrides. La combinaison du matériel génétique d’espèces distinctes peut conférer de meilleures capacités à la progéniture (vigueur hybride ou hétérosis), pouvant à terme potentiellement mener à des changements adaptatifs et à l'émergence de pathogènes dans des zones non endémiques, ce qui en fait une menace émergente à l’échelle mondiale. Ce travail de thèse se focalise sur la schistosomiase, seconde maladie parasitaire humaine et sa récente émergence en Europe (Corse, France). Après l’identification et la caractérisation génomique d’un parasite hybride entre deux agents distincts de la maladie, S. haematobium chez l’homme et S. bovis chez les bovins, nous avons mené une approche intégrative afin de caractériser à plusieurs échelles les capacités invasives et la virulence de tels parasites. A partir de souches du terrain, nous avons mis en place un protocole d’évolution expérimentale visant à générer des hybrides de première et deuxième générations au laboratoire. Nous avons analysé les modifications de traits d’histoire de vie de ces parasites ainsi que les conséquences moléculaires (génomique et transcriptomique) de ce « clash génomique » et nous montrons que l’hybridation peut être une force évolutive majeure pour les parasites. / Global changes contribute in modifying species geographical distribution. New interactions between species that have never been in contact before can potentially lead to atypical cases of reproduction, including hybridization. This phenomenon can have strong epidemiological consequences as it can potentially lead to the genesis of hybrid pathogens. The combination of genetic material of distinct species can confer increased capacities to the offspring (hybrid vigor or heterosis), eventually leading to adaptive changes and the emergence of pathogens in non-endemic areas, making them an emerging global threat. This thesis work focuses on schistosomiasis, the second human parasitic disease after malaria and its recent emergence in Europe (Corsica, France). After the identification and genomic characterization of a hybrid parasite between two distinct agents of the disease, S. haematobium in humans and S. bovis in cattle, we conducted an integrative approach to characterize at several scales the invasive capacities and virulence of such parasites. Starting from the field, we set up an experimental evolution protocol aimed at generating first- and second-generation hybrids in the laboratory. We analysed life history trait modifications of these parasites as well as the molecular consequences (genomics and transcriptomics) of this "genomic clash" and we show that hybridization can be a major evolutionary force for parasites.

Le cadre général de cette thèse est la question de la relation génotype-phénotype, abordée à travers l'analyse du phénomène d'hétérosis chez la levure, dans une approche associant biologie, mathématiques et statistiques. Antérieurement à ce travail, un très gros jeu de données hétérogènes, correspondant à différents niveaux d'organisation (protéomique, caractères de fermentation et traits d'histoire de vie), avait été recueilli sur un dispositif demi-diallèle entre 11 souches appartenant à deux espèces. Ce type de données est idéalement adapté pour la modélisation multi-échelle et pour tester des modèles de prédiction de la variation de phénotypes intégrés à partir de caractères protéiques et métaboliques (flux), tout en tenant compte des structures de dépendance entre variables et entre observations. J’ai d'abord décomposé, pour chaque caractère, la variance génétique totale en variances des effets additifs, de consanguinité et d'hétérosis, et j’ai montré que la distribution de ces composantes permettait de définir des groupes bien tranchés de protéines dans lesquels se plaçaient la plupart des caractères de fermentation et de traits d'histoire de vie. Au sein de ces groupes, les corrélations entre les variances des effets d'hétérosis et de consanguinité pouvaient être positives, négatives ou nulles, ce qui a constitué la première mise en évidence expérimentale d’un découplage possible entre les deux phénomènes. Le second volet de la thèse a consisté à interfacer les données de protéomique quantitative avec un modèle stœchiométrique du métabolisme carboné central de la levure, en utilisant une approche de modélisation à base de contraintes. M'appuyant sur un algorithme récent, j’ai cherché, dans l'espace des solutions possibles, celle qui minimisait la distance entre le vecteur de flux et le vecteur des abondances observées des protéines. J’ai ainsi pu prédire un ensemble de flux et comparer les patrons de corrélations entre caractères à plusieurs niveaux d'intégration. Les données révèlent deux grandes familles de caractères de fermentation ou de traits d'histoire de vie dont l'interprétation biochimique est cohérente en termes de trade-off, et qui n'avaient pas été mises en évidence à partir des seules données de protéomique quantitative. L'ensemble de mes travaux permet de mieux comprendre l'évolution de la relation entre génotype et phénotype. / The general framework of this thesis is the issue of the genotype-phenotype relationship, through the analysis of the heterosis phenomenon in yeast, in an approach combining biology, mathematics and statistics. Prior to this work, a very large set of heterogeneous data, corresponding to different levels of organization (proteomics, fermentation and life history traits), had been collected on a semi-diallel design involving 11 strains belonging to two species. This type of data is ideally suited for multi-scale modelling and for testing models for predicting the variation of integrated phenotypes from protein and metabolic (flux) traits, taking into account dependence patterns between variables and between observations. I first decomposed, for each trait, the total genetic variance into variances of additive, inbreeding and heterosis effects, and showed that the distribution of these components made it possible to define well-defined groups of proteins in which most of the characters of fermentation and life history traits took place. Within these groups, the correlations between the variances of heterosis and inbreeding effects could be positive, negative or null, which was the first experimental demonstration of a possible decoupling between the two phenomena. The second part of the thesis consisted of interfacing quantitative proteomic data with the yeast genome-scale metabolic model using a constraint-based modelling approach. Using a recent algorithm, I looked, in the space of possible solutions, for the one that minimized the distance between the flux vector and the vector of the observed abundances of proteins. I was able to predict unobserved fluxes, and to compare correlation patterns at different integration levels. Data allowed to distinguish between two major types of fermentation or life history traits whose biochemical interpretation is consistent in terms of trade-off, and which had not been highlighted from quantitative proteomic data alone. Altogether, my thesis work allows a better understanding of the evolution of the genotype-phenotype map.

<p>Heterosis, or hybrid vigor, is a phenomenon observed in both plant and animal systems where hybrid offspring perform better when compared to their parents. For hybrid plants, this can result in increased biomass, crop yields, and vigor when compared to the inbred parents. Even though heterosis has been used in agriculture for over a century, the molecular mechanisms that result in hybrid vigor remain elusive even after years of investigation. A molecular understanding of heterosis is desirable because it will speed up the process of breeding compatible inbred lines for developing hybrid seeds, and it will provide us with the knowledge to potentially engineer inbred lines that can mimic the beneficial phenotypic effects of heterosis, eliminating the need for farmers to buy new hybrid seeds every year. The goal of this research project is to identify genes that are required for heterotic phenotypes in maize. Our working hypothesis is that a mutation in genes that are essential for heterosis will cause an altered heterotic phenotype in hybrid maize plants. To test this hypothesis, we applied combined approaches of EMS mutagenesis, trait phenotyping in field and controlled conditions, bulk segregant analysis, whole genome sequencing, and bioinformatics analysis. First, we applied a forward genetics approach to identify mutant hybrids with altered heterosis and detected potential causal genes <em>via</em> whole genome sequencing. We identified one mutation occurring in a protein coding gene (gene ID <em>Zm00001eb305590</em>) located in a region of interest on chromosome 7, whose genotypes across various samples assayed fit the observed segregation pattern of hybrid traits. This mutation leads to a moderate or high-level codon change, indicating that this gene may play a role in mediating heterosis in maize. By investigating this gene with further studies, the learned knowledge could speed up the process of hybrid maize breeding by selecting compatible inbred lines through sequencing or by engineering hybrids that have favorable alleles for this gene.</p>