The objectives of this study were to identify signatures of selection in Bos taurus beef and dairy cattle populations and to annotate regions of selection with gene, function and QTL information. Differences in minor allele frequencies, population-average FST, population-specific FST, and integrated extended haplotype homozygosity scores were applied to a subset of the bovine HapMap data to characterize signatures of selection in 7 Bos taurus beef and 5 Bos taurus dairy cattle populations. Numerous single nucleotide polymorphisms (SNP) exhibited evidence of selection across the genome and regions of BTA2 and BTA14 that are considered to be under positive selection in beef and dairy cattle, respectively, were highlighted. The current density of SNP limited our ability to annotate regions putatively under selection because most SNP in the assay were intergenic. This is likely because of the betweenbreed SNP discovery method that was used, which typically identifies SNP with higher allele frequencies.

Depuis la domestication du pommier, l’homme a progressivement sélectionné des variétés plus performantes, notamment pour la qualité du fruit, la productivité ou la résistance aux pathogènes. Les bases génétiques de ces caractères ont été explorées par cartographie en descendances F1 ne permettant d’explorer qu’une infime partie de la diversité génétique disponible.L’objectif de la thèse portait sur l’analyse des bases génétiques de caractères de qualité du fruit et de résistance du pommier à la tavelure et au feu bactérien dans des collections représentant une diversité plus large. Le génotypage de core collections de variétés anciennes s’est fait à l’aide de deux puces 8k et 480kSNPs ou grâce à du ré-séquençage de gènes. Des traces de différenciation génétique entre pommes à cidre et à couteau ont été identifiées et partiellement reliées à la voie des polyphénols. Après analyse de l’étendue du déséquilibre de liaison à large et fine échelle, une approche de génétique d’association a permis l’identification de régions génomiques associées à la variation de plusieurs caractères de qualité du fruit, dont le haut du groupe de liaison 16 rassemblant l’acidité (locus Ma), la fermeté, la jutosité et l’amertume (gène LAR). Pour la résistance au feu bactérien, une région contenant un homologue du gèneNPR1 (activateur de défenses) a été identifiée.Cette thèse a ainsi permis de préciser la localisation potentielle de QTLs identifiés préalablement par cartographie génétique et d’identifier de nouvelles ressources utiles dans de futurs programmes de sélection assistée par marqueurs. / Since apple domestication, humans have progressively selected improved varieties, especially for traits linked with fruit quality, productivity or resistance to pathogens. The genetic bases underlying these traits have been explored thanks to genetic mapping in F1 segregating populations that only allows the study of a small part of the available genetic diversity. The aim of this work was to analyze the genetic bases of fruit quality and disease resistance against apple scab and fire blight, in collections of old apple varieties representing a much larger diversity. Genotyping of core collections was performed either with arrays of 8k and 480k SNPs or by resequencing of chosen genes. Signs of genetic differentiation were identified between cider and dessert apples and were partially linked to the polyphenols pathway. After studying linkage disequilibrium, both on a large and a small scale, an association genetics approach allowed the identification of genomic regions associated with the variation of several fruit quality traits. Especially, the top of linkage group 16 was found to be linked with acidity (locus Ma), firmness, juiciness and bitterness (LAR gene). Concerning the resistance of apple to fire blight, a region containing a homolog of the NPR1 gene (defense activator) was identified. This thesis allowed the refining of the putative localization of previously identified QTLs and the identification of new genetic resources that could be useful in future selection programs using marker assisted selection.

nÃo hà / As raÃas de ovinos localmente adaptadas brasileiras, tambÃm conhecidas como nativas ou crioulas, descendem de animais trazidos durante o perÃodo colonial e, desde aquela Ãpoca, vÃm sendo submetidas a processos evolutivos sistemÃticos e nÃo sistemÃticos., o que resultou na formaÃÃo de genÃtipos altamente adaptados Ãs mais diversas condiÃÃes ambientais brasileiras. Embora estas raÃas nÃo possuam o mesmo potencial produtivo das raÃas exÃticas melhoradas, elas sÃo consideradas extremamente importantes devido Ãs relaÃÃes sociais e culturais que guardam com as populaÃÃes do campo. AlÃm disso, as raÃas localmente adaptadas possuem caracterÃsticas adaptativas importantÃssimas para a manutenÃÃo de sistemas produtivos tradicionais. A otimizaÃÃo da utilizaÃÃo dos recursos genÃticos naturalizados depende de um conhecimento profundo destas populaÃÃes e, portanto, a caracterizaÃÃo morfolÃgica, produtiva e molecular sÃo ferramentas imprescindÃveis para o sucesso da conservaÃÃo e utilizaÃÃo deste recurso genÃtico. Com base nisso, o objetivo desta tese foi aprofundar os estudos de caracterizaÃÃo molecular das principais raÃas de ovinos localmente adaptadas brasileiras: Crioula Lanada, Morada Nova e Santa InÃs. Assim, o capÃtulo I intitulado âIdentificaÃÃo de assinaturas de seleÃÃo em animais de produÃÃoâ consiste em uma revisÃo cujo objetivo à descrever os principais efeitos da seleÃÃo natural/artificial nos genomas das espÃcies de animais de produÃÃo, apresentar os principais mÃtodos de anÃlise de assinaturas de seleÃÃo e discutir os recentes avanÃos nesta Ãrea de estudo. Foram realizados dois estudos que resultaram nos capÃtulos II e III desta tese. O capÃtulo II, intitulado âIdentificaÃÃo de assinaturas de seleÃÃo em ovinos de raÃas localmente adaptadas brasileirasâ, teve como objetivo a identificaÃÃo e caracterizaÃÃo de regiÃes genÃmicas provÃveis de estar sob seleÃÃo nas trÃs principais raÃas brasileiras localmente adaptadas de ovinos e caracterizar estar regiÃes com a finalidade de identificar genes envolvidos com diferenÃas produtivas/adaptativas entre estas raÃas. A identificaÃÃo das regiÃes sujeitas à seleÃÃo foi feita com base em dois tipos de metodologia: diferenciaÃÃo entre populaÃÃes (FST) e desequilÃbrio de ligaÃÃo (iHS e Rsb). Foram identificados 78 genes candidatos envolvidos com funÃÃes como: resposta imune, desenvolvimento do sistema nervoso, percepÃÃo sensorial e desenvolvimento de pelos/lÃ. O capÃtulo III, intitulado: âIdentificaÃÃo de subestrutura de populaÃÃes em ovinos de raÃas localmente adaptadas brasileirasâ, teve como objetivos identificar e caracterizar a presenÃa de subestruturaÃÃo genÃtica dentro das trÃs principais raÃas brasileiras localmente adaptadas de ovinos. Foi observada, de uma forma geral, a presenÃa de diferenciaÃÃo genÃtica bastante considerÃvel ao comparar os rebanhos de cada raÃa analisada. AlÃm disso, tanto na raÃa Crioula Lanada quanto na raÃa Santa InÃs, pode ser observada a presenÃa de grupos bem distintos de indivÃduos, sugerindo a efetiva presenÃa de diferentes ecÃtipos/linhagens dentro destas raÃas. / The Brazilian locally adapted sheep breeds, also known as native and creole, are descendant from animals brought during the settlement period and, since then, are been subjected to evolutive (both systematic and non systematic) processes, what resulted in the formation of highly adapted genotypes to the diverse environmental Brazilian conditions. Although these breeds donât posses the same productive potential when compared with the exotic improved breeds, they are considered extremely important from a social and cultural point of view. Moreover, the locally adapted breeds are essential for the maintenance of traditional production systems. The optimization of the utilization of naturalized genetic resources depends on a deep knowledge of these populations, and then, the morphological, productive and molecular characterizations are essential to the success of conservation and utilization of these locally adapted genotypes. Therefore, the principal aim of this thesis was to deepen molecular the knowledge of the three main locally adapted Brazilian sheep breeds: Brazilian Creole, Morada Nova and Santa Ines. Thus, Chapter I entitled "Identification of selection signatures in livestock species" is a literature review that is proposed to describe the main effects of natural/artificial selection in the genomes of species of farm animals, present the main methods of signature selection analysis and discuss recent advances in this area of study. Two studies were conducted and resulted in the chapters II and III of this thesis. The chapter II, entitled âIdentification of selection signatures in brazilian locally adapted sheep breedsâ, aimed the identification and characterization of putative genomic regions that underwent selection and the identification of candidate genes related to productive/adaptative differences between these breeds. The identification of signatures of selection was performed through two approaches: population differentiation (FST) and linkage disequilibrium (iHS and Rsb). Seventy eight genes, related to functions as: immune response, nervous system development, sensorial perception and wool/hair development were identified. The chapter III, entitled âIdentification of population substructure in brazilian locally adapted sheep breedsâ, aimed the identification and characterization of of genetic substructure within the three main locally adapted Brazilian sheep breeds: Brazilian Creole, Morada Nova and Santa Ines. The level of genetic differentiation between herds of the same breeds was, in general, high. Both in the Brazilian Creole and in the Santa Ines breeds the presence of distinct groups on animals could be observed, what suggests the occurrence of different ecotypes/lineages within these breeds.

La génomique des populations rend possible la mise en évidence de traces de sélection dans le génome. Les travaux effectués considèrent en général une échelle de temps longue (~ 10³ générations). En comparaison, peu d’intérêt a été porté aux études expérimentales de court terme (~ 10 générations). De telles expériences sont pourtant susceptibles de nous renseigner sur la base génétique de caractères complexes. Nous proposons une méthode de vraisemblance basée sur un modèle de Wright-Fisher pour détecter la sélection à partir d’échantillons génétiques temporels acquis sur une période de dix générations. Nous montrons par simulation que notre méthode permet de différencier les signaux dus à la combinaison de la sélection et de la dérive génétique de ceux dus à la dérive seule. Nous montrons également par simulation qu’il est possible d’estimer le coefficient de sélection appliqué à un locus testé. De plus, nous illustrons l’intérêt de notre méthode pour la détection de marqueurs candidats à la sélection au travers de deux études génomiques sur données réelles, chez le diable de Tasmanie (Sarcophilus harrisii) et chez la truite arc-en-ciel (Oncorhynchus mykiss). Ces applications mettent en évidence des régions génomiques candidates pour des phénotypes complexes dans des contextes différents. Dans l’ensemble, nos résultats montrent qu’il est possible de détecter des gènes sujets à une sélection directionnelle intense à partir d’échantillons génétiques temporels, même si la sélection est de courte durée et si les populations examinées ont un faible effectif. / Population genomics makes it possible to detect traces of selection in the genome. Studies in this field have mainly focused on long time scale (~ 10³ generations). In comparison, short-term experimental studies (~ 10 generations) have attracted much less interest. Such experiments are, however, likely to inform us about the genetic basis of complex characters. We propose a likelihood method based on a Wright-Fisher model to detect selection from genetic temporal samples collected over ten generations. We show through simulation that our method can disentangle signals due to the combination of genetic drift and selection to those due to drift alone. We also show through simulation that it is possible to estimate the selection coefficient applied to a tested locus. In addition, we illustrate the interest of our method for the detection of candidate markers for selection through two genome scans performed on real data, in the Tasmanian devil (Sarcophilus harrisii) and in the rainbow trout (Oncorhynchus mykiss). These practical applications highlight candidate genomic regions for complex phenotypes in different contexts. Collectively, our results show the possibility of detecting genes submitted to strong directional selection from genetic time-series, even if selection is applied on a short time period and if the examined populations are small.