Le moustigre tigre Aedes albopictus, un des vecteurs de la Dengue et du Chikungunya, est une espèce invasive qui a colonisé le monde entier en 30 ans à partir de son berceau asiatique. Les éventuelles bases génétiques de ce succès sont inconnues. Afin d’étudier l’ampleur de la différenciation génétique entre populations asiatiques et européennes et la part prise par la sélection naturelle dans cette différenciation, nous avons développé de nouveaux marqueurs génétiques reposant sur le polymorphisme d’insertion des éléments transposables. Pour cela, nous avons dans un premier temps conçu un outil bioinformatique –dnaPipeTE— nous permettant de dresser le portrait de la fraction répétée du génome d’Ae. albopictus à partir d’une faible proportion des lectures brutes issues d’un projet de séquençage en cours. Le polymorphisme d’insertion de cinq des familles d’ET décrites a ensuite été étudié par la technique de transposon display couplée à du séquençage Illumina, chez 140 individus issus de trois populations vietnamiennes et cinq populations européennes. L’immense majorité des 128 000 marqueurs analysés montre une différenciation génétique très faible entre Europe et Asie. Nous avons néanmoins pu mettre en évidence un centaine d’insertions ayant des fréquences extrêmement différentes entre ces continents. La majorité d’entre elles ségrège à forte fréquence en Europe, suggérant une adaptation du moustique à son environnement tempéré / The Asian tiger mosquito, one of the main vectors of Dengue and Chikungunya, is an invasive species that colonized the world during the last 30 years from its cradle in Asia. Whether this success has an underlying genetic basis remains to be investigated. In order to study the extent of the genetic differentiation between Asian and European populations and the contribution of natural selection to this differentiation, we developed new genetic markers based on transposable elements insertion polymorphism. We first conceived a bioinformatic pipeline –dnaPipeTE— that allowed to grasp a comprehensive picture of the repetitive fraction of the Tiger’s genome through the analysis of a low proportion of raw reads from a ongoing sequencing project. The insertion polymorphism of five transposable element families was then studied by Illumina based transposon display, in 140 individuals from three Vietnamese populations and five European populations. The vast majority of the 128,000 markers showed a very low genetic differentiation between Europe and Asia. However 92 of them displayed extreme frequency differences between the continents. The majority of them segregate at high frequencies in Europe, a pattern suggestive of adaptive evolution towards temperate environments

L’étude des modifications phénotypiques et génomiques associées à l’adaptation des pathogènes aux résistances est une étape fondamentale pour mieux comprendre et anticiper le phénomène de contournement des résistances. Le nématode à kyste Globodera pallida est un important pathogène de la pomme de terre, vis-à-vis duquel un QTL majeur de résistance, GpaVvrn, a été identifié chez Solanum vernei. Cependant, la capacité des populations de G. pallida à s’adapter à cette résistance en quelques générations seulement a été mise en évidence par évolution expérimentale. Dans ce contexte, ce travail de thèse avait pour objectifs (1) d’étudier les traits d’histoire de vie du nématode impactés par l’adaptation, afin de tester l’existence éventuelle d’un coût de virulence, et (2) d’identifier les régions génomiques impliquées dans l’adaptation, par une approche originale combinant évolution expérimentale et scans génomiques sur des lignées virulentes et avirulentes. Contre toute attente, nous avons montré que l’adaptation à la résistance issue de S. vernei entraînait une augmentation de la fitness des individus virulents sur hôte sensible. Nous avons également pu identifier des régions génomiques candidates à l’adaptation à la résistance de la plante hôte, contenant des gènes codant pour des effecteurs, et notamment des SPRYSECs, connus chez les nématodes à kyste pour être impliqués dans la suppression des défenses des plantes mais aussi dans la virulence du nématode. À terme, ces résultats s’avéreront utiles pour la conception de stratégies durables de déploiement de variétés de pommes de terre résistantes. / Studying phenotypic and genomic modifications associated with pathogen adaptation to resistance is a crucial step to better understand and anticipate resistance breakdown. The cyst nematode Globodera pallida is an important pest of potato crops, for which a major resistance QTL, GpaVvrn, has been identified in Solanum vernei. However, the capability of G. pallida populations to adapt to this resistance in only few generations has been highlighted through experimental evolution. In this context, the purposes of this work were (1) to study the nematode life-history traits impacted by adaptation, in order to test for potential existence of a virulence cost, and (2) to identify genomic regions involved in adaptation, through an original approach combining experimental evolution and genome scans on virulent and avirulent lineages. Unexpectedly, we highlighted that adaptation to resistance from S. vernei leads to an increase of virulent individual’s fitness on susceptible host. We were also able to pinpoint candidate genomic regions to adaptation to host plant resistance, containing genes encoding effectors, and especially SPRYSECs, known in cyst nematodes to be involved in suppression of host defense but also in nematode virulence. These results will ultimately be useful in order to conceive sustainable strategies of use of potato resistant cultivars

Ziel unserer molekulargenetischen Studien ist es, Gene der genetisch komplexen idiopathisch generalisierten Epilepsien (IGE) im Genom des Menschen zu lokalisieren und die verantwortlichen Genstörungen durch die Mutationsanalyse von positionell und funktionell plausiblen Kandidatengenen zu identifizieren. Unsere Kopplungsanalysen konnten einen IGE-Locus (Locus-Symbol: EJM1) in der chromosomalen Region 6p21.3 bestätigen und die Kandidatengenregion auf ein chromosomales Segment von 10 centiMorgan (cM) eingrenzen. Ein positionell und funktionell plausibles Kandidatengen ist das Gen einer Untereinheit des heterodimeren GABAB Rezeptors (Gen-Symbol: GABA-BR1). Die systematische Mutationsanalyse des GABA-BR1 Gens und eine Assoziationsstudie mit drei Sequenzpolymorphismen in den Exonen 1a1, 7 und 11 ergaben keinen Anhalt für eine Beteiligung des GABA-BR1 Gens bei der Epileptogenese der IGE. Kopplungshinweise in den chromosomalen Regionen 20q13, 8q24 und 15q14 konnten wir in unserem Familienkollektiv nicht bestätigen. Die Mutationsanalyse der Kandidatengene CHRNA4 und KCNQ2 in der Kandidatengenregion 20q13 und von zwei Kalziumkanal-Genen (CACNA1A, CACNB4) ergaben keinen Hinweis auf disponierende Sequenzvarianten bei IGE-Patienten. Unsere systematische Genomanalyse bei 130 Familien mit mehreren IGE-Angehörigen zielte auf die positionelle Eingrenzung von Genstörungen, die an der Disposition eines breiten IGE-Spektrums beteiligt sind. Bei 360 der 694 Familienangehörigen lag ein IGE-Phänotyp vor. Bei 617 Familienangehörigen wurden für die systematische Genomanalyse insgesamt 416 Mikrosatelliten-Polymorphismen mit einem durchschnittlichen Abstand von 10 cM genotypisiert. Die parameter-freien Kopplungsanalysen ergaben einen signifikanten Kopplungsbefund in der chromosomalen Region 3q26 (P = 1,7 x 10-5 bei D3S3725) sowie zwei Kopplungshinweise in den chromosomalen Regionen 2q36.1 (P = 5,4 x 10-4 bei D2S1371) und 14q23 (P = 5,6 x 10-4 bei D14S63). Positionell und funktionell plausible Kandidatengene sind die Gene des Kalium-Kanals KCNA1B und des Chlorid-Kanals CLCN2 in der Region 3q26, das Gen des Chlorid-Bikarbonat Austauschers SLC4A3 in der Region 2q36, und das Gen des Natrium-Kalzium Austauschers SLC8A3 in der Region 14q23. Der molekulargenetische Nachweis von Genmutationen für die IGE wird konkrete Einblicke in die molekularen Mechanismen der Epileptogenese eröffnen und die Voraussetzungen dafür schaffen, rational begründete Therapieansätze zu entwickeln. / The aim of our molecular genetic studies is to map genes of the genetically complex idiopathic generalized epilepsies on the human genome and to identify the causative gene variants by mutation analyses of positional and functional plausible candidate genes. Our linkage studies confirmed an IGE-locus (locus symbol: EJM1) in the chromosomal region 6p21.3 and to refine the candidate region to a chromosomal segment of 10 centiMorgan (cM). A positional and functional candidate gene is the gene encoding a subunit of the heterodimeric GABAB receptor (gene symbol: GABA-BR1). The systematic mutation screening of the GABA-BR1 gene and an association analysis with three sequence polymorphisms in exons 1a1, 7 and 11 provided no evidence that the GABA-BR1 gene confers susceptibility to the epileptogenesis of IGE. We failed to replicate previous linkage findings in the chromosomal regions 20q13, 8q24 and 15q14 in our family sample. Mutation analysis of the candidate genes CHRNA4 and KCNQ2 and two genes encoding calcium channel subunits (CACNA1A, CACNB4) did not detect common susceptibility alleles in IGE patients. Our systematic genome scan was designed to identify susceptibility loci that predispose to a broad spectrum of common IGE syndromes. Our study included 130 families with two or more siblings affected by an IGE. In total, 360 out of 694 family members were affected by an IGE-trait. 617 family members were genotyped for 416 microsatellite polymorphisms with an average distance of 10 cM. Non-parametric linkage analysis provided significant evidence for a novel IGE susceptibility locus on chromosome 3q26 (ZNPL = 4.19 at D3S3725; P = 0.000017) and suggestive evidence for two IGE loci on chromosome 14q23 (ZNPL = 3.28 at D14S63; P = 0.000566), and chromosome 2q36 (ZNPL = 2.98 at D2S1371; P = 0.000535). Positional and functional candidate genes include the potassium channel gene KCNA1B and the chloride channel gene CLCN2 in the region 3q26, the chloride-bicarbonate anion exchanger gene SLC4A3 in the region 2q36, and the sodium-calcium exchanger gene SLC8A3 in the region 14q23. The molecular genetic detection of susceptibility genes for IGE will provide clues to elucidate the complex molecular pathways of epileptogenesis, and, finally, will help to develop rational treatment strategies.

<p>Systemic lupus erythematosus (SLE) is a complex autoimmune disease with unknown etiology. The aim of this thesis was to identify susceptibility regions through genetic mapping, using model-based linkage analysis on nuclear and extended SLE multicase families.</p><p>In the first paper we performed a genome scan on 19 genetically homogenous Icelandic and Swedish families. One region at 2q37 was identified with a significant linkage with contribution from both populations (Z=4.24). Five other regions 2q11, 4p13, 9p22, 9p13 and 9q13 showed suggestive linkage (Z>2.0).</p><p>In the second paper, 87 families from 10 different countries were analysed only for chromosome 1. One region at 1q31 showed significant linkage (Z=3.79) with contribution from families from all populations, including Mexicans and Europeans. Four other regions 1p36, 1p21, 1q23, and 1q25, showed levels of suggestive linkage. Linkage for most regions was highly dependent on what population was used, which indicated strong genetic heterogeneity in the genetic susceptibility for SLE.</p><p>In the two last papers, we used the positional candidate gene strategy, in order to investigate candidate genes in two regions linked to SLE. For the Bcl-2 gene (at 18q21) we could not detect any association with SLE using three different markers. However, when we investigated the tightly linked low-affinity family of FcγR genes (at 1q23), we could find association for two risk alleles in the FcγRIIA and FcγRIIIA genes. The risk alleles were transmitted to SLE patients on one specific haplotype and therefore are not independent risk alleles.</p><p>The results show that model-based linkage analysis is a strong approach in the search for susceptibility genes behind complex diseases like SLE.</p>

<p>In summary there currently exist techniques to discover miRNA however both require many calculations to be performed during the identification limiting their use at a genomic level. Machine learning techniques are currently providing the best results by combining a number of calculated and statistically derived features to identify miRNA candidates, however almost all of these still include computationally intensive secondary-structure calculations. It is the aim of this project to produce a miRNA identification process that minimises and simplifies the number of computational elements required during the identification process.</p>

Systemic lupus erythematosus (SLE) is a complex autoimmune disease with unknown etiology. The aim of this thesis was to identify susceptibility regions through genetic mapping, using model-based linkage analysis on nuclear and extended SLE multicase families. In the first paper we performed a genome scan on 19 genetically homogenous Icelandic and Swedish families. One region at 2q37 was identified with a significant linkage with contribution from both populations (Z=4.24). Five other regions 2q11, 4p13, 9p22, 9p13 and 9q13 showed suggestive linkage (Z&gt;2.0). In the second paper, 87 families from 10 different countries were analysed only for chromosome 1. One region at 1q31 showed significant linkage (Z=3.79) with contribution from families from all populations, including Mexicans and Europeans. Four other regions 1p36, 1p21, 1q23, and 1q25, showed levels of suggestive linkage. Linkage for most regions was highly dependent on what population was used, which indicated strong genetic heterogeneity in the genetic susceptibility for SLE. In the two last papers, we used the positional candidate gene strategy, in order to investigate candidate genes in two regions linked to SLE. For the Bcl-2 gene (at 18q21) we could not detect any association with SLE using three different markers. However, when we investigated the tightly linked low-affinity family of FcγR genes (at 1q23), we could find association for two risk alleles in the FcγRIIA and FcγRIIIA genes. The risk alleles were transmitted to SLE patients on one specific haplotype and therefore are not independent risk alleles. The results show that model-based linkage analysis is a strong approach in the search for susceptibility genes behind complex diseases like SLE.

<p>In summary there currently exist techniques to discover miRNA however both require many calculations to be performed during the identification limiting their use at a genomic level. Machine learning techniques are currently providing the best results by combining a number of calculated and statistically derived features to identify miRNA candidates, however almost all of these still include computationally intensive secondary-structure calculations. It is the aim of this project to produce a miRNA identification process that minimises and simplifies the number of computational elements required during the identification process.</p>

Magister Scientiae - MSc / In summary there currently exist techniques to discover miRNA however both require many calculations to be performed during the identification limiting their use at a genomic level. Machine learning techniques are currently providing the best results by combining a number of calculated and statistically derived features to identify miRNA candidates, however almost all of these still include computationally intensive secondary-structure calculations. It is the aim of this project to produce a miRNA identification process that minimises and simplifies the number of computational elements required during the identification process. / South Africa

Chez les espèces sexuées, une sélection sexuellement antagoniste (SA) peut agir si les deux sexes ont des optimums en fitness différents pour un même trait. De plus, si l'architecture génétique de ce trait est partagée entre les sexes, un conflit sexuel intralocus (IASC) peut se produire, menant à l'évolution d'un dimorphisme sexuel. Un modèle de génétique des populations classique prédit que le chromosome X offre un environnement plus favorable à l'accumulation de locus sous sélection SA en comparaison aux autosomes. Nous nous sommes dans un premier temps intéressée à la détection d'une signature d'IASC dans le génome humain, c'est-à-dire des différences de fréquences alléliques entre les sexes. En effectuant un balayage du génome, nous avons mis en évidence un enrichissement en locus montrant une signature d'IASC sur le chromosome X en comparaison aux autosomes. Un mécanisme possible à l'origine des différences de fréquences alléliques entre les sexes dans une population est une distorsion de transmission sexe-spécifique. Dans un second temps, nous avons donc mis au point une méthode de détection de locus pour lesquels les parents transmettent préférentiellement un allèle à leurs fils, et un autre allèle à leurs filles, en utilisant une base de données de séquençage de trios parents-enfant. Nos résultats indiquent que des processus de distorsion de transmission sexe-spécifique seraient à l'origine d'une grande partie des différences de fréquences alléliques entre les sexes observées chez les enfants. Cela suggère que des processus sexuellement antagonistes agissant sur la survie pourraient avoir lieu entre la production des gamètes et la naissance chez l'Homme. / Sexually Antagonistic (SA) selection can occur when, within a species, the two sexes have different fitness optima for a trait. If a trait under SA selection is encoded by the same set of genes in the two sexes, an Intralocus Sexual Conflict (IASC) can arise, leading to the evolution of sexual dimorphism. A classical theoretical model predicts that the X chromosome should be a hotspot for the accumulation of loci under IASC, as compared to the autosomes. In this dissertation, we first aimed at detecting differences in allelic frequencies between males and females, a signature of IASC, in the human genome using a genome scan. We show that loci exhibiting signatures of ongoing IASC are preferentially located on the X chromosome as compared to autosomes. Moreover, they are enriched in genes involved in the determination of traits known to be sexually dimorphic in humans, including reproduction, metabolism and immune system, supporting an implication of sexually antagonistic selection in the evolution of sexual dimorphisms in humans. One possible mechanism leading to differences in allelic frequencies between the sexes is a sex-specific transmission distortion. Therefore, we aimed at detecting loci for which parents preferentially transmit one allele to their sons and another allele to their daughters in a sequencing dataset containing trios (parents-child). We found that sex-specific transmission distortions are at the origin of a large proportion of the differences in allelic frequencies between the sexes observed in children. This suggests that sexually antagonistic processes on survival may occur between the production of gametes and birth in humans.

La recherche des signatures génétiques de l'adaptation locale est d'un grand intérêt pour de nombreuses études de génétique des populations. Les approches pour trier les loci sélectifs à partir de leur contexte génomique, se concentrent sur les valeurs extrêmes de l'indice de fixation, FST, à travers les loci. Cependant, le calcul de l'indice de fixation devient difficile lorsque la population est génétiquement continue, lorsque la prédéfinition des sous-populations est une tâche difficile et en présence d'individus mélangés dans l'échantillon. Dans cette thèse, nous présentons une nouvelle méthode pour identifier les loci sous sélection basée sur une extension de la statistique FST à des échantillons avec des individus mélangés. Considérant notre objectif d'explorer des méthodes statistiques pour identifier l'adaptation locale dans la population mélangée, nous avons inclus des données spatiales pour calculer les coefficients d'ascendance et les fréquences d'allèles. Pour enrichir notre travail, nous avons investigué les effets du déséquilibre de liaison et des méthodes d'élagage de LD dans les analyses de génomes pour la sélection. / Finding genetic signatures of local adaptation is of great interest for many population genetic studies. Common approaches to sorting selective loci from their genomic background focus on the extreme values of the fixation index, FST, across loci. However, the computation of the fixation index becomes challenging when the population is genetically continuous, when predefining subpopulations is a difficult task, and in the presence of admixed individuals in the sample. In this thesis, we present a new method to identify loci under selection based on an extension of the FST statistic to samples with admixed individuals. Considering our goal of exploring statistical methods to identify local adaptation in admixed population, we included spatial data to compute ancestry coefficients and allele frequencies. To enrich our work, we investigated the effects of linkage disequilibrium and LD-pruning methods in genome scans for selection.