Recent advances in genomics now allow for the identification of the genes and mutations that underlie the heritability of agronomically important traits in livestock. The corresponding genes are said to map to Quantitative Trait Loci (QTL), and the mutations referred to as Quantitative Trait Nucleotides (QTN). The most commonly used approach relies on positional cloning which typically proceeds in three steps: QTL mapping by linkage analysis, QTL fine-mapping by linkage disequilibrium or association analysis, and QTN identification combining haplotype analysis and functional assays. Knowledge of QTL and QTN provides insights into the genetic architecture of complex traits and physiology of production traits, and opens novel possibilities for enhanced selection referred to as Marker Assisted Selection (MAS). This thesis is devoted to QTN identification of a QTL that was previously mapped to pig chromosome 2 and fine-mapped to a 250 Kb segment encompassing the imprinted IGF2 gene. The QTL was shown to have a major post-natal effect on muscle mass and fat deposition, and to be subject to parental imprinting as only the padumnal chromosome affects the phenotype. To identify the QTN we have first generated 32 Kb and 56 Kb of finished porcine sequence encompassing the IGF2 and H19 genes, respectively. The corresponding sequences were annotated including definition of gene models, identification of interspersed repeats and determination of 97 sequence elements that are highly conserved between pig, human and mouse. We have then resequenced 28 Kb encompassing the IGF2 gene for 15 boar chromosomes for which the QTL genotype had been determined by progeny-testing or Marker Assisted Segregation Analysis (MASA). This revealed 258 polymorphisms of which only one (Int3-3072G>A) cosegregated perfectly with QTL genotype. The corresponding single nucleotide polymorphism (SNP) is a G to A transition affecting one of the highly conserved sequence elements located just downstream of differentially methylated region 1 in intron 3. We have demonstrated that the Int3-3072 A allele associated with increased muscle mass is also associated with increased IGF2 mRNA levels in post-natal striated muscle (but not in pre-natal muscle nor in pre- and post-natal liver). However, the Int3-3072G>A SNP does not alter imprinting nor allele-specific methylation. Using a luciferase reporter assay, we then demonstrated that the Int3-3072 A allele reduces the cis activity of a silencer element, and using an electrophoretic mobility shift assay (EMSA), that it abrogates binding of a nuclear factor assumed to be a trans-acting silencing factor. Taken together both genetic and functional evidence strongly support the conclusion that the Int3-3072G>A SNP is the causative SNP. The thesis is concluded by a discussion that (i) highlights the factors that make domestic animals a unique resource for the molecular dissection of complex phenotypes, (ii) comments the Asian origin of the Int3-3072A allele associated with increased muscle mass, (iii) describes recent advances in characterizing the trans-acting silencing factor binding to the Int3-3072G allele, (iv) pinpoints statistical issues related to the detection of imprinted QTL, (v) reports on the utility of the Int3-3072G>A SNP for MAS applied to pig breeding, and (vi) makes projections on how latest progress in genome analysis will affect positional identification of QTN in the near future. Grâce aux progrès récents en génomique, il est maintenant possible didentifier les gènes et mutations qui sous-tendent lhéritabilité des caractères de production chez les animaux de rente. Ces gènes se localisent au niveau de Loci de Traits Quantitatifs (QTL), et les mutations correspondantes sont qualifiées de Nucléotides de Traits Quantitatifs (QTN). La démarche expérimentale la plus couramment utilisée est le clonage positionnel. Celui-ci comprend trois étapes: cartographie de QTL par analyses de liaison génétique, cartographie fine de QTL par études dassociation exploitant le déséquilibre de liaison, et identification de QTN par combinaison danalyses haplotypiques et fonctionnelles. Lidentification de QTL et QTN non seulement révèle larchitecture génétique des phénotypes complexes que sont les caractères de production, ainsi que les rouages moléculaires qui les sous-tendent, mais ouvre également des possibilités nouvelles de sélection plus performante dite Assistée par Marqueurs (MAS). Cette thèse est consacrée à lidentification dun QTN correspondant à un QTL dabord localisé sur le chromosome 2 du porc, et ensuite cartographié finement dans un segment chromosomique de 250 Kb comprenant le gène IGF2. Le QTL en question a un effet post-natal majeur sur la croissance musculaire et le dépôt graisseux. Il est soumis à lempreinte parentale, lallèle paternel étant le seul à influencer le phénotype. Afin didentifier le QTN, nous avons tout dabord généré 32 Kb et 56 Kb de séquences finies, comprenant respectivement les gènes IGF2 et H19. Les séquences correspondantes ont été annotées bioinformatiquement, y compris la définition de modèles gèniques, lidentification de séquences répétées dispersées, ainsi que de 97 éléments de séquence fortement conservés chez le porc, lhomme et la souris. Nous avons ensuite re-séquencé 28 Kb chevauchant le gène IGF2 pour 15 chromosomes dont le génotype au niveau du QTL fut préalablement déterminé par testage de descendance ou Ségrégation Assistée par Marqueurs. Cet exercice a révélé 258 polymorphismes dont un seulement (Int3-3072G>A) correspondait parfaitement aux génotypes QTL. Ce polymorphisme est une transition G à A affectant un des 97 éléments hautement conservés, situé juste en aval de la région différentiellement méthylée (DMR1) dans lintron 3. Nous avons ensuite démontré que lallèle Int3-3072 A, associé à une augmentation de la masse musculaire, est également associé à une augmentation des taux dARNm IGF2 dans le muscle strié post-natal (mais non dans le muscle strié pré-natal, ni dans le foie pré- et post-natal). Par contre, le polymorphisme Int3-3072G>A naffecte ni état dempreinte ni de méthylation allèle-spécifique du gène. Nous avons ensuite démontré à laide dun test rapporteur de type luciférase que lallèle Int3-3072 A réduit lactivité dun élément silenceur agissant en cis, et à laide dun test de type EMSA quil empêche la liaison dun facteur nucléaire. Conjointement, ces données génétiques et fonctionnelles démontrent que le polymorphisme Int3-3072G>A SNP correspond bien au QTN. Nous concluons la thèse par une discussion dans laquelle nous (i) démontrons pourquoi les animaux domestiques offrent des possibilités uniques pour la dissection moléculaire de phénotypes complexes, (ii) commentons lorigine asiatique de lallèle Int3-3072A associé à une augmentation du développement musculaire, (iii) décrivons les progrès récent dans lidentification du facteur nucléaire reconnaissant spécifiquement lallèle Int3-3072G, (iv) attirons lattention sur les artéfacts statistiques associés à la détection de QTL soumis à lempreinte, et (v) discutons limpact de nouvelles technologies génomiques sur le clonage positionnel de gènes.

The noise in the Langmuir Probe and Plasma Wave Instrument (LP-PWI) on board ESA:s future Jupiter satellite JUICE (Jupiter ICy Moons Explorer) was investigated. Thermal Johnson-Nyquist noise and shot noise, caused by fluctuations in the probe-plasma currents, were combined with the quasi-thermal noise (QTN) due to thermal fluctuations in the electric field in the plasma, using a small signal equivalent circuit model. The contributions and effects of each of the considered noise sources were examined and compared for a number of representative space plasma conditions, including the cold dense plasma of Ganymede's ionosphere and the hot tenuous plasma out in the Jovian magnetosphere. The results showed that in the cold dense plasma of Ganymede's ionosphere, the antenna was long compared to the Debye length and the quasi-thermal noise had a clearly pronounced peak and a steep high-frequency cut-off. For an antenna biased to 1 V with respect to the plasma, the shot noise due to the ambient plasma was the dominant source of noise. For a an antenna at the floating potential the photoelectron shot noise coalesced with the shot and Nyquist noises of the ambient plasma to form almost a single curve. In the hot tenuous plasma out in Jupiter's magnetosphere, the antenna was short compared to the Debye length and the QTN spectrum was much flatter, with little or no peak at the plasma frequency and a very weak high-frequency cut-off. For an antenna biased to 1 V, the shot noise due to photoelectron emission dominated at Callisto's orbital position whereas at Ganymede's and Europa's orbital positions the Nyquist and shot noises of the ambient plasma particles were the dominant noise components. For an antenna at the floating potential, the shot and Nyquist noises of the ambient plasma also dominated the output noise, except at Europa's orbital position, where the quasi-thermal noise was the largest noise component for frequencies at and above the plasma frequency. The numerical calculations were performed using MATLAB. The code was made available in a Git repository at https://github.com/eliasodelstad/irfuproj_JUICE_noise.

Domestic animals have become very different from their wild ancestors during domestication and animal breeding. This provides a good model to unravel the molecular mechanisms underlying phenotypic variation. In my thesis I have studied genes affecting two important traits, leanness in pigs and hair greying-associated melanoma in horses. In the first part of the thesis, I focused on an intronic mutation leading to more muscle growth and less fat deposition in domestic pigs to identify a transcription factor (TF) that binds to the regulatory element overlapping with the mutation. The aim has been to further study the function of the previously unknown TF in mouse myoblast cells and in insulin-producing cells (Paper I-III). We discovered a new TF ZBED6 binding to intron 3 of the IGF2 gene, in which a single nucleotide substitution in pigs abrogates the binding and causes increased leanness in domestic pigs. Silencing of ZBED6 expression in mouse myoblasts increased Igf2 expression, cell proliferation and migration, and myotube formation. This result is in line with the increased leanness phenotype in mutant pigs. Chromatin Immunoprecipitation-sequencing (ChIP-seq) using an anti-ZBED6 antibody identified 1200 ZBED6 target genes besides IGF2 and many are TFs controlling fundamental biological processes. In the first follow-up study we found ZBED6 mainly affected the expression of muscle protein genes by directly regulating Igf2 and Twist2 expression, in agreement with our previous observation of faster myotube formation in ZBED6-silenced cells. ChIP-seq with antibodies against six different histone modifications revealed that ZBED6 preferentially binds to active promoters and modulates transcriptional activity by a novel mechanism rather than by recruiting repressive histone modifications. The second follow-up study revealed that ZBED6 affects the morphology and insulin content and release in pancreatic ß cells. In the second part (Paper IV), we investigate the functional significance of an intronic duplication in the Syntaxin 17 (STX17) gene causing hair greying and melanoma in horses. We found two Microphtalmia-associated transcription factor (MITF) binding sites within the duplication and showed that the duplicated sequence up-regulates reporter gene expression in a melanocyte-specific manner both by reporter assays in mouse melanocytes and in transgenic zebrafish. These results established that the intronic duplication acts as a melanocyte-specific enhancer that becomes much stronger when it is duplicated.

The noise in the Langmuir Probe and Plasma Wave Instrument (LP-PWI) on board ESA:s future Jupiter satellite JUICE (Jupiter ICy Moons Explorer) was investigated. Thermal Johnson-Nyquist noise and shot noise, caused by fluctuations in the probe-plasma currents, were combined with the quasi-thermal noise (QTN) due to thermal fluctuations in the electric field in the plasma, using a small signal equivalent circuit model. The contributions and effects of each of the considered noise sources were examined and compared for a number of representative space plasma conditions, including the cold dense plasma of Ganymede's ionosphere and the hot tenuous plasma out in the Jovian magnetosphere. The results showed that in the cold dense plasma of Ganymede's ionosphere, the antenna was long compared to the Debye length and the quasi-thermal noise had a clearly pronounced peak and a steep high-frequency cut-off. For an antenna biased to 1 V with respect to the plasma, the shot noise due to the ambient plasma was the dominant source of noise. For a an antenna at the floating potential the photoelectron shot noise coalesced with the shot and Nyquist noises of the ambient plasma to form almost a single curve. In the hot tenuous plasma out in Jupiter's magnetosphere, the antenna was short compared to the Debye length and the QTN spectrum was much flatter, with little or no peak at the plasma frequency and a very weak high-frequency cut-off. For an antenna biased to 1 V, the shot noise due to photoelectron emission dominated at Callisto's orbital position whereas at Ganymede's and Europa's orbital positions the Nyquist and shot noises of the ambient plasma particles were the dominant noise components. For an antenna at the floating potential, the shot and Nyquist noises of the ambient plasma also dominated the output noise, except at Europa's orbital position, where the quasi-thermal noise was the largest noise component for frequencies at and above the plasma frequency. The numerical calculations were performed using MATLAB. The code was made available in a Git repository at https://github.com/eliasodelstad/irfuproj_JUICE_noise.