La levure S. cerevisiae est la seule espèce capable de terminer la fermentation alcoolique du jus de raisin qui est l’étape principale de la vinification. A cause de la forte variabilité technologique retrouvée chez cette espèce, des travaux de sélection sont réalisés dans le but d’utiliser des levains performants pour l’industrie. Ces souches montrent des différences importantes à la fois dans leurs cinétiques fermentaires et leur bilans en métabolites, ce qui impacte la qualité des vins. La réponse phénotypique des levures varie également de manière considérable et non homogène face aux variations environnementales. La compréhension des mécanismes génétiques expliquant cette réponse différenciée est une question scientifique non triviale. Elle revêt une importance particulière en oenologie, où les conditions de vinifications sont très changeantes (millésimes, cépages, terroirs, conduites de vinifications…). Afin de pouvoir proposer des levains garantissant le succès des fermentations dans un large éventail de conditions, nous proposons ici de mieux comprendre ces mécanismes d’interaction Gène x Environnement dans un contexte oenologique. L’identification de locus génétiques (Quantitative Trait Loci (QTL)) contrôlant des caractères quantitatifs est rendue possible par des approches de cartographie de QTLs. Celles-ci nécessitent l’étude d’une vaste descendance en ségrégation qui doit être caractérisée sur le plan génétique et phénotypique. L’établissement d’un lien statistique entre des marqueurs génétiques et un phénotype permet la localisation de QTLs influant les caractères étudiés. Au cours de cette thèse, une méthode de phénotypage pour suivre les fermentations de plusieurs centaines d’individus a été mise au point. Grâce à elle, les performances fermentaires de deux descendances génotypées par séquençage à haut débit ont été mesurées en faisant varier les conditions de fermentations. Cela a permis l’identification de nombreux QTLs et d’estimer leur impact sur la robustesse des souches. L’implication des allèles de trois gènes qui montrent une forte interaction avec l’environnement et qui possèdent des effets pléiotropiques liés au métabolisme du SO2 a été prouvée moléculairement. Les résultats obtenus font l’objet d’une discussion générale sur l’utilisation de QTLs pour la sélection de levures plus performantes. / The yeast S. cerevisiae is the only species able to complete the alcoholic fermentation of grape must which is the main step of the wine-making process. Because of the high technological variability found in this species, selection work is carried out with the aim of using efficient yeasts for the industry. These strains show important differences both in their fermentation kinetics and their metabolite yield which affects the wines quality. In addition to these important phenotypic variations, the phenotypic response of yeasts varies considerably and not homogeneously against environmental variations. Understanding the genetic mechanisms that explain these differentiated responses to environmental variations is a non-trivial scientific question. This is of particular importance in oenology, where the winemaking conditions are highly variable (vintages, grape variety, terroirs, oenological practices...). In order to obtain yeasts ensuring the success of the fermentations under a wide range of conditions, we propose here to better understand these mechanisms of interaction Gene x Environment in an oenological context. The identification of genetic locus (Quantitative Trait Loci (QTL)) controlling quantitative characters is made possible by QTL mapping approaches. These approaches require the study of a large progeny in segregation that must be characterized genetically and phenotypically. The establishment of a statistical link between genotype and phenotype allows the localization of QTLs that have an impact on phenotyped characters. During this thesis a phenotyping method that allows us to follow the fermentations of several hundred individuals has been developed. Thanks to it, two progenies genotyped by whole genome sequencing have been phenotyped in different environmental conditions. This lead to the identification of many QTLs and to the estimation of their impact in strain robustness. The implication of the alleles of 3 genes showing a strong interaction with environment and pleiotropic effects linked to the SO2 metabolism has been proved molecularly. The results achieved are discussed in the context of QTL exploitation for the selection of more efficient yeast.

Plants are the primary producers of biomass and thereby the basis of all life. Many varieties are cultivated, mainly to produce food, but to an increasing amount as a source of renewable energy. Because of the limited acreage available, further improvements of cultivated species both with respect to yield and composition are inevitable. One approach to further progress in developing improved plant cultivars is a systems biology oriented approach. This work aimed to investigate the primary metabolism of the model plant A.thaliana and its relation to plant growth using quantitative genetics methods. A special focus was set on the characterization of heterosis, the deviation of hybrids from their parental means for certain traits, on a metabolic level. More than 2000 samples of recombinant inbred lines (RILs) and introgression lines (ILs) developed from the two accessions Col-0 and C24 were analyzed for 181 metabolic traces using gas-chromatography/ mass-spectrometry (GC-MS). The observed variance allowed the detection of 157 metabolic quantitative trait loci (mQTL), genetic regions carrying genes, which are relevant for metabolite abundance. By analyzing several hundred test crosses of RILs and ILs it was further possible to identify 385 heterotic metabolic QTL (hmQTL). Within the scope of this work a robust method for large scale GC-MS analyses was developed. A highly significant canonical correlation between biomass and metabolic profiles (r = 0.73) was found. A comparable analysis of the results of the two independent experiments using RILs and ILs showed a large agreement. The confirmation rate for RIL QTL in ILs was 56 % and 23 % for mQTL and hmQTL respectively. Candidate genes from available databases could be identified for 67 % of the mQTL. To validate some of these candidates, eight genes were re-sequenced and in total 23 polymorphisms could be found. In the hybrids, heterosis is small for most metabolites (< 20%). Heterotic QTL gave rise to less candidate genes and a lower overlap between both populations than was determined for mQTL. This hints that regulatory loci and epistatic effects contribute to metabolite heterosis. The data described in this thesis present a rich source for further investigation and annotation of relevant genes and may pave the way towards a better understanding of plant biology on a system level. / Pflanzen sind die Primärproduzenten von Biomasse und damit Grundlage allen Lebens. Sie werden nicht nur zur Gewinnung von Nahrungsmitteln, sondern zunehmend auch als Quelle erneuerbarer Energien kultiviert. Aufgrund der Begrenztheit der weltweit zu Verfügung stehenden Anbaufläche ist eine zielgerichtete Selektion und Verbesserung der verwendeten Sorten unabdingbar. Um solch eine kontinuierliche Verbesserung zu gewährleisten, ist ein grundlegendes Verständnis des biologischen Systems Pflanze nötig. Diese Arbeit hatte zum Ziel, den Primärmetabolismus der Modellpflanze A. thaliana mit Methoden der quantitativen Genetik zu untersuchen und in Beziehung zu Wachstum und Biomasse zu stellen. Insbesondere sollte Heterosis, die Abweichung von Hybriden in ihren Merkmalen vom Mittelwert der Eltern, auf Stoffwechselebene charakterisiert werden. Mit Hilfe der Gas Chromatographie/ Massen Spektrometrie (GC-MS) wurden über 2000 Proben von rekombinanten Inzucht Linien (RIL) und Introgressions Linien (IL) der Akzessionen Col 0 und C24 bezüglich des Vorkommens von 181 Metaboliten untersucht. Die beobachtete Varianz erlaubte die Bestimmung von 157 metabolischen QTL (mQTL), genetischen Regionen, die für die Metabolitkonzentrationen relevante Gene enthalten. Durch die Untersuchung von Testkreuzungen der RILs und ILs konnten weiterhin 385 heterotische metabolische QTL (hmQTL) identifiziert werden. Im Rahmen dieser Arbeit wurde eine robuste Methode zur Auswertung von GC-MS Analysen entwickelt. Es wurde eine hoch signifikante kanonische Korrelation (r=0.73) zwischen Biomasse und Metabolitprofilen gefunden. Die unterschiedlichen Ansätze zur QTL Analyse, RILs und ILs, wurden verglichen. Dabei konnte gezeigt werden, daß die Methoden komplementär sind, da mit RILs gefundene mQTL zu 56% und hmQTL zu 23% in ILs bestätigt wurden. Durch den Vergleich mit Datenbanken wurden für 67% der mQTL Kandidatengene identifiziert. Um diese zu überprüfen wurden acht dieser Gene resequenziert und insgesamt 23 Polymorphismen darin bestimmt. Die Heterosis in den Hybriden ist für die meisten Metabolite gering (<20%). Für hmQTL konnten weniger Kandidatengene als für mQTL bestimmt werden und sie zeigten eine geringere Übereinstimmung in den beiden Populationen. Dies deutet darauf hin, daß regulatorische Loci und epistatische Effekte einen wichtigen Beitrag zur Heterosis besteuern. Die gewonnenen Daten stellen eine reiche Quelle für die weitergehende Untersuchung und Annotation relevanter Gene dar und ebnen den Weg für ein besseres Verständnis des Systems Pflanze.

Nob1 (New Zealand obese 1) bezeichnet einen Adipositas-QTL auf Chr. 5 der Maus (LODBMI >3,3), der in einem Rückkreuzungsexperiment der Mausstämme NZO (adipös) und SJL (schlank) identifiziert wurde. Um Kandidatengene für Adipositas zu finden, wurden mehr als 300 Nob1-Transkripte mit Hilfe von Genexpressionsanalysen auf Unterschiede in stoffwechselrelevanten Geweben zwischen beiden Mausstämmen untersucht. Sieben Gene zeigten eine differentielle Expression: 2310045A20Rik, Tbc1d1, Ppp1cb, Mll5, Insig1, Abhd1 und Alox5ap. Die codierenden Bereiche dieser Gene wurden anschließend auf Sequenzunterschiede zwischen NZO und SJL untersucht. Nur im Gen Tbc1d1, das im Peak-Bereich des Nob1 lokalisiert ist, wurde eine SJL-spezifische Deletion von sieben Basen detektiert, die zu einer Leserasterverschiebung und einem vorzeitigen Abbruch des Proteins in der funktionellen Rab-GAP-Domäne führt (Loss-of-Function-Mutation). Interessanterweise wurde eine Variante von TBC1D1 (R125W) in Kopplungsanalysen mit Adipositas beim Menschen assoziiert (Stone et al., 2006). TBC1D1 zeigt eine hohe Homologie zu TBC1D4 (AS160), das im Insulinsignalweg eine wichtige Rolle spielt. In 17 weiteren Genen im Peak-Bereich des Nob1 wurde keine weitere SJL-spezifischen Mutation detektiert. Bei NZO-Tieren erfolgte die Tbc1d1-mRNA-Expression vorwiegend in glycolytischen Fasern des Skelettmuskels. Zudem wurden zwei gewebsspezifisch exprimierte Tbc1d1-Isoformen identifiziert, die sich durch alternatives Splicen der Exone 12 und 13 unterscheiden. Die im Rahmen dieser Arbeit gefundenen Ergebnisse machen Tbc1d1 zu einem plausiblen Kandidatengen für den Nob1-QTL. Welche Funktion Tbc1d1 im Glucose- und Fettstoffwechsel des Skelettmuskels hat, muss in weiteren Analysen untersucht werden. / Nob1 (New Zealand obese 1) has been identified as an obesity QTL on chromosome 5 (LODBMI >3,3) in a backcross experiment of obese NZO and lean SJL mice. To identify candidate genes for obesity expression profiling experiments with RNA from metabolic tissues were performed with more than 300 Nob1-genes. Seven genes showed differences in mRNA expression levels between both strains: 2310045A20Rik, Tbc1d1, Ppp1cb, Mll5, Insig1, Abhd1, and Alox5ap. Sequencing of the coding regions of these genes revealed a SJL-specific deletion of seven basepairs in the Tbc1d1 gene that is located in the peak region of Nob1. This mutation leads to a frameshift resulting in a truncated protein that lacks the important Rab-GAP-domain (Loss-of-Function-mutation). Interestingly, linkage analysis of the R125W-variant of TBC1D1 has been recently associated with human obesity. TBC1D1 shows high homology to TBC1D4 (AS160) that plays an important role in the insulin signaling pathway. No other SJL-specific mutations were detected in 17 further genes in the Nob1 peak region. In NZO mice Tbc1d1 mRNA is predominantly expressed in glycolytic fibres of skeletal muscle. Two isoformes were identified differing in alternative spliced exons 12 and 13 and showing a tissue specific mRNA expression. The results presented in this work make Tbc1d1 a very feasible candidate gene to be causal for Nob1. The function of Tbc1d1 in the metabolism of carbohydrates and fat has yet to be analyzed.

The growth and development of two sorghum drought tolerant genotypes BTx642 (post-flowering drought tolerant, “stay green”) and RTx7000 (pre-flowering drought tolerant) were characterized and compared. Differences in phenology and the growth and development of leaves and stalks were identified that could contribute to variation in shoot biomass, grain yield and response to water deficit. An F12 recombinant inbred line (RIL) population derived from the two parents was genotyped using the Illumina Genome Analyzer II platform and the information used to generate a genetic map useful for analysis of quantitative trait loci (QTL). Seventy-two different traits were measured in the RIL population at anthesis and at grain maturity. Plants were grown in well-watered environments in greenhouse conditions and in field conditions near College Station, TX in 2008-2010. QTL mapping was used to analyze the genetic basis of trait variation in the population and to detect associations between traits. A total of 477 QTL were identified that in combination modulate leaf size (length, width, and area), shoot biomass accumulation (shoot, stalk, stem, leaf, and leaf sheath), panicle weight, root size and architecture (length, surface area, and volume, number of tips, forks and nodal roots, and root biomass), stalk and stem length, and flowering time. Six flowering time QTL were identified and variation in time to anthesis affected the expression of several other traits including leaf size and biomass accumulation. However, QTL infrequently had an impact on traits associated with different organs. The specificity observed is consistent with independent genetic control of traits associated with leaves, stems and roots. Nine QTL that modulated shoot biomass accumulation were detected that were not affected by flowering time. Of these, four shoot biomass QTL co-localized with leaf size traits. Eight QTL for panicle biomass were detected with two coincident with QTL for upper leaf size. A QTL for leaf width at anthesis was found to co-localize with a stay green locus.

Domestication is the process by which animals become adapted to the environment provided by humans. The process of domestication has let to a number of correlated behavioural, morphological and physiological changes among many domesticated animal species. An example is the changes of plumage colour in the chicken. Plumage colour is one of the most readily observable traits that make distinction between breeds as well as between strains within a breed. Understanding the genetic architecture of pigmentation traits or indeed any trait is always a great challenge in evolutionary biology. The main aim of this study was to map quantitative trait loci (QTLs) affecting the red and metallic green coloration in the chicken plumage. In this study, a total of 572 F8 intercross chickens between Red Junglefowl and White Leghorn were used. Phenotypic measurements were done using a combination of digital photography and photography manipulating software. Moreover, all birds were genotyped with 657 molecular markers, covering 30 autosomes. The total map distance covered was 11228 cM and the average interval distance was 17 cM. In this analysis, a total of six QTLs (4 for red and 2 for metallic green colour) were detected on four different chromosomes: 2, 3 11 and 14. For red colour, the most significant QTL was detected on chromosome 2 at 165 cM. An additional QTL was also detected on the same chromosome at 540 cM. Two more QTLs were detected on chromosomes 11 and 14 at 24 and 203 cM respectively. Additionally, two epistatic pairs of QTLs were also detected. The identified four QTLs together can explain approximately 36% of the phenotypic variance in this trait. In addition, for metallic green colour, one significant and one suggestive QTLs were detected on chromosomes 2 and 3 at 399 and 247 cM respectively. Moreover, significant epistatic interactions between these two QTLs were detected. Furthermore, these two QTLs together can explain approximately 24% of the phenotypic variance in this trait. These findings suggest that the expression of pigmentation in the chicken plumage is highly influenced by both the epistatic actions and pleiotropic effects of different QTLs located on different chromosomes.

Made available in DSpace on 2015-03-26T13:32:14Z (GMT). No. of bitstreams: 1 texto completo.pdf: 1865501 bytes, checksum: 1ea217f4e435634fb653ba16ecac4ac4 (MD5) Previous issue date: 2012-02-24 / Many studies are focused on the search for QTL(quantitative trait loci) that affects growth traits in swine, and almost all studies have found QTL with significant effects. However, most of these studies use information related to the body weight on specific ages or average weight gain. Thus, it becomes interesting to evaluate all the growth information with the focus on longitudinal data simultaneously. This study aims to use random regression models (RRM) in order to detect QTL (quantitative trait loci) for growth traits in swine from a population F2 Piau x Commercial. To this end, it was considered a RRM with random polygenic effects, permanent environment and QTL, being the covariance matrix associated with the latter known as IBD (identical-by-descent). The presence of a significant QTL was found by likelihood ratio test considering the model described above as being the complete and this same without the QTL effect as null model. Comparisons between these models were made at the positions of the markers (6 microsatellite markers) and at positions between markers. In the position with greater evidence of QTL effect was calculated the heritability and the genetic polygenic and QTL values for body weight throughout the growth period studied. The results showed a significant effect of QTL at position 65 of chromosome 7. / Muitos estudos são voltados para a busca de QTL (locos de características quantitativas) que afetam características de crescimento em suínos, sendo que a quase totalidade tem encontrado QTL com efeitos significativos. No entanto, a maioria destes estudos utiliza informações referentes a peso corporal em idades específicas ou ganho de peso médio. Dessa forma, torna-se interessante avaliar simultaneamente todas as informações de crescimento sob o enfoque de dados longitudinais. O presente trabalho tem como objetivo utilizar modelos de regressão aleatória (MRA) com o intuito de detectar QTL para características de crescimento em suínos de uma população F2 Piau x Comercial. Para tanto, considerou-se MRAs com efeitos aleatórios poligênico, de ambiente permanente e de QTL, sendo a matriz de covariância associada a este último denominada de IBD (identical-by-descent). A presença de um QTL com efeito significativo foi verificada mediante teste de razão de verossimilhanças considerando o modelo descrito como sendo o completo e o mesmo sem o efeito de QTL como sendo o modelo nulo. As comparações entre estes modelos foram realizadas nas posições dos marcadores (6 marcadores microssatélites) e nas posições entre marcadores. Na posição com maior evidência de efeito de QTL foi calculada a herdabilidade e os valores genéMany studies are focused on the search for QTL(quantitative trait loci) that affects growth traits in swine, and almost all studies have found QTL with significant effects. However, most of these studies use information related to the body weight on specific ages or average weight gain. Thus, it becomes interesting to evaluate all the growth information with the focus on longitudinal data simultaneously. This study aims to use random regression models (RRM) in order to detect QTL (quantitative trait loci) for growth traits in swine from a population F2 Piau x Commercial. To this end, it was considered a RRM with random polygenic effects, permanent environment and QTL, being the covariance matrix associated with the latter known as IBD (identical-by-descent). The presence of a significant QTL was found by likelihood ratio test considering the model described above as being the complete and this same without the QTL effect as null model. Comparisons between these models were made at the positions of the markers (6 microsatellite markers) and at positions between markers. In the position with greater evidence of QTL effect was calculated the heritability and the genetic polygenic and QTL values for body weight throughout the growth period studied. The results showed a significant effect of QTL at position 65 of chromosome 7.ticos poligênicos e de QTL para peso em todo o período de crescimento estudado. Os resultados mostraram um efeito significativo de QTL na posição 65 do cromossomo 7.

A l’échelle du globe, la diminution des ressources en eau est devenue un des principaux facteurs limitants pour les productions agricoles. Jusqu’à présent, les approches génomiques à haut débit conduites chez les espèces modèles ont permis d’identifier des centaines de gènes potentiellement impliqués dans la survie des plantes en conditions de sécheresse,mais très peu ont des effets bénéfiques sur la qualité et le rendement des cultures.Néanmoins, l’application d’un déficit hydrique bien contrôlé peut permettre d’améliorer la qualité des fruits charnus par dilution et/ou accumulation de composés gustatifs majeurs.Dans ce contexte, la première partie du travail de thèse avait pour but de déchiffrer les déterminants génétiques de la réponse au déficit hydrique chez la tomate en explorant les interactions ‘génotype x niveau d’irrigation’ (G x I) et ‘QTL x niveau d’irrigation’ (QTL x I) dans deux populations. La première population consistait en un ensemble de lignées recombinantes (RIL) issues du croisement entre deux accessions cultivées, tandis que la seconde était composée de diverses accessions à petits fruits principalement originaires d'Amérique du Sud. Les plantes ont été phénotypées pour un ensemble de caractères agronomiques (vigueur des plantes et qualité des fruits) et génotypées pour des milliers de SNP. Les données ont été analysées en utilisant les méthodologies de la cartographie de liaison et d'association, permettant l'identification de QTL et gènes candidats putatifs pour la réponse de la tomate au déficit hydrique. La deuxième partie du travail de thèse avait pour objectif d'explorer la régulation des gènes dans les fruits et les feuilles de tomates en condition de déficit hydrique. Dans ce but, des données de séquençage du transcriptome ont été recueillies sur les deux génotypes parentaux de la population RIL et leur hybride F1. Les données ont été analysées pour identifier les gènes et les allèles exprimés de manière différentielle. Puis, l'expression de 200 gènes a été mesurée dans les fruits et les feuilles de l’ensemble des lignées de la population RIL par qPCR micro-fluidique à haut débit. Des eQTL et des interactions ‘eQTL x niveau d’irrigation’ ont été identifiés pour ces gènes par cartographie de liaison. Les colocalisations entre les QTL phénotypiques et les QTL d’expression ont été analysées. Les connaissances produites au cours de cette thèse contribuent à une meilleure compréhension des interactions des plantes de tomate avec leur environnement et fournissent des bases pour l'amélioration de la qualité des fruits en conditions d’irrigation limitée. / Water scarcity will constitute a crucial constraint for agricultural productivity in a nearfuture. High throughput approaches in model species have identified hundreds of genespotentially involved in survival under drought conditions, but very few having beneficialeffects on quality and yield in crops plants. Nonetheless, controlled water deficits mayimprove fleshy fruit quality through weaker dilution and/or accumulation of nutritionalcompounds. In this context, the first part of the PhD was aimed at deciphering the geneticdeterminants of the phenotypic response to water deficit in tomato by exploring thegenotype by watering regime (G x W) and QTL by watering regime (QTL x W) interactions intwo populations. The first population consisted in recombinant inbreed lines (RIL) from across between two cultivated accessions and the second was composed of diverse small fruittomato accessions mostly native from South America. Plants were phenotyped for majorplant and fruit quality traits and genotyped for thousands of SNP. Data were analyzed withinthe linkage and association mapping frameworks allowing the identification of QTLs andputative candidate genes for response to water deficit in tomato. The second part of the PhDhad the objective to explore gene regulation in green fruit and leaves of tomato plantsstressed by water deficit. For this purpose, RNA-Seq data were collected on the two parentalgenotypes of the RIL population and their F1 hybrid. Data were analyzed to identifydifferentially expressed genes and allele specific expression (ASE). Then, the expression of200 genes was measured in leaves and fruits of the whole RIL population by high throughputmicrofluidic qPCR. eQTLs and eQTL by watering regime interactions were mapped for thosegenes using linkage mapping. Colocalisations with the phenotypic QTLs were analyzed. Theknowledge produced during this PhD will contribute to a better understanding of the tomatoplant interaction with their environment and provide bases for improvement of fruit qualityunder limited water supply.

Muitas são as características quantitativas que são, significativamente, influenciadas por fatores genéticos, em geral, existem vários genes que colaboram para a variação de uma ou mais características quantitativas. As informações ausentes a respeito dos genótipos nos marcadores moleculares é um problema comum em estudo de mapeamento genético e, por conseguinte, no mapeamento dos locus que controlam estas características fenotípicas (QTL). Os dados que não foram observados ocorrem, principalmente, devido a erros de genotipagem e de marcadores não informativos. Para solucionar este problema foi utilizado o método do modelo oculto de Markov para inferir estes dados. Os métodos de acurácias evidenciaram o sucesso da aplicação desta técnica de imputa- ção. Uma vez imputado, na inferência bayesiana estes dados não serão mais tratados como uma variável aleatória resultando assim, numa redução no espaço paramétrico do modelo. Outra grande dificuldade no mapeamento de QTL se deve ao fato de que não se conhece ao certo a quantidade destes que influenciam uma dada característica, fazendo com que surjam diversos problemas, um deles é a dimensão do espaço paramétrico e, consequentemente, a obtenção da amostra a posteriori. Assim, com o objetivo de contornar este problema foi proposta a utilização do método Monte Carlo via cadeia de Markov com Saltos Reversíveis, uma vez que este permite flutuar, entre cada iteração, modelos com diferentes quantidades de parâmetros. A utilização da abordagem bayesiana permitiu detectar cinco QTL para a característica estudada. Todas as análises foram implementadas no programa estatístico R. / There are many quantitative characteristics which are significantly influenced by genetic factors, in general, there are several genes that contribute to the variation of one or more quantitative trait. The missing information about the genotypes in molecular markers is a common problem in studying genetic mapping and therefore the mapping of loci that control these phenotypic traits (QTL). The data were not observed occur mainly due to errors in genotyping and uninformative markers. To solve this problem the method of occult Markov model to infer this information was used. Techniques accuracies demonstrated the successful application of this technique of imputation. Once allocated, in the Bayesian inference this data will no longer be treated as a random variable thus resulting in a reduction in the parameter space of the model. Another great difficulty in mapping QTL is due to the fact that no one knows exactly the amount of these which influence a given characteristic, so that several problems arise, one of them is dimension of the parameter space and, consequently, obtaining the sample a posterior. Thus, in order to solve this problem using the method via Monte Carlo Markov chain Reversible Jump was proposed, since this allows fluctuate between each iteration, models with different numbers of parameters. The use of the Bayesian approach allowed five QTL detected for the studied trait. All analyzes were implemented in the statistical software R.

Made available in DSpace on 2015-03-26T13:42:05Z (GMT). No. of bitstreams: 1 texto completo.pdf: 294516 bytes, checksum: 2ec13b3c525f57f69aa1f3dad7a90997 (MD5) Previous issue date: 2008-07-28 / Conselho Nacional de Desenvolvimento Científico e Tecnológico / QTL are statistical associations of a genomic region and the phenotypic variation between segregating populations. The variation in a quantitative trait of interest can be related with the genotype of a molecular marker if this marker is close and linked to quantitative trait loci (QTL). To identify these associations, the mapping of chromosomes 9 and 10 was conducted in a F2 population composed of 714 animals derived from Piau X Commercial (Large White Landrace X Pietrain) crosses. The population was evaluated by performance, carcass, internal organs, viscera, carcass cuts and meat quality traits. Six microsatellites loci on chromosome 9 and three microsatellites loci on chromosome 10 were studied. The loci were analyzed for genic frequency, observed heterogosity, expected heterozigosity and polymorphic information content. Linkages maps were also constructed through the CRIMAP 2.4 program for the informative markers. The orders of all microsatellite loci were in accordance with the published USDA-MARC map. However, sex average maps of chromosomes 9 and 10 were, respectively, 27.75% and 124.60% longer than the published USDA-MARC. Association analyses were performed using interval mapping by regression for QTL detection. Three significant QTL to chromosomal levels were detected on chromosome 9 for total (bone-in) loin weight (P<0.01), boneless loin weight (P<0.05) and small intestine length (P<0.05), responding, respectively, by 6.7%, 4.0% and 4.9% of phenotypic variance. Two significant QTL to chromosomal levels have been detected on chromosome 10 for higher backfat thickness on the shoulder region (P<0.05) and redness (P<0.05), both responding by 2.4% of phenotypic variance and one significant QTL to genomic level for liver weight (P<0.01) responding by 6.9% of phenotypic variance. The generated information of significant QTL will be useful for future studies dealing with fine mapping and identification of genes that could provide a better understanding of physiology and production traits of pigs. / QTL são associações estatísticas entre dados relativos a uma região genômica e a variabilidade fenotípica existente entre populações segregantes. Para identificação e avaliação dos efeitos de tais associações, foi feito o mapeamento dos cromossomos 9 e 10 de suínos pertencentes a uma população F2, oriunda do cruzamento entre as raças Piau e Comercial (Landrace X Large White X Pietrain), composta por 714 animais. A população foi avaliada em relação a características de desempenho, carcaça, órgãos e vísceras, cortes de carcaça e qualidade da carne. Foram estudados um total de 9 locos microssatélites distribuídos nos cromossomos, sendo seis localizados no cromossomo 9 e três no cromossomo 10. Os locos foram avaliados em relação à freqüência alélica, heterozigosidade observada, heterozigosidade esperada e conteúdo de informação polimórfica, sendo que aqueles considerados informativos foram utilizados na construção dos mapas de ligação, a partir do programa CRIMAP versão 2.4. A ordem dos marcadores no presente mapa foi semelhante àquela apresentada pelo mapa do USDA-MARC. No entanto, os mapas médios entre sexos dos cromossomos 9 e 10 obtidos no presente estudo possuem comprimentos superiores, respectivamente, 27,75% e 124,60% em relação aos mapas do USDA-MARC. As análises de associação foram feitas utilizando mapeamento de intervalo por regressão para detecção de QTL, com o auxílio do programa QTL EXPRESS. Foram detectados três QTL significativos ao nível cromossômico no cromossomo 9 para peso total do carré (P<0,01), peso do lombo (P<0,05) e comprimento total do intestino delgado (P<0,05), respondendo, respectivamente, por 6,7%, 4,0% e 4,9% da variação fenotípica. No cromossomo 10, foram detectados dois QTL significativos ao nível cromossômico para maior espessura de toucinho na região da copa, na linha dorso-lombar (P<0,05) e índice de vermelho (P<0,05), ambos respondendo por 2,4% da variação fenotípica, e um QTL significativo ao nível genômico para peso de fígado (P<0,01), respondendo por 6,9% da variação fenotípica. As informações dos QTL significativos encontrados servem para estudos futuros como o mapeamento fino e a identificação de genes que ajudem no melhor entendimento da fisiologia e das características de produção de suínos.

Made available in DSpace on 2015-03-26T13:42:06Z (GMT). No. of bitstreams: 1 texto completo.pdf: 856973 bytes, checksum: 67a532cc638045d0929e3d65118e3c24 (MD5) Previous issue date: 2008-07-18 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The occurrence of the rust caused by Puccinia Psidii can represent a limiting factor for the eucalypt plantations. Planting of resistant genotypes is the most advisable control measure against the disease. This way, the study and the detection of genes that are responsible for the rust resistance, aiming the selection of resistant genotypes, became desirable. This study has the purpose of detect and the map locus responsible to the rust resistance caused by Puccinia Psidii in an interspecific cross of Eucalyptus sp., by using molecular microsatellites markers. Phenotypic information was evaluated from 115 individuals derived progeny resulting from the crossing of a feminine resistant genitor E. urophylla and a masculine hybrid genitor between E. urophylla and E. grandis, as well genotypic information about 22 microsatellites markers. QTL detection was accomplished by using ANOVA, original and modified (weighted by marker informativity) Haseman & Elston regression and Fulker & Cardon regression. Single markers methodologies detected significant association for markers EMBRA 125 and EMBRA 321, both of the linkage group three. The Haseman & Elston regression showed the values of pF = 20,6515 and H2 = 14,73% for the EMBRA 125 marker pF = 70,1694 and H2 = 40,58 for the EMBRA 321 marker. Additionally, the Fulker and Cardon regression allowed the detection of the with QTL with pF = 29,4788 and H2 = 17,58%. The QTL locus was positioned 0,01cM from EMBRA 125. The EMBRA 321 marker could not be evaluated by mean the interval methodology. The application of the markers EMBRA 125 and EMBRA 321 in procedures of assisted selection is putative and it should be investigated. / A ocorrência da ferrugem causada pelo fungo Puccinia Psidii pode representar um fator limitante para as plantações de eucalipto. O plantio de genótipos resistentes a esse fungo é a medida mais adequada de controle dessa doença. Neste sentido, o estudo e a detecção de genes responsáveis pela resistência a este patógeno, permitindo a seleção precoce de genótipos resistente, é desejável. Desta forma, este trabalho objetiva a detecção e o mapeamento de locos de resistência ao patógeno Puccinia Psidii em um cruzamento interespecífico de Eucalyptus sp. por meio de marcadores moleculares microssatélites. Foi utilizada a informação fenotípica da progênie de 117 indivíduos resultante do cruzamento de um genitor feminino E. grandis resistente ao patógeno e um genitor masculino híbrido entre E. urophylla e E. grandis susceptível e a informação genotípica de 22 marcadores microssatélites. A detecção de QTL controlador da característica foi realizada por meio da metodologia da ANOVA, regressão de Haseman & Elston, original e modificada, ponderada pela informatividade do marcador, e regressão de Fulker & Cardon. As análises de marca simples detectaram associação significativa para os marcadores EMBRA 125 e EMBRA 321, ambos do grupo de ligação três do Eucalyptus. A regressão de Haseman e Elston apresentou valores de pF = 20,6515 e H2 = 14,73% para o marcador EMBRA 125 e pF = 70,1694 e H2 = 40,58 para o marcador EMBRA 321. Adicionalmente, a metodologia de Fulker e Cardon permitiu a detecção do QTL, com valor de pF de 29,4788 e H2 de 17,58%. O loco QTL foi posicionado a 0,01cM do marcador EMBRA 125. O marcador EMBRA 321 não pôde ser avaliado por meio da metodologia de intervalo. A aplicação dos marcadores EMBRA 125 e EMBRA 321 em procedimentos de seleção assistida é putativa e deve ser investigada.