Submitted by Gabriela Lopes (gmachadolopesufpel@gmail.com) on 2017-02-08T14:02:33Z No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) TESE_CarlosBusanello.pdf: 2235732 bytes, checksum: e2445dbcb147a88becd9a9bd9fe1e349 (MD5) / Approved for entry into archive by Aline Batista (alinehb.ufpel@gmail.com) on 2017-02-13T12:05:47Z (GMT) No. of bitstreams: 2 TESE_CarlosBusanello.pdf: 2235732 bytes, checksum: e2445dbcb147a88becd9a9bd9fe1e349 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2017-02-13T12:05:47Z (GMT). No. of bitstreams: 2 TESE_CarlosBusanello.pdf: 2235732 bytes, checksum: e2445dbcb147a88becd9a9bd9fe1e349 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2016-09-06 / Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul - FAPERGS / O conhecimento da capacidade geral de combinação-CGC e capacidade específica de combinação-CEC são fundamentais para conhecer as melhores combinações em um grupo de linhagens elite de milho para um programa de melhoramento. Para identificar estas relações foi utilizado um grupo de 10 linhagens cruzadas entre si em um delineamento dialélico incluindo os recíprocos, totalizando 90 híbridos. Estes híbridos foram testados em três ambientes, Pato Branco-PR, Campos Novos-SC e Frederico Westphalen-RS representando a região Sul do Brasil na safra agrícola 2012/2013. Os efeitos aditivos foram mais importantes que os efeitos não aditivos para a variação dos híbridos. O genitor 6 foi o que apresentou a maior estimativa do efeito da CGC, com alelos favoráveis ao incremento de peso de espiga e peso de grão. Para estas mesmas características, levando em consideração a CEC, a hibridação envolvendo os genitores 1x2 promoveu aumento no ambiente 1, e a hibridação envolvendo os genitores 4x8 promoveu redução considerável destas características. A ação do ambiente interferiu na expressão da maioria dos caracteres, indicando a necessidade de conhecer os fatores genéticos e ambientais na composição de novos híbridos de milho. Para mapeamento de QTLs foi utilizado 73 linhas de introgressão provenientes do cruzamento entre B73 e Gaspé Flint seguido de retrocruzamento, esta população foi avaliada em duas condições hídricas de campo principalmente para arquitetura do sistema radicular, bem como, caracteres morfológicos e componentes do rendimento em Ravenna, Itália. Com a genotipagem das linhas pôde-se confeccionar um mapa no qual representa 80% do genoma do Gaspé Flint introgredido em B73 contendo 329 bins independentes. A utilização do software REST para quantificar as variáveis do sistema radicular em raízes de milho em condições de campo foi eficaz, rápida e precisa. A análise de QTLs indica 35 possíveis regiões principalmente nos cromossomos 1, 2 e 4 para as características de raiz, levando em consideração todas as 31 características, foram encontrados 132 possíveis QTLs distribuídos por todos os cromossomos. Para a condição de estresse hídrico observa- se que raízes que apresentam ângulo aberto, grandes áreas e peso seco sendo superficiais, reduzem o rendimento de grãos. / The understanding about general-GCA and specific-SCC combining ability are key to identify the best combinations in an elite lineage group of a maize breeding program. In order to identify these relationships, a group comprising 10 lineages crossed with each other in a diallel design, including the reciprocal crosses, totalling 90 hybrids, were used. The hybrids were tested in three different environments, Pato Branco-PR, Campos Novos-SC and Frederico Westphalen-RS, representing the Southern Region of Brazil in the agricultural harvest of 2012/2013. For hybrid variance, additive were more important than non-additive effects. Parent 6 showed the highest estimated effect of GCA, with favorable alleles for increments of ear and grain weight. For these same traits, taking into account the SCC, the hybridization involving 1x2 parents promotes an increase in the environment 1. On the other hand, the hybridization involving 4x8 parents promotes a pronounced reduction of these traits. The expression of most traits analyzed were affected by environmental action and it indicates that the understanding of genetic and environmental factors is necessary for the development of new maize hybrids. For QTL mapping, 73 introgressed lines from the crossing between B73 and Gaspé Flint followed by backcross were used and evaluated under two field water regimes. The major traits analyzed were root architecture, plant morphological traits and yield components. Based in the genotyping analysis of the lines, it was possible to obtain a map in which 80% of the Gaspé Flint genome is introgressed in B73 comprising 329 independent bins. The software REST was employed to quantify the variables of the maize root system under field conditions and it was effective, fast and accurate. The QTL analyses indicate 25 probable regions mainly in the chromossomes 1, 2 and 4 for the root traits. Taking into account all of the 31 traits, 90 probable QTLs, distributed in all chromossomes, were found. For watering stress condition, it was possible to observe that roots with open angle, bigger area and dry mass, as well as superficial, reduces grain yield.

Orientador: Sergio Marangoni / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-04T06:47:38Z (GMT). No. of bitstreams: 1 Silva_AdrianaMoreiradaSilvae_D.pdf: 6318592 bytes, checksum: 2d42ae741dfb799cf38492581dbb5324 (MD5) Previous issue date: 2005 / Resumo: As plantas são capazes de responder e resistir ao ataque de patógenos ativando uma diversidade de estratégias de defesa. A maioria delas exibe uma estratégia geral onde são ativadas respostas bioquímicas de maneira coordenada, incluindo a reprogramação do metabolismo celular, o reforço das barreiras celulares e produção de compostos antimicrobianos e proteínas que agem diretamente sobre o patógeno. Mas existem também respostas específicas das plantas a determinados patógenos, onde são ativadas vias de defesa específicas.Apesar da crescente quantidade de dados em literatura descrevendo genes envolvidos na patogênese vegetal, pouco se sabe sobre as modificações ao nível de proteoma associadas com estas interações. Neste trabalho é apresentado um estudo proteômico comparativo de plantas de milho, de dois genótipos contrastantes em relação à resistência ao fungo Puccinia polysora, em que foram caracterizadas as diferenças no perfil de expressão de proteínas em sementes dos dois genótipos. Através de uma ampla caracterização dos perfis de proteína por diferentes métodos eletroforéticos, foram reveladas 12 proteínas diferencialmente expressas no genótipo de maior resistência. Destas, 5 foram identificadas por espectrometria de massas por MALDI-TOF, sendo 3 delas identificadas como proteínas com atividade de defesa: uma lipoxigenase de 96 kDa, uma proteína Vicilin-like de 66 kDa e uma proteína Heat-Shockde 70 kDa. No segundo capítulo da tese, apresentamos um estudo complementar de mapeamento de QTLs em plantas de milho para a identificação dos genes reguladores da síntese de DIMBOA, um composto secundário que atua na defesa de plantas contra fungos e insetos. Neste estudo foi construído um mapa genético de ligação de uma população F2 resultante do cruzamento de uma linhagem com alta produção de DIMBOA e outra linhagem de baixa produção deste composto. O mapa, com um tamanho total de 1432,9 centimorgans, foi construído com 123 marcadores SSR. Com este mapa foi possível identificar quatro QTLs potencialmente relacionadas com a regulação da via de síntese de DIMBOA, sendo uma no cromossomo 1 (bin 1.08), duas no cromossomo 6 (bin 6.01 e bin 6.02) e uma no cromossomo 10 (bin 10.05) / Abstract: Plants have the ability to respond to invasion by pathogens through activation of a variety of defense strategies. Most plants exhibit a general defense strategy in which a wide range of biochemical responses are induced in a coordinated manner, including reprogramming of cellular metabolism, accumulation of barrier-forming substances and production of antimicrobial compounds and proteins that act directly to prevent pathogen invasion. Some plants show also specific pathogen responses, in a different strategy pathway. Although there is an increasing amount of literature dealing with genes involved in bacterial and fungal pathogenesis, very few reports have addressed proteome modifications associated with such interactions. In the present work we show a comparative proteomic analysis of maize plants, resistant and susceptible genotypes to Puccinia polysora fungi infection and the characterization of differences in protein expression profiles of seeds. Protein profiles of both genotypes were analyzed by a broad range of electrophoresis methods and we could identify 12 proteins differentially expressed in resistant genotype. Five of them were identified by MALDI-TOF mass spectrometry and 3 of them were identified as defense related proteins, a 96 kDa lipoxygenase, 66 kDa Vicilin-like protein and 70 kDa Heat-Shock protein. We also present a complementary study of QTL mapping for identification of regulatory genes controlling DIMBOA synthesis in maize. In this study is shown a linkage map of a F2 population resultant from crossing between two maize lines presenting high DIMBOA production and low DIMBOA production. This map presents 1432,9 centimorgans and was constructed using 123 SSR markers. Using this map we could identify four QTLs possibly related with DIMBOA production, one QTL on bin 1.08 of chromossome 1, two QTLs on bins 6.01 and 6.02 on chromossome 6, and one last QTL on bin 10.05 on chromossome 10 / Doutorado / Bioquimica / Doutor em Biologia Funcional e Molecular

Over the last ten years, genome-wide association studies (GWAS) have been used to identify genetic variants associated with many diseases as well as quantitative phenotypes, by exploiting naturally occurring genetic variation in large cohorts of individuals. More recently, the GWAS approach has also been applied to highthroughput RNA sequencing (RNA-seq) data in order to find loci associated with different levels of gene expression, called expression quantitative trait loci (eQTL). Because of the large amount of data that is required for such high-resolution eQTL studies, most of them have so far been carried out in humans, where the cost of data collection could be justified by a possible future impact in human health. However, due to the rapidly falling price of high-throughput sequencing it is now also becoming feasible to perform high-resolution eQTL studies in higher model organisms. This enables the study of gene regulation in biological contexts that have so far been beyond our reach for practical or ethical reasons, such as early embryonic development. Taking advantage of these new possibilities, we performed a high-resolution eQTL study on 80 inbred fruit fly lines from the Drosophila Genetic Reference Panel, which represent naturally occurring genetic variation in a wild population of Drosophila melanogaster. Using a 3′ Tag RNA-sequencing protocol we were able to estimate the level of expression both of genes as well as of different 3′ isoforms of the same gene. We estimated these expression levels for each line at three different stages of embryonic development, allowing us to not only improve our understanding of D. melanogaster gene regulation in general, but also investigate how gene regulation changes during development. In this thesis, I describe the processing of 3′ Tag-Seq data into both 3′ isoform expression levels and overall gene expression levels. Using these expression levels I call proximal eQTLs both common and specific to a single developmental stage with a multivariate linear mixed model approach while accounting for various confounding factors. I then investigate the properties of these eQTLs, such as their location or the gene categories enriched or depleted in eQTLs. Finally, I extend the proximal eQTL calling approach to distal variants to find gene regulatory mechanisms acting in trans. Taken together, this thesis describes the design, challenges and results of performing a multivariate eQTL study in a higher model organism and provides new insights into gene regulation in D. melanogaster during embryonic development.

A partir de uma linha macho de corte e outra de postura, foi desenvolvida uma população experimental F2 com objetivo de mapear locos de características quantitativas (QTLs) para características de interesse comercial. Foi gerado um total de 2.063 animais F2 em 17 incubações que foram criados como frangos de corte até a 6ª semana de idade, quando foram avaliadas seis características de desempenho. As famílias utilizadas para o estudo, foram as que obtiveram maior número de marcadores microssatélites informativos em trabalhos anteriores envolvendo os cromossomos 1 a 5 com a mesma população. Vinte marcadores dos cromossomos 19, 23, 24, 26, 27 e 28 foram testados nos indivíduos parentais e F1 das famílias escolhidas para checar se eram ou não informativos. Após a genotipagem das 5 famílias escolhidas, foram construídos os mapas de ligação e realizada a análise de mapeamento de QTL por intervalo para cada cromossomo utilizando o método de regressão e o modelo genético F2. Dois modelos foram testados: um incluindo apenas o efeito aditivo do QTL e outro modelo que incluiu também o efeito de dominância. Caso fosse identificado QTL com nível de significância no mínimo sugestivo no genoma, os modelos foram confrontados para confirmar o efeito de dominância do QTL. Foram conduzidas também análises complementares com o intuito de detectar interação do QTL x sexo e QTL x família. Foram estimados a porcentagem da variância fenotípica e o intervalo de confiança para cada QTL. No cromossomo 26 foi mapeado QTL significativo a 5% no cromossomo para ganho de peso dos 35 aos 41 dias, e no cromossomo 27 foi identificado, para a característica peso vivo aos 35 dias um QTL sugestivo no genoma. Os QTL localizados nos cromossomo 26 e 27 foram localizados a 0.0 e 103.0 cM e explicaram 1,95 e 2,03% da variação fenotípica, respectivamente. / With the objective of mapping quantitative trait loci (QTLs) for economically valuable characteristics, an F2 chicken population was developed by crossing a broiler sire line and a layer dam line. A total of 2.063 F2 chickens from 17 incubations were reared as broilers and slaughtered at 6 week of age, when six performance traits were measured. Five families were chosen for this study based on previous work to determine the most informative families. Twenty markers from chromosomes 19, 23, 24, 26, 27 and 28 were tested in the parental and F1 chickens from the chosen families to select the informative markers. After genotyping parental, F1 and F2 chickens, the linkage maps were constructed and QTL Interval mapping analysis was conducted for each chromosome using regression methods and the F2 genetic model. Two different models were tested: one including only the additive effect of the QTL and another model that also included the dominance effect. If at least a genome-wide suggestive QTL was detected, they were compared through standard F tests to confirm the dominance effect of the QTL. Complementary analyses were conducted to investigate the existence of QTL x sex and QTL x family interactions. The percentage of the phenotypic variance explained by the QTL and the confidence intervals were estimated for each QTL. A 5% chromosome-wide significant QTL for weight gain from 35 to 41 d was mapped to chromosome 26 and a QTL that exceeded the genome-wide suggestive threshold for body weight at 35 d was mapped to chromosome 27. This QTL positioned at 103 cM explained 2.03% of the phenotypic variance of the trait and presented a confidence interval from 0 to 111 cM.

Genetic influence of Trypanosoma brucei brucei infection in mice The African trypanosomes are zoonotic parasites transmitted by Tse-Tse flies. Two of the three subspecies, Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense, cause sleeping sickness in humans whereas the third subspecies, Trypanosoma brucei brucei is not infective to humans. These parasites are members of Kinetoplastida. Trypanosomes are extracellular parasite witch have complex life cycles involving both insect and mammalian hosts. African trypanosomes after infection penetrate mainly vascularized organs and get into brain where cause serious pathology. Parasite can manipulate with immune system of mammal host in wide spectrum of interactions witch are not clearly understood so far. Discovering of a new immune mechanisms, whitch participite in reaction on african trypanosomes, can reveal some general characteristics of immune system. The results of these studies can help to prepare effective drugs and vaccines against this disease. The best way to observe pathological manifestation and genetical analysis is study on animal models . Study on suitable animal model to find genes which are responsible for control of immune response to T. brucei can help us to find homologous genes in humans. It was found that immune responces to...

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L’étude des rendements en blé a mis en évidence une stagnation apparue dans les années 1990, notamment en France, et principalement lié aux stress hydrique et thermique. Dans ce contexte, améliorer la tolérance du blé européen à ces stress est de première importance. Cette étude avait pour but d’étudier le déterminisme génétique de la tolérance à ces stress chez le blé. Pour ce faire, trois populations de blé tendre du CIMMYT combinant des caractères d’adaptation à ces stress ont été cultivées en conditions irriguée, sèche et stress thermique irriguée plusieurs années. Des caractères physiologiques et agronomiques ont été mesurés sur un réseau de 15 essais. Une méthodologie de caractérisation environnementale a été développée et a permis l’identification de six scenarii de stress au sein du réseau. Une covariable environnementale représentative de chacun a été extraite. L’utilisation des modèles de régression factorielles a permis la décomposition de l’interaction génotype x environnement ainsi que la mise en évidence d’une sensibilité différentielle au stress dans le germplasm. Une recherche de QTL multi-environnementale a conduit à la détection de régions génomiques contrôlant les caractères physiologiques et agronomiques ainsi que leurs interactions avec l’environnement. De la caractérisation environnementale à la détection de QTL, cette étude a abouti au développement d’un outil pour les sélectionneurs permettant l’évaluation du potentiel des génotypes face à une gamme d’environnement, mais aussi à l’identification de régions génomiques impliquées dans le contrôle de la tolérance aux stress hydrique et thermique chez le blé tendre. Ceci pourrait améliorer la tolérance à ces stress au sein du germplasm européen. / A stagnation of wheat yield was reported in France and other countries worldwide since the 1990’s, which incriminated mainly drought and heat stress. Improving the European wheat tolerance to them is of first importance. This study aimed to investigate the genetic determinism of the tolerance to such stresses. Three CIMMYT bread wheat populations combining complementary heat and drought adaptive habits were grown in Northern Mexico under irrigated, drought and heat-irrigated treatments from 2011 to 2013. The trial network comprised 15 trials and both physiological and agronomic traits were scored. First, an environmental characterization methodology was developed and resulted in the identification of six main environmental scenarios in the network. A representative environmental covariate was extracted from each of them. Then, a factorial regression model leaded to the dissection of the genotype-by-environment interaction and highlighted differential stress sensitivity of the germplasm. Finally, a multi-environmental QTL detection resulted in the discovery of genomic regions involved in the control of both physiological and agronomic traits and the study of their sensitivity to the environment. From the environmental characterization to the QTL detection, this study resulted in the development of a tool for breeders which may enable the evaluation of the potential of any genotypes in front of a range of environment, but also the identification of genomic regions involved in the control of the tolerance to drought and heat stress in bread wheat. This may help in improving the tolerance of the European bread wheat germplasm to drought and heat stress.