The influence of genotype variation on phenotype has been a longstanding question in biology but it is now one of the greatest challenges of the post-genomics era. Discovering the link between common gene variants that affect phenotypes within and between populations is likely to provide insight into the molecular physiology of phenotypic traits and the mechanisms by which they evolve. The overall goal of this thesis is to link naturally occurring genotypic variation with the organism??s phenotype. The specific goal of this thesis is to connect natural variation in the mitochondrial genotype with the organismal phenotype using the model organism Drosophila simulans. Mitochondria are intracellular organelles found in most eukaryotes and produce over 90% of the energy needed by cells. Determining the connection of mitochondrial genotype to whole organism phenotype is of particular interest because of the broad use of mitochondrial (mt) DNA as a molecular marker in evolutionary biology and population genetics, the organelle??s central role in cellular energy production, the potential for the mitochondria to influence organismal distribution particularly in the face of climate change and in human degenerative disease. I use the model organism D. simulans because it has high genetic variability, can be easily sampled from the wild and manipulated in the lab, and the energy producing reactions that take place in its mitochondria are highly conserved among metazoa. I studied naturally occurring mutations to understand the influence of these changes in natural populations. The four studies in this thesis have employed a Genotype-Biochemistry-Phenotype (GBP) model to link naturally occurring variation in the mitochondrial genotype with organism phenotype in D. simulans mitochondria. Three major conclusions can be drawn from the thesis that follow the genotype to biochemistry to phenotype model. Firstly, a subset of the mutations in genes that comprise the mitochondrial genotype is functionally significant. Secondly, the biochemical efficiency of OXPHOS is regulated by mitochondrial homeostasis. Thirdly, key organismal life history traits influenced by the mitochondrial genotype and this is mediated through the biochemistry of OXPHOS.

In the current study, behavioral responses of several species of calanoid copepods to mimics of oceanographic structure were observed and evaluated in the context of foraging and aggregation. Zooplankton distributions in oceanic habitats are often attributed to physical forcing; however, physical factors only act to drive ecological patterns at large scales (m to km). At fine to intermediate scales (cm to m) zooplankton behavior is believed to govern observed distributions, but the mechanisms and ecological significance of these behaviors are not well understood. In a water column, biological activity is often concentrated into one or a few regions, called thin layers, on the order of a meter thick, and zooplankton, such as copepods, must be able to reliably locate and exploit these patches for survival. Thin layers commonly are associated with oceanic structure such as flow gradients, fluid density jumps, or chemical composition gradients. Utilization of mechanosensory or chemosensory cues associated with thin layers may increase foraging success, thus translating into a significant ecological advantage. A laboratory apparatus was developed to create isolated and combined thin layer properties. Copepods then were exposed to laboratory mimics of thin layers. All of the tested species of copepods exhibited behavioral responses associated with area-restricted search behavior to one of the physical gradients (flow velocity or fluid density), but not both. Similar responses were observed for chemical exudate layer experiments and included increased proportional residence times, swimming speeds, and turn frequency. Food layers induced feeding responses from all tested species (increased proportional residence time, decreased swimming speed). Responses to various combinations of gradients were not fully synergistic, but suggested that some copepods employ a cue hierarchy to locate food-rich areas. Velocity or density gradients acted as initial cues for narrowing search regions, while chemical exudates induced responses that strengthened or removed the initial reactions. A simple foraging model was used to illustrate how such behavioral changes can lead to observed aggregations at larger temporal and spatial scales. Consequently, these results suggest that individual responses to oceanographic structure may have far reaching influence on population dynamics, succession, and biodiversity in coastal and pelagic ecosystems.

Cells switch phenotypes or behaviors to adapt to various environmental stimuli. Often there are multiple alternative phenotypes, hence a cell chooses one phenotype among them, a process which we term a ``decision switch'. At the cellular level, decision switches are governed by gene regulation, hence they are intrinsically stochastic. Here we investigate two aspects of decision switches: how copy number of genetic components facilitates multiple phenotypes and how temporal dynamics of gene regulation with stochastic fluctuations affect switching a cell fate. First, we demonstrate that gene expression can be sensitive to changes in the copy number of genes and promoters, and alternative phenotypes may arise due to bistability within gene regulatory networks. Our analysis in phage-lambda-infected E. coli cells exhibit drastic change in gene expression by changing the copy number of viral genes, suggesting phages can determine their fates collectively via sharing gene products. Second, we examine decision switches mediated by temporal dynamics of gene regulation. We consider a case when temporal gene expression triggers a corresponding cell fate, and apply it to the lysis-lysogeny decision switch by phage lambda. Our analysis recapitulates the systematic bias between lysis and lysogeny by the viral gene copy number. We also present a quantitative measure of cell fate predictability based on temporal gene expression. Analyses using our framework suggest that the future fate of a cell can be highly correlated with temporal gene expression, and predicted if the current gene expression is known.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniversitet, 2009. / Härtill 4 uppsatser.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniv., 2009. / Härtill 5 uppsatser.

The influence of genotype variation on phenotype has been a longstanding question in biology but it is now one of the greatest challenges of the post-genomics era. Discovering the link between common gene variants that affect phenotypes within and between populations is likely to provide insight into the molecular physiology of phenotypic traits and the mechanisms by which they evolve. The overall goal of this thesis is to link naturally occurring genotypic variation with the organism??s phenotype. The specific goal of this thesis is to connect natural variation in the mitochondrial genotype with the organismal phenotype using the model organism Drosophila simulans. Mitochondria are intracellular organelles found in most eukaryotes and produce over 90% of the energy needed by cells. Determining the connection of mitochondrial genotype to whole organism phenotype is of particular interest because of the broad use of mitochondrial (mt) DNA as a molecular marker in evolutionary biology and population genetics, the organelle??s central role in cellular energy production, the potential for the mitochondria to influence organismal distribution particularly in the face of climate change and in human degenerative disease. I use the model organism D. simulans because it has high genetic variability, can be easily sampled from the wild and manipulated in the lab, and the energy producing reactions that take place in its mitochondria are highly conserved among metazoa. I studied naturally occurring mutations to understand the influence of these changes in natural populations. The four studies in this thesis have employed a Genotype-Biochemistry-Phenotype (GBP) model to link naturally occurring variation in the mitochondrial genotype with organism phenotype in D. simulans mitochondria. Three major conclusions can be drawn from the thesis that follow the genotype to biochemistry to phenotype model. Firstly, a subset of the mutations in genes that comprise the mitochondrial genotype is functionally significant. Secondly, the biochemical efficiency of OXPHOS is regulated by mitochondrial homeostasis. Thirdly, key organismal life history traits influenced by the mitochondrial genotype and this is mediated through the biochemistry of OXPHOS.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniversitet, 2006. / Härtill 4 uppsatser.

Orientador: Ananda Virginia de Aguiar / Resumo: As espécies nativas podem ser utilizadas para diversos usos em sistemas de produção, bem como para recuperação ambiental. Porém, poucas dessas espécies são exploradas economicamente devida à falta de oferta de sementes com qualidade genética no mercado. De maneira geral, a caracterização genética de populações e a seleção de indivíduos mais produtivos a partir de testes de progênies é a primeira etapa do processo para obtenção de indivíduos mais produtivos para sistemas de produção. Assim, os objetivos desse trabalho foram estimar a variação e a divergência genética, as relações genéticas e fenotípicas entre os caracteres quantitativos, bem como a interação genótipo x ambiente de testes de progênies de polinização aberta de Cordia trichotoma e Dalbergia nigra. As avaliações foram realizadas durante os quatro primeiros anos após o plantio. Os caracteres avaliados foram: diâmetro do coleto a 30 cm do solo, diâmetro a altura do peito 1,30 m do solo, altura total das plantas, altura do primeiro verticilo e sobrevivência. Para a estimativa dos componentes de variância e das análises multivariadas utilizou-se o método REML/BLUP (Melhor predição linear não viciada/máxima verossimilhança restrita). As análises foram realizadas entre as progênies da mesma espécie. Dois testes de progênies de C. trichotoma e D. nigra, em sistema de consórcio, foram instalados em 2012 na empresa Vale Rio Doce, em Linhares-ESpirito Santo, em duas áreas, em duas textura de solos. O delineamento experiment... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Native species can be used for various purposes in production systems, as well as for environmental recovery. However, few of these species are economically exploited due to the lack of genetic quality of seeds in the marketplace. In general, the genetic characterization of populations and the selection of more productive individuals from progeny tests are the first stage of the process to obtain more productive individuals for production systems. The objectives of this work were to estimate the variation and genetic divergence, identify the genetic and phenotypic relationships among the quantitative traits, as well as analyze the genotype x environment interaction of open pollinated progenies of Cordia trichotoma and Dalbergia nigra. The assessments were conducted during the first four years after planting. The evaluation traits were: collection diameter at 30 cm from the soil, diameter at 1.30 m from the soil, total height of the plants, height of first whorl and survival. To estimate the components of variance and multivariate analyzes, the REML/BLUP method (Restricted Maximum Likelihood/Best Linear Unbiased Prediction) was used. The analyses were carried out among the progenies of the same species. The two progenies of Cordia trichotoma and Dalbergia nigra, in a consortium system, were installed in 2012 at Vale Rio Doce, in the municipality of Linhares, Espirito Santo, in two areas, using two distinct soils. The experimental Randomized Complete Block design (RCB) were div... (Complete abstract click electronic access below) / Doutor

A raça Holandesa apresenta alto rendimento na produção de leite, por isto, diversos países têm optado pela importação de sêmen para substituir as raças leiteiras locais. Esta estratégia seria eficaz se o sêmen importado fosse utilizado nas mesmas circunstâncias em que foram selecionados. Caso exista interação genótipo ambiente significativa, é esperada uma nova classificação dos touros, porém se o efeito da interação genótipo ambiente não é levada em consideração, os valores genéticos preditos (EBVs) podem ser tendenciosos, reduzindo a resposta de seleção. Diante disso, os objetivos deste trabalho foram comparar modelos de diferentes ordens de ajuste por meio de funções polinomiais de Legendre, utilizando modelos de regressão aleatória e estimar os coeficientes de herdabilidade para os teores de gordura, proteína, ácido graxo saturado, ácido graxo insaturado, e produção de leite. Além de estimar o valor genético dos animais, sob a interferência do estresse térmico. Foram utilizadas informações fenotípicas coletadas mensalmente ao longo da lactação e modelos com polinômios ortogonais de Legendre de primeira a sexta ordem, para verificar a interferência de estresse térmico, foram utilizadas informações de temperatura e umidade do dia de coleta. Os modelos que melhor se ajustaram foram os de primeira e segunda ordem. As estimativas de herdabilidade variaram de 0,02 a 0,52 para teor de gordura; de 0,03 a 0,63 para teor de proteína; de 0,05 a 0,63 para ácido graxo saturado; de 0,019 a 0,364 para ácido graxo insaturado e de 0,133 a 0,390 para produção de leite nos diferentes modelos estudados. As estimativas de valores genéticos variaram de -0,5 a 0,5 em ambiente sem estresse térmico e de -0,2 a 0,2 em ambiente com estresse térmico para o teor de gordura; de -0,4 a 0,4 para ambiente sem estresse térmico e de -0,2 a 0,2 em ambiente com estresse térmico para o teor de proteína; de -0,3 a 0,3 em ambiente sem estresse térmico e de -0,2 a 0,2 em ambiente com estresse térmico para ácido graxo saturado; de -0,1 a 0,1 em ambiente sem estresse térmico e de -0,1 a 0,1 em ambiente com estresse térmico para ácido graxo insaturado e de - 6 a 6 em ambiente sem estresse térmico e de -2 e 2 em ambiente com estresse térmico para produção de leite. De acordo com os resultados, as herdabilidades indicam que o teor de gordura, proteína, ácido graxo saturado produção de leite podem ser utilizados como critério de seleção. Com o uso de informações de temperatura e umidade do ar, foi possível verificar a presença de interação genótipo ambiente para teor de gordura, proteína, ácido graxo saturado e produção de leite aos 205 dias em lactação. / Due to the high milk production of Holstein cattle, many countries have chosen to import semen to replace local dairy breeds. This strategy would be effective if these semen was used in the same circumstances in which they were selected. However, if there is significant genotype environment interaction, it is expected a new bulls ranking, but if the effect of genotype environment interaction is not considered, the estimated breeding values (EBVs) may be tendentious, reducing the selection response. The objectives of this study were estimate breeding value under heat stress and heritability coefficients, and also to compare models of different adjustment orders through Legendre polynomials, using random regression models for fat, protein, saturated fatty acid, unsaturated fatty acid and milk production. There were used phenotypic information collected monthly through the lactation period and Legendre orthogonal polynomials models from the first to sixth order. To verify the interference of heat stress, there was used temperature and humidity information on the day of the evaluation was performed. The first and second order models were the ones that better fitted. Heritability estimates were from 0.02 to 0.52 for fat; 0.03 to 0.63 for protein; 0.05 to 0.63 for saturated fatty acid; 0.019 to 0.364 for unsaturated fatty acid and 0.133 to 0.390 for milk production on the different models tested. Estimates of the genetic value were from -0.5 to 0.5 on environment without heat stress and -0.2 to 0.2 on environment with heat stress for fat; -0.4 to 0.4 on environment without heat stress and -0.2 to 0.2 on environment with heat stress for protein; -0.3 to 0.3 on environment without heat stress and -0.2 to 0.2 on environment with heat stress for saturated fatty acid; -0.1 to 0.1 on environment without heat stress and of -0.8 to 0.8 on environment with heat stress for unsaturated fatty acid; -6 to 6 on environment without heat stress and -2 to 2 on environment with heat stress for milk production. The heritability indicates that the fat, protein, saturated fatty acid and milk production can be used as selection criteria. With the use of temperature and humidity information, it was possible to verify the presence of genotype environment interaction for fat, protein, saturated fatty acid and milk production at 205 days in milk.

A produtividade e a qualidade tecnológica do trigo são influenciadas por fatores genéticos, ambientais e de manejo. A participação do ambiente na definição de caracteres componentes do rendimento e atributos qualitativos de farinha requer extensiva avaliação de genótipos em vários locais durante anos. O objetivo deste trabalho foi avaliar o efeito de anos (2007 a 2011) e regiões de cultivo (Abelardo Luz- SC, Cascavel-PR, Castro-PR, Guarapuava-PR, Não Me Toque- RS e Palotina-PR) sobre a qualidade industrial e produtividade de grãos em conjuntos de ensaios de trigo (Triticum aestivum L.), com vistas a recomendação de cultivares e identificação de regiões que maximizem a qualidade de panificação. Foram realizadas as análises de variância conjunta e calculadas as estatísticas de comparação de médias, associação entre caracteres e adaptabilidade e estabilidade dos genótipos às diferentes regiões de cultivo, utilizando analises gráficas GGE Biplot e análises AMMI. Os resultados indicam que todos os caracteres avaliados foram influenciados pelo genótipo (G), ambiente (E) interação GxE. Os caracteres determinantes da qualidade de panificação de trigo têm sua variação fenotípica controlada principalmente pelo efeito genético. As cultivares CD 150, CD 108 e IPR 85 apresentaram excelente comportamento quanto à qualidade de panificação. O ambiente de teste Não-Me-Toque é ideal para seleção de genótipos com foco no rendimento de grãos e massa do hectolitro. Ambientes ideais para a seleção de genótipos com foco na qualidade de panificação incluem, em ordem, Abelardo Luz, Cascavel e Guarapuava. / The productivity and technological quality of wheat is influenced by genetic, environmental and management factors. The environmental contribution in the definition of component traits of yield and quality attributes of flour requires extensive evaluation of genotypes in multiple locations for years. The objective of this study was to evaluate the effect of years (2007-2011) and growing regions (Abelardo Luz- SC , Cascavel - PR, Castro - PR, Guarapuava - PR , Não-Me-Toque - RS and Palotina - PR) on the quality industrial and grain yield in sets of trials of wheat ( Triticum aestivum L.), with a view to recommending cultivars and identification of regions that maximize the quality of baking. Analyses of joint variance and calculated statistical comparison of means , association between character and adaptability and stability of genotypes to different growing regions, using graphical GGE Biplot analysis and AMMI analysis were performed. The results indicate that all traits were influenced by genotype (G), environment (E) interaction GxE. The determinants of quality characters of wheat bread have their phenotypic variation mainly controlled by genetic effects. The CD 150, CD 108 and IPR 85 cultivars showed excellent behavior in relation to baking quality. The test environment Não-Me-Toque is ideal for selection of genotypes with a focus on yield and hectoliter mass. Ideal environments for the selection of genotypes with a focus on quality of bread making, in order, Abelardo Luz, Cascavel and Guarapuava.