Orientador: Mario Luiz Teixeira de Moraes / Resumo: As ações antrópicas no bioma Cerrado levaram a perturbações do seu ecossistema e a fragmentação das florestas, colocando em risco de extinção a espécie Myracrodruon urundeuva. O objetivo do estudo foi avaliar os caracteres silviculturais para estimar os parâmetros genéticos nos bancos de germoplasma provenientes de populações naturais em Bauru-SP e Selvíria-MS, a fim de adquirir informações que possibilitem a formação de pomares de sementes melhoradas visando a qualidade da madeira. Aos 31 anos de idade, analisou-se os caracteres altura total (ALT), diâmetro médio da copa (DMC), diâmetro na altura do peito (DAP), forma do fuste (FOR), densidade básica da madeira (DBM), relação cerne/alburno (RC/Ab) e sobrevivência (SOB). Utilizou-se o procedimento REML/BLUP via metodologia dos modelos lineares mistos para estimar os componentes de variância, os parâmetros genéticos e as estimativas de correlações genéticas entre os caracteres. Para as análises de divergência genética foi utilizado o programa Genes. Os testes de progênies de ambas as populações apresentaram variação genética. Os caracteres referentes a qualidade de madeira (DBM e RC/Ab) foram os que apresentaram maiores herdabilidades, com cerca de 0,80 e coeficiente de variação genética (16,57% a 70,10%). As correlações genéticas mostraram diferentes resultados em ambas as populações, com Selvíria sendo a população com maiores correlações positivas significativas, permitindo o uso de seleção direta e indireta tanto para os ca... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Anthropic actions in the Cerrado biome led to disturbances of its ecosystem and the fragmentation of forests, putting the species Myracrodruon urundeuva at risk of extinction. The objective of the study was to evaluate the silvicultural traits to estimate the genetic parameters in the germplasm banks from natural populations in Bauru-SP and Selvíria-MS, in order to acquire information that allows the formation of improved seed orchards aiming at the quality of the wood. At 31 years of age, the characters total height (ALT), average crown diameter (DMC), diameter at chest height (DAP), stem shape (FOR), basic wood density (DBM), ratio heartwood / sapwood (RC / Ab) and survival (SOB). The REML / BLUP procedure was used via mixed linear models methodology to estimate the components of variance, genetic parameters and estimates of genetic correlations between the characters. For the genetic divergence analyzes, the Genes program was used. The progeny tests of both populations showed genetic variation. The characters referring to wood quality (DBM and RC / Ab) were those with the highest heritability, with about 0,80 and coefficient of genetic variation (16,57% to 70,10%). The genetic correlations showed different results in both populations, with Selvíria being the population with the highest significant positive correlations, allowing the use of direct and indirect selection for both growth and wood quality characters. In the dissimilarity analyzes, the Selvíria population was t... (Complete abstract click electronic access below) / Mestre

La variabilité phénotypique existante au sein d’une population est d’une importance cruciale ; elle permet l’adaptation à de nouvelles conditions par la sélection naturelle de traits bénéfiques. La variabilité phénotypique est le résultat du polymorphisme génétique de chaque individu, couplé à l’influence de divers facteurs environnementaux. Ces travaux ont pour objectif d’élucider quels sont les facteurs génétiques responsables de la variabilité phénotypique de chaque individu afin de comprendre comment celle-ci évolue de génération en génération et peut s’accentuer au-delà des prédispositions parentales. Finalement, les résultats obtenus seront utilisés pour prédire un phénotype à partir d’un génotype inconnu. Nous avons utilisé des techniques de phénomique et de génomique de haut débit pour décomposer avec une précision inédite la variabilité phénotypique d’une large population de souches diploïdes de Saccharomyces cerevisiae. Le génotype exact de plus de 7000 souches uniques a ainsi été obtenu via le croisement et le séquençage de souches haploïdes distinctes. Nous avons mesuré la capacité de croissance de ces souches et identifié les composants génétiques influant sur ce trait. De plus, nous avons identifié des « loci de caractères quantitatifs » additifs et non-additifs, et étudié la fréquence du phénomène d’hétérosis et ses mécanismes. Enfin, en utilisant les données phénotypiques et génotypiques de la même population de levures, nous avons pu prédire les traits de chaque individu avec une presque parfaite exactitude. Ces travaux ont ainsi permis d’identifier avec précision les facteurs génétiques modulant la variation phénotypique d’une population diploïde, et de prédire un trait à partir du génotype et de l’ensemble des données phénotypiques. En plus de ce projet, nous travaillons aussi sur l’identification des bases génétiques à l’origine de la non-viabilité des gamètes, ainsi que sur la compréhension des caractères complexes chez des souches hybrides intra-espèce. De par l’étude de 9000 gamètes séquencés issus de six hybrides différents, nous avons pour objectif de caractériser leur profil de recombinaison et d’observer quelle est l’influence du fond génétique sur ce dernier. De plus, nous avons caractérisé la capacité de croissance de ces gamètes dans neuf conditions environnementales différentes et nous prévoyons de disséquer l’architecture génétique de ces traits dans différents fonds génétiques. / The phenotypic variation between individuals in a population is of crucial importance. It allows populations to evolve to novel conditions by the natural selection of beneficial traits. Variation in traits can be caused by genetic or environmental factors. This work endeavors to study the genetic factors that underlie phenotypic variation in order to understand how variation can be created from one generation to the next; to know what genetic mechanisms are most prominent; to learn how variation can extend beyond the parents; and finally, to use this in order to predict phenotypes of unknown genetic constellations. We used large scale phenomics and genomics to give an unprecedented decomposition of the phenotypic variation in a large population of diploid Saccharomyces cerevisiae strains. Constructing phased outbred lines by large scale crosses of sequenced haploid strains allowed us to infer the genetic makeup of more than 7,000 colonies. We measured the growth of these strains and decomposed the phenotypic variation into its genetic components. In addition, we mapped additive and nonadditive quantitative trait loci, we investigated the occurrence of heterosis and its genetic basis, and using the same populations we used phenotypic and genetic data to predict traits with near perfect accuracy. By using the phased outbred line approach, we succeeded in giving a conclusive account of what genetic factors define phenotypic variation in a diploid population, and in accurately predicting phenotypes from genetic and phenotypic data. Beyond the phased outbred line project, I am currently investigating the genetic basis of gamete inviability and complex traits in intraspecies yeast hybrids. Using 9,000 sequenced gametes from six different hybrids we aim to characterize their recombination landscape and how the genetic background influences it. Furthermore, we have phenotyped these gametes in nine conditions and will dissect the genetic architecture of these traits across multiple genomic backgrounds.

The evolution of antibiotic resistance provides a well-documented, rapid, and recent example of a selection driven process that has occurred in many bacterial species. An exhaustive collection of Moraxella catarrhalis that spans a transition to chromosomally encoded penicillin resistance was used to analyze genetic changes accompanying the transition. The population was characterized by high haplotypic diversity with 148 distinct haplotypes among 372 isolates tested at three genomic regions. The power of a temporally stratified sample from a single population was highlighted by the finding of high genetic diversity throughout the transition to resistance, population numbers that remained high over time, and no evidence of departures from neutrality in the allele frequency spectra throughout the transition. The direct temporal analysis documented the persistence, antibiotic status, and haplotypic identity of strains undergoing apparent clonal expansions. Several haplotypes that were β-lactamase nonproducers in early samples converted to producers in later years. Maintenance of genetic diversity and haplotype conversions from sensitive to resistant supported the hypothesis that penicillin resistance determinants spread to a diverse array of strains via horizontal exchange. Genetic differentiation between sample years, estimated by FST, was increasing at a rate that could cause complete haplotype turnover in less than 150 years. Widespread linkage disequilibrium among sites within one locus (copB) suggested recent mutation followed by clonal expansion. Nonrandom associations between haplotypes and resistance phenotypes provided further evidence of clonal expansion for some haplotypes. Nevertheless, the population structure was far from clonal as evidenced by a relatively low frequency of disequilibria both within sites at a second locus (M46) as well as between loci. The haplotype-antibiotic resistance association that was accompanied by gradual haplotype turnover is consistent with a hypothesis of genetic drift at marker loci with directional selection at the resistance locus.

A functional central nervous system (CNS) is composed of numerous types of neurons. Neurons are derived from a limited number of multipotent neural stem cells. Previous studies have suggested three major strategies nature uses to diversify neurons: lineage identity specification that gives an individual neural stem cell distinct identity based on its position in the developing CNS; temporal identity specification that gives neurons derived from a neural stem cell distinct identities based on their birth-order within the lineage; and binary cell fate specification that gives different identities to the two sister postmitotic neurons derived from the terminal division of a common precursor. Through the combination of the three strategies, almost unlimited neuron types can be generated. To understand neuronal diversification, we have to understand the underlying molecular mechanisms of each of the three strategies. The fruit fly Drosophila melanogaster, has been an excellent model for studying neuronal diversity, mainly due to its easily traceable nervous system and an impressive collection of genetic tools. Studies in fly have provided us fundamental insights into lineage identity, temporal identity, and binary cell fate specifications. Nevertheless, previous studies mostly centered on the embryonic ventral nerve cord (VNC) because of its simpler organization. Our understanding of the generation of neuronal diversity in the fly brain is still rudimentary. In this thesis work, I focused on the mushroom body (MB) and three antennal lobe neuronal lineages, studying their neuronal diversification during postembryonic brain development. In Chapter I, I reviewed the previous studies that have built our current understanding of the neuronal diversification. In Chapter II, I showed that MB temporal identity changes are instructed by environmental cues. In Chapter III, to search for the potential factors that mediate the environmental control of the MB temporal identity changes, I silenced each of the 18 nuclear receptors (NRs) in the fly genome using RNA interference. Although I did not identify any NR important for the regulation of MB temporal identities, I found that unfulfilled is required for regulating axon guidance and for the MB neurons to acquire all major subtype-specific identities. In Chapter IV, I demonstrated that the Notch pathway and its antagonist Numb mediate binary cell fate determination in the three classical antennal lobe neuronal lineages— anterodorsal projection neuron (adPN), lateral antennal lobe (lAL), and ventral projection neuron (vPN)—in a context-dependent manner. Finally, in Chapter V, I did detailed lineage analysis for the lAL lineage, and identified four classes of local interneurons (LNs) with multiple subtypes innervating only the AL, and 44 types projection neurons (PNs) contributing to olfactory, gustatory, and auditory neural circuits. The PNs and LNs were generated simultaneously but with different tempos of temporal identity specification. I also showed that in the lAL lineage the Notch pathway not only specifies binary cell fates, but is also involved in the temporal identity specification.

Salinity is a major concern in agriculture since it adversely affects plant growth, development, and yield. Domestication of crops exerted strong selective pressure and reduced their genetic diversity. Meanwhile, wild species continued to adapt to their environment becoming valuable sources of genetic variation, with the potential for enhancing modern crops performance in today’s changing climate. Some wild species are found in highly saline environments; remarkable examples are the endemic wild tomatoes from the Galapagos Islands, forming the Solanum cheesmaniae and Solanum galapagense species (hereafter termed Galapagos tomatoes). These wild tomatoes adapted to thrive in the coastal regions of the Galapagos Islands. The present work includes a thorough characterization of a collection of 67 accessions of Galapagos tomatoes obtained from the Tomato Genetics Resource Center (TGRC). Genotyping-by-sequencing (GBS) was performed to establish the population structure and genetic distance within the germplasm collection. Both species were genetically differentiated, and a substructure was found in S. cheesmaniae dividing the accessions in two groups based on their origin: eastern and western islands. Phenotypic studies were performed at the seedling stage, subjecting seedlings to 200 mM NaCl for 10 days. Various traits were recorded and analysed for their contribution to salinity tolerance, compared to control conditions. Large natural variation was found across the collection in terms of salt stress responses and different possible salt tolerant mechanisms were identified. Six accessions were selected for further work, based on their good performance under salinity. This experiment included scoring several plant growth and yield-related traits, as well as RNA sequencing (RNAseq) at the fruit-ripening stage, under three different NaCl concentrations. Accession LA0421 showed an increased yield of almost 50% in mild salinity (150 mM NaCl) compared to control conditions. The transcriptome data obtained could reveal the genes involved in the salt stress-related yield increase. The knowledge obtained so far will be useful for scientists and breeders to select accessions of interest based on recorded traits. It will allow the use of Galapagos tomatoes as genetic sources for salinity tolerance traits in commercial tomatoes, thereby contributing to feed and nourish the growing human population in the years to come.

Bread wheat (Triticum aestivum L.) is an important cereal crop that provides over 20% of the global calorie intake. With the world population constantly growing, yield production must increase to meet food demands. Wheat plays a significant role on nutritional and food security especially in rural areas, however, bread wheat grains are known to be inherently deficient in micronutrients, particularly Fe and Zn, which makes them important biofortification targets. To date, South African wheat genotypes have not been explored for their nutritional micronutrient variation; hence there is a need to investigate the variation of nutritional quality and its association with yield components. Bread wheat cultivars, TugelaDN and Elands were used in this study based on their known high yield potential, resistance to insect pests and diseases as well as their good-to-excellent bread-making quality. The goal of this study was to use a doubled haploid (DH) mapping population, developed from a cross between cultivars Tugela-DN and Elands, to identify single nucleotide polymorphism (SNP) and genotyping-by-sequencing (GBS)-based markers linked to high nutritional quality and yield-related traits. This was achieved by (i) determining grain micronutrient (Fe and Zn) concentration variation in 139 lines of a DH mapping population; (ii) evaluating the mapping population for yield-related traits; (iii) determining the correlation between micronutrient and yield-related traits among the genotypes; (iv) identifying SNP GBS-based markers linked to the high minerals and yield-related traits. The analysis of variance (ANOVA) showed significant (P<0.001) differences between genotypes for all traits evaluated. A wide variation was observed for both GFeC and GZnC. The statistical analysis revealed significant variation for Zn concentration (P < 0.001) among genotypes and not significant Fe concentration. DArT-Seq was used to genotype Tugela-DN and Elands cultivars and 139 DH genotypes. Quantitative trait loci (QTL) were detected using SNP GBS-based markers on chromosome 2D, 5B, 5D, 6A, and 6B for GZnC, and on chromosome 2D, 5B, 5D and 7D for GFeC. Most QTLs identified for GFeC and GZnC shared the genomic interval and some of them also co-located with few yield-related traits. The results of this study will contribute to breeding programmes to improve nutritional quality of bread wheat and food security of the country. / Life and Consumer Sciences

The hierarchy of biological organization, from molecules to ecosystems, describes the relationships among various biological systems. Of particular interest is assessing how the factors that primarily determine the nature of one hierarchical level also have transcendent qualities that affect the ecology and evolution of higher hierarchical levels. The goal of this dissertation was to use a bottom-up approach to examine the transcendent effects of two factors that strongly determine the nature of their associated level of biological organization. The first, phenotypic plasticity, is a primary factor that determines the phenotype of an individual. The second factor, genetic diversity, largely determines the phenotypic distributions associated with populations. Controlled laboratory experiments on taxa from a freshwater tri-trophic food web were employed to examine the transcendent effects of phenotypic plasticity and genetic diversity on the biological hierarchy because relationships between individuals and populations from different trophic levels are well documented for numerous freshwater species. The results show that phenotypic plasticity can induce changes in population means and variances that promote population persistence and evolvability, and that plasticity provides a mechanistic explanation of community stability in response to changing environments. Similarly, genetic diversity may act as a signal that induces phenotypic plasticity in individuals, modulates community richness and ecosystem properties, and suggests a potential mechanism for the changes in biodiversity. Thus, results from this dissertation show that plasticity and genetic variation can shape the attributes of other biological groups higher in the biological hierarchy, and, in some cases, may also provide a mechanistic explanation for variability observed in higher levels of the biological hierarchy. These results highlight the importance of integrating traditionally disparate biological disciplines and may help to unify biology as a field.

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