Orientador: Alexandre Magno Sebbenn / Resumo: In Uruguay, reforestation with Eucalyptus sp. is of fundamental importance to produce paper, pulp and wood. The productivity of these continually grows due to application of breeding techniques, such as hybridization. This study aimed to investigate genetic parameters, productivity, stability, adaptability and to identify SNP markers associated with the diameter breast height (DBH) for to select Eucalypts grandis x Eucalyptus globulus full-sibs hybrid clones. The study was conducted in a clonal test, repeated at two different soils, in the state of Rio Negro, Uruguay. The population was phenotypically characterized to the DBH at 48 months of age and cambium tissues of each individual were sampled for genotyping with EuCHIP60K chip. The mean growth in DBH was similar between both places. The genotype-environment interaction was the simple type, with high genotype correlation in clones’ performance between environments (0.708), indicating the possibility of the same clones being selected for both places. Mean heritability between clones (0.724), coefficient of individual genetic variation (10.9%) and relative variation (0.916), showed the possibility of obtaining gains by selecting clones with higher growth, which was estimated in 3.1% for both sites together. A total of 15,196 markers SNPs were used in the genomic selection for the DBH, but after cleaning of SNPs data, the number was reduced for 15,196 (23.5%). The predictive capacity was expected to be low or negative (-0.15)... (Resumo completo, clicar acesso eletrônico abaixo) / Doutor

O avanço na ciência trouxe novas descobertas sobre mecanismos celulares, o que permitiu o desenvolvimento de novos produtos e serviços acerca do melhoramento genético animal. A tecnologia genômica, embora recente, traz para a atividade leiteira a possibilidade de aumentar os ganhos em seleção genética e a rentabilidade econômica. No Brasil, já são comercializados testes genômicos que possibilitam, por meio da coleta de material genético, uma predição das características genéticas dos bovinos jovens com a identificação de características produtivas dos animais, antes da sua expressão. No entanto, por se tratar de uma tecnologia nova, ainda não se sabe a opinião dos pecuaristas sobre a tecnologia, sobre o melhoramento genético, nem se conhece o nível de conhecimento e tecnificação do produtor. Portanto, a presente pesquisa levantou informações sobre o perfil das propriedades de atividade leiteira passíveis de utilizarem os testes genômicos, identificando suas principais necessidades frente à utilização do serviço. Os dados foram coletados com questionários quantitativos e qualitativos, aplicados de forma aleatória a 100 propriedades produtoras de leite, distribuídas na região do Triângulo Mineiro. Após a coleta, foram realizados testes estatísticos de análise descritiva com tabelas de contingência e correlação, com os dados não paramétricos obtidos. Através destes, identificou-se que as propriedades são heterogêneas, com níveis de tecnificação crescentes e que contam cada vez mais com o apoio da assistência técnica. Parte dos pecuaristas ainda não utilizam ferramentas para melhoria da seleção genética como: inseminação artificial, IATF, TE ou outras e embora os testes genômicos já estejam disponíveis comercialmente, apenas 25% dos entrevistados dizem ter conhecimentos básicos sobre a técnica. Para que os testes genômicos atendam às necessidades do consumidor final e sejam comercializados, é importante que além do aumento na disseminação de conhecimento sobre o produto, o seu preço seja acessível, o produtor sinta confiança no resultado e que os grupo de animais a ser avaliado atenda aos requisitos mínimos exigidos pela tecnologia, para assim, se conseguir utilizar o produto com mais alta acurácia. / The breakthrough in science has brought new discoveries about cellular mechanisms, allowing the development of new products and services about animal genetic improvement. Genomic technology, although recent, brings to dairy activity the possibility of increasing gains in genetic selection and economic profitability. In Brazil, genomic tests are already commercialized, which make it possible, through the collection of genetic material, to predict the genetic characteristics of young cattle with the identification of productive characteristics of the animals before their expression. However, because it is a new technology, the opinion of cattle ranchers about technology, genetic improvement, and the level of knowledge and technification of the producer is not yet known. Therefore, the present research raised information on the profile of dairy activity properties that could use genomic tests, identifying their main needs in relation to the use of the service. The data were collected with quantitative and qualitative questionnaires, randomly applied to 100 milk properties, distributed in the Triângulo Mineiro region. After the collection, statistical tests of descriptive analysis and contingency and correlation tables were performed with the non-parametric data obtained. Through these, it was identified that the properties are heterogeneous, with increasing levels of technification and increasingly rely on the support of technical assistance. Some of the cattle ranchers still do not use tools to improve genetic selection such as artificial insemination, IATF, ET or others, and although genomic tests are already commercially available, only 25% of the interviewees have a basic knowledge of the technique. To sell the genomic tests, is important to understand the needs of the final consumer and to be marketed, it is important that the costumer increases the knowledge of the product, the price need to be accessible, the producer feels confidence in the result and that the groups of animals to be evaluated meet the minimum requirements required by the technology in order to be able to use the product with the highest accuracy.

No description available.

Quantitative genetics aims to bridge the genome to phenome gap. The advent of high-throughput genotyping technologies has accelerated the progress of genome to phenome mapping, but a challenge remains in phenotyping. Various high-throughput phenotyping (HTP) platforms have been developed recently to obtain economically important phenotypes in an automated fashion with less human labor and reduced costs. However, the effective way of designing HTP has not been investigated thoroughly. In addition, high-dimensional HTP data bring up a big challenge for statistical analysis by increasing computational demands. A new strategy for modeling high-dimensional HTP data and elucidating the interrelationships among these phenotypes are needed. Previous studies used pedigree-based connectetdness statistics to study the design of phenotyping. The availability of genetic markers provides a new opportunity to evaluate connectedness based on genomic data, which can serve as a means to design HTP. This dissertation first discusses the utility of connectedness spanning in three studies. In the first study, I introduced genomic connectedness and compared it with traditional pedigree-based connectedness. The relationship between genomic connectedness and prediction accuracy based on cross-validation was investigated in the second study. The third study introduced a user-friendly connectedness R package, which provides a suite of functions to evaluate the extent of connectedness. In the last study, I proposed a new statistical approach to model high-dimensional HTP data by leveraging the combination of confirmatory factor analysis and Bayesian network. Collectively, the results from the first three studies suggested the potential usefulness of applying genomic connectedness to design HTP. The statistical approach I introduced in the last study provides a new avenue to model high-dimensional HTP data holistically to further help us understand the interrelationships among phenotypes derived from HTP. / Doctor of Philosophy / Quantitative genetics aims to bridge the genome to phenome gap. With the advent of genotyping technologies, the genomic information of individuals can be included in a quantitative genetic model. A new challenge is to obtain sufficient and accurate phenotypes in an automated fashion with less human labor and reduced costs. The high-throughput phenotyping (HTP) technologies have emerged recently, opening a new opportunity to address this challenge. However, there is a paucity of research in phenotyping design and modeling high-dimensional HTP data. The main themes of this dissertation are 1) genomic connectedness that could potentially be used as a means to design a phenotyping experiment and 2) a novel statistical approach that aims to handle high-dimensional HTP data. In the first three studies, I first compared genomic connectedness with pedigree-based connectedness. This was followed by investigating the relationship between genomic connectedness and prediction accuracy derived from cross-validation. Additionally, I developed a connectedness R package that implements a variety of connectedness measures. The fourth study investigated a novel statistical approach by leveraging the combination of dimension reduction and graphical models to understand the interrelationships among high-dimensional HTP data.

BACKGROUND:Metagenomics has a great potential to discover previously unattainable information about microbial communities. An important prerequisite for such discoveries is to accurately estimate the composition of microbial communities. Most of prevalent homology-based approaches utilize solely the results of an alignment tool such as BLAST, limiting their estimation accuracy to high ranks of the taxonomy tree.RESULTS:We developed a new homology-based approach called Taxonomic Analysis by Elimination and Correction (TAEC), which utilizes the similarity in the genomic sequence in addition to the result of an alignment tool. The proposed method is comprehensively tested on various simulated benchmark datasets of diverse complexity of microbial structure. Compared with other available methods designed for estimating taxonomic composition at a relatively low taxonomic rank, TAEC demonstrates greater accuracy in quantification of genomes in a given microbial sample. We also applied TAEC on two real metagenomic datasets, oral cavity dataset and Crohn's disease dataset. Our results, while agreeing with previous findings at higher ranks of the taxonomy tree, provide accurate estimation of taxonomic compositions at the species/strain level, narrowing down which species/strains need more attention in the study of oral cavity and the Crohn's disease.CONCLUSIONS:By taking account of the similarity in the genomic sequence TAEC outperforms other available tools in estimating taxonomic composition at a very low rank, especially when closely related species/strains exist in a metagenomic sample.

published_or_final_version / abstract / Statistics and Actuarial Science / Doctoral / Doctor of Philosophy

No description available.

Exposure of cells to hydrogen peroxide can cause oxidative damage to cellular constituents including lipids, protein, and DNA. At elevated concentrations, hydrogen peroxide can trigger cell death by apoptosis or necrosis. Apoptotic cell death can be prevented by overexpression of the oncoprotein Bcl-2. The exact mechanism by which Bcl-2 blocks cell death is controversial. Some researchers believe that Bcl-2 possesses antioxidant properties that protect cells from apoptosis. The purpose of this thesis was to assess oxidative stress and apoptosis following hydrogen peroxide exposure in Jurkat T cells overexpressing Bcl-2. One of the major objectives was to ascertain whether or not Bcl-2 overexpression elevated the antioxidant capacity of Jurkat T cells to provide protection from oxidant-induced cell death. Hydrogen peroxide treated Jurkat cells became apoptotic at moderate levels of oxidant (25-100 uM H2O2), and necrotic at higher doses (greater than 200 uM H2O2). Bcl-2 overexpression prevented caspase activation and cell death at the apoptotic doses of H2O2, but not the necrotic doses. Caspase inhibition studies demonstrated that Bcl-2 overexpression provided a greater level of resistance from H2O2-induced cell death than the broad-spectrum caspase inhibitor z-VAD.fmk. A systematic study was carried out examining the antioxidant status of Jurkat cells overexpressing Bcl-2. Several Bcl-2 transfectants were utilised for the study, so that any differences seen could be correlated to the level of Bcl-2 expression. Surprisingly, there were no statistically significant differences among the Bcl-2 transfectants for any of the antioxidant enzymes. Jurkat cells overexpressing Bcl-2 exhibited the same level of oxidative damage to lipids and protein in response to H2O2 exposure as the parental Jurkat cells. Interestingly, Jurkat cells overexpressing Bcl-2 continued to grow in culture after H2O2 exposure, despite harboring damage to cellular constituents. Consistent with these results, H2O2 treated Jurkat cells overexpressing Bcl-2, which failed to undergo apoptosis, were more prone to genomic instability. Together, these findings suggest that Bcl-2 overexpression protects Jurkat cells from H2O2-induced cell death by blocking apoptosis. Jurkat cells overexpressing Bcl-2 were no better at detoxifying oxidants and showed the same level of oxidative damage following H2O2 exposure. As a result, the overexpression of Bcl-2 considerably enhanced the mutagenicity of H2O2.

No description available.

Analyzing regions in the genome with low levels of recombination helps understand the prevalence of sexual reproduction. Here, I show that variability in regions of reduced recombination in Drosophila can be explained by interference among strongly deleterious mutations; selection becomes progressively less effective in influencing the behaviour of neighbouring sites as the number of closely linked sites on a chromosome increases. I also show that the accumulation of loss-of-function mutations on the neo-Y chromosome of Drosophila miranda is compatible with a model of selection against such mutations alone, without the need to invoke the action of selective sweeps. I describe the discovery of two new sex-linked genes in the plant Silene latifolia, SlCyt and SlX9/SlY9. SlCyt has been recently translocated from an autosome to the X and shows signs of a selective sweep. Its possible role in having caused recombination arrest between the evolving X and Y chromosome is discussed. SlX9 still has an intact Y-linked copy that is presumably functional. Nucleotide diversity at SlY9 is very low, whereas SlX9 has an unusually high diversity and shows signs of introgression from S. dioica into S. latifolia, but the effect of this seems very localized.