A inclusão de grupos genéticos na avaliação de reprodutores tem sido comumente empregada para a representação de possíveis diferenças genéticas entre os animais não contabilizadas pela ausência de informações de parentesco. Entretanto, a definição destes grupos ainda é arbitrária, sendo inexistentes trabalhos que avaliem as estratégias de agrupamento genético quanto aos seus efeitos sobre a eficiência de seleção. Dessa forma, o objetivo desta pesquisa foi comparar estratégias de agrupamento genético na predição de valores genéticos, determinando-se a estrutura adequada à avaliação genética. Para tanto, foram utilizados dados de peso ao nascimento, peso ao desmame, ganho de peso pós-desmame, circunferência escrotal e escore de musculosidade de uma população de bovinos compostos da raça Montana Tropical. Foram avaliadas as estratégias de agrupamento envolvendo safra de nascimento do animal (SAF); sexo do parental desconhecido (SEX); fazenda de nascimento do animal (FAZ); caminho de seleção (SEL); composição racial (RACA) safra de nascimento do animal e sexo do parental desconhecido (SAFSEX); fazenda de nascimento do animal e sexo do parental desconhecido (FAZSEX); safra e fazenda de nascimento do animal (SAFFAZ); e safra, fazenda de nascimento do animal e sexo do parental desconhecido (SAFFAZSEX). Para cada estratégia, foram realizadas cem análises para a predição de valores genéticos simulando-se a perda de informação de parentesco de 10, 30 e 50% dos indivíduos. Posteriormente, estes valores genéticos foram comparados aos obtidos em uma análise envolvendo a matriz de relacionamentos completa, de maneira a se estimar a eficiência de seleção e as correlações entre os valores genéticos e a classificação dos animais. As estratégias de SAF e RACA apresentaram eficiências de seleção e correlações altas independente da característica e amostra de animais com parentesco desconhecido consideradas, mostrando-se adequadas à avaliação e seleção de reprodutores. Perdas de seleção elevadas foram observadas para SAFFAZ e SAFFAZSEX, possivelmente devido à formação de muitos grupos com poucos animais, dificultando-se assim a estimativa dos efeitos dos grupos genéticos. A partir dos resultados é possível concluir que a definição da estratégia de agrupamento deve considerar as decisões vinculadas à seleção de reprodutores e o número de grupos genéticos formados, de forma que os mesmos representem as diferenças genéticas da população e permitam a adequada predição dos valores genéticos. / The inclusion of genetic groups in sire evaluation has been widely used to represent genetic differences among animals not accounted by the absence of parentage information. However, the definition of these groups is still arbitrary, and research assessing the effects of genetic grouping strategies on the selection efficiency is rare. Thus, the aim of this study was to compare genetic grouping strategies in breeding values prediction, determining the appropriate structure for the genetic evaluation. Data on birth weight, weaning weight, post-weaning weight gain, scrotal circumference and muscling score of Montana Tropical composite beef cattle population were used. Grouping strategies involving birth season of the animal (SAF), sex of the unknown parent (SEX), birth farm of the animal (FAZ), path selection (SEL), breed composition (RACA), birth season of the animal and sex of the unknown parent (SAFSEX), birth farm of the animal and sex of the unknown parent (FAZSEX), birth season and farm of the animal (SAFFAZ), and birth season and farm of the animal and sex of the unknown parent (SAFFAZSEX) were evaluated. For each strategy, one hundred analyses were performed to predict breeding values, simulating a loss of genealogy information of 10, 30 and 50% of individuals. Thereafter, these breeding values were compared to those obtained in an analysis involving the complete relationship matrix, in order to estimate the selection efficiency and the correlations between breeding values and animal rankings. The grouping strategies SAF and RACA showed high selection efficiencies and correlations, regardless of the trait and sample of animals with unknown parentage considered, and therefore, they are suitable for sire evaluation and selection. High selection losses were observed for SAFFAZ and SAFFAZSEX, possibly due to the formation of many groups with few animals, since this could lead to some confounding with other fixed effects and hamper the estimation effects of genetic groups. These results allow to conclude that the definition of grouping strategy must consider the decisions regarding the selection and the number of genetic groups formed, so that genetic groups represent the genetic differences in population and allow an adequate prediction of breeding values.

No description available.

Identifying reliable screening tools and characterizing tolerant germplasm sources is essential for developing wheat (Triticum aestivum L.) varieties suited for the hot areas of the world. Our objective was to evaluate heat tolerance of promising wild tetraploid wheat (Triticum turgidum L.) accessions that could be used as sources of heat tolerance in common- and durum-wheat (Triticum durum) breeding programs. We screened 109 wild tetraploid wheat accessions collected by the International Center for Agriculture Research in the Dry Areas (ICARDA) from the hottest wheat growing areas in Africa and Asia, as well as, two common wheat checks for their response to heat stress by measuring damage to the thylakoid membranes, flag leaf temperature depression (FLTD), and spike temperature depression (STD) during exposure to heat stress for 16 beginning at anthesis. Measurements were taken on the day of anthesis then 4, 8, 12, and 16 days post anthesis (DPA) under controlled optimum and heat-stress conditions. Individual kernel weight (IKW) and heat susceptibility index (HSI) measurements were also obtained. Prolonged exposure to heat stress was associated with increased damage to thylakoid membranes, as indicated by the high ratio of constant fluorescence (O) to peak variable fluorescence (P). A positive and significant correlation was found between O/P ratio and both FLTD and STD under heat-stress conditions. A negative and significant correlation was found between FLTD and HSI and between STD and HSI based on the second and third measurements (4 and 8 DPA). Correlations obtained after the third measurement were not significant because heat-stress accelerated maturity and senescence. For a pedigree-based mapping strategy a family approach was then developed by crossing and back-crossing heat-tolerant and heat-susceptible germplasm. A set of 800 lines resulting from the pedigree-based family approach was phenotyped using FLTD, chlorophyll content and yield and its components under heat stress. Genotyping of these lines was accomplished using simple sequence repeat (SSRs) markers. Some QTLs associated with heat stress tolerance were identified. This study identified potential heat-tolerant wild tetraploid wheat germplasm and QTL conditioning heat tolerance that can be incorporated into wheat breeding programs to improve cultivated common and durum wheat.

Le groupe " scoparius " est composé de Cytisus scoparius (Genisteae, Fabaceae) et des taxons qui lui sont apparentés dans le genre Cytisus. Des études taxinomiques et morphométriques ont permis de délimiter 10 espèces réparties en trois sections Alburnoides, Spartopsis et Verzinum. Une phylogénie moléculaire basée sur des marqueurs chloroplastiques trnD-T, trnS-G et nucléaires ITS, LEGCYCIAa, LEGCYCIAb et LEGCYCIAc a montré que les sections Alburnoides et Verzinum, toutes deux monophylétiques (à condition d'inclure C. striatus dans la section Alburnoides), sont des groupes frères alors que la section Spartopsis, paraphylétique ou monophylétique selon la position de C. commutatus (sect. Corothamnus) est plus éloignée. Quatre hybrides cultivés sont issus de croisements entre espèces du groupe " scoparius ". La comparaison de données ITS issues de clonage a confirmé les deux parents proposés par la littérature pour trois de ces hybrides et un des parents du dernier hybride. Le marqueur chloroplastique trnD-T s'est révélé efficace pour déterminer le sens du croisement à l'origine de trois des hybrides du groupe. L'addition des quatre hybrides dans les analyses phylogénétiques a montré que les hybrides entre taxons proches forment un clade avec leur parent maternel et ne modifient pas les relations entre taxons non hybrides. En revanche, l'ajout d'hybrides entre taxons éloignés peut provoquer des effondrements de clades ainsi que des changements de topologie. Le groupe " scoparius " comprend également plus de 150 cultivars dont 40 ont été caractérisés. L'analyse de données ISSR, trnD-T et SSR a permis de confirmer et de compléter les données généalogiques de 28 de ces cultivars et ainsi de reconstituer un pedigree à 7 générations.

Diss. (sammanfattning) Umeå : Umeå universitet, 2010.

MATOS, Rosângela da Luz. Juventude, arte e poesia: a constituição histórica do CRIA – Centro de Referência Integral de Adolescentes. 2008. 173f. – Tese (Doutorado) – Universidade Federal do Ceará, Programa de Pós-graduação em Sociologia, Fortaleza (CE), 2008. / Submitted by Márcia Araújo (marcia_m_bezerra@yahoo.com.br) on 2013-10-21T11:40:29Z No. of bitstreams: 1 2008-TESE-RLMATOS.pdf: 1149031 bytes, checksum: c509ade374e5078e5c3735042dd6e6ec (MD5) / Approved for entry into archive by Márcia Araújo(marcia_m_bezerra@yahoo.com.br) on 2013-10-21T13:19:03Z (GMT) No. of bitstreams: 1 2008-TESE-RLMATOS.pdf: 1149031 bytes, checksum: c509ade374e5078e5c3735042dd6e6ec (MD5) / Made available in DSpace on 2013-10-21T13:19:03Z (GMT). No. of bitstreams: 1 2008-TESE-RLMATOS.pdf: 1149031 bytes, checksum: c509ade374e5078e5c3735042dd6e6ec (MD5) Previous issue date: 2008 / This research was used in Method History (arch-genealogy), to learn the meanings of teaching practices and proposals offered to young people who are integrated into programs and / or educational projects in a non-school institution. The empirical field was the CRIA – Centro de Referência Integral de Adolescentes, an NGO working since 1994 with artistic training for young people 10-18 years of age in the city of Salvador. The procedures for doing file were executed by means of descriptive exercises, taking as reference documents, records of interviews, ethnographic observations and diaries made ​​over a year, with the activities of NGOs in the arts practiced. These exercises reinforced a narrative text in which CRIA is understood as an institution that exists from historicities local, regional and individual asserting the claim that educating through art is an argument that extends the meaning of life and puts, adolescents and young given the need to forge himself in relation to culture and the present. The education activities undertaken by NGOs have a handy reference of the city, theatrical experimentation, clown and poetry; implementation of policies of art and culture in the context of formal education and community which young people are linked. / Esta pesquisa se utiliza do Método Histórico, proposto por Michel Foucault, para conhecer o CRIA – Centro de Referência Integral de Adolescentes, ONG que trabalha, desde 1994, com formação artística para jovens, de 10 a 18 anos de idade, na cidade de Salvador. Os procedimentos de fazer arquivo foram executados por de meio de exercícios descritivos, tomando por referência documentos, registros de entrevistas, observações e diários etnográficos realizados ao longo de um ano, junto às atividades de artes praticadas na ONG. Esses exercícios consolidaram um texto narrativo no qual o CRIA é compreendido como instituição que existe a partir de historicidades locais, regionais e individuais afirmando a tese de que educar através da arte é um argumento que amplia os sentidos da vida e conduz adolescentes e jovens ao experimento de auto-criação de si, de seu laços com a cultura e com o presente. As ações de educação empreendidas pela ONG têm por referência práticas de cidade, experimentação teatral e poética e a implementação de políticas de arte e cultura no âmbito da educação formal de jovens. Neste sentido apresenta-se uma discussão sobre a juventude no terreno da historia social e no campo da sociologia, em especial a relação educação escolar e trabalho capitalista, bem como juventude e práticas de cultura com vistas a explicitar os nomes da juventude que a modernidade ocidental celebrou como verdadeiros. Finalmente apresenta-se um ensaio sobre a juventude que, inspirado em Nietzsche, procura pôr em cena diálogos da razão trágica a que o CRIA expõe os jovens que fazem formação em artes. Palavras chaves: Juventude; Arte; Educação; Método Histórico, Razão Trágica.

Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgico / CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior / Esta pesquisa se utiliza do MÃtodo HistÃrico, proposto por Michel Foucault, para conhecer o CRIA â Centro de ReferÃncia Integral de Adolescentes, ONG que trabalha, desde 1994, com formaÃÃo artÃstica para jovens, de 10 a 18 anos de idade, na cidade de Salvador. Os procedimentos de fazer arquivo foram executados por de meio de exercÃcios descritivos, tomando por referÃncia documentos, registros de entrevistas, observaÃÃes e diÃrios etnogrÃficos realizados ao longo de um ano, junto Ãs atividades de artes praticadas na ONG. Esses exercÃcios consolidaram um texto narrativo no qual o CRIA à compreendido como instituiÃÃo que existe a partir de historicidades locais, regionais e individuais afirmando a tese de que educar atravÃs da arte à um argumento que amplia os sentidos da vida e conduz adolescentes e jovens ao experimento de auto-criaÃÃo de si, de seu laÃos com a cultura e com o presente. As aÃÃes de educaÃÃo empreendidas pela ONG tÃm por referÃncia prÃticas de cidade, experimentaÃÃo teatral e poÃtica e a implementaÃÃo de polÃticas de arte e cultura no Ãmbito da educaÃÃo formal de jovens. Neste sentido apresenta-se uma discussÃo sobre a juventude no terreno da historia social e no campo da sociologia, em especial a relaÃÃo educaÃÃo escolar e trabalho capitalista, bem como juventude e prÃticas de cultura com vistas a explicitar os nomes da juventude que a modernidade ocidental celebrou como verdadeiros. Finalmente apresenta-se um ensaio sobre a juventude que, inspirado em Nietzsche, procura pÃr em cena diÃlogos da razÃo trÃgica a que o CRIA expÃe os jovens que fazem formaÃÃo em artes. Palavras chaves: Juventude; Arte; EducaÃÃo; MÃtodo HistÃrico, RazÃo TrÃgica. / This research was used in Method History (arch-genealogy), to learn the meanings of teaching practices and proposals offered to young people who are integrated into programs and / or educational projects in a non-school institution. The empirical field was the CRIA â Centro de ReferÃncia Integral de Adolescentes, an NGO working since 1994 with artistic training for young people 10-18 years of age in the city of Salvador. The procedures for doing file were executed by means of descriptive exercises, taking as reference documents, records of interviews, ethnographic observations and diaries made ​​over a year, with the activities of NGOs in the arts practiced. These exercises reinforced a narrative text in which CRIA is understood as an institution that exists from historicities local, regional and individual asserting the claim that educating through art is an argument that extends the meaning of life and puts, adolescents and young given the need to forge himself in relation to culture and the present. The education activities undertaken by NGOs have a handy reference of the city, theatrical experimentation, clown and poetry; implementation of policies of art and culture in the context of formal education and community which young people are linked.

Genealogy reconstruction is widely used in biology when relationships among entities are studied. Phylogenies, or evolutionary trees, show the differences between species. They are of profound importance because they help to obtain better understandings of evolutionary processes. Pedigrees, or family trees, on the other hand visualize the relatedness between individuals in a population. The reconstruction of pedigrees and the inference of parentage in general is now a cornerstone in molecular ecology. Applications include the direct infer- ence of gene flow, estimation of the effective population size and parameters describing the population’s mating behaviour such as rates of inbreeding. In the first part of this thesis, we construct genealogies of various types of cancer. Histopatho- logical classification of human tumors relies in part on the degree of differentiation of the tumor sample. To date, there is no objective systematic method to categorize tumor subtypes by maturation. We introduce a novel algorithm to rank tumor subtypes according to the dis- similarity of their gene expression from that of stem cells and fully differentiated tissue, and thereby construct a phylogenetic tree of cancer. We validate our methodology with expression data of leukemia and liposarcoma subtypes and then apply it to a broader group of sarcomas and of breast cancer subtypes. This ranking of tumor subtypes resulting from the application of our methodology allows the identification of genes correlated with differentiation and may help to identify novel therapeutic targets. Our algorithm represents the first phylogeny-based tool to analyze the differentiation status of human tumors. In contrast to asexually reproducing cancer cell populations, pedigrees of sexually reproduc- ing populations cannot be represented by phylogenetic trees. Pedigrees are directed acyclic graphs (DAGs) and therefore resemble more phylogenetic networks where reticulate events are indicated by vertices with two incoming arcs. We present a software package for pedigree reconstruction in natural populations using co-dominant genomic markers such as microsatel- lites and single nucleotide polymorphism (SNPs) in the second part of the thesis. If available, the algorithm makes use of prior information such as known relationships (sub-pedigrees) or the age and sex of individuals. Statistical confidence is estimated by Markov chain Monte Carlo (MCMC) sampling. The accuracy of the algorithm is demonstrated for simulated data as well as an empirical data set with known pedigree. The parentage inference is robust even in the presence of genotyping errors. We further demonstrate the accuracy of the algorithm on simulated clonal populations. We show that the joint estimation of parameters of inter- est such as the rate of self-fertilization or clonality is possible with high accuracy even with marker panels of moderate power. Classical methods can only assign a very limited number of statistically significant parentages in this case and would therefore fail. The method is implemented in a fast and easy to use open source software that scales to large datasets with many thousand individuals.:Abstract v Acknowledgments vii 1 Introduction 1 2 Cancer Phylogenies 7 2.1 Introduction..................................... 7 2.2 Background..................................... 9 2.2.1 PhylogeneticTrees............................. 9 2.2.2 Microarrays................................. 10 2.3 Methods....................................... 11 2.3.1 Datasetcompilation ............................ 11 2.3.2 Statistical Methods and Analysis..................... 13 2.3.3 Comparison of our methodology to other methods . . . . . . . . . . . 15 2.4 Results........................................ 16 2.4.1 Phylogenetic tree reconstruction method. . . . . . . . . . . . . . . . . 16 2.4.2 Comparison of tree reconstruction methods to other algorithms . . . . 28 2.4.3 Systematic analysis of methods and parameters . . . . . . . . . . . . . 30 2.5 Discussion...................................... 32 3 Wild Pedigrees 35 3.1 Introduction..................................... 35 3.2 The molecular ecologist’s tools of the trade ................... 36 3.2.1 3.2.2 3.2.3 3.2.1 Sibship inference and parental reconstruction . . . . . . . . . . . . . . 37 3.2.2 Parentage and paternity inference .................... 39 3.2.3 Multigenerational pedigree reconstruction . . . . . . . . . . . . . . . . 40 3.3 Background..................................... 40 3.3.1 Pedigrees .................................. 40 3.3.2 Genotypes.................................. 41 3.3.3 Mendelian segregation probability .................... 41 3.3.4 LOD Scores................................. 43 3.3.5 Genotyping Errors ............................. 43 3.3.6 IBD coefficients............................... 45 3.3.7 Bayesian MCMC.............................. 46 3.4 Methods....................................... 47 3.4.1 Likelihood Model.............................. 47 3.4.2 Efficient Likelihood Calculation...................... 49 3.4.3 Maximum Likelihood Pedigree ...................... 51 3.4.4 Full siblings................................. 52 3.4.5 Algorithm.................................. 53 3.4.6 Missing Values ............................... 56 3.4.7 Allelefrequencies.............................. 58 3.4.8 Rates of Self-fertilization.......................... 60 3.4.9 Rates of Clonality ............................. 60 3.5 Results........................................ 61 3.5.1 Real Microsatellite Data.......................... 61 3.5.2 Simulated Human Population....................... 62 3.5.3 SimulatedClonalPlantPopulation.................... 64 3.6 Discussion...................................... 71 4 Conclusions 77 A FRANz 79 A.1 Availability ..................................... 79 A.2 Input files...................................... 79 A.2.1 Maininputfile ............................... 79 A.2.2 Knownrelationships ............................ 80 A.2.3 Allele frequencies.............................. 81 A.2.4 Sampling locations............................. 82 A.3 Output files..................................... 83 A.4 Web 2.0 Interface.................................. 86 List of Figures 87 List of Tables 88 List Abbreviations 90 Bibliography 92 Curriculum Vitae I

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