Os programas de melhoramento da cana-de-açúcar demandam aproximadamente 12 anos para a obtenção de um novo cultivar. Assim, os marcadores moleculares podem ser usados como uma ferramenta valiosa, uma vez que possibilitamo estudo da arquitetura genética de caracteres quantitativos, ajudando a reduzir este tempo. Embora a cana-de-açúcar seja uma cultura perene, para a qual o desempenho genotípico é avaliado através de ensaios estabelecidos ao longo de diferentes locais e cortes, a maior parte dos estudos de mapeamento de QTLs ignora a existência de interação entre QTLs, corte e local (QTL × H × L). Neste contexto, o presente trabalho apresenta uma estratégia que foi desenvolvida para a detecção de QTLs em cana-de-açúcar, com base em modelos mistos e mapeamento por intervalo, considerando diferentes estruturas de (co)variância que permitem supor heterogeneidade de variâncias genéticas e existência de correlações genéticas entre cortes e locais. A metodologia de modelos mistos foi aplicada aos dados de uma população segregante obtida a partir do cruzamento entre dois cultivares pré-comerciais de cana-de-açúcar, constituída por 100 indivíduos avaliados em dois locais (Piracicaba e Jaú, SP, Brasil) e em três cortes para produção (toneladas de cana por hectare, TCH), produção de açúcar (toneladas de Pol por hectare, TPH), porcentagem de fibra e Pol (teor de sacarose). A análise fenotípica resultou na seleção do modelo não-estruturado, que assume heterogeneidade de variâncias e existência de correlação genética específica para cada combinação de corte e local, para todos os caracteres avaliados. Na análise de mapeamento, foram detectados 50 QTLs, incluindo 14 QTLs para TCH, 15 para TSH, 10 para Pol e 11 para Fibra. Além disso, os resultados mostram que os efeitos das interações entre QTL e corte (QTL × H), QTL e local (QTL × L) e QTL, corte e local (QTL × H × L) foram importantes para todos os caracteres avaliados. Do total de QTLs identificados, 33 (66 %) apresentaram algum tipo de interação e apenas 17 (34 %) mostraram mesmo efeito entre as diferentes combinações de corte e local. Estes resultados fornecem informações importantes para o entendimento da base genética de caracteres quantitativos relacionados com produção e teor de sacarose em cana-de-açúcar. / Sugarcane breeding programs take at least twelve years to develop new commercial cultivars. Thus, molecular markers can be used as a valuable tool since they offer the possibility to study the genetic architecture of quantitative traits, helping to reduce this time. Although the performance of genotypes in sugarcane breeding programs has been evaluated across a range of locations and harvest years, since sugarcane is a perennial crop, many of the QTL detection methods ignore QTL by harvest by location interaction (QTL × H × L). In this work, a strategy for QTL detection in sugarcane was developed, based on mixed models and interval mapping, considering different (co)variance structures for the modeling of heterogeneous genetic variances and genetic correlations between harvests and locations. The mixed model approach was applied to a data set provided by a segregating population developed from a cross between two pre-commercial Brazilian cultivars, consisted of 100 individuals planted in two locations in 2003 (Piracicaba and Jaú, SP, Brazil) and evaluated in the first, second and third subsequent harvest years for cane yield (tonnes of cane per hectare, TCH), sugar yield (tonnes of sugar per hectare, TSH), fiber percent and Pol (sucrose content). Phenotypic analysis provided the selection of the unstructured model, which allows the assumption of heterogeneity of variance and presence of a specific genetic correlation for each combination of harvest and location. In the QTL mapping procedure, 50 QTLs were detected, including 14 QTLs for TCH, 15 for TSH, 10 for Pol and 11 for Fiber. In addition, the results show that QTL by harvest (QTL × H), QTL by location (QTL × L) and QTL by harvest by location (QTL × H × L) interaction effects were important for all evaluated traits. From the total of QTLs identified, 33 (66%) had some interaction and only 17 (34%) showed stable effects across the different combinations of harvest and location. These results can provide useful information to understand the genetic control of complex traits related with sugarcane production and sucrose content.

Os objetivos do presente trabalho compreenderam a obtenção de estimativas de parâmetros genéticos e fenotípicos, como variâncias, correlações, herdabilidades e respostas à seleção, em uma população derivada do cruzamento entre as linhagens 14 e 56 de soja, contrastantes para produção de grãos. Os tratamentos consistiram de uma amostra de 89 progênies F2:4 e 11 testemunhas comerciais, que foram avaliadas em experimentos em látice triplo 10 x 10 no ano agrícola 2007/08 na Estação Experimental Anhembi do Departamento de Genética da ESALQ/USP, localizada em Piracicaba, SP. A parcela experimental foi constituída de uma linha de 2 m de comprimento, espaçada de 0,5 m, contendo 35 plantas no estande ideal, após o desbaste. Foram avaliados os seguintes caracteres: dias até a maturação (DM), altura das plantas na maturação (AM), acamamento (AC) e produção de grãos (PG). As estimativas dos coeficientes de herdabilidade entre médias de progênies foram: elevada para AM (77,4%), mediana para DM (32,3%) e baixas para AC e PG (18,1% e 19,0%, respectivamente). Entretanto, os coeficientes de variação genética foram muito baixos para DM e AC (0,37% e 1,61%, respectivamente), e mais altos para AM e PG (6,80% e 6,83%, respectivamente), indicando a ocorrência de pouca variabilidade genética para DM e AC e, conseqüentemente, poucas perspectivas de resposta à seleção. O coeficiente de correlação genética entre AM e PG foi alto (rg = 0,67), indicando que a seleção para PG deve resultar em plantas mais altas. A estimativa da resposta com seleção das 20% progênies mais produtivas foi de 4,5%, e a resposta correlacionada em AM foi de 3,8%. Devido à baixa variabilidade genética, as respostas correlacionadas esperadas em DM e AC foram muito pequenas. Os resultados indicam que a população pode ser melhorada somente para os caracteres PG e AM. / This paper was carried out in order to estimate genetic and phenotypic parameters, such as variances, heritabilities, correlations and expected response to selection in a population derived from the cross between inbred lines 14 and 56 of soybeans, divergent for grain yield. Entries consisted of a sample of 89 F2:4 progenies and 11 commercial checks, evaluated in a triple 10 x 10 lattice design in the 2007/08 growing season at Anhembi Experimental Station of the Genetics Department (ESALQ/USP), near Piracicaba, SP. Plots were single 2-meter-long rows spaced 0.5 m apart, with 35 plants after thinning. The following traits were evaluated: days to maturity (DM), plant height at maturity (AM), lodging (AC) and grain yield (PG). Heritability estimates on a progeny mean basis were high for AM (77.4%), medium for DM (32.3%) and low for AC and PG (18.1% and 19.0%, respectively). However, genetic coefficients of variation were very low for DM and AC (0.37% and 1.61%, respectively) and higher for AM and PG (6.80% and 6.83%, respectively), which indicates low genetic variability for DM and AC and, consequently, small perspectives of response to selection. Genetic correlation coefficient between AM and PG was high (rg = 0.67), indicating that selection for higher PG will result in taller plants. Expected response based on selection of the 20% high yielding progenies was 4.5%, and the correlated response in AM was 3.8%. The correlated response in DM and AC were very low, due to the low genetic variability. General results have shown that the population can be improved only for the traits PG and AM.

Abstract Many waders are in decline, and the number of endangered species and populations is increasing. Their protection and management requires knowledge of both ecological and genetic state of the populations. In this thesis, I studied the distribution-wide genetic variation, structure and phylogeography of the Temminck’s Stint (Calidris temminckii) and Terek Sandpiper (Xenus cinereus) using microsatellites and sequence data from the mitochondrial control region and cytochrome oxidase I gene. I compared these regionally endangered species to other waders with varying evolutionary histories, breeding systems and habitat preferences to examine the levels of genetic variation and structure at different spatial scales. In addition, I studied the genetic structure of the endangered Baltic population of the Southern Dunlin (Calidris alpina schinzii) with microsatellites. I used genetic information in all three study species to determine units for conservation. The Temminck’s Stint and Terek Sandpiper, both not restricted to the Arctic, had low distribution-wide structuring. They also had quite low levels of variation when compared to other species breeding at similar latitudes, indicating reductions in population sizes during past climate changes. Especially the peripheral breeding populations were differentiated and showed signs of inbreeding and genetic drift when compared to the main range. The Temminck’s Stint populations at the Bothnian Bay and Yakutia, and Terek Sandpiper populations in Finland and Belarus, should be treated as separate management units. The broader interspecific comparison of waders suggests that habitat availability, mating system and the extent of philopatry may affect the genetic composition of species. The genetic analyses of the Southern Dunlin indicated strong effects of philopatry and inbreeding throughout the range. Local subpopulations at the Bothnian Bay and in Sweden need to be considered as separate management units. Management efforts at the Baltic should be focused on increasing connectivity and providing large enough breeding habitats for potential immigrants and recruits. / Tiivistelmä Useat kahlaajapopulaatiot ovat pienentyneet ja uhanalaistuneet maailmanlaajuisesti. Lajien ja populaatioiden ekologiaa ja genetiikkaa on tunnettava, jotta suojelutoimia voidaan kohdistaa oikein. Tutkin väitöskirjassani lapinsirrin (Calidris temminckii) ja rantakurvin (Xenus cinereus) geneettistä rakennetta, muuntelua ja fylogeografiaa levinneisyysalueen laajuisesti mikrosatelliittien ja mitokondrion kontrollialueen ja sytokromioksidaasi I -geenin sekvenssien avulla. Tutkin, mitkä tekijät vaikuttavat geneettisen rakenteeseen ja muunteluun vertaamalla näitä lajeja muihin kahlaajiin, joilla on erilaisia lisääntymisstrategioita, jotka pesivät vaihtelevissa ympäristöissä ja joista monet eroavat toisistaan myös fylogeografialtaan. Lisäksi tutkin Itämeren rannalla pesivän etelänsuosirrin (Calidris alpina schinzii) geneettistä populaatiorakennetta mikrosatelliittien avulla. Käytin geneettistä tietoa hyväksi luonnonsuojeluyksikköjen määrittämisessä kaikille kolmelle tutkimuslajilleni. Lapinsirrin ja rantakurvin fylogeografinen historia oli samankaltainen. Geneettisen muuntelun määrä oli vähäisempää verrattuna muihin, samankaltaisissa ympäristöissä pesiviin kahlaajiin. Molemmat lajit ovat todennäköisesti kärsineet historiallisten ilmaston-muutosten aiheuttamasta populaatioiden pienenemisestä. Erityisesti levinneisyysalueen reunoilla pesivät populaatiot olivat erilaistuneita, ja niissä näkyi sukusiitoksen ja geneettisen satunnaisajautumisen merkkejä. Perämeren ja Jakutian lapinsirri- sekä Valko-Venäjän ja Suomen rantakurvipopulaatioita tulee kohdella erillisinä suojeluyksiköinään. Vertailu muihin kahlaajiin osoitti, että niin pesimä- ja talvehtimisalueiden laajuus kuin lisääntymisstrategiat ja paikkauskollisuus voivat vaikuttaa lajien geneettiseen koostumukseen. Etelänsuosirrin geneettiset analyysit paljastivat merkkejä sukusiitoksesta, joita paikkauskollisuus ja populaatioiden pienuus ovat voimistaneet. Perämeren ja Ruotsin populaatioita tulee kohdella erillisinä suojeluyksiköinään. Suojelutoimet on kohdistettava tarpeeksi suurien, hyvälaatuisten pesimäpaikkaverkostojen ylläpitämiseen.

Force est de constater que les dépérissements forestiers augmentent. Ces observations vont de pairs avec l’accroissement des événements climatiques extrêmes. Aussi dans ce contexte, il est nécessaire d’identifier denouveaux caractères de resistance à la sécheresse. La résistance à la cavitation est actuellement le meilleurmarqueur de la survie d’une espèce à la sécheresse.Cette thèse avait deux objectifs : (i) comprendre le mécanisme de propagation de la cavitation dans le xylèmechez les gymnospermes. (ii) Quantifier la variation phénotypique in situ de ce caractère chez Pinus pinaster ainsique (iii) quantifier la variation génétique, et sa plasticité phénotypique.La démarché a été la suivante (i) une étude interspécifique de la résistance à la cavitation a été couplé à desmesures micro-anatomiques. (ii) Pour le volet intraspécifique, nous avons phénotypé 6 populations dans deuxtest de populations-descendances, ainsi qu’en population naturelles in situ.La propagation de l’embolie chez les Pinaceae et les ex-Taxodiaceae pourrait être due au passage du germe d’air(rupture capillaire) à travers des nanopores dans le torus. En effet, la pression de rupture d’un ménisque air-sèveest corrélée à l’entrée de l’air dans le xylème (P12). Alors que la variation interspécifique est grande, la résistanceà la cavitation varie faiblement au sein d’une espèce. Ainsi les populations provenant de climat contrasté neprésentent pas ou peu de différence génétique (en test de provenance) ou en populations naturelles in situ. Cecaractère présente une plasticité phénotypique mais faible comparée à celle de la croissance en hauteur parexemple. La comparaison entre la variation génétique entre populations et la variation des marqueurs neutresentre ces mêmes populations montrent que la variation de ce caractère semble réduite par l’architecturegénétique sous-jacente. La resistance à la cavitation est vraisemblablement un trait canalisé. / Several review reported global forest die-back that are caused, directly or indirectly, by extreme climatic events(like heat waves or prolonged drought). In this context, there is an urgent need to identify new traits to tracedrought tolerance. Resistance to cavitation is one of the best proxy for survival during extreme drought.The aim of this work was (i) to understand how spreads cavitation in the vascular pathway of gymnosperms (ii)to quantify the phenotypic variation of resistance to cavitation for Pinus pinaster species, (iii) to determine theamount of the genetic variation and phenotypic plasticity available for this trait.A micro-anatomy study was coupled to measurement of resistance to cavitation for various species to foundwhere air-seeding occurs in the bordered pit. To quantify the variability of resistance to cavitation, wephenotyped 506 genotypes using to replicated provenance-progeny trials and on natural in situ populations.The spread of embolism for Pinaceae and ex-Taxodiaceae could be due to minute pore in tori, which are remainsof secondary plasmodesmata. We found that the pressure needed to break a water/air meniscus in these minutepores is correlated with the xylem air entry (P12). Despite the great variability of resistance to cavitation betweenspecies, we found low variability within species. Most of the variability is within population, rather than betweenpopulations. The phenotypic plasticity of resistance to cavitation is low compare to growth traits. Comparisonbetween QST and FST shows that populations exhibit less variation compare to what it is expected under geneticdrift. The variation of resistance to cavitation seems to be narrowed by the genetic architecture, which is the signof canalisation.

Orientadores: Maria Imaculada Zucchi, Anete Pereira de Souza / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-27T12:00:33Z (GMT). No. of bitstreams: 1 Pavinato_VitorAntonioCorrea_D.pdf: 6829608 bytes, checksum: 7fdb8c74593eb4dc2fe78e2302d3995f (MD5) Previous issue date: 2014 / Resumo: A associação entre subpopulações de insetos e plantas-hospedeiras pode ocorrer por adaptação e esta, pode ser uma etapa anterior ao surgimento de raças-hospedeiras e especialização. Pouco se sabe sobre o papel da mudança da composição da paisagem, mediada pela atividade agrícola recente, na divergência adaptativa e fluxo gênico de insetos fitófagos. Dessa forma, o presente trabalho teve como objetivos: i) desenvolver marcadores moleculares microssatélites para o estudo genético de um inseto fitófago, Diatraea saccharalis; ii) quantificar e caracterizar a estrutura genética, o fluxo gênico e os fatores que contribuem para a divergência genética das subpopulações da espécie; iii) identificar variação genética sob seleção natural que possa estar contribuindo para a divergência genética de subpopulações associadas a cana-de-açúcar e milho e; iv) desenvolver recurso genômico através de bibliotecas genômicas RADtag para a busca, desenvolvimento e caracterização de marcadores moleculares associados a genes candidatos. Dos 20 locos microssatélites, dez foram selecionados para serem utilizados no estudo de ecologia molecular. Os índices de diferenciação mostraram que, tanto a estruturação genética espacial, quanto a determinada pelo hospedeiro, foram significativas. Dos 301 locos AFLP utilizados para a genotipagem de quatro subpopulações, 19 foram identificados como outliers nas comparações par-a-par e desses, cinco locos foram identificados pelos dois métodos empregados na detecção de outliers, e podem, desta forma, estar associados à adaptação à planta-hospedeira. Os resultados das análises de agrupamento utilizando os locos outliers mostraram o agrupamento dos indivíduos em grupos que representam a planta-hospedeira onde foram coletados. Os mesmos resultados foram obtidos com uma amostra dos SNPs isolados através do protocolo de RADtag. Os dados genômicos obtidos até o momento estão sendo utilizados, juntamente com o estudo de genômica comparativa, na identificação e desenho de primers específicos para genes candidatos. Os resultados mostraram os efeitos da expansão e mudança recente da paisagem agrícola na diversidade genética de uma espécie de inseto fitófago. A atividade agrícola pode ser fonte de seleção divergente suficiente para levar à especialização e especiação de insetos. Os resultados deste trabalho sugerem estar havendo divergência ecológica entre as subpopulações de D. saccharalis coletadas em milho e cana-de-açúcar e que esta divergência, por ser recente, não é completa. Além disso, esses resultados mostram a necessidade de estudos complementares para isolar as fontes de seleção divergente, os mecanismos de isolamento reprodutivo, e a arquitetura genética que liga a seleção divergente ao isolamento reprodutivo / Abstract: The association between subpopulations of insects and their host plants can occur by adaptation and this may lead to host-races formation and specialization. Little is known about the role of the changing landscape composition mediated by recent agricultural activity in adaptive divergence and gene flow of phytophagous insects. This study aimed to: i) develop microsatellite markers for the genetic study of a phytophagous insect, Diatraea saccharalis; ii) quantify and characterize the genetic structure, gene flow and the factors that contribute to the genetic divergence of subpopulations of the species; iii) identify genetic variation that may be experiencing natural selection and thus be contributing to genetic divergence of subpopulations associated with sugarcane and maize; iv) develop genomic resource through RADtag libraries to search, characterize and develop molecular markers linked to candidate genes. Ten of 20 microsatellite loci were selected for use in the study of molecular ecology. The genetic differentiation showed that both spatial genetic structure and that determined by the host-plant were significant. Of the 301 AFLP loci used for genotyping four subpopulations, 19 were identified as outliers in pairwise comparisons and five were identified by the two methods employed for outliers detection and thus, can be associated with host-plant adaptation. Cluster analysis using outlier loci showed the grouping of individuals into groups that represent the host plant where they were collected. Data from a sample of SNPs isolated by RADtag protocol showed the same results. The genomic data obtained so far are being used together with the study of comparative genomics for the identification and design of specific primers for candidate genes. The results showed the effects of expansion and recent changes in agricultural landscape in genetic diversity of phytophagous insect species. Farming can generate enough source for ecologically based divergence that could lead to specialization and speciation in insects species. The results of this study suggest that there is ecological divergence between subpopulations of D. saccharalis collected from corn and sugarcane, but it is not complete. In addition, these results showed the need for further studies to isolate the sources of divergent selection, the mechanisms of reproductive isolation, and the genetic architecture linking the divergent reproductive isolation with selection / Doutorado / Genetica Animal e Evolução / Doutor em Genetica e Biologia Molecular

Os genes de receptores olfatórios (OR) pertencem a uma família de proteínas de membrana formada por cerca de 1000 genes no genoma de camundongo. Os genes OR são expressos de forma monogênica e monoalélica nos neurônios olfatórios (OSNs). No entanto, ainda não está claro o mecanismo que permite essa forma de expressão peculiar, sobretudo, qual o papel da metilação de DNA nesse processo. Nosso estudo determinou o padrão de metilação de DNA da região promotora e codificadora do gene Olfr17. Em células de epitélio olfatório (MOE) de camundongos adultos, observamos na região codificadora (CDS) do gene uma frequência de metilação em dinucleotídeos CpG 58%, enquanto que na sua região promotora ela foi bem mais baixa. Os níveis de metilação do Olfr17 em MOE de embrião (E15.5) e fígado foram similares aos observados em MOE de animais adultos. Em seguida, analisamos se a metilação de DNA pode regular a expressão gênica do Olfr17. Utilizando animais transgênicos onde os neurônios olfatórios que expressam Olfr17 também expressam GFP, pudemos selecionar neurônios olfatórios GFP+ e analisar a metilação do gene Olfr17, que está ativo nestas células. Verificamos que o padrão geral de metilação do Olfr17, tanto na região CDS como na região promotora, não se altera quando este gene está ativo. Este resultado indica que alterações na metilação do gene Olfr17 não são necessárias para que este receptor seja expresso. Finalmente, verificamos que a região promotora do gene Olfr17, de duas linhagens de camundongos diferentes, a C57BL/6 e a 129, possuem dois polimorfismos de base única (SNPs) que alteram o conteúdo CpG. Devido a estes SNPs, a linhagem 129 apresenta dois sítios CpG adicionais, inexistentes na linhagem C57BL/6. Nossas análises mostraram que estes CpGs são frequentemente metilados, o que torna o promotor do Olfr17 de 129 significativamente mais metilado que o promotor de C57BL/6. Em seguida, nós analisamos o nível de expressão no MOE dos dois alelos de Olfr17, o 129 e o C57BL/6, utilizando ensaios de RT-qPCR. Estes experimentos demonstraram que o nível de expressão do alelo 129, que possui 3 CpGs metiladas em seu promotor, é menor que o do alelo C57BL/6, que apresenta apenas uma CpG que é pouco metilada em seu promotor. Nossos resultados sugerem que as alterações na região promotora influenciam a probabilidade com que o gene OR é escolhido para ser expresso no MOE. / Olfactory receptor (OR) genes belong to a large family of membrane proteins composed of 1000 genes in the mouse genome. The OR genes are expressed in the olfactory sensory neurons (OSNs) in a monogenic and monoallelic fashion. However, the mechanisms that govern OR gene expression are unclear. Here we asked whether DNA methylation plays a role in the regulation of OR gene expression. We first determined the DNA methylation pattern in the coding (CDS) and promoter regions of the odorant receptor gene Olfr17. In olfactory epithelium (MOE) cells, the CpG methylation level in the CDS is 58% but is much lower in the promoter region of the gene. In embryonic MOE (E15.5) and liver, the levels of Olfr17 DNA methylation are similar to the ones shown in adult MOE. We next analyzed whether DNA methylation is involved in Olfr17 regulation. We isolated GFP+ neurons from transgenic mice that coexpress GFP with Olfr17, and analyzed the DNA methylation pattern of the Olfr17, which is active in these cells. We found that the general methylation pattern, both, in the coding and promoter regions is not altered in the active gene. These results indicate that changes in DNA methylation are not required for the activation of Olfr17. Finally, we found that the Olfr17 promoter region from two different mouse strains, C57BL/6 and 129, has two single-nucleotide polymorphisms (SNPs) that alter the CpG content. The SNPs lead to the existence of two additional CpGs in the 129 allele, which are absent in the C57BL/6 allele. These CpGs are frequently methylated, making the 129 Olfr17 promoter significantly more methylated than the Olfr17 promoter from C57BL/6. We next performed RT-qPCR experiments to analyze the expression levels of the 129 and C57BL/6 Olfr17 alleles in the MOE. These experiments showed that the expression level of the 129 Olfr17 allele, which contains three methylated CpGs in its promoter region, is lower than the one from C57BL/6, which contains only one, undermethylated CpG, in its promoter. Our results suggest that these promoter modifications regulate the probability of the OR gene choice.

O HBoV é um novo parvovírus que foi isolado pela primeira vez em 2005 nas secreções respiratórias de pacientes humanos que tiveram pneumonia. Desde então, é associado a doenças do trato respiratório superior e doença gastrointestinal em pacientes adultos e pediátricos, desde a sua descoberta na Suécia e posteriormente em diversos países no Mundo. Quase todos os estudos foram realizados em amostras de secreção do trato respiratório, normalmente, de crianças com menos de 2 anos de idade e a maioria com infecção respiratória. As taxas de prevalência variam de 1,5% a 19% nos diferentes países. A Análise filogenética deste novo vírus demonstrou que tratava-se de um parvovirus, mais estreitamente relacionado ao parvovírus bovino e ao minuto vírus canino e por isso foi denominado de Bocavírus Humano. A variabilidade genética do HBoV é baixa e estudos filogenéticos indicam que duas linhagens circulam paralelamente ao redor do mundo. Entretanto, como ainda é um vírus relativamente novo, devem se feitos estudos mais detalhados de suas variantes. Em nosso estudo, com a finalidade de determinar a prevalência e conhecer a variabilidade genética do HBoV circulante, foram analisados de janeiro de 2008 a fevereiro de 2010, 935 amostras de aspirado de nasofaringe de crianças com menos de 2 anos de idade, com doença respiratória aguda, internadas no Hospital da Santa Casa de Misericórdia de São Paulo. Pela técnica de PCR, obtivemos 47 (4,7%) amostras positivas para HBoV e dessas 27 amostras apresentaram coinfecção com outros vírus respiratórios, 45 amostras foram seqüenciadas na região da VP1/VP2 de um fragmento de 658 nt. A análise filogenética, quando comparada com seqüência do genBank representativas de vários países, mostrou a circulação, em nossa amostragem, de grupos de HBoV semelhantes aos que circulam no Japão e Taiwan. A variabilidade genética entre as nossas amostras foram inferiores a 1%, tanto entre si como quando comparadas com as amostras do genBank. / HBoV is a new parvovirus which was first isolated in 2005 from respiratory secretions from human patients who had pneumonia. It has been associated with respiratory and gastrointestinal diseases in adult and pediatric patients since its discovery in Sweden and later in several countries worldwide. Almost all studies were performed on samples of secretions from the respiratory tract, usually in children under 2 years of age. Prevalence rates vary from 1.5% to 19% in different countries. The phylogenetic analysis of this new virus showed that it was a parvovirus, more closely related to bovine parvovirus and canine minute virus, and therefore called Human Bocavirus. The genetic variability of HBoV is low and phylogenetic studies indicate that there are two strains circulating alongside around the world. However, as it is still a relatively new virus, more detailed studies of its variants should be carried out. In our study, 935 samples of nasopharyngeal aspirate from children under 2 years old with acute respiratory disease, patients at Santa Casa de Misericordia Hospital, São Paulo, were analyzed from February 2008 to February 2010 in order to determine the prevalence and genetic variability of HBoV stock. Using the PCR method, we obtained 47 (4.7%) positive samples for HBoV from which 27 showed coinfection with other respiratory viruses; 45 samples from a fragment of 658 nt were sequenced in the VP1/VP2 region. The phylogenetic analysis, when compared with GenBank sequences representing several countries, showed the presence in our samples of groups of HBoV similar to those circulating in Japan and Taiwan. Genetic variation in our samples were below 1%, both among themselves and when compared with samples from GenBank.

O Vírus Respiratório Sincicial Humano (HRSV) é considerado o principal causador de doenças agudas do trato respiratório inferior durante a infância, sendo o principal responsável por um elevado índice de hospitalização de crianças com até cinco anos de idade. Possui distribuição mundial, podendo acometer todas as faixas etárias, entretanto as crianças de 6 semanas a 9 meses são as que desenvolvem problemas mais sérios, como pneumonia e bronquiolite. A epidemia de HRSV apresenta uma sazonalidade bem clara, ocorrendo anualmente no período de outono tardio, inverno ou início da primavera, mas não durante o verão. No presente estudo foi realizada a análise da região G2 da glicoproteína G do HRSV. Um total de 44 amostras positivas para o HRSV do Hospital Universitário (HU) da Universidade de São Paulo (USP), nos anos de 2007-2008, foram seqüenciadas e posteriormente analisadas, sendo então comparadas com seqüências obtidas do NCBI/GeneBank. A análise filogenética mostrou que os genótipos GA2 e GA5, do grupo A, foram os predominantes nos anos de 2007 e 2008, alternando o padrão verificado nos anos anteriores, onde os genótipos do grupo B foram altamente predominantes. A comparação das mutações sinônimas e não sinônimas mostrou uma grande evidência de seleção positiva nos genótipos GA2 e GA5 do grupo A. / Human Respiratory Syncytial Virus (HRSV) is considered the most common cause of lower respiratory tract disease in infants and young children and are the main guilty for the elevated children hospitalizations rate under 5 years of age. The HRSV has a world-wide distribution, being able to attack all the ages however the 6 weeks to 9 months children of are the ones that develop more serious problems as pneumonia and bronquiolite. The HRSV outbreak presents a well defined season, occurring annually in the delayed falls period, winter or springs beginning, but not during the summer. In the present study, we performed a phylogenetic analysis from G2 region of HRSV G glycoprotein. Forty four samples positive for HRSV from University Hospital (UH) of University of Sao Paulo (USP) in 2007-2008, were submitted to sequencing by PCR and compared with GenBank sequences. Phylogenetic analysis revealed that HRSV group A genotypes GA2 and GA5 was the predominant in 2007-2008, alternating the standard verified in the previous years, where the group B genotypes had been highly predominant. Comparison of the synonymous/nonsynonymous mutation ratios showed greater evidence for positive selection pressure for group A genotypes GA2 and GA5.

Analyse de la diversité inter et intra-spécifique des paramètres de l’architecture des systèmes racinaires chez les Solanacées. Les racines des plantes jouent un rôle important pour garantir productivité et résistance à de nombreux stress. Dans le nouveau contexte agricole, l’importance de ce système racinaire et de sonarchitecture sont remises au premier plan. Notre étude porte sur la dynamique de l’architecture racinaire des solanacées, qui contient un ensemble d’espèces horticoles importantes pour l’alimentation. Notre travail porte sur 32 génotypes, parmi 3 groupes d’espèces: aubergines, piments et tomates.Dans cette étude, nous proposons tout d’abord une analyse de la diversité inter et intraspécifique de l’architecture racinaire à travers l’évaluation d’un ensemble de traits qui sont aussi les paramètres d’un modèle dynamique de simulation (ArchiSimple : Pagès et al, 2012). Cette première évaluation a été faite en pots, en utilisant un milieu très favorable à la croissance des plantes et à l’enracinement. Nous montrons que les traits racinaires choisis présentent en effet des variations d’origine génétique, généralement plus fortes entre espèces qu’au sein des espèces. Nous avons également observé des corrélations entre certains traits qui révèlent des compromis ou des coordinations dans les processus de développement.Pour aller plus loin dans la signification des traits racinaires choisis et leur stabilité vis‐à‐vis des conditions environnementales, nous avons également évalué ces traits en conditions de culture hydroponique. C’est un milieu reconnu comme radicalement différent, intéressant pour les possibilités de visualisation des racines qu’il offre. Un dispositif avec des rhizotrons hydroponiques a été construit spécifiquement pour cette expérimentation. Nous avons confirmé, dans ces nouvelles conditions, les différences d’origine génétique entre les différents génotypes utilisés. De plus, nous avons comparé de manière systématique les valeurs de traits mesurés avec celles de la précédente expérimentation. Certains traits se révèlent stables ou très corrélés (e.g. diamètres, distances interramification)alors que d’autres présentent des différences beaucoup plus fortes (e.g. vitesses de croissance, vitesses d’émergence des racines adventives).Une troisième expérimentation, utilisant différentes combinaisons de greffage entre génotypes, nous a permis d’approfondir la question du contrôle des traits par des interactions au sein de la plante: soit à courte distance au sein du système racinaire, soit à plus longue distance parle système aérien. Deux traits importants ont été étudiés (le diamètre apical et la densité de ramification) en utilisant des combinaisons de génotypes ayant des valeurs contrastées par rapport à ces traits. Il en ressort des réponses très différentes, avec un effet marqué du greffon sur les111RésuméBui H.H. (2015), Diversité inter- et intra-spécifique des paramètres racinaires chez les Solanacées diamètres, révélant qu’une partie au moins du contrôle de ce trait est effectuée par le système aérien, et un effet faible ou inexistant du greffon sur la densité de ramification, révélant un contrôle local de ce trait, par des interactions à courte distance entre les racines. Cette expérimentation par greffage a montré un potentiel très intéressant pour mettre en lumière divers mécanismes de contrôle des traits au sein de la plante entière.Cette étude mérite d’être prolongée par des analyses plus systématiques des déterminismes de variation des traits de l’architecture racinaire, et par des simulations par modèle qui permettront de synthétiser les conséquences des variations de traits sur les performances globales des systèmes racinaires pour la prospection du sol. / Analysis of the inter and intra specific diversity of the parameters of the root system architecture in the Solanaceae.Plant roots play an important role to ensure the productivity and the resistance to manystresses. In new agricultural context, the importance of root system and its architecture are placed tothe forefront. Our study focuses on the root architecture dynamics of Solanaceae, which contains aseries of important horticultural species for the alimentation. Our work was based on 32 genotypesbelonging to three groups of species: aubergines, capsicums, and tomatoes.In this study, we propose firstly an analysis of inter‐ and intra ‐ specific diversity of rootarchitecture through evaluating a set of traits which are also the parameters of a dynamic simulationmodel (ArchiSimple: Pagès et al, 2012). The experiment in pots with a very favorable condition forplant growth and rooting was conducted for the first evaluation. It showed that the selected roottraits present an effect of genetic ‐ originated variations and this effect is usually stronger amongspecies than within species. We also found correlations between certain traits, which revealcompromises or coordinations in the developmental processes.In order to go deeper into the signification of selected root traits and their stability toenvironmental conditions, we also evaluated these traits in hydroponic culture. This environment isradically different, and interesting for its possibilities to visualize the roots. An experimental setupwith hydroponic rhizotrons was specially built for this experiment. In the new conditions, the genetic‐ originated differences between different genotypes used also were found. In addition, wecompared systematically the traits values with those of the previous experiment. Certain traits arestable or highly correlated (e.g., apical diameter, inter‐branch distance), while others are muchdifferent (e.g., root growth rate, emission rate of adventitious roots).In a third experiment, we used different grafting combinations between genotypes todeepen the question of the control of root traits by interactions within plant: either short distancecontrol within root system or long distance control by aerial system. Two important root traits (apicaldiameter and branching density) have been studied by grafting between genotypes which havecontrasting values on these traits. The different responses appear: a significant effect of scion ondiameters, which indicate that at least of this trait is controlled by shoot system, and a weak effect orno effect of scion on branching density, revealing the local control of this trait, by short distanceinteractions between the roots. This experiment showed a great potential of grafting to highlightvarious control mechanisms of root traits within whole plant.AbstractBui H.H. (2015), Diversité inter- et intra-spécifique des paramètres racinaires chez les Solanacées 113This study deserve to be extended by more systematic analysis of determinisms of variationsof root architecture traits, and by using simulation model which allow to integrate the consequencesof traits variations on global performances of root system for prospecting of soil.

Cette thèse visait à développer nos connaissances quant au contrôle génétique et environnemental et la structuration géographique de la variabilité phénotypique pour des caractères fonctionnels chez le peuplier noir (Populus nigra L.). Trois caractères fonctionnels ont été étudiés : la phénologie de croissance, WUE et la résistance à la cavitation. La variabilité phénotypique exprimée pour la phénologie de croissance et WUE a été évaluée au sein d’une collection européenne de peuplier noir regroupant 1085 génotypes échantillonnés dans 13 métapopulations et installés en test clonal en pépinière dans deux sites expérimentaux. Nos résultats ont révélé une importante variabilité génétique ainsi qu’une importante plasticité phénotypique des caractères phénologiques et de WUE au sein des métapopulations. Une différenciation génétique modérée à forte des métapopulations a été observée pour la phénologie de croissance et WUE. Les différences entre métapopulations se structuraient selon des patrons plus ou moins complexes, qui semblaient refléter, pour la phénologie de croissance, une adaptation locale des métapopulations aux conditions de photopériode et de température. Tenant compte des capacités de phénotypage limitées pour la résistance à la cavitation, la variabilité génétique exprimée pour ce caractère a été évaluée au sein d’une population naturelle de peuplier noir regroupant 33 génotypes et installée en test clonal en pépinière dans un site expérimental. Nous avons détecté une variation significative du niveau de résistance à la cavitation entre génotypes. De manière générale, aucune relation phénotypique significative n’a été détectée entre la phénologie de croissance, WUE et la résistance à la cavitation au niveau intra-population, suggérant le maintien d’une diversité de combinaisons fonctionnelles. Le développement d’une puce à 10 331 marqueurs SNPs distribués à l’échelle du génome de P. nigra, notamment dans des régions candidates pour la phénologie de croissance, devrait permettre, à court terme, de confirmer l’adaptation locale des populations de peuplier noir et d’explorer ses bases génétiques. / This work aimed at improving our understanding of the genetic and environmental control as well as the geographic structure of phenotypic variation for functional traits in black poplar (Populus nigra L.). Three functional traits were studied: bud phenology, water-use efficiency (WUE) and xylem resistance to drought-induced cavitation. The phenotypic variation expressed for bud phenology and WUE was evaluated in a European P. nigra collection composed of 1085 cloned individuals sampled in 13 natural metapopulations and established in clonal test in nursery at two experimental sites. Substantial genetic variation and substantial phenotypic plasticity for bud phenology and WUE were observed within all metapopulations. Moderate to strong genetic differentiation of metapopulations was evidenced for phenological traits and WUE. Patterns of genetic differentiation were more or less complex depending on traits and seemed to reflect, for phenological traits, local adaptation of metapopulations to photoperiod and temperature. Taking into account the limited phenotyping capacity for xylem resistance to cavitation, genetic variation expressed for this trait was evaluated within one single natural population of black poplar composed of 33 genotypes which were established in clonal test in nursery at one experimental site. Significant variations were observed between genotypes for the degree of cavitation resistance. Overall, no significant relationship was detected between bud phenology, WUE and cavitation resistance at the within-population level, indicating the maintenance of a diversity of functional combinations. The development of an array covering 10 331 SNPs distributed across the P. nigra genome, notably in candidate regions for bud phenology, will enable in the short-term to confirm local adaptation of P. nigra populations and to identify its genetic basis.