A narrow germplasm base and a complex allotetraploid genome have historically made the discovery of single nucleotide polymorphism (SNP) markers difficult in cotton (Gossypium hirsutum). We conducted a genome reduction experiment to identify SNPs from two accessions of G. hirsutum and two accessions of G. barbadense. Approximately 2 million sequence reads were assembled into contigs with an N50 of 508 bp and analyzed for SNPs. A total of 11,834 and 1,679 SNPs between the accessions G. hirsutum and G. barbadense, respectively, were identified with highly conservative parameters (a minimum read depth of 8x at each SNP and a 100% identity of all reads within an accession at the SNP). Additionally, 4,327 SNPs were identified between accessions of G. hirsutum in and assembly of Expressed Sequence Tags (ESTs). 320 and 252 KASPAR assays were designed for SNP mapping in non-genic and genic regions respectively. 187 markers in total (136 non-genic, 51 genic) were mapped using KBioscience KASPar genotyping assays in a segregating F2 population using the Fluidigm EP1 system. EST The target genome of EST markers was successfully predicted bioinformaticly diploid reference sequences. Examination of nucleotide substitutions and SNP frequencies further confirms validity of new markers. A genetic map was constructed using a large G. hirsutum segregating F2 population. Genetic maps generated by these newly identified markers will be used to locate quantitative, economically important regions within the cotton genome.

L'alimentation en eau constitue le principal facteur limitant la croissance, voire la survie des<br />plantes. Les modèles climatiques prévoient pour les 50 à 100 années à venir une baisse des<br />précipitations et des températures estivales accrues dans la moitié sud de la France. La durée<br />de vie d'une forêt de pin maritime, de sa plantation jusqu'à la coupe d'exploitation est<br />justement de 50 ans. Il est donc important de savoir si ces organismes pourront faire face à ces<br />brusques changements climatiques ; en d'autres termes si les variétés améliorées plantées<br />aujourd'hui pourront maintenir le niveau actuel de productivité dans un milieu plus pauvre en<br />eau, et tolérer des épisodes de sécheresse intense. La capacité de ces organismes à faire face à<br />ces perturbations brutales dépendra à la fois de leur plasticité phénotypique et de leur diversité<br />génétique. Dans le cadre de cette thèse, nous avons étudié la plasticité moléculaire du système<br />racinaire de jeunes plants de pin maritime élevés en milieu hydroponique et soumis à un stress<br />osmotique par ajout de polyéthylène glycol. Un plan factoriel croisant deux écotypes (France<br />et Maroc) par cinq niveaux de stress a permis d'analyser les réponses du transcriptome et du<br />protéome à court et long terme. Nos investigations ont porté sur l'accumulation des transcrits<br />de 7000 gènes et de 1200 protéines. L'analyse statistique des données a permis d'identifier<br />des gènes dont la plasticité moléculaire est génétiquement contrôlée, révélant des stratégies de<br />réponse différentes de chaque écotype. La valeur adaptative de ces gènes pourra alors être<br />confirmée par l'interprétation des patrons de diversité nucléotidique de ces gènes candidats.

Made available in DSpace on 2014-06-11T19:26:09Z (GMT). No. of bitstreams: 0 Previous issue date: 2007-07-20Bitstream added on 2014-06-13T18:54:09Z : No. of bitstreams: 1 jovino_dfr_me_jabo.pdf: 637580 bytes, checksum: dc449a2a52a9354da867effed1512963 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Sob condições de estresse hídrico, a cana-de-açúcar pode sofrer mudanças fisiológicas e bioquímicas, tais como diminuição nas atividades fotoquímicas, redução da fixação de CO2 e acúmulo de osmólitos e osmoprotetores. O objetivo deste trabalho foi identificar, através da técnica de macroarranjo de cDNA, o perfil de expressão de genes promotores das diferentes vias metabólicas em palmitos da variedade de cana-de-açúcar SP80-3280 submetidas ao estresse hídrico nos dias 5, 9, 13 e 17 após o início da condição de supressão de água, sendo considerado o dia 1 como controle. Os resultados do macroarranjo mostraram que as proteínas mais expressas sob déficit hídrico pertencem a quatro categorias das quais as ESTs mais importantes foram selecionadas. As quatro categorias descritas abaixo estão discutidas neste trabalho. As ESTs da via do metabolismo de açúcar e amido (invertase de parede celular (INV), sacarose fosfato sintase (SFS), sacarose fosfato fosfatase (SFF), trealose fosfato sintase (TFS), trealose fosfato sintase/fosfatase (TFS/F) e hexoquinase (HXQ)) pertencem a categoria de bioenergética. Colina monooxigenase (CMO) e betaína aldeído desidrogenase (BADH) as quais pertencem a via do metabolismo de glicina betaína, foram selecionadas a partir da categoria do metabolismo secundário. A terceira categoria compreende as ESTs do metabolismo de aminoácido (D-pirrolina-5- carboxilato sintase (P5CS), ornithina -aminotransferase (OAT) e prolil 4-hidroxilase (PH)) as quais pertencem a via da biossíntese de prolina, e a quarta categoria, resposta ao estresse, compreende as ESTs aleno oxido sintase (AOS), aleno oxido ciclase (AOC) e lipoxigenase (LOX), pertencentes a via de biossíntese do jasmonato. / Under water deficit, sugarcane undergoes physiological and biochemical alterations such as photochemical activity reduction, CO2 fixation reduction and the accumulation of osmolytes and osmoprotectants. This work was undertaken to identify the gene expression profile in sugarcane (var. SP80-3280) under water deficit through the cDNA macroarray technique. Leafroll tissues were collected from plants subjected to 5, 9, 13 and 17 days of water restriction, and day 1 was used as control. Macroarray results showed that most proteins expressed under water restriction belong to four categories, from which the most important ESTs were selected. The four categories described below are discussed in this work. Sugar and starch metabolism pathway ESTs (cell wall invertase (CWI), sucrose phosphate synthase (SPS), sucrose phosphate phosphatase (SPP), trehalose phosphate synthase (TPS), trehalose phosphate synthase phosphatase (TSP/P) and hexoquinase (HXQ) were selected from the bioenergetics category. Choline monooxygenase (CMO) and betaine aldehyde dehydrogenase (BADH), which belong to the glycine betaine metabolism pathway, were selected from the secondary metabolism category. The third category comprised the amino acid metabolism ESTs D- pyrroline-5-carboxylate synthase (P5CS), Ornithine - aminotransferase (OAT) and Prolyl 4-hydroxylase (PH), which belong to the proline biosynthesis pathway, and the fourth category, stress response, comprised the ESTs for Allene oxide synthase (AOS), Allene oxide cyclase (AOC) and Lipoxygenase (LOX), which belong to the jasmonate biosynthesis pathway.

No description available.

La première partie de la thèse traite de la recherche de biomarqueurs du cancer. Lors de la transcription, il apparaît que certains nucléotides peuvent être remplacés par un autre nucléotide. On s'intéresse alors à la comparaison des probabilités de survenue de ces infidélités de transcription dans des ARNm cancéreux et dans des ARNm sains. Pour cela, une procédure de tests multiples menée sur les positions des séquences de référence de 17 gènes est réalisée via les EST (Expressed Sequence Tag). On constate alors que ces erreurs de transcription sont majoritairement plus fréquentes dans les tissus cancéreux que dans les tissus sains. Ce phénomène conduirait ainsi à la production de protéines dites aberrantes, dont la mesure permettrait par la suite de détecter les patients atteints de formes précoces de cancer. La deuxième partie de la thèse s'attache à l'étude de l'allergie à l'arachide. Afin de diagnostiquer l'allergie à l'arachide et de mesurer la sévérité des symptômes, un TPO (Test de Provocation Orale) est réalisé en clinique. Le protocole consiste à faire ingérer des doses croissantes d'arachide au patient jusqu'à l'apparition de symptômes objectifs. Le TPO pouvant se révéler dangereux pour le patient, des analyses discriminantes de l'allergie à l'arachide, du score du TPO, du score du premier accident et de la dose réactogène sont menées à partir d'un échantillon de 243 patients, recrutés dans deux centres différents, et sur lesquels sont mesurés 6 dosages immunologiques et 30 tests cutanés. Les facteurs issus d'une Analyse Factorielle Multiple sont également utilisés comme prédicteurs. De plus, un algorithme regroupant simultanément en classes des intervalles comprenant les doses réactogènes et sélectionnant des variables explicatives est proposé, afin de mettre ensuite en compétition des règles de classement. La principale conclusion de cette étude est que les mesures de certains anticorps peuvent apporter de l'information sur l'allergie à l'arachide et sa sévérité, en particulier ceux dirigés contre rAra-h1, rAra-h2 et rAra-h3.

Made available in DSpace on 2015-03-26T13:42:23Z (GMT). No. of bitstreams: 1 texto completo.pdf: 636309 bytes, checksum: ca1e7c510537c62820f228b759c5a23d (MD5) Previous issue date: 2011-07-25 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / O suíno (Sus scrofa) é considerado um animal de grande importância para produção de carne, sendo seu potencial de crescimento muscular objeto de grande interesse e geralmente associado com características determinadas na fase pré-natal durante a miogênese. Para o estudo de genes responsáveis por estas características, as etiquetas de sequências expressas (Expressed Sequence Tags - EST) fornecem informações diretas sobre o transcriptoma e indiretas sobre a relação entre o genoma e diferentes fenótipos, proporcionando o conhecimento sobre genes diferencialmente expressos (GDE) bem como sequências genômicas transcritas para o controle da expressão gênica como, por exemplo, alguns RNAs não codificantes. Características de tecidos musculares em suínos podem ser influenciadas diretamente por genes, e estes sendo regulados como, por exemplo, através de miRNAs, em diferentes fases de desenvolvimento. O presente trabalho teve como objetivo a identificação e a anotação in sílico de GDE e sequências não codificantes, com enfoque aos miRNAs, de bibliotecas de cDNA construídas a partir do músculo esquelético semi-membranoso de três diferentes raças de suínos (Duroc, Large White e naturalizada brasileira Piau) bem como a análise dos níveis de expressão dos genes identificados e miRNAs em sete fases de desenvolvimento do Longissimus Dorsi (21, 40, 70 e 90 dias pré-natal e 107, 121 e 171 dias pós-natal) de animais de linha comercial. Foram identificados 34 GDE sendo 21 pertencentes a uma rede gênica musculo-específica. Destes, 13 genes tiveram seus perfis de expressão analisados com o uso do qRT-PCR durante os sete períodos citados, formando quatro grupos de expressão semelhantes, um com maior expressão na fase pós-natal e três na fase pré-natal. Nas análises das sequências não codificantes um resultado importante foi a identificação de dois novos miRNAs em suínos, os quais tiveram suas sequências maduras similares aos miRNAs hsa-miR-1207-5p e hsa-miR-665 foram classificadas como verdadeiras pelo programa MiPred e formaram estruturas secundárias. Destes, encontrou-se 289 e 214 genes regulados por eles respectivamente, dos quais quatro são músculo-específicos. Os novos miRNAs tiveram seus perfis de expressão analisados com o uso do PCR em tempo real durante os sete períodos citados juntamente com outros três já identificados em suínos. Seus níveis de expressão mostraram diferenças entre os estágios pré- e pós-natal. Estes estudos podem fornecer valiosas informações possibilitando um maior entendimento dos mecanismos moleculares envolvidos no desenvolvimento muscular. As análises de GDE em fases pré e pós-natal sugerem a presença de genes atuando especificamente em determinados estágios de desenvolvimento do músculo, contribuindo para melhor explicar suas funções. A identificação de dois novos miRNAs, somados a outros já identificados e postados nos bancos de dados em suínos, podem contribuir para um maior entendimento dos modos de regulação gênica, sendo de importância para os estudos de genética e melhoramento animal, permitindo o entendimento da fisiologia da deposição de músculo para produção de carne em suínos. / The pig (Sus scrofa) is considered an important animal for meat production. This interest revolves around the potential for muscle growth, which usually is associated with certain characteristics during prenatal myogenesis. To study the genes responsible for these characteristics, expressed sequence tags (EST) provide direct information about the transcriptome and indirectly on the relationship between the genome and different phenotypes, supplying knowledge about differentially expressed genes (DEG) as well as other transcribed genomic sequences for the control of gene expression, e.g., some non-coding RNAs. Characteristics of muscle tissue in pigs may have been directly influenced by genes, and those being regulated, for example, by miRNAs, in different stages of development. This study aimed to identify by in silico annotation, DEG and non-coding sequences, focusing on miRNAs, using cDNA libraries constructed from semi-membranous skeletal muscle of three different pig breeds (Duroc, Large White and naturalized Brazilian Piau ) as well as analysis of gene expression profiles of identified genes and miRNAs during seven stages of development (21, 40, 70 and 90 days prenatal and 107, 121 and 171 days postnatal) from commercial line animals Longissimus Dorsi muscle. Twenty-one identified genes out of 34 DEGs belongs to the muscle-specific path. From these, 13 genes had their expression profiles analyzed by qRT-PCR during the seven periods, forming four clusters of similar expression, with one having greater expression in the postnatal period and three in the prenatal. In the analysis of non-coding sequences, an important result was the identification of two new miRNAs in pigs, which had their sequences similar to mature miRNAs hsa-miR-1207- 5p and hsa-miR-665 which had their precursor sequences forming secondary structures and classified as real precursor sequence by MiPred program. From these, we found 289 genes and 214 respectively regulated by them, of which four are muscle-specific. The new miRNAs and other three which have been identified in previous studies in pigs had their expression levels analyzed by quantitative real time PCR during the mentioned seven periods. Their levels of expression differed between pre-and postnatal stages. These studies may provide valuable information allowing a better understanding of the molecular mechanisms involved in muscle development. Analyses of DEG in the pre-and postnatal periods suggest the presence of genes acting specifically on certain stages of muscle development, contributing to better explain their functions. The identification of two new miRNAs, together with other previously identified and posted on the databases in pigs, may contribute to a better understanding of gene regulation and is important for studies of genetics and animal breeding, allowing the understanding of the muscle deposition physiology to meat production in pigs.

Leaf rust caused by Puccinia hordei is an important disease of barley (Hordeum vulgare) in many regions of the world. Yield losses up to 62% have been reported in susceptible cultivars. The Rph5 gene confers resistance to the most prevalent races (8 and 30) of barley leaf rust in the United States. Therefore, the molecular mapping of Rph5 is of great interest. Genetic studies were performed by analysis of 93 and 91 F2 plants derived from the crosses 'Bowman' (rph5) x 'Magnif 102' (Rph5) and 'Moore' (rph5) x Virginia 92-42-46 (Rph5), respectively. Linkage analysis positioned the Rph5 locus to the extreme telomeric region of the short arm of barley chromosome 3H at 0.2 cM proximal to RFLP marker VT1 and 0.5 cM distal from RFLP marker C970 in the Bowman x Magnif 102 population. Synteny between rice chromosome 1 and barley chromosome 3 was employed to saturate the region within the sub-centimorgan region around Rph5 using sequence-tagged site (STS) markers that were developed based on barley expressed sequence tags (ESTs) syntenic to the phage (P1)-derived artificial chromosome (PAC) clones comprising distal region of the rice chromosome 1S. Five rice PAC clones were used as queries to blastn 370,258 barley ESTs. Ninety four non-redundant EST sequences were identified from the EST database and used as templates to design 174 pairs of primer combinations. As a result, 10 EST-based STS markers were incorporated into the 'Bowman' x 'Magnif 102' high-resolution map of the Rph5 region. More importantly, six markers, including five EST-derived STS sequences, co-segregate with Rph5. Genes, represented by these markers, are putative candidates for Rph5. Results of this study demonstrate the usefulness of rice genomic resources for efficient deployment of barley EST resources for marker saturation of targeted barley genomic region. / Ph. D.

No description available.