A produção brasileira de carne de frango tem uma grande importância econômica no mundo todo devido principalmente aos avanços do melhoramento genético. O surgimento de novas tecnologias de sequenciamento (sequenciamento de nova geração) tem se tornado uma ferramenta poderosa, pois por meio da identificação de SNPs (polimorfismo de nucleotídeo único) e INDELs (deleções/inserções) possibilita a adição de novas informações ao melhoramento genético. A deposição de músculo, em especial o músculo de peito, é uma das características que mais merecem destaque por causa da sua importância nutricional e econômica. Sendo assim o objetivo deste trabalho foi ressequenciar o genoma de 18 aves de duas linhagens distintas experimentais e identificar SNPs e INDELs em uma região de QTL no cromossomo 2 da galinha associado anteriormente com deposição de músculo do peito, além de caracterizar variantes potencialemente funcionais e propor mutações candidatas para estudos futuros. Para isso, dezoito galinhas de duas diferentes linhagens experimentais (corte e postura), ambas desenvolvidas pela Embrapa Suíno e Aves, foram sequenciadas pela plataforma de nova geração da Illumina. SNPs e INDELs foram identificados por meio de ferramentas de bioinformática em uma região de QTL no cromossomo 2 da galinha (105.848.755-112.648.761 pb) que foi previamente associada com deposição de músculo de peito. O sequenciamento dos 18 animais gerou em torno 2,7 bilhões de reads e após a filtragem por qualidade foram mantidas 77% das reads. Em seguida, as reads foram alinhadas ao genoma referência (Gallus_gallus-4.0, NCBI) pela ferramenta Bowtie2 e gerou em média 10,6X de cobertura de sequenciamento na região-alvo. , Foram identificados 722.832 SNPs e 63.727 INDELs para os 18 animais por meio do programa SAMtools, e após uma filtragem rigorosa, foram mantidos 77% dos SNPs (n=558.767) e 60% das INDELs (n=38.402). Com base nas variantes únicas para os 18 animais (85.765 SNPs e 7.824 INDELs) foi realizada a anotação funcional por meio da ferramenta ANNOVAR. Dentre os SNPs não sinônimos (n=153) e stopgain (n=3), 15 foram classificados como deletérios. Um dos SNPs deletérios que já foi depositado em banco de dados foi identificado no gene RB1CC1, que tem sua função relacionada ao desenvolvimento do músculo de peito. Utilizando a ferramenta DAVID foi possível analisar 37 genes relacionados aos SNPs não sinônimos, stopgain, INDELs frameshift e não frameshift. Dentre estes genes, três (DTNA, RB1CC1 e C-MOS) foram selecionados por terem suas funções relacionadas ao desenvolvimento muscular e suas mutações foram analisadas. Sendo assim, futuros estudos podem ser realizados nestes genes candidatos e nas mutações identificadas, por meio de análises de associação e validação em populações comerciais, permitindo assim uma melhor explicação o efeito do QTL estudado. / The Brazilian chicken meat production has a great economic importance in worldwide mainly due to advances in breeding. The emergence of new techniques of sequencing (nextgeneration sequencing) becomes a powerful tool because through identification of SNPs (single nucleotide polymorphism) and INDELs (deletions/insertions) allows the addition of new information for genetic improvement. The muscle deposition, particularly the breast muscle, is one of the features that are most noteworthy because of its nutritional and economic importance. Therefore the aim of this study was to perform the genome resequencing of 18 chicken from two distinct experimental lines and identify SNPs and INDELs in a QTL region on chromosome 2 previously associated with breast muscle, and characterize the variants to identify potentially function ones and propose candidate mutations for future studies. To achieve these objectives, eighteen chickens of two different experimental lines (broiler and layer), both developed by Embrapa Swine and Poultry were sequenced by Illumina next-generation platform. SNPs and INDELs were identified by bioinformatic tools in a QTL region on chicken chromosome 2 (105,848,755-112,648,761 bp) which was previously associated with breast muscle deposition. Sequencing of the eighteen animals generated around 2.7 billion of reads, and 77% of the reads were retained after filtering. The reads were aligned against the chicken genome reference (Gallus_gallus-4.0, NCBI) by Bowtie2 tool resulting in a 10.6X coverage across the target region. Using SAMtools, 722,832 SNPs and 63,727 INDELs were identified in the all individuals, and after a stringent filtration, 77% of SNPs (n=558,767) and 60% of INDELs (n=38,402) were maintained. Based on unique variants for all the animal (85,765 SNPs and 7,828 INDELs) were performed the functional annotation by ANNOVAR tool. Among the non-synonymous SNPs (n=153) and stopgain (n=3), fifteen were predicted like a deleterious mutation. One of deleterious SNPs has already deposited in public database, and it was identified in RB1CC1 gene, which function is related to breast muscle development. Using the DAVID tool was possible to analyze the 37 genes related to the non-synonymous SNPs, stopgain, frameshift and non-frameshift INDELs. Among these genes, three (DTNA, RB1CC1 and C-MOS) were selected due their functions related to muscle development and their mutations were analyzed. Therefore, further association studies can be performed with these candidate genes and their mutations, and also validation in commercial populations, allowing a better explanation of QTL effects.

Submitted by admin tede (tede@pucgoias.edu.br) on 2018-06-22T19:18:01Z No. of bitstreams: 1 LORRAYNNE GUIMARÃES OLIVEIRA.pdf: 972251 bytes, checksum: 3d1335f8344b25e2c479fd95096c777d (MD5) / Made available in DSpace on 2018-06-22T19:18:01Z (GMT). No. of bitstreams: 1 LORRAYNNE GUIMARÃES OLIVEIRA.pdf: 972251 bytes, checksum: 3d1335f8344b25e2c479fd95096c777d (MD5) Previous issue date: 2018-03-08 / At the end of 1987 was one of the most serious radiological accidents in history, occurred in Goiânia-Goiás-Brazil, causing the contamination of the environment, succeending in the external irradiation and the internal contamination of several people. The direct and indirect effects of radiation initiate a series of biochemical and molecular signaling events that can repair the damage or culminate in permanent physiological changes or cell death. Mammalian cells have integrated response systems that detect DNA damage, activate signaling cascades, and realize repair. Chromosomal rearrangements induced by exposure to ionizing radiation can occur by Double Strand Break in the DNA (DSB). The main DNA repair mechanism responsible for the repair of DSBs is Nonallelic Homologous Recombination (NAHR). Through the NAHR process, the Low Copy Repeats known also with Segmental Duplications (LCRs / SDs) can lead to DNA rearrangements, such: deletions, duplications, inversions and translocations. Chromosomal Microarray Analysis (CMA) based on SNP array, is established on the identification of Copy Number Variantion (CNV), including gains and losses. The goal of this study was to investigate the effect of the presence of LCRs in the formation of new CNVs observed in the offspring of individuals exposed to low doses of IR of Cesium-137. The exposed group consisted of 12 families, of which at least one parent was directly exposed to IR Césio-137, including a total of 40 individuals (12 couples and 16 children born after the accident). The absorbed dose for the exposed individuals was estimated at ≤0.2 Gray. A group with 8 families of individuals not exposed to IR was used as control. The statistical tests used were Chi-Square, Pearson's Chi-Square, ANOVA, Spearman's Correlation, Kruskal Wallis, Likelihood Ratio and Linear Linear Association. All analyzes were performed with a significance level of 5% (p <0.05). We identified 50 (10.6%) and 23 (9.7%) CNVs that were being flanked by LCRs for the case and control groups, respectively. The test showed no significant difference. The comparison of gain and loss CNVs flanked by LCRs showed a significant difference where LCRs were significantly more associated with gain CNVs. The presence of LCRs was often associated with more longer CNVs, suggesting that CNVs originating from NAHR tend to be bigger. The CNV rates mutation and paternal meiosis in F1 generation of the case and control groups showed a significant difference. Men exposed to IR transmit more CNVs again small when compared to transmission based on maternal exposure and between controls. The estimation of rate mutation in LCR-mediated CNVs analyzed in F1 generation and in their biological parents was a useful biomarker in the retrospective evaluation of parental exposure to IR in human populations, especially for Burden mutation rate estimation. / No final de 1987 houve um dos mais graves acidentes radiológicos da história, ocorrido em Goiânia-Goiás-Brasil, ocasionando a contaminação do ambiente, sucedendo na irradiação externa e a contaminação interna de várias pessoas. Os efeitos diretos e indiretos da radiação iniciam uma série de eventos de sinalização bioquímica e molecular que podem reparar o dano ou culminar em mudanças fisiológicas permanentes ou morte celular. As células de mamíferos integraram sistemas de resposta que detectam danos no DNA, ativam cascatas de sinalização e efetuam o reparo. Os rearranjos cromossômicos induzidos pela exposição à radiação ionizante podem ocorrer por quebras na dupla fita do DNA (DSB). O principal mecanismo de reparo do DNA, responsável pela reparação de DSBs é a Recombinação Homóloga Não Alélica (NAHR). Através do processo de NAHR, as Repetições de poucas cópias conhecidas também com Duplicações Segmentares (LCRs / SDs) podem levar a rearranjos de DNA, como: deleções, duplicações, inversões e translocações. A análise Cromossômica em Microarranjos (CMA) baseada em SNP array, fundamenta-se na identificação de Variação no Número de Cópias (CNV), incluindo ganhos e perdas. O objetivo deste trabalho foi investigar o efeito da presença de LCR na formação de CNVs novas observadas na prole de indivíduos expostos a baixas doses de RI de Césio-137. O grupo exposto foi constituído por 12 famílias, dos quais pelo menos um dos progenitores foi diretamente exposto à RI de Césio-137, incluindo um total de 40 indivíduos (12 casais e 16 filhos nascidos após o acidente). A dose absorvida para os indivíduos expostos foi estimada em ≤0,2 Gray. Um grupo com 8 famílias, de indivíduos não-expostos à radiação ionizante foi usado como controle. Os testes estatísticos utilizados foram Qui–Quadrado, Qui-Quadrado de Pearson, ANOVA, Correlação de Spearman, Kruskal Wallis, Razão de verossimilhança e Associação Linear por Linear. Todas as análises foram realizadas com nível de significância de 5% (p<0,05). Identificamos 50 (10,6%) e 23 (9,7%) CNVs que estavam sendo flanqueadas por LCRs, para os grupos caso e controle, respectivamente. O teste não demonstrou diferença significante. A comparação de CNVs de ganho e perda flanqueadas por LCRs mostrou diferença significativa onde LCRs estavam significativamente mais associadas as CNVs de ganhos. A presença de LCRs esteve associada frequentemente em CNVs mais longas, sugerindo que CNVs originadas a partir de NAHR tendem a ser maiores. As taxas de mutações de CNV e a meiose paterna na geração F1 dos grupos caso e controle demonstram diferença significativa. Homens expostos à RI transmitem mais CNVs de novo pequenas quando comparado com a transmissão em função da exposição materna e entre controles. A estimativa da taxa de mutação em CNVs mediadas por LCRs analisada na geração F1 e em seus pais biológicos foi um biomarcador útil na avaliação retrospectiva de exposição parental

Atualmente, o Brasil é considerado o maior exportador mundial e terceiro maior produtor mundial de carne de frango. Este destaque é resultado, principalmente, do melhoramento animal baseado na estimação do valor genético a partir da mensuração de fenótipos e informações de pedigree. Entretanto, é comum que a seleção não seja feita para cada característica isoladamente devido à correlação genética entre elas. Esta correlação tem como causas a pleiotropia ou a ligação genética. Com este trabalho objetivou-se detectar associações entre características fenotípicas de interesse para a avicultura e SNPs em uma região do cromossomo 1 (168 - 208 cM e 57 - 71 Mbp), onde possíveis QTL ligados foram previamente mapeados. Utilizou-se o Beadchip de SNPs de 60k para genotipar 14 animais da geração Parental (machos TT e fêmeas CC) e 28 F1 da população TCTC desenvolvida pela Embrapa Suínos e Aves. A linhagem TT apresentou maior variabilidade genotípica que CC, porém, os F1 foram superiores às linhagens Parentais com base no número de heterozigotos e MAF. O polimorfismo com maior ocorrência em ambas as gerações foram as transições com 84,3%. Foram selecionados 144 SNPs mais informativos com base na heterozigosidade dos cinco casais F1 que geraram os 453 F2. Houve redução de heterozigotos e MAF em F2, em função da média de F1, decorrente de certo grau de parentesco e endogamia entre os animais que compuseram esta geração. Os blocos de haplótipos construídos demonstraram que os machos TT apresentaram 25 blocos, fêmeas CC (17), F1 (32) e F2 (23) com tamanho médio de 278, 467, 242 e 160 kpb, respectivamente. Foi evidenciado que 236 (42,7%) correlações fenotípicas foram significativas, das quais o maior número constatado foi entre PB_MS e outras 17 características e, o maior valor estimado foi entre PB_MS e EE_MS (-0,90). Do total esperado de 3.456 testes de associação, 609 (17,6%) foram considerados significativos (p < 0,05), sendo 424 (69,6%) com efeito aditivo e 185 com efeito de dominância (30,4%). PV41 apresentou maior número de associações (123), enquanto DOR não foi associado a nenhum SNP. Proporcionalmente, o maior número de SNPs foi associado próximo ao QTL pleiotrópico 2 para 17 características. Já os maiores níveis de significância (p < 9,59 x 10-8) para o efeito aditivo foram evidenciados para SNPs localizados próximos ao QTL pleiotrópico 1 e associados somente com PV41, a saber: Gga_rs13869715 (A < C), Gga_rs13870613 (T < C), Gga_rs14827719 (A < G), GGaluGA019336 (T < C) e GGaluGA019533 (A < C). Foram detectadas associações ainda não descritas na literatura para GP3541, CA3541, INT, PES, CAB, FIG, COR, MOE, PUL, HEM, COL, TRI, TC, PB_MS, EE_MS, CZ_MS. Finalmente, foram indicados possíveis genes candidatos posicionais e funcionais, tais como, IGF1, MYBPC1, MTPN, SOX-5, FGFR1OP2 e TTLL12 que poderão ser empregados na análise de expressão gênica. / Actually, Brazil is considered the world\'s first- and third-biggest exporter and producer of poultry meat, respectively. These performances are mainly consequence of animal breeding based on the estimation of breeding value combining phenotypes and pedigree information. However, usually the selection is not carried out for each trait separately due to genetic correlation between them. This correlation is caused by pleiotropy or linkage. We aimed to detect associations between phenotypic traits of interest to poultry industry and SNPs on a region of chromosome 1 (168 - 208 cM and 57 - 71 Mbp), where putative linked-QTL were previously mapped. A chicken 60k SNP BeadChip was used to genotype 14 animals from Parental generation (TT males and CC females) and 28 F1 of the TCTC population that was developed by Embrapa Swine and Poultry. The TT line showed greater genotypic variability than CC, however, F1 were higher than Parental generation based on the number of heterozygotes and MAF. The polymorphism more frequent in both generations was the transitions with 84.3%. The 144 most informative SNPs were selected based on heterozygosity of the five F1 couples which generated the 453 F2. There was a reduction of heterozygotes and MAF in F2, based on the F1 mean value, as consequence of some degree of relationship and inbreeding between animals that formed this generation. Haplotype blocks demonstrated that the TT males showed 25 blocks, CC female (17) F1 (32) and F2 (23) with an average size of 278, 467, 242 and 160 kbp, respectively. It was observed that 236 (42.7%) phenotypic correlations were significant. Out of these, the highest number was found between PB_MS and other 17 traits and the highest estimated value was between PB_MS and EE_MS (-0.90). Out of 3,456 expected association tests, 609 (17.6 %) were considered significant (p < 0.05), being 424 (69.6%) with additive effect and 185 with dominance effect (30.4%). PV41 presented the highest number of associations (123), while DOR was not associated to any SNP. Proportionally, the highest number of SNPs was associated close to the pleiotropic QTL 2 with 17 traits. On the other hand, the highest significance levels (p < 9.59 x 10-8) for the additive effect were evidenced for SNPs located close to the pleiotropic QTL 1 and associated only with PV41 (Gga_rs13869715 (A < C), Gga_rs13870613 (T < C), Gga_rs14827719 (A < G), GGaluGA019336 (T < C) and GGaluGA019533 (A < C)). Novel associations were detected for GP3541, CA3541, INT, PES, CAB, FIG, COR, MOE, PUL, HEM, COL, TRI, TC, PB_MS, EE_MS, CZ_MS when we compared our results with literature. Finally, putative positional and functional candidate genes were indicated such as IGF1, MYBPC1, MTPN, SOX-5, FGFR1OP2 and TTLL12, which may be used in gene expression analysis.

As síndromes mielodisplásicas (SMD) constituem um grupo heterogêneo de doenças hematológicas de origem clonal, caracterizado por hematopoese ineficaz, citopenia e risco de evolução para leucemia mieloide aguda (LMA). As anormalidades citogenéticas adquiridas são marcadores prognósticos bem estabelecidos em SMD. No entanto, a técnica de citogenética metafásica apresenta limitações, incluindo baixa resolução e necessidade de divisão celular, sendo que defeitos cromossômicos podem não ser detectados. Tecnologias baseadas em microarranjo (array) de DNA, como o Single Nucleotide Polymorphism Array (SNP-A), são importantes para avaliação do genoma normal e neoplásico. O SNP-A foi desenvolvido para o estudo de todo o genoma, apresenta uma resolução superior a citogenética metafásica convencional, pode ser realizado em células na interfase, e detecta alterações cromossômicas não visualizadas pela citogenética metafásica. Além disso, o SNPA fornece dados de genotipagem para detecção de perda neutra de heterozigose, também denominada de dissomia uniparental somática. Regiões cromossômicas com deleção, perda neutra de heterozigose ou ganho são comuns em pacientes com neoplasias hematológicas e sugeriu genes candidatos a supressores de tumor e oncogenes. O objetivo do presente estudo foi a caracterização da coorte de pacientes com suspeita clínica de SMD e o uso integrado do método de citogenética convencional e SNP-A no serviço de hematologia da nossa instituição na investigação de alterações citogenéticas em pacientes com SMD e doenças relacionadas. Durante o período do estudo, foram recebidas um total de 114 amostras de pacientes com suspeita clínica de SMD. A análise clínica, morfológica e citogenética permitiu confirmar o diagnóstico de SMD ou doenças relacionadas em 43 pacientes (SMD [n=34], SMD/NMP [n=5], LMA com alterações mielodisplásicas [n=4]). Vinte e um pacientes foram classificados como citopenia idiopática de significado indeterminado (CISI) e 50 indivíduos apresentaram outros diagnósticos. SNP-A foi realizado em 17 pacientes com SMD e doenças relacionadas. Dentre os pacientes selecionados para o SNP-A, anormalidades cromossômicas foram observadas em 6/17 (35%) casos pelo cariótipo convencional e em 8/17 (47%) casos pela técnica de SNP-A. SNP-A não detectou quatro alterações cromossômicas previamente identificadas pela citogenética convencional: duas translocações balanceadas e duas alterações numéricas. SNP-A confirmou os demais achados identificados pela citogenética convencional e detectou um total de 32 novas lesões (1 ganho, 19 perdas e 12 UPDs) em 6 pacientes com SMD ou doenças relacionadas. SNP-A pode complementar a citogenética convencional na detecção de anormalidades cromossômicas em neoplasias mieloides. / Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal hematopoietic diseases, characterized by inefficient hematopoiesis, peripheral blood cytopenias and a risk to progress to acute myeloid leukemia (AML). Acquired chromosomal abnormalities have prognostic value in MDS. However, metaphase cytogenetics has some limitations including low resolution and the requirement of cell division, and chromosomal abnormalities may not be detected. New technologies based on array, the Single Nucleotide Polymorphism Array (SNP-A), are able to evaluate the whole genome. The SNP-A has superior resolution compared to metaphase cytogenetics, may be used in interphase cells, and may detect chromosomal abnormalities not detected by metaphase cytogenetics. In addition, the SNP-A read-out includes genotyping calls and hybridization signal strength, corresponding to gene copy number, allowing detecting copy neutral loss of heterozigosity (CN-LOH), also known as uniparental dissomy (UPD). Deletions, copy neutral loss of heterozigosity or gain are frequent in patients with haematopoietic neoplasms and has already suggested the location of tumor suppressor genes and oncogenes. The aim of this study was to characterize the cohort of patients with clinical suspicion of MDS and to establish the integrative use of the conventional cytogenetic and the SNP-A in the investigation of chromosomal abnormalities in patients with MDS and related diseases followed at our institution. The clinical, morphological and cytogenetic evaluation allowed us to confirm the diagnosis of MDS or related disease in 43 patients (MDS [n=34], MDS/MPN [n=5], AML with myelodysplastic changes [n=4]). Twenty-one patients were diagnosed with idiopathic cytopenia with undetermined significance (ICUS) and 50 patients had other diagnosis. SNP-A were performed in 17 patients with MDS and related disease. Chromosomal abnormalities were observed in 6/17 (35%) cases by metaphase cytogenetics, and in 8/17 (47%) of the cases by SNP-A. SNP-A did not detected two balanced translocations and two numerical alterations previously observed by metaphase cytogenetics. SNP-A confirmed all the other findings observed by metaphase cytogenetics and SNP-A detected a total of 32 new lesions (1 gain, 19 losses and 12 UPDs) in 6 MDS and related diseases. SNP-A may complement metaphase cytogenetics to improve the detection of chromosomal abnormalities in myeloid neoplasms.

Les études préexistantes identifient quatre taxons de base (C. reticulata les mandariniers, C. maxima les pamplemoussiers, C. medica les cédratiers et C. micrantha) à l'origine de l'ensemble des formes cultivées suite à des événements de réticulations. Il en résulte des structures génotypiques complexes, généralement fixées par l'apomixie, fortement hétérozygotes et formées d'une mosaïque de grands fragments chromosomiques d'origines phylogénétiques différentes. La structuration de la variabilité phénotypique suggère que la différenciation initiale des taxons ancestraux est à l'origine d'une part importante de la variabilité utile des agrumes. La connaissance de l'origine des formes cultivées et de leurs structures phylogénomiques est donc indispensable à la bonne gestion des collections et à l'optimisation des programmes d'amélioration génétique. A cette fin, cette thèse explore différentes approches d'analyse de la diversité des génomes. Elle a bénéficié de l'évolution rapide des NGS et propose une utilisation raisonnée des outils disponibles en fonction des questions de recherches. Une analyse plus poussée a été conduite sur les limettiers et citronniers. Le pyroséquençage 454 (Roche) d'amplicons a été utilisé pour décrypter la structure en mosaïque interspécifique du chromosome 2 de 50 variétés à partir d'une information haplotypique multiloci et pour identifier des marqueurs diagnostiques des taxons ancestraux. Ces marqueurs ont permis, en association avec des SSR et indels, d'apporter un nouvel éclairage sur l'origine des limettiers et citronniers, par un génotypage exhaustif des collections Inra/Cirad et Ivia. Enfin, les données de re-séquençage complet Illumina de sept variétés de limettiers et de citronniers comparées à celles de représentants des taxons ancestraux nous ont permis de reconstituer la structure interspécifique de leurs génomes et de schématiser leurs caryotypes phylogénomiques. Les différentes approches ont conduit à des conclusions convergentes. Nos résultats confirment les hypothèses concernant la séquence évolutive à l'origine des bigaradiers (C. aurantium), des orangers (C. sinensis) et des pomelos (C. paradisi) à partir des pools géniques de C. maxima et C. reticulata. Ils mettent en évidence de fréquentes introgressions de C. maxima dans le génome de mandariniers considérées comme représentatifs de C. reticulata. Les contributions relatives de ces deux taxons ancestraux aux génomes de nombreuses variétés de petits agrumes (mandariniers, tangors et tangelos) ont pu être estimées. Les limettiers et citronniers résultent de multiples évènements de réticulation et C. medica est identifié comme parent mâle de la majorité des variétés diploïdes. Deux grands groupes de citronniers, sont différenciés, ceux issus d'hybridations directes C. reticulata × C. medica et ceux impliquant trois taxons ancestraux (C. maxima, C. reticulata et C. medica). Le bigaradier serait le parent femelle à l'origine des citronniers type Lisbonne (C. limon). Les limettiers de type Mexicain (C. aurantifolia) seraient issus d'une hybridation directe C. micrantha × C. medica. Enfin, les limes à gros fruits, triploïdes, ont deux origines. Les types Tahiti résulteraient probablement de la fécondation d'un ovule de citronnier type Lisbonne par un gamète diploïde de limettier type Mexicain. L'autre grand type serait issu d'un backcross entre C. aurantifolia (gamète diploïde) et C. medica. Ces connaissances sur la structure génomique des espèces secondaires permettent d'envisager une reconstruction d'idéotypes à partir du germplasm des taxons ancestraux. Elles ouvrent également la voie à des études de génétique d'association s'appuyant sur la phylogénomique des gènes impliqués dans l'élaboration des caractères de qualité, de résistance et d'adaptation. Enfin, les marqueurs diagnostiques d'espèces développés trouveront de nombreuses applications pour la caractérisation des collections et diverses études de génétiques. / Citrus fruit, the most important fruit crop in the world, show a wide phenotypic diversity. Previous studies (molecular markers) identified four ancestral taxa (Citrus reticulata Blanco, mandarins; C. maxima (Burm.) Merr., pummelos; C. medica L., citrons; C. micrantha Wester, papedas) as the ancestors of all cultivated Citrus after reticulate evolutions. As a result, modern citrus varieties have complex and highly heterozygous genotypic structures, generally fixed by apomixis, and formed by a mosaic of large chromosomal fragments of different phylogenetic origins. Furthermore, the structuration of the phenotypic variability suggests that the initial differentiation of the basic taxa is the main source of most of the variability of the useful citrus phenotypic diversity. A thorough knowledge of the origin of cultivated citrus and their phylogenomic structure are essential for the management of biological resources and breeding program optimization. This thesis explores different approaches for analyzing genome diversity in order to identify the phylogenetic origins of the various horticultural citrus groups and to decipher their phylogenomic genome's structures. We focused on limes and lemons. This thesis takes advantage of the rapid evolution of NGS and proposes a rational use of available tools, based on research questions. Roche 454 parallel sequencing of amplicons provides multi-loci haplotype information on 500 base fragments. It was used to decipher the interspecific mosaic structure of chromosome 2 for fifty varieties and to identify ancestral taxa diagnostic SNP markers. The genotyping of all limes and lemons of the Inra/Cirad and Ivia germplasms with these markers, in association with SSR and indel markers, allowed to propose new hypothesis on the origins of limes and lemons. Data from Illumina whole genome re-sequencing of 7 varieties of limes and lemons, compared to those of representatives of the ancestral taxa, allowed to infer the interspecific structure of their genomes and to map out, for the first time, their phylogenomic karyotypes. The different approaches led to similar conclusions. Our results confirm previous hypothesis about the evolutionary steps at the origin of sour orange (C. aurantium), sweet orange (C. sinensis) and grapefruit (C. paradisi) involving C. maxima and C. reticulata gene pools. They highlight frequent introgressions of C. maxima in the genome of mandarin varieties despite the fact they were considered as representative of C. reticulata. We were also able to quantify the relative proportions of these two ancestral taxa in the genome of many varieties of small citrus fruit (mandarin hybrids, tangors and tangelos). Our work on limes and lemons demonstrate that C. medica is the male parent of this varietal group at the diploid level. Two groups of lemons are clearly differentiated: one from direct hybridizations between C. reticulata and C. medica, and one from crosses between hybrids (C. maxima × C. reticulata) and C. medica. Sour orange seems to be the female parent of ‘Eureka' type lemons (C. limon). The ‘Mexican' limes (C. aurantifolia) seems to come from a direct hybridization C. micrantha × C. medica. Finally, triploid big fruit limes have two major origins. The ‘Tahiti' type probably results from an ‘Eureka' type lemon (C. limon) ovule fecundated by a diploid gamete of a ‘Mexican' type lime (C. aurantifolia), while the other type would come from a back-cross between C. aurantifolia (diploid gamete) and C. medica. This new insights in genomic structure of secondary species makes to consider possible a reconstruction of these ideotypes from ancestral taxa germplasm. They also open new ways for association genetic studies based on phylogenomics of genes involved in the development of quality, resistance and adaptation traits. Finally, developed specific taxa diagnostic markers will find many applications for the characterization of collections and further genetic studies.

Reversion-inducing cysteine-rich with Kazal motif (RECK) is a cell surface anchoring protein, which known for the ability to inhibit matrix metalloproteinases (MMPs) and participate in angiogenesis regulation. The inhibition of membrane type-1 matrix metalloproteinase (MT1-MMP), MMP-2, MMP-7 and, MMP-9 by RECK has been demonstrated. Our previous studies show that RECK expression is suppressed by Ras and Her-2/neu oncogene. In addition, oncogenic Ras activates downstream ERK signaling pathway to increase Sp1/HDAC promoter binding affinity which results in reduction of RECK gene transcription and increase of tumor progression and metastasis. From the clinical investigation, RECK expression is down-regulated in a number of cancer types. In breast cancer, RECK expression is associated with the prognosis of the patients. Recently, single nucleotide polymorphisms (SNPs) of RECK promoter have been suggested to be linked with survival rate and prognosis of breast cancer patients. Whether SNP of the RECK promoter has any effect on RECK expression and its clinical significance is still unclear. . In this study, we investigate -402 SNP at RECK promoter and find this SNP directly affects RECK expression through progesterone receptor binding. Additionally, we also address the -402 SNP in the sample collected from patients and analyze its association with clinicopathological parameters to clarify its clinical significance. Our results suggest that RECK SNP may be an valuable prognosis factor for breast cancer.

The human metabolic syndrome is characterized by a heterogenic complex of symptoms, including central obesity. Obesity itself is linked to major features of the metabolic syndrome such as insulin resistance, dyslipidemia or type 2 diabetes mellitus. It has been shown that obesity risk and resulting metabolic alterations are associated with adipose tissue distribution, adipocyte size and secretion of adipocytokines, which are in turn influenced by environmental factors and genetic susceptibility. It might be assumed that currently known genetic variants associated with obesity and/or BMI (body mass index) as well as fat distribution explain up to 20 % of the variability in BMI and so, studies employing novel strategies are inevitable. In addition to the role of genetic variation, mRNA levels of several genes have been shown to be differentially expressed in subcutaneous (SC) and visceral (Vis) adipose tissue and to be correlated with obesity-related traits. It is scarcely investigated whether the obesity risk variants also might account for the variability in mRNA expression. The present thesis deals with novel obesity candidate genes, characterized by a differential mRNA expression in various fat depots. The association of genetic variants in these genes with obesity as part of the metabolic syndrome, and related traits was investigated in well characterized German cohorts. The main method used for genotyping was described in detail in a comprehensive review providing explicit troubleshooting and description of modified protocols for specific experimental needs. Further, the influence of genotypes on the gene expression levels was examined. While the differential expression for FTO could be described for the first time, the variant rs8050136 was shown to be significantly associated with obesity but not with the expression. Genetic variants in FASN were shown to be significantly associated with obesity and related traits in a cohort of European ancestry for the very first time. Moreover, one polymorphism showed effects on the ratio of Vis/SC FASN mRNA expression. While CNR1 is controversially discussed in the literature, the present work showed rather moderate effects of genetic variants on obesity. BMPR2 could be described as a novel obesity candidate gene. Amongst others, one variant was associated with obesity in a case-control design and with BMPR2 mRNA expression in Vis adipose tissue. In conclusion, the present study revealed novel genetic variants promoting obesity, and therefore a metabolic risk, which might be partly explicable through an influence of these variants on the mRNA expression levels of the genes in the adipose tissue depots. These findings contribute to better understanding of the genetic background of obesity which is essential in order to translate experimental data into diagnostic, preventive and treatment strategies.

Viele Publikationen haben bereits den Einfluss verschiedener Zytokingenvariationen auf die Ensteheung einer Graft versus Host Disease untersucht. Ich habe den Einfluss verschiedener Zytokin- und Zytokinrezeptorgenvariationen des Interleukin 10-Gens auf die Ausprägung von GvHD und die Überlebensrate nach allogener Blutstammzelltranplantation bei Patienten mit einer hämatologischen Neoplasie untersucht. Die GvHD zählt zu einer gefürchteten Komplikation bei Patienten nach einer allogenen Stammzelltransplantation. Sie kann als akute Form innerhalb von 100 Tagen nach Transplantation, sowie als chronische Form im späteren Verlauf auftreten. Sowohl die akute wie auch die chronische GvHD können bis zum Tode des Patienten führen oder durch Organschäden und die langandauernde intensive Immunsuppression die Lebensqualität der Patienten sehr beeinträchtigen. Es fehlt bis heute das genaue Verständnis, warum einige Patienten eine schwerwiegende GvHD entwickeln, während andere Patienten von einer nur leichtgradig auftretenden GvHD auf Grund eines damit assoziierten GvL-Effektes sogar profitieren. Das Interleukin 10 spielt neben anderen Zytokinen aufgrund seiner antiinflammatorischen Funktion eine wichtige Rolle in der Pathophysiologie der GvHD. Durch IL 10 kommt es zu einer Herunterregulation von MHC Klasse 2 und Kostimulatorischen Molekülen auf der Zelloberfläche, womit die Fähigkeit antigenpräsentierender Zellen zur Antigenpräsentation supprimiert wird. Interleukin 10 bewirkt außerdem eine Hemmung der Produktion proinflammatorischer Faktoren wie z.B. Interferon a, oder TNF-a, sowie eine Suppression der Transkription von NF- kB. Für diese Analyse wurden die GvHD-relevanten klinischen Daten von 360 konsekutiven Patienten ausgewertet, die zwischen 2001 und 2011 in der Universitätsmedizin Göttingen eine allogene Transplantation erhielten und eine Einteilung in die Schweregrade der akuten und der chronischen GvHD vorgenommen. Es wurde eine Genotypisierung ausgewählter Single Nucleotide Polymorphisms des IL 10–Gens und des IL 10–Rezeptorgens mittels SNaPshot-Analyse und TaqMan® Genotyping Assays vorgenommen. Durch univariate, gefolgt von multivariaten logistischen Regressionsanalysen der Daten mit Bezug zum klinischen Verlauf wurden Genvarianten mit Einfluss auf das Auftreten und den Schweregrad der GvHD identifiziert. Für die Überlebenszeitanalysen wurde ein simpler Logrank–Test verwendet, um Variablen mit einem p-Wert < 0,20 herauszufiltern, mit denen anschließend eine Cox–Regressionsanalyse durchgeführt wurde. In Voruntersuchungen (v.a. Hansen et al) war der SNP IL-10 -597 Genotyp A (= IL-10 -592) im Patienten, in Kombination mit dem G-Allel im SNP IL-10Rβ K47E (=IL-10Rβ c238) im Spender, bereits als wichtiger protektiver Faktor gegen eine schwere aGvHD in Matched-related-Donor (MRD)-transplantierten Patienten beschrieben worden. Der protektive Effekt dieser Kombination war in unserem Datensatz über alle Patienten hinweg nur als Tendenz erkennbar, während sich der alleinige protektive Effekt des R K47E G-Allel im Spender bei Patienten mit malignen Lymphomen als signifikant erwies. Dieser Unterschied in unseren Analysen, kann an der inhomogenen Zusammenzusetzung des Kollektivs aus MRD- und MUD- transplantierten Patienten liegen. Der protektive Effekt der oben genannten Kombination wurde bisher nur in reinen MRD-Kollektiven nachgewiesen und war in reinen MUD-Kollektiven nicht vorhanden. Weiterhin erwies sich für die chronische GvHD der proximale SNP IL-10 -1087 Genotyp GG des Patienten als assoziiert mit einem erhöhten Auftreten von chronischer GvHD. Dieser Genotyp ist mit einer erhöhten IL 10 Produktion assoziiert. Laut Ergebnissen von Martin und Zhou et al., ist ein erhöhter IL 10–Spiegel mit einer cGvHD assoziiert. Unter den in dieser Untersuchung erstmalig analysierten Polymorphismen des IL 10-Rezeptorgens wurde ein signifikant erhöhtes Risiko für das Auftreten einer schweren akuten GvHD (Grad III und IV) für Patienten festgestellt, die mit einem Spender des Genotyps IL 10 Rα G351R AA transplantiert worden waren. Dieses Risiko war weiter erhöht für die Patienten festzustellen, die zur T-Zell-Depletion im Rahmen der Konditionierung ATG erhalten hatten. Der Einsatz des als prophylaktisch gegen das Auftreten einer schweren GvHD genutzen ATGs war bei dieser Patientengruppe also mit einer zusätzlichen Risikoerhöhung für das Auftreten einer schweren GvHD assoziiert. Der IL 10 Rezeptor besteht aus einer - und einer -Einheit. Analysen der -Einheit des IL 10-Rezeptors beziehen sich größtenteils auf den Rα G159S. Der Rα G351R wurde bisher nicht funktionell oder in genetischen Assoziationsstudien untersucht, weshalb die funktionelle Bedeutung dieses Polymorphismus bisher nicht bekannt ist. Eine funktionelle Rolle dieses Polymorphismus erscheint aber prinzipiell möglich, da er im codierenden Bereich des Gens liegt und mit einem Austausch der Aminosäure Glycin gegen Arginin verbunden ist. Die Bedeutung der in dieser Arbeit erstmalig untersuchten SNPs, insbesondere des Polymorphismus IL 10 Rα G351R AA, sollte in unabhängigen Patientenkollektiven hinsichtlich seiner klinischen Relevanz weiter überprüft werden, auch um die Assoziation mit einer höheren Inzidenz an schwerer akuter GvHD bei Patienten, die ATG erhielten, detaillierter zu untersuchen. Um den Effekt besser zu verstehen, sollte diese Genvariante auch in ihrer Funktionalität in vitro untersucht werden. Neben dem Interleukin 10 sind noch viele weitere Zytokine an der Entstehung bzw. der Verhinderung einer GvHD beteiligt und es ist wichtig, hier mit der Genotypisierung von Kandidatengenen fortzufahren, um weitere funktionell bedeutsame Genvarianten zu identifizieren. Im Erfolgsfalle wird durch die Identifizierung dieser Varianten die Erstellung eines genetischen Profils der Patienten vor der geplanten Stammzelltransplantation möglich. Mit Hilfe dieses Profils kann eine bessere Einschätzung des individuellen Risikos getroffen und gegebenenfalls die Medikation frühzeitig dementsprechend angepasst werden.

A current trend in biological science is the increased use of computational tools for both the production and analysis of experimental data. This is especially true in the field of genomics, where advancements in DNA sequencing technology have dramatically decreased the time and cost associated with DNA sequencing resulting in increased pressure on the time required to prepare and analyze data generated during these experiments. As a result, the role of computational science in such biological research is increasing. This thesis seeks to address several major questions with respect to the development and application of single nucleotide polymorphism (SNP) resources in non-model organisms. Traditional SNP discovery using polymerase chain reaction (PCR) amplification and low-throughput DNA sequencing is a time consuming and laborious process, which is often limited by the time required to design intron-spanning PCR primers. While next-generation DNA sequencing (NGS) has largely supplanted low-throughput sequencing for SNP discovery applications, the PCR based SNP discovery method remains in use for cost effective, targeted SNP discovery. This thesis seeks to develop an automated method for intron-spanning PCR design which would remove a significant bottleneck in this process. This work develops algorithms for combining SNP data from multiple individuals, independent of the DNA sequencing platforms, for the purpose of developing SNP genotyping arrays. Additionally, tools for the filtering and selection of SNPs will be developed, providing start to finish support for the development of SNP genotyping arrays in complex polyploids using NGS. The result of this work includes two automated pipelines for the design of intron-spanning PCR primers, one which designs a single primer pair per target and another that designs multiple primer pairs per target. These automated pipelines are shown to reduce the time required to design primers from one hour per primer pair using the semi-automated method to 10 minutes per 100 primer pairs while maintaining a very high efficacy. Efficacy is tested by comparing the number of successful PCR amplifications of the semi- automated method with that of the automated pipelines. Using the Chi-squared test, the semi-automated and automated approaches are determined not to differ in efficacy. Three algorithms for combining SNP output from NGS data from multiple individuals are developed and evaluated for their time and space complexities. These algorithms were found to be computationally efficient, requiring time and space linear to the size of the input. These algorithms are then implemented in the Perl language and their time and memory performance profiled using experimental data. Profiling results are evaluated by applying linear models, which allow for predictions of resource requirements for various input sizes. Additional tools for the filtering of SNPs and selection of SNPs for a SNP array are developed and applied to the creation of two SNP arrays in the polyploid crop Brassica napus. These arrays, when compared to arrays in similar species, show higher numbers of polymorphic markers and better 3-cluster genotype separation, a viable method for determining the efficacy of design in complex genomes.

[Truncated abstract] Tumor Necrosis Factor (TNF) is a potent pro-inflammatory cytokine involved in a range of biological functions including the differentiation, proliferation and survival of many cell types. The TNF gene lies in the class III region of the major histocompatibility complex (MHC), approximately 250 Kbp centromeric of the HLA-B locus and 850 Kbp telomeric of HLA-DR. Due to the genomic location and biological relevance of TNF, it is thought that genetic heterogeneity at this locus may be associated with autoimmune and infectious diseases. A G-to-A single nucleotide polymorphism (SNP) at position -308 (relative to the transcriptional start site) in the TNF promoter has been well described. The less common -308A variant has been shown to be linked with the HLA-A1, B8, DR3 haplotype which in turn has been associated to a high TNF producing phenotype. Determining whether the -308 polymorphism contributes to elevated levels of expression has therefore been a priority for many research groups. Some investigators have shown differences in transcription between the -308G and -308A alleles while others could not. These contradicting results have led to conflicting views regarding the functional relevance of the -308 SNP. In this study, statistical analysis of 18 independent transient transfections of -308 biallelic TNF reporter constructs have provided evidence for a functional consequence of the polymorphism. ... In addition, chromatin accessibility of this region was maximal at greater levels of transcription suggesting a role for both chromatin structure and YY1 binding in -308G regulation. Surprisingly, chromatin structure did not seem to play a role in -308A regulation nor was there any significant binding of YY1, suggesting the -308 region does not affect transcriptional control of TNF. Taken as a whole, the G-to-A SNP relieves YY1 binding and demonstrates an allele-specific regulatory mechanism controlling expression. A growing list of promoter polymorphisms exists in the human genome having associations with certain diseases. Determining the functional consequence of these SNPs has proven difficult and utilized mainly in vitro approaches. In this thesis, a unique approach to investigating the functionality of promoter polymoprhisms has been developed, utilizing in vivo techniques which test their effects in a more natural system. It is hoped that the identification of the allele-specific YY1-mediated control of the -308 region of the TNF promoter may provide insight into overexpression as a consequence of the polymorphism and its role in the genetic susceptibility to MHC-associated autoimmune disease.