Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2018-11-01T15:06:18Z No. of bitstreams: 2 Dissertação - Karla da Silva Carneiro - 2017.pdf: 3925004 bytes, checksum: 34919ba64c10b1240fa3e19cf38d927a (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2018-11-01T15:53:42Z (GMT) No. of bitstreams: 2 Dissertação - Karla da Silva Carneiro - 2017.pdf: 3925004 bytes, checksum: 34919ba64c10b1240fa3e19cf38d927a (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2018-11-01T15:53:42Z (GMT). No. of bitstreams: 2 Dissertação - Karla da Silva Carneiro - 2017.pdf: 3925004 bytes, checksum: 34919ba64c10b1240fa3e19cf38d927a (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2017-12-21 / Financiadora de Estudos e Projetos- Finep / In Brazil, the history of sugarcane is related to the social, economic and politic country development. Sugarcane cultivation is considered as the first organized economic activity in the country. The main purpose of sugarcane cultivation is for sugar and biofuel production, but in recent years the energy production from its biomass has also been explored, increasing the attention for this crop. Modern cultivated sugarcane varieties are hybrids from interspecific crosses between S. officinarum and S. spontaneum. The genetic breeding has given many contributions to sugarcane production and exploration, by the development of superior genotypes. The main sources of variability used in breeding programs are the germplasm banks. However, to explore these resources efficiently it is necessary to have basic information on the available levels of genetic diversity and on its structure, to support decisions on how they can be used in breeding programs. The purpose of this work was to characterize the genetic diversity and structure of a base population from the Ridesa/UFG sugarcane breeding program. A sample of 160 sugarcane clones were genotyped using 37,914 SNP markers. The population showed medium levels of genetic diversity. The average Nei’s gene diversity index was estimated to be 0,173, while the medium observed heterozygosity was a little higher (0,236). The genetic divergence, estimated by Roger’s modified distance varied from 0,20 to 0,30. SNP markers were efficient to identify individuals that are genetic divergent or similar, even without genealogy information. The population structure analysis, performed with the software Structure, suggested the existence of two clusters. Each clone had a fraction of its genome inside these two clusters, corroborating the fact that modern sugarcane cultivars are essentially hybrids. Our results suggest that, given the low level of genetic structure among clones, from the breeding programs standpoint, the evaluated population can be managed as weakly structured, although some small groups, including a small number of clones, had been detected. Among the evaluated clones, the least divergent pairs were those formed by the genotypes 023 and 011, and 066 and 036. The most divergent pairs were formed by the clones 131 and 084, and 131 and 063. / A história da cana-de-açúcar está intimamente relacionada com o desenvolvimento social, econômico e político do Brasil, sendo considerada por muitos como a primeira atividade economicamente organizada no país. A cana-de-açúcar é matéria prima para a produção de açúcar e etanol, tendo sido também utilizada nos últimos anos para a produção de energia. As modernas variedades de cana-de-açúcar são híbridos poliploides decorrentes do cruzamento interespecífico entre S. officinarum e S. spontaneum. O melhoramento genético tem contribuído de maneira importante para o setor, pelo desenvolvimento de genótipos superiores. O ponto de partida destes programas de melhoramento são os bancos de germoplasma. Para que esse recurso seja explorado de forma eficiente é preciso que as informações básicas, que irão permitir o dimensionamento da magnitude da diversidade genética disponível, sejam geradas. O presente trabalho teve como objetivo realizar a caracterização genética molecular de uma população base do programa de melhoramento genético da Ridesa/UFG, representada por uma amostra de 160 clones, pela utilização de 37.914 marcadores SNPs. A diversidade genética revelada por estes marcadores, em que a dosagem de cada alelo não é detectável em cada genótipo, em decorrência da poliploidia, foi de magnitude intermediária, com índice de diversidade genética de Nei estimado em 0,173. A estimativa de heterozigosidade média observada apresentou valor mais elevado 0,236. As estimativas de divergência genética obtidas pela distância de Rogers modificada por Wright variaram entre 0,20 e 0,30. Na análise de agrupamento foram identificados sete grupos de clones. O uso de SNPs foi eficiente em identificar pares de indivíduos geneticamente divergentes, mesmo sem dispor de informações de genealogia. A análise de estruturação genética pelo software Structure sugeriu, a princípio, a existência de dois grupos. Cada clone, no entanto, se revelou constituído por uma mistura relativamente homogênea dos dois grupos identificados, confirmando a natureza híbrida das cultivares modernas de cana-de-açúcar. Estes resultados sugerem que, dada o reduzido nível de estruturação da diversidade genética ao nível de clones, do ponto de vista de melhoramento, a população possa ser considerada como um grupo fracamente estruturado, com a presença de poucos grupos envolvendo pequeno número de genótipos. Entre os clones avaliados, os pares menos divergentes são constituídos pelos genótipos 023 e 011, e 066 e 036. Os pares mais divergentes são constituídos pelos clones 131 e 084, e 131 e 063.

Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2016-04-01T12:01:10Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) ZILMA ANJOS.pdf: 965838 bytes, checksum: 562afc25b2650739b531bde86e398a7b (MD5) / Made available in DSpace on 2016-04-01T12:01:11Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) ZILMA ANJOS.pdf: 965838 bytes, checksum: 562afc25b2650739b531bde86e398a7b (MD5) Previous issue date: 2014-12-04 / Ficolinas são moléculas de reconhecimento do sistema complemento capazes de promover opsonização, fagocitose e destruição de patógenos mediado pela ativação da via das lectinas. Polimorfismos de nucleotídeo único (SNPs) nos genes FCN1 e FCN2, que codificam as ficolinas 1 e 2, têm sido relacionadas com a susceptibilidade a doenças infecciosas e autoimunes. Nosso estudo teve como objetivo investigar a associação funcional dos polimorfismos de base única (SNPs) ou tagSNPs entre FCN1 e FCN2 e o desenvolvimento de diabetes mellitus tipo 1 (DM1). Dois SNPs no gene FCN1, rs2989727 e rs1071583 e três no FCN2, rs17514136, rs3124954 e rs7851696 foram estudados em 204 crianças e adolescentes com diagnóstico de DM1 e 193 indivíduos saudáveis do Nordeste do Brasil. Não encontramos associações diretas com o desenvolvimento do DM1 ou com a insurgência de doenças relacionadas com DM1, como doença celíaca (DC) e tireoidite autoimune (AIDT). No entanto, o genótipo T / T (rs1071583) da FCN1 foi associado com uma idade precoce quando do diagnóstico DM1 em comparação com C / C ou genótipos C / T (p = 0,02), em torno de dois anos de diferença. Assim, se a hipótese de que o genótipo T / T (rs1071583) não está diretamente envolvido nas etapas iniciais de DM1 início, mas, após o gatilho induzir DM1, os indivíduos com este genótipo podem aumentar / acelerar a resposta autoimune contra células – do pâncreas. Apesar dos nossos resultados indicarem importância de FCN1 no contexto do DM1, estudos adicionais de réplicas devem ser realizados para esclarecer o papel da ficolina no DM1. / Ficolins are innate immune proteins able to activate the complement system by the lectin pathway. Single nucleotide polymorphisms (SNPs) of FCN1 and FCN2 genes, encoding for ficolin 1 and 2, have been related with susceptibility to infectious and autoimmune diseases. Our study aims at investigating the association between FCN1 and FCN2 functional of single nucleotide polymorphisms (SNPs) or tagSNPs and the development of type 1 diabetes mellitus (T1D). Two SNPs at FCN1, rs2989727 and rs1071583 and three at FCN2, rs17514136, rs3124954 and rs7851696 were studied in 204 children diagnosed with T1D and 193 healthy individuals all from the Brazilian Northeast. No direct associations were found with the T1D onset or with the insurgence of T1D related celiac disease (CD) and autoimmune thyroiditis (AIDT). However, the genotype T/T (rs1071583) of FCN1 was associated with an early age at T1D diagnosis compared with C/C or C/T genotypes (p = 0.02), around two years of difference Thus, we hypothesize that the T/T genotype (rs1071583) is not directly involved in the initial steps of T1D onset, but, after the trigger inducing T1D, individuals carrying this genotype could increase/accelerate the pancreatic autoimmune response. Despite our results indicate some importance of FCN1 in the context of T1D, additional replica studies should be performed to clarify the role of ficolins in T1D.

Submitted by Irene Nascimento (irene.kessia@ufpe.br) on 2016-06-28T18:09:11Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) dissertação Kamila_04.02.16 versao final completa.pdf: 2092777 bytes, checksum: 9e9782d9821d10b1a59b8f2a1a1ca8f7 (MD5) / Made available in DSpace on 2016-06-28T18:09:11Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) dissertação Kamila_04.02.16 versao final completa.pdf: 2092777 bytes, checksum: 9e9782d9821d10b1a59b8f2a1a1ca8f7 (MD5) Previous issue date: 2015-10-10 / CAPES / O processo inflamatório associado à liberação de citocinas está diretamente envolvido na patogênese da artrite reumatóide (AR). Um estudo anterior do nosso grupo relatou que pacientes com AR apresentaram níveis elevados da citocina IL-22 em relação aos controles e este aumento foi associado a um pior quadro clinico. Polimorfismos em interleucinas ou nos receptores específicos podem modificá-los funcionalmente, e assim, contribuir para o desenvolvimento da AR. O objetivo deste estudo foi identificar polimorfismos no receptor da citocina IL-22 que possam estar associados ao risco de desenvolver AR. Cento e trinta e oito portadores de AR foram recrutados pelo Serviço de Reumatologia do HC - UFPE, cumprindo os critérios do Colégio Americano de Reumatologia foram genotipados para os polimorfismos no IL22RA1 (rs4292900 e rs10794665) através da metodologia TaqMan®; o grupo controle foi formado por cento e vinte e oito indivíduos sadios. Os SNPs foram identificados por meio de consulta ao site HapMap, com uma frequência do alelo menor (MAF) de pelo menos 0,1% em caucasianos. Todas as frequências genéticas foram verificadas quanto ao equilíbrio de Hardy-Weinberg e a comparação das proporções foi realizada através do qui-quadrado (X²) ou teste exato de Fisher. Resultados: O genótipo TT (rs4292900) foi significativamente associado a AR quando comparados aos controles (37.79% e 21.36%, respectivamente, p=0,0054, odds ratio=2.23). Os pacientes heterozigotos CT e homozigotos TT para o polimorfismo rs4292900 apresentaram níveis significativamente elevados da citocina IL-22 comparados ao homozigoto CC (p=0.0018 e p=0.0324, respectivamente). Quanto aos parâmetros clínicos o genótipo CT (rs4292900) apresentou valores maiores do índice de atividade da doença (CDAI) comparado aos homozigotos; o mesmo ocorreu com o rs1079466. Observamos que os indivíduos TT para o rs 4292900 apresentaram maiores valores do hemossedimentação (VSH) comparados aos heterozigotos (p=0.016). Conclusão: Nossos resultados sugerem uma associação entre o rs4292900 e uma maior susceptibilidade a artrite reumatóide. Os dois SNPs não foram associados a pior quadro clínico da doença, no entanto o genótipo TT do rs4292900 foi associado com o altos níveis do VSH. / The inflammatory process associated with the release of cytokines is directly involved in the pathogenesis of rheumatoid arthritis (RA). A previous study from our group reported that RA patients had higher levels of IL-22 cytokine compared to controls and this increase was associated worse clinical condition. Interleukins or polymorphisms in the specific receptors can modify them functionally, therefore contributing to the development of the RA. The objective of this study was to identify polymorphisms in the IL-22 cytokine receptor that may be associated with risk of developing RA. One hundred and thirty-eight patients with RA were recruited at the Rheumatology Service HC - UFPE, meeting the American College of Rheumatology criteria they were genotyped for polymorphisms in IL22RA1 (rs4292900 and rs10794665) through the TaqMan method; the control group consisted of one hundred twenty-eight healthy individuals. SNPs were identified by query of the HapMap site with a minor allele frequency (MAF) of at least 0.1% in Caucasians. All genetic frequencies were checked for Hardy-Weinberg and the comparison of proportions was performed using the chi-square (X²) or Fisher's exact test. Results: The TT genotype (rs4292900) was significantly associated with RA compared to controls (37.79% and 21:36% respectively, p = 0.0054, odds ratio = 2.23). Patients heterozygous CT, and homozygous TT for the polymorphism rs4292900 had significantly elevated levels of the cytokine IL-22 compared to the homozygous CC (p = 0.0018 and p = 0.0324, respectively). As for the clinical parameters the CT genotype (rs4292900) showed higher values of disease activity index (CDAI) compared to homozygous; so has the rs1079466. We observe that the TT individuals for rs4292900 showed higher erythrocyte sedimentation rate (ESR) values compared to heterozygotes (p = 0.016). Conclusion: Our results suggest an association between rs4292900 and increased susceptibility to rheumatoid arthritis. The two SNPs were not associated worse clinical disease, however the rs4292900 TT genotype was associated with high levels of ESR.

O estudo das características de temperamento e resistência de bovinos ao carrapato visa a obtenção de animais possuidores de genótipos que levam a altas produções mas que sejam também adaptados ao meio ambiente de criação extensiva no Brasil. Esses animais produtivos e adaptados poderiam otimizar os custos e tornar a produção mais rentável. O temperamento é uma característica importante dentro do sistema de produção de gado de corte. Animais nervosos ou muito reativos são indesejáveis, principalmente por apresentarem risco às pessoas que os manejam e para si próprios, gerando custos adicionais para sua produção. O carrapato que mais compromete a produtividade da pecuária bovina é o Boophilus microplus. A infestação com esses ectoparasitas é considerada, atualmente, um dos principais entraves à intensificação das pecuárias de leite e de corte. A validação de marcadores moleculares ligados ao temperamento e a resistência ao carrapato torna possível estudar com mais precisão os efeitos dos genes envolvidos nesta característica. A proposta do presente trabalho foi estimar os parâmetros genéticos e caracterizar as frequências gênicas e genotípicas de vários polimorfismos e estudar seus efeitos nas características de temperamento e em várias maneiras de mensuração da resistência ao carrapato, em bovinos da raça Nelore. As estimativas de herdabilidade, no geral, tiveram média-baixa herdabilidade, com exceção de temperamento. Foi verificada a presença dos polimorfismos, desenvolvidos em bovinos de origem Bos taurus, nos animais da raça Nelore. Para diversos polimorfismos foi possível identificar o alelo favorável para uma dada característica. Justificando, assim, o uso de marcadores moleculares para um resultado mais acelerado em programas de melhoramento genético. / The study on traits like docility and resistante to ticks aims to help selection os animals with better genotypes to those traits, to increase productivity, but also keep adptation of those animals to the environment of extensive production systems used in the Brazilian beef production. Those animals, adapted to thse environmental conditions, should also optimize costs and increase profitability of the whole system. Docility, or temperament is an important trait in beef cattle production. Wild or nervous animals are very reactive, and can be risky to handle, not only to cattleman, but also for them, causing wounds and a decrease of their carcasses or production. The tick infestiation, specially with the species Boophilus microplus, can cause important losses for beef industry, being considered an important problem for that production. The validation of the use of genetic markers in selection for traits linked to temperament and tick resistance, by the study of association of the genotypes and the phenotypes or estimated genetic values allows to understand those relationships and indicate the possible use of those markers in selection of those traits. The objectives of this study were to estimate genetic parameters and define gene and genotype frequencies of several polymorphisms of single basis DNA markers (SNPs) of traits linked to docility and tick resistance, besides developing different methodologies to measure tick resistance in Nellore beef cattle reared in a tropical area on southeastern Brazil. Heritability estimates varied, in general, from low to medium for all traits, but temperament, where the estimates were high. Several markers, originally discovered in Bos Taurus, showed polymorphism in the Nellore population studied. For several os the studied markers, it was possible to indicate the allele that was favorable to the traits. In this study, the evidences suggest that the use of genetic markers should speed up the response to selection for those traits in breeding programs.

Amaciamento natural devido proteólise miofibrilar pelas enzimas calpaínas (cálcio-dependentes) e descoloração devido oxidação do pigmento mioglobina podem ocorrer em carne maturada. Em bovinos, o tipo biológico Bos indicus apresenta maior atividade de calpastatina (CAST, inibidora das calpaínas) no músculo e concentração de melanina (modulador de vitamina D3) na pele do que Bos taurus. Maior concentração de melanina na pele reduz fotossíntese de vitamina D3 e, subsequentemente, poderia reduzir as concentrações de seus metabólitos 25-hidróxivitamina D3 (25-D) e 1,25-di-hidróxi-vitamina D3 (1,25-D; modulador de cálcio) no plasma de Bos indicus. Nos casos de maiores concentrações de 1,25-D plasmático, uma melhor absorção de cálcio da dieta com aumento de suas concentrações no plasma e músculo poderia resultar em atividade melhorada das calpaínas. Além disso, maiores concentrações de 1,25-D plasmático poderiam colaborar para minimizar oxidação de carne devido sua propriedade antioxidante. Então, além da maior atividade de CAST no músculo, os Bos indicus poderiam ter mais duas desvantagens para produzir carne mais macia e menos oxidada: concentrações maiores de melanina na pele e menores de 1,25-D no plasma. Desta forma, o objetivo deste trabalho foi estudar as relações entre as concentrações de melanina total (MELT) e suas frações [faeumelanina (FAE) e eumelanina (EUM)] na pele, metabólitos da vitamina D3 (25-D e 1,25-D) no plasma, cálcio plasmático e muscular e maciez [Índice de Fragmentação Miofibrilar (MFI) e força de cisalhamento (FC)] e cor (valores de L*, a* e b*) em carne maturada (1, 7 e 14 dias) e suas associações com polimorfismos de um único nucleotídeo (SNPs) nos genes candidatos receptor da melanocortina-1 [MC1R; rs109688013 (C/T) e rs110710422 (G/-)], proteína ligante à vitamina D3 [DBP; rs136359868 (T/C) e rs135330728 (T/C)] e CAST [rs109384915 (T/C)]. Bovinos Nelore (n=86), abatidos com 516 ± 39 kg aos 24 ± 1 meses, foram usados para determinação dos genótipos e mensuração das características. Na pele, a fração EUM foi positivamente correlacionada com MELT, mais do que a fração FAE. As frações de melanina na pele foram correlacionadas negativamente. A fração FAE foi correlacionada negativamente com 1,25-D plasmático, mas não foi correlacionada com 25-D plasmático. Melanina e suas frações na pele e metabólitos da vitamina D3 no plasma não foram correlacionadas com cálcio plasmático e muscular. Todavia, cálcio no plasma e músculo foram correlacionados positivamente com MFI e valores de L* e b* e negativamente com FC e valores de a*. A EUM e MELT na pele foram correlacionadas negativamente com FC e valores de a* e b* e positivamente com valores de L*, enquanto que 25-D no plasma foi correlacionada positivamente com MFI e valores de a* e b* e negativamente com valores de L*. A FAE foi correlacionada positivamente com MFI e negativamente com os valores de L*, a* e b*. No gene MC1R, o alelo T do SNP rs109688013 apresentou-se fixado (100%) na população, enquanto que o alelo G e sua deleção (-) do SNP rs110710422 tiveram frequência de 97,7 e 2,3%, respectivamente. SNPs do gene MC1R resultaram nos genótipos do loco Extension (E/E = T/T + G/G e E/e = T/T + G/-), que foi associado com 1,25-D plasmático e valores de b* no dia 1. No gene DBP, o alelo C do SNP rs136359868 foi menos frequente (3,5%) do que o alelo T, enquanto que os alelos C e T do SNP rs135330728 tiveram uma frequência de 73,8 e 26,2%, respectivamente. SNPs do gene DBP foram associados com MELT na pele e valores de L* e a* em diferentes dias. No gene CAST, os alelos C e T do SNP rs109384915 tiveram a mesma frequência. O SNP rs109384915 foi associado com MFI ao dia 7 e a substituição do alelo T por C reduziu os valores de MFI e a* no dia 7 e os valores de b* no dia 1. Ao final, maiores concentrações de FAE na pele e 25-D no plasma melhoraram proteólise miofibrilar e cor de carne, enquanto as maiores concentrações de EUM e MELT na pele resultaram em uma carne mais macia com uma pior cor. Associações do loco Extension e dos SNPs no gene DBP com cor de carne parecem consequência das diferenças em 1,25-D no plasma e melanina na pele. SNP do CAST associou-se com proteólise miofibrilar e cor de carne maturada, mas não com FC. / Natural tenderization by myofibrillar proteolysis through the calpains enzymes (calcium-dependent) and discoloration by oxidation of myoglobin pigment may occur in aged meat. In cattle, the Bos indicus biological type has higher calpastatin activity (CAST, inhibitor of calpains) in muscle and melanin concentration (modulator of vitam in D3) in skin than Bos taurus. Higher melanin concentration in skin reduces photosynthesis of vitamin D3 and, subsequently, could reduce the concentrations of its metabolites 25-hydroxy-vitamin D3 (25-D) and 1,25-di-hydroxy-vitamin D3 (1,25-D; modulator of calcium) in plasma from Bos indicus cattle. In cases of higher plasma 1,25-D concentrations, an improved absorption of calcium from the diet followed by increased plasma calcium concentrations could result in enhanced activity of calpains. Furthermore, higher plasma 1,25-D concentrations could collaborate to minimize meat oxidation due to its antioxidant propriety. Then, in addition to higher CAST activity in muscle, the Bos indicus cattle could have two more disadvantages to produce tender and less oxidized meat: higher melanin concentrations in skin and lower 1,25-D concentrations in plasma. Hence, the objective of this work was to study the relationships between the concentrations of total melanin (MELT) and its fractions [pheomelanin (PHEO) and eumelanin (EUM)] in skin, vitamin D3 metabolites (25-D and 1,25-D) in plasma, plasma and muscle calcium, and tenderness [Myofibrillar Fragmentation Index (MFI) and shear force (SF)] and color (L*, a*, and b* values) in aged meat (1, 7, and 14 days) and their associations with single nucleotide polymorphisms (SNPs) in candidate genes as melanocortin-1 receptor [MC1R; rs109688013 (C/T) and rs110710422 (G/-)], vitamin D3-binding protein [DBP; rs136359868 (T/C) and rs135330728 (T/C)], and CAST [rs109384915 (T/C)]. Nellore cattle (n=86), slaughtered with 516 ± 39 kg at 24 ± 1 months, were used for genotyping and traits measurements. In skin, the EUM fraction was positively correlated with MELT than the PHEO fraction. The melanin fractions in skin were negatively correla ted. The PHEO fraction was negatively correlated with plasma 1,25-D, but not with plasma 25-D. Melanin and its fractions in skin and vitamin D3 metabolites in plasma were not correlated with plasma and muscle calcium. Nevertheless, plasma and muscle calcium were positively correlated with MFI, and L* and b* values and negatively correlated with SF and a* values. The EUM and MELT in skin were negatively correlated with SF, and a* and b* values and positively correlated with L* values, while 25-D in plasma was positively correlated with MFI, and a* and b* values and negatively correlated with L* values. The PHEO was positively correlated with MFI and negatively correlated with L*, a*, and b* values. In MC1R gene, the rs109688013 SNP allele T was fixed (100%) in the population, while the rs110710422 SNP allele G and its deletion (-) had a frequency of 97.7 and 2.3%, respectively. MC1R SNPs resulted in genotypes of the Extension locus (E/E = T/T + G/G and E/e = T/T + G/-), which was associated with plasma 1,25-D and b* values at the day 1. In DBP gene, the rs136359868 SNP allele C was less frequent (3.5%) than allele T, while rs135330728 SNP alleles C and T had a frequency of 73.8 and 26.2%, respectively. DBP SNPs were associated with MELT in skin, and L* and a* values at different days. In CAST gene, the rs109384915 SNP alleles C and T had a similar frequency. The rs109384915 SNP was associated with MFI at the day 7 and the substitution from allele T to C reduced the MFI and a* values at the day 7 and the b* values at the day 1. At last, higher skin PHEO and plasma 25-D concentrations improved the myofibrillar proteolysis and meat color, while higher skin EUM and MELT concentrations resulted in a meat with improved tenderness and worsened color. Associations of the Extension locus and polymorphisms in DBP gene with the meat color seem to be a consequence of the differences in plasma 1,25-D and skin melanin. CAST SNP is associated with myofibrillar proteolysis and meat color, but not with SF.

5 à 10% des cancers du sein sont héréditaires mais parmi ceux-ci seulement la moitié est expliquée par une altération constitutionnelle d’un gène de prédisposition connu tels que les gènes BRCA1 et BRCA2. L’importante hétérogénéité génétique qui caractérise les famillesBRCAx rend difficile la réalisation d’études familiales groupées et ne permet pas l’identification de nouveaux gènes de prédisposition au cancer du sein selon les méthodes classiques de liaison génétique ou d’association. Les techniques de séquençage de nouvelle génération (NGS) à l’échelle de l’exome ou du génome entier, autorisent en revanche l’étude de familles individuelles à la recherche de mutations constitutionnelles privées mais le nombre considérable de variants génétiques identifiés impose leur tri sur des critères de pathogénicité ou de récurrence. Un autre critère de tri peut être représenté par l’identification de régions candidates définies en fonction de réarrangements génomiques tumoraux communs à plusieurs tumeurs au sein d’une même famille. Le génotypage tumoral par puces SNP (pour single nucleotide polymorphism) permet en effet la détection d’haplotypes conservés dans des régions récurrentes de LOH (pour loss of heterozygosity) communes à plusieurs tumeurs familiales et donc l’identification de régions candidates suspectes d’abriter des mutations germinales dans des gènes de prédisposition au cancer. La combinaison de ces deux approches, génotypage tumoral puis NGS, a été appliquée à une série de 17 familles avec agrégation de cancers du sein pour lesquelles au moins deux échantillons tumoraux étaient disponibles. Aucun nouveau gène de prédisposition au cancer du sein n’a été identifié mais une mutation délétère constitutionnelle du gène ATM a ainsi été retrouvée, associée à une perte de l’allèle sauvage dans les 2 tumeurs d’une famille BRCAx. L’analyse de 17 tumeurs du sein supplémentaires provenant de 10 familles avec agrégation de cancers du sein et mutation constitutionnelle du gène ATM identifiée chez le cas index, a révélé que l’allèle sauvage d’ATM était fréquemment perdu dans ces tumeurs (>80% contre 20% attendu en situation sporadique ; p<0.001). Ce résultat plaide fortement en faveur de l’implication d’ATM dans la carcinogénèse de ces cancers du sein tel un gène suppresseur de tumeur et suggère que les mutations constitutionnelles d’ATM sont impliquées dans des formes familiales de cancer du sein. / Hereditary breast cancers (BCs) account for 5-10% of all diagnosed BCs, yet only 50% of such tumors arise in the context of a germline mutation in known tumor suppressor genes such as BRCA1 or BRCA2. The vast genetic heterogeneity which characterizes BRCAx families makes grouped studies impossible to perform. Next generation sequencing (NGS) techniques, however, allow individual families to be studied in order to identify private mutations. Single nucleotide polymorphism (SNP) arrays allow the detection of conserved haplotypes within recurrent regions of loss of heterozygosity, common to several familial tumors, therefore identifying genomic loci likely to harbor a germline mutation in cancer predisposition genes. The combination of both exome sequencing and SNP arrays for a series of 17 familial BC did not allow the identification of a novel BC predisposition gene, but revealed a germline ATM mutation associated with a loss of the wild-type allele in a BRCAx family. The analysis of 17 additional breast tumors from ten BC families in which a germline ATM mutation had been identified revealed a high frequency of wild-type allele loss in these tumors (>80% compared to the 20% expected in sporadic BC; p <0.001). This result argues strongly in favor of the involvement of ATM in the carcinogenesis of these tumors as a tumor suppressor gene and suggests that germline ATM mutations are involved in a subset of familial BC.

Les technologies actuelles permettent d’explorer le génome entier pour y découvrir des variants génétiques associés aux maladies. Cela implique des outils bioinformatiques adaptés à l’interface de l’informatique, des statistiques et de la biologie. Ma thèse a porté sur l’exploitation bioinformatique des données génomiques issues de la cohorte GRIV du SIDA et du projet international IHAC (International HIV Acquisition Consortium). Posant les prémices de l'imputation, j’ai d’abord développé le logiciel SUBHAP. Notre équipe a montré que la région HLA était essentielle dans la non progression et le contrôle de la charge virale et cela m’a conduit à étudier le phénotype non-progresseur non « elite ». J’ai ainsi révélé un variant du gène CXCR6 qui, en dehors du HLA, est le seul résultat identifié par approche génome-entier et répliqué. L’imputation des données du projet IHAC (10000 patients infectés et 15000 contrôles) a été réalisée et des premières associations sont en cours d’exploration. / Nowadays with the newest technologies, the entire genome can be explored to uncover genetic variants which may be linked to diseases. This requires bioinformatics tools which are adequate for studies which are at the border between computing, statistics and biology. My thesis work focused on the bioinformatical analysis of genomic data from the GRIV AIDS cohort and from the IHAC (International HIV Acquisition Consortium) project. I first laid the foundation for imputation work by developing the SUBHAP software. Our team showed that the HLA region was essential in non-progression and viral charge control. This led me to study the non progressor non elite phenotype. Thus, I uncovered a variant of the CXCR6 gene which is, apart from HLA, the only result identified with a GWAS approach so far and which has been reproduced. The imputation of data from the IHAC project (10000 infected patients and 15000 control subjects) was also performed and the first associations are now being studied.

La peau est un excellent modèle d’étude du vieillissement général. En plus de facteurs environnementaux, les facteurs génétiques jouent un rôle majeur dans le vieillissement cutané. Dans le cadre de ma thèse, j’ai eu accès à une cohorte exceptionnelle de 502 femmes caucasiennes très bien caractérisées sur le plan cutané, pour effectuer deux études d’association « génome-entier ». La première étude a montré le rôle joué par le système immunitaire, et en particulier le gène HLA‑C, dans la sévérité des lentigines du visage. La seconde a mis en évidence une association entre le gène H2AFY2 et la sévérité de l’affaissement de la paupière supérieure. La recherche de voies de signalisation biologiques associées à différents indicateurs du vieillissement cutané a souligné le rôle de la mélanogénèse et des mécanismes de réparation de l’ADN.Ces résultats ouvrent de nouvelles perspectives dans la compréhension des mécanismes inhérents au vieillissement cutané et général. / The skin is an excellent model to study general ageing. In addition to environmental factors, genetic factors play a key role in skin ageing mechanisms. During my PhD, I have had access to a unique cohort of 502 Caucasian women very-well characterized regarding their facial features to perform two genome-wide association studies. The first one pointed to the role of the immune system, and especially the HLA‑C gene, in the severity of facial lentigines. The second one identified an association between the H2AFY2 gene and the severity of superior eyelid drooping. I also looked for associations between biological pathways and several skin ageing indicators which underlined the role of the melanogenesis and several mechanisms of DNA repair.Overall, these results lead to new insights in the understanding of the molecular mechanisms underlying skin and global ageing.

Les Amélogenèses imparfaites constituent un groupe d’altération de l’émail dentaire d’origine génétique. Cette pathologie peut exister de manière isolée ou associée à d’autres symptômes dans le cadre de syndromes. Certains gènes impliqués sont déjà connus, cependant de nouvelles mutations et de nouveaux gènes restent à identifier. L’étude de familles informatives dans le cadre de ce projet de recherche sur le massif crânio-facial et bucco-dentaire, associée à des stratégies d’identification génétique telles que la sélection de gènes candidats, les zones d’homozygotie, le séquençage haut débit, ont permis d’obtenir des résultats probants. Des investigations futures passant par l’augmentation des cohortes, le développement des outils de séquençage de nouvelle génération, l’étude des modèles cellulaires et animaux permettront d'améliorer la compréhension de l’amélogenèse. / Amelogenesis imperfecta (AI) represents hereditary conditions affecting the quality and quantity of enamel. This disease can exist in isolation or in association with other symptoms in the form of syndromes. Several genes involved in AI are already known, however mutations in these genes are not sufficient to explain all cases of AI. This suggests that mutations in yet unidentified genes underlie AI. The study of informative families included in this research project on cranio-facial and oro-dental anomalies, by using genetic strategies such as candidate gene mutational analysis,homozygosity mapping and next generation sequencing, allowed the discovery of novel genes and mutations in AI. Future investigations based on the recruitment of new families, the development of new next generation sequencing tools and the establishment of cellular and animal models will improve our understanding of amelogenesis.

Ziel dieser Arbeit war es, verschiedene Aspekte der Verwendung von genetischen Markern in der genomischen Charakterisierung und Analyse von verschiedenen Tierpopulationen zu untersuchen. Zu Beginn werden die verschiedenen Anwendungsbereiche von genetischen Markern in der Tierzucht beschrieben. In der ersten Analyse wurden acht Hühnerrassen für 9‘216 Single Nucleotide Polymorphism (SNPs) und 29 Microsatelliten (Single Sequence Repeats, SSRs) typisiert. Um die Rassen zu differenzieren wurden zwei unterschiedliche Methoden herangezogen: (i) die Bayesian Model-based Clustering Analyse, die im Programm STRUCTURE (Version 2.3) implementiert ist und (ii) eine Hauptkomponenten-Analyse (Principal Component Analysis, PCA), bei der eine Differenzierung der Rassen aufgrund ihres Euklidischen Abstandes zueinander durchgeführt wurde. Die Ergebnisse der STRUCTURE Analyse zeigten, dass die Wiederholbarkeit bei SNPs, unabhängig von Ihrer Anzahl, höher war als bei den SSR. Bei der Zuordnung eines Individuums zu einer der Rassen wurden die höchsten Werte für 29 SSRs und 100 SNPs errechnet. Die PCA-basierte Methode ergab, dass 2.4 SNPs je SSR benötigt werden, um eine vergleichbare Differenzierung zu erreichen. Dieses Ergebnis ist vergleichbar mit Untersuchungen, die an Menschen oder Rindern durchgeführt wurden. Unter Verwendung aller SNPs konnte im Vergleich zu allen vorhandenen SSRs eine genetisch inhomogene Rasse detektiert werden. Aufgrund dieser Ergebnisse und der deutlich größeren Anzahl an verfügbaren SNPs verglichen mit SSRs kann davon ausgegangen werden, dass SNP-basierte Ansätze weiter an Bedeutung gewinnen werden. Des Weiteren wurde eine umfassende Kartierung von Selektionssignaturen auf den Autosomen des Göttinger Minischweins durchgeführt. Für die Suche nach Selektions-signaturen wurden die mittels des Illumina Porcine BeadChip 60K (Illumina, San Diego, USA) gewonnenen SNP Daten anhand von zwei Methoden untersucht: Zum einen wurde der Long Range Haplotype Test (LRH) angewendet, der im Softwarepacket SWEEP integriert ist. Zum anderen wurden die genomischen Anteile der drei Ausgangsrassen für jeden SNP aufgrund einer Bayes‘schen Methode geschätzt. Es konnte eine signifikante Veränderung der Anteile der Ausgangsrassen verglichen mit den berechneten pedigree-basierten Erwartungswert festgestellt werden. Hierbei fiel auf, dass die Zuteilung der Allele zu einer der drei Ausgangsrassen sowohl zwischen als auch innerhalb der Chromosomen hoch variabel ist. Es wurde angenommen, dass eine lokale Abweichung der Zusammensetzung als Hinweis darauf interpretiert werden kann, dass diese Region unter gerichteter Selektion stand. Mit Hilfe dieses Indikators und den Ergebnissen des LRH-Testes konnte eine Vielzahl von Regionen identifiziert werden, die unter Selektion standen. Einige dieser Regionen beherbergen Kandidatengene, die funktionell mit den Zuchtzielen der Göttinger Minischweine im Zusammenhang stehen, z.B. SOCS2, TXN, DDR2 und GRB10, die mit der Körpergröße in Verbindung gebracht werden, oder das PRLR Gen, das die Wurfgröße beeinflusst. Die Ergebnisse dieser Untersuchungen lassen Rückschlüsse darauf zu, dass die Beziehung der Gene SOCS2 und GRB10 zu dem IGF-1 Gen der mögliche Grund für den Zwergwuchs im Göttinger Minischwein sein könnte. In einem weiteren Schritt wurden die Ergebnisse der Kartierung der Selektionssignaturen auf den Autosomen des Göttinger Minischweins validiert. Hierfür wurde die Cross Population Extended Haplotype Homozygosity (XPEHH) berechnet. Diese Methode basiert, genau wie der LRH-Test, auf dem Auffinden von Regionen ausgedehnter Haplotypenhomozygotie. Die beiden Ansätze unterscheiden sich dadurch, dass beim LRH-Test innerhalb einer Rasse und beim XPEHH im Vergleich zweier Rassen Selektionssignaturen aufgedeckt werden. Als Vergleichsrassen wurden Tiere der Rassen Göttinger Minischwein, Deutsche Landrasse und Large White mit dem Illumina Porcine BeadChip 60K (Illumina, San Diego, USA) genotypisiert. Mit Hilfe des XPEHH-Tests konnten weitere Regionen identifiziert werden, die unter Selektion standen. Aufgrund des Vergleichs von Großschweinerassen mit dem Göttinger Minischwein und dem erneuten Auffinden des SOCS2 Gens wird die Vermutung bestärkt, dass es sich hierbei um eines der wichtigsten Gene für den Zwergwuchs beim Göttinger Minischwein handelt. Zusammenfassend ergibt sich, dass SNP-basierte Ansätze einen deutlich besseren Einblick in die genomische Architektur von Populationen ermöglichen. Dadurch wird ein besseres Verständnis von Selektion und Differenzierung von Rasse auf genomischer Ebene erreicht.