L’approche GWAS est un outil essentiel pour la découverte de gènes associés aux maladies, mais elle pose des problèmes de puissance statistique quand il est impossible d’échantillonner génétiquement des dizaines de milliers de sujets. Les résultats présentés ici—ALDsuite, un programme en utilisant une correction nouvelle et efficace pour le déséquilibre de liaison (DL) ancestrale de la population locale, en permettant l'utilisation de marqueurs denses dans le MALD, et la démonstration que la méthode simpleM fournit une correction optimale pour les comparaisons multiples dans le GWAS—réaffirment la valeur de l'analyse en composantes principales (APC) pour capturer l’essence de la complexité des systèmes de grande dimension. L’APC est déjà la norme pour corriger la structure de la population dans le GWAS; mes résultats indiquent qu’elle est aussi une stratégie générale pour faire face à la forte dimensionnalité des données génomiques d'association. / GWAS is an essential tool for disease gene discovery, but has severe problems of statistical power when it is impractical to genetically sample tens of thousands of subjects. The results presented here—a novel, effective correction for local ancestral population LD allowing use of dense markers in MALD using the ALDsuite and the demonstration that the simpleM method provides an optimum Bonferroni correction for multiple comparisons in GWAS, reiterate the value of PCA for capturing the essential part of the complexity of high- dimensional systems. PCA is already standard for correcting for population substructure in GWAS; my results point to it’s broader applicability as a general strategy for dealing with the high dimensionality of genomic association data.

L’approche GWAS est un outil essentiel pour la découverte de gènes associés aux maladies, mais elle pose des problèmes de puissance statistique quand il est impossible d’échantillonner génétiquement des dizaines de milliers de sujets. Les résultats présentés ici—ALDsuite, un programme en utilisant une correction nouvelle et efficace pour le déséquilibre de liaison (DL) ancestrale de la population locale, en permettant l'utilisation de marqueurs denses dans le MALD, et la démonstration que la méthode simpleM fournit une correction optimale pour les comparaisons multiples dans le GWAS—réaffirment la valeur de l'analyse en composantes principales (APC) pour capturer l’essence de la complexité des systèmes de grande dimension. L’APC est déjà la norme pour corriger la structure de la population dans le GWAS; mes résultats indiquent qu’elle est aussi une stratégie générale pour faire face à la forte dimensionnalité des données génomiques d'association. / GWAS is an essential tool for disease gene discovery, but has severe problems of statistical power when it is impractical to genetically sample tens of thousands of subjects. The results presented here—a novel, effective correction for local ancestral population LD allowing use of dense markers in MALD using the ALDsuite and the demonstration that the simpleM method provides an optimum Bonferroni correction for multiple comparisons in GWAS, reiterate the value of PCA for capturing the essential part of the complexity of high- dimensional systems. PCA is already standard for correcting for population substructure in GWAS; my results point to it’s broader applicability as a general strategy for dealing with the high dimensionality of genomic association data.

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No. of bitstreams: 2 Tese - Letícia Mendes de Castro - 2016.pdf: 2261024 bytes, checksum: 4cfaccebd66c7e3ea4eda9b31d53d16d (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2016-03-04 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Brazil has one of the largest commercial cattle herds worldwide, but its meat quality is highly variable. The national herd is largely composed of Bos indicus breeds, which in general have less tender meat than Bos taurus cattle, decreasing the product value. This study was carried out to identify relevant regions and biological pathways associated with meat tenderness in Polled Nellore cattle. It was also aimed to evaluate the effect of different quality control protocols in GWAS for meat tenderness in Polled Nellore cattle. The data consisted of Warner-Bratzler shear force (WBSF) values of Longissimus muscle after 7 days of ageing, from 427 Polled Nellore animals. The animals were genotyped using either the Illumina BovineHD Beadchip (777k) or the GGP-Indicus Chip (77k). SNPs were excluded when Call Rate < 90%, then the imputation from the GGP to the HD Chip was performed using the FImput’s software. To study the different quality control protocols and their influence in GWAS, 590,915 markers were used. The effect of different QCs were verified using 16 protocols with three thresholds for MAF (MAF < 0.01; < 0.05 and < 0.10) and HWP (p < 0.01; < 0.0001 and < 0.00001) and their possible combinations. GWASs were performed using the PD3/EMMAx method with the remaining markers of each QC. For GWAS performed for pathway analysis, 369,007 markers were used after SNPs were excluded when Call rate < 90%, HWP p < 0.01 and MAF < 0.01. Group of slaughter and sex were included as fixed effects. Significant markers (p < 0.0001) were found in all analysis, in which the chromosomes with more significant SNPs of the different QCs were 3, 17, 20, 21, 25 and 27, and in the pathway study were located on chromosomes 3, 13, 17, 20, 21 and 25 explaining great proportion of variation, indicating possible QTLs associated with meat tenderness in those genomic regions. The analyses of different QCs showed that there is an effect of quality control over GWAS, and the filter for MAF influenced the results more broadly. A pathway enrichment analysis based on SNPs from GWAS was performed using FatiGO’s procedure. 22,365 annotated genes, including 1,010 significant genes were used. Thus, 22 GO terms and two IP entries were deemed enriched. Several of these functional categories, such as protein tyrosine and serine/threonine kinase activity, calcium ion binding and growth factors can be related to WBSF in Polled Nellore cattle. These results help to elucidate the metabolic pathways related to this trait, which is of extreme economic and social importance to Brazil as Nellore is the dominant beef cattle breed in the country. / O Brasil tem um dos maiores rebanhos bovinos comerciais do mundo, mas a qualidade da carne é altamente variável. O rebanho nacional é em grande parte composto de raças Bos indicus, que em geral têm carne menos macia do que o gado Bos taurus, diminuindo o valor do produto. Objetivou-se nesse estudo identificar regiões genômicas e vias biológicas relevantes associadas com a maciez da carne em bovinos da raça Nelore Mocho. Além disso, objetivou-se também avaliar diferentes protocolos de controle de qualidade dos SNPs e as possíveis influências nos resultados de GWAS. Os dados consistiram em valores de WBSF do músculo Longissimus dorsi, após maturação de sete dias, de 427 animais Nelore Mocho. Os animais foram genotipados em marcadores SNP Illumina BovineHD Beadchip (777k) ou Chip GGP-Indicus (77k). Todos os SNPs passaram por um Call Rate de 90% para posterior imputação utilizando o software FImput. Para averiguar os diferentes protocolos de qualidade e suas influências no GWAS foram utilizados 590.915 marcadores. Os efeitos dos diferentes QCs foram verificados utilizando 16 protocolos com três limiares para MAF (MAF < 0,01;< 0,05 e < 0,10) e HWP (p < 0,01; < 0,0001 e < 0,00001) e suas possíveis combinações. Os GWASs foram realizados utilizando método P3D/EMMAx com os marcadores restantes de cada QC. No GWAS realizado para posterior análise das vias utilizou-se 369.007 marcadores após a exclusão de SNPs baseada nos filtros Call Rate < 90%, HWP p < 0,01 e MAF < 0,01. Grupo de abate e sexo foram incluídos no modelo como efeitos fixos. Marcadores significativos (p < 0,0001) foram localizados em todas as análises, e os cromossomos com maior quantidade de SNPs significativos dos diferentes QCs foram 3, 17, 20, 21, 25 e 27. No estudo de vias foram localizados SNPs significativos nos cromossomos 3, 13, 17, 20, 21 e 25, que explicaram maior proporção da variação, indicando que existem QTLs associados à maciez da carne nessas regiões do genoma. As análises dos diferentes QCs evidenciaram efeito do controle de qualidade dos SNPs sobre o GWAS e o filtro para MAF influenciou de maneira mais ampla os resultados. Foi realizada uma análise de enriquecimento de vias baseando-se nos SNPs do GWAS, utilizando o procedimento FatiGO. Apenas os genes com no mínimo um SNP significativo (p < 0,01) foram considerados. Foram utilizados 22.365 genes anotados, incluindo 1.010 genes significativos. Um total de 22 termos GO e duas entradas IP foram consideradas enriquecidas com genes significamente associados com a maciez da carne. Várias dessas categorias funcionais como atividade da proteína tirosina quinase e serina/treonina quinase, ligantes ao íon cálcio e fatores de crescimento, podem estar relacionadas com WBFS em bovinos da raça Nelore Mocho. Estes resultados ajudam elucidar as vias relacionadas com essa característica de extrema importância econômica para o Brasil, já que o Nelore é a raça de gado de corte dominante no país.

Com a disponibilidade de tecnologias de genotipagem robustas, fornecendo milhares de marcadores moleculares a um baixo custo por amostra, tornou-se mais acessível escanear o genoma todo. Logo, as abordagens de mapeamento associativo, baseado no cálculo do desequilíbrio de ligação, e a busca de regiões do genoma que apresentam sinais de seleção foram favorecidas. Essas ferramentas apresentam um grande potencial a ser explorado em programas de melhoramento de soja, auxiliando na obtenção de informações valiosas em relação à arquitetura genética dos caracteres de interesse agronômico e à dinâmica dos processos de seleção. Portanto, os objetivos deste estudo foram: (i) verificar os efeitos da relação genética entre genótipos no desequilíbrio de ligação; (ii) obter informações em relação a arquitetura genética para dez caracteres por meio da abordagem de mapeamento associativo; e (iii) identificar regiões sob seleção diferencial em uma população representada por cultivares brasileiras comparadas a de uma população de genótipos exóticos de diferentes origens geográficas. Para isto, 95 genótipos de soja foram genotipados utilizando a plataforma da Affymettrix (180 K Axiom&reg; Soybean Genotyping Array). O efeito da estrutura populacional sobre DL foi investigado utilizando como correções as matrizes resultantes do software STRUCTURE, DAPC, PCA e a matriz de parentesco. Para o mapeamento associativo, os genótipos foram fenotipados para dez caracteres. Foram realizadasvárias abordagens para detecção de sinais de seleção: estimação da diferenciação populacional nas regiões do genoma por meio do índice de fixção (FST) e cross-population composite likelihood ratio test (XP-CLR); identificação de regiões do genoma com redução de diversidade nucleotídica (&mu;); e a presença de blocos de haplótipos. Ao utilizar medidas de correções para estimação do DL no genoma da soja observamos a influência da estrutura da população e do parentesco nos padrões de DL. Pelo mapeamento associativo, foram identificados 181 marcadores associados para dez caracteres avaliados em soja. Além disso, foi verificada a complexa interação entre regiões envolvidas no controle de caracteres quantitativos (QTL) e ambientes. Regiões diferencialmente selecionadas foram identificadas entre a população de genótipos brasileiros e de materiais de origens diversas, demonstrando que essas passaram por processos de seleção divergente. / The availability of robust genotyping technologies providing thousands of markers with a low-cost per sample, whole-genome scans are becoming more accessible. Hence, associative mapping approaches, based on the calculation of linkage disequilibrium (LD), and the detection of signals of selection were favored. These tools have a great potential to be explored in soybean breeding programs, helping to obtain valuable information about the genetic architecture of the characters of agronomic interest and of the dynamics of selection processes. Therefore, the objectives of this study were: (i) to verify the effects of the genetic relationship among genotypes on soybean linkage disequilibrium; (ii) to obtain information about the genetic architecture in ten soybean traits with an association mapping approach; and (iii) to identify regions under differential selection between a population represented by Brazilian cultivars compared to a population of exotic genotypes from different geographic origins. For this, 95 soybean genotypes were genotyped using an Affymetrix (180 K Axiom&reg; Soybean Genotyping Array) platform. The effect of the population structure on LD was investigated using as corrections the matrices resulting from the software STRUCTURE, DAPC, PCA and a kinship matrix. We phenotyped ten soybean traits in order to carry the association mapping. Several approaches were carried aiming to detect selection signals: estimation of population genetic differentiation in the genomic regions with fixation index (FST) and cross-population composite likelihood ratio test (XP-CLR); identification of genomic regions with reduced nucleotide diversity (&mu;); and the presence of haplotype blocks.Using the LD corrections, it was showed the influence of population structure and kinship on LD patterns in soybean. By the association mapping, we identified 181 markers associated with the ten traits evaluated in soybean. In addition, complex interactions between QTL and environments were verified. Differentially selected regions were identified between theBrazilian genotypes population and the population of materials from diverse origins, demonstrating that they underwent divergent selection processes.

O conhecimento da diversidade genética e da estrutura populacional das variedades mantidas em bancos de germoplasma é de fundamental importância para sua efetiva utilização em programas de melhoramento. O mapeamento por associação, também conhecido como mapeamento por desequilíbrio de ligação, é um dos principais métodos para relacionar genes e alelos às características de interesse, através da co-segregação de marcadores genéticos polimórficos com os genes envolvidos na variação das características em estudo. O Banco de Germoplasma de Arroz do Departamento de Genética da ESALQ contém 192 acessos japoneses que foram estudados com o objetivo de entender sua diversidade, estruturação genética e determinar a associação genômica de caracteres agronômicos relacionados a produção de grãos. A caracterização molecular foi conduzida através da tecnologia DArT-seq, que gerou dados de marcadores SNPs (single-nucleotide polymorphism) e silico DArTs. Em seguida, após a filtragem, 5.578 SNPs de alta qualidade foram utilizados para calcular as estimativas de diversidade no pacote hierfstat e a estrutura do painel de acessos através da análise discriminante de componentes principais (DAPC), que consiste em determinar existência de cluster em um grupo de genótipos em que não há informação a priori sobre existência de grupos. A diversidade genética nos acessos foi evidenciada pelo valor de heterozigosidade esperada (HS) (0,0279) e a estruturação foi evidenciada pela formação de três subgrupos. O mapeamento associativo foi realizado com o uso do pacote GAPIT, sendo considerados seis caracteres: número de dias para florescimento (NDF), estatura de planta (EP), comprimento da panícula (CP), peso de parcela (PP), massa de mil grãos (MMG) e CICLO, bem como 24.266 marcadores silico DArTs e 1.965 marcadores SNPs. Foram detectadas um total de 113 associações significativas genótipo-fenótipo (P<0,001) quando utilizado marcadores silico DArTs em todas as seis características analisadas e, um total de 21 associações significativas genótipo-fenótipo (P<0,001) quando utilizado marcadores SNPs para apenas quatro das seis características analisadas: EP, CICLO, MMG e PP. Considerando-se os 113 silico DArTs associados significativamente na análise, 90 foram localizados em regiões intergênicas e 23 foram localizados dentro de genes. Enquanto que, dos 21 SNPs significativos, 11 foram localizados em regiões intergênicas e 10 foram localizados dentro de genes. A informação gerada neste estudo foi útil para testar associações ao longo do genoma do arroz. O modelo linear misto (MLM) empregado no mapeamento associativo acredita-se ter conseguido controlar eficientemente os falsos positivos no mapeamento utilizando os marcadores SNPs. As informações geradas neste estudo servem de base para avaliações mais aprofundadas, utilizando o conjunto de marcadores significativos como ponto de partida para determinação dos genes mais importantes para a produtividade em arroz. / The knowledge of the genetic diversity and population structure of varieties maintained in germplasm banks is crucial for their effective use in breeding programs. Association mapping, also known as linkage disequilibrium mapping, is one of the main methods for relating genes and alleles to the characteristics of interest, through the co-segregation of polymorphic genetic markers with the genes involved in the variation of the characteristics under study. The Rice Germplasm Bank of the Department of Genetics of ESALQ contains 192 Japanese accessions that were studied with the purpose of understanding its diversity, genetic structuring and determining the genomic association of agronomic traits related to grain production. The molecular characterization was conducted by DArTseq technology, which generated data of SNPs (single-nucleotide polymorphism) markers and silico DArTs. Then, after filtering, 5,578 high-quality SNPs were used to calculate the diversity estimates in hierfstat package and the accession panel structure through discriminant analysis of principal components (DAPC), which consists of determining the cluster existence in a group of genotypes where there is no a priori information about the existence of groups. The genetic diversity in the accessions was evidenced by the expected heterozygosity value (HS) (0.0279) and the population structure was evidenced by the formation of three clusters. The association mapping was performed using the GAPIT package, considering six characters: number of days for flowering (NDF), plant height (EP), panicle length (CP), plot weight (PP), mass of thousand grains (MMG) and CYCLE, as well as 24.266 silico DArTs markers and 1.965 SNPs markers. We detected a total of 113 significant associations genotype-phenotype (P <0.001) when used silico DArTs markers in all six analyzed characteristics and a total of 21 significant associations genotype-phenotype (P<0.001) when used SNPs markers for only four of the six analyzed characteristics: EP, CYCLE, MMG and PP. Considering the 113 silico DArTs significantly associated in the analysis, 90 were located in intergenic regions and 23 were localized within genes. While of the 21 significant SNPs, 11 were located in intergenic regions and 10 were located within genes. The information generated in this study was useful for testing associations throughout the rice genome. The mixed linear model (MLM) used in association mapping is believed to have been able to efficiently control false positives in the mapping using the SNPs markers. The information generated in this study serves as a basis for further evaluation using the set of significant markers as a starting point for determining the most important genes for rice yield.

Un important dispositif de détection de QTL caprin laitier basé sur 2 254 chèvres génotypées sur puce SNP 50K et issues de 20 mâles d'IA séquencés a été mis en place. Des QTL avaient déjà été détectés pour de nombreux caractères laitiers ou de morphologie. Un certain nombre de caractères restait néanmoins à étudier ou à approfondir. Dans un premier temps, une analyse de type GWAS a été réalisée sur cinq caractères. Pour deux d'entre eux, les trayons surnuméraires et le débit de traite, nos résultats sont en faveur d'un déterminisme polygénique. Pour deux phénotypes de coloration indésirables en race Saanen et la présence de pampilles, une région du génome a été trouvée comme très significativement associée au phénotype (chromosomes 11, 13 et 10 respectivement). Le gène ASIP est un candidat fonctionnel et positionnel très prometteur pour le QTL du chromosome 13 qui agit sur la coloration rose des animaux Saanen. En revanche, malgré une analyse plus poussée des deux autres zones via l'analyse de séquences et des génotypages, aucune mutation causale candidate n'a pu être identifiée. Enfin, nous avons étudié deux mutations associées à des différences de taux butyreux qui avaient été précédemment identifiées dans le gène DGAT1 caprin. Après avoir produit in vitro les différentes versions de la protéine en système " baculovirus/cellules de lépidoptère ", l'activité enzymatique des différents variants a été testée sur le diglycéride DAG 10 :10. Nos résultats confirment l'effet délétère des mutations sur la production de triglycérides et signent ainsi la causalité de ces mutations. Ces travaux ont permis de mettre en évidence de nouvelles régions du génome impliquées dans le contrôle de caractères d'intérêt pour la filière et ont prouvé la causalité de deux mutations. L'ensemble de ces résultats pourra aider la filière à mieux gérer ces phénotypes dans le schéma. / A large daughter design based on 2 254 genotyped dairy goats genotyped on a 50K SNP chip and their 20 sequenced fathers was carried out for mapping traits of interest in French dairy goats and QTL have been detected for some dairy and morphologic traits. However, in-depth studies were needed and some unstudied traits remained. A GWAS analysis was performed on five different traits. For two of them: supernumerary teats and milk flow, results showed a polygenic determinism. For the three others: two undesired coat color in the Saanen breed and the presence of wattles, a genome region was very significantly associated with each of these phenotypes (chromosomes 11, 13 and 10 respectively). The ASIP gene is a strong functional and positional candidate for the QTL on chromosome 13 for the pink coat trait. Despite in-depth analyses for the two other regions using sequences data and genotyping, no candidate causal mutation has been identified. Finally, two mutations previously identified in the DGAT1 gene and statistically associated with differences of milk fat content have been investigated. After in vitro production of the different version of the protein by a baculovius system, the enzymatic activity was assessed on diglyceride DAG 10:10. The results attest the deleterious effect of these mutations on triglyceride production and prove the causality of the mutations. This work lead to the identification of new genome regions associated with traits of interest and will be useful for the breeding organization.

Dans un contexte de réduction des intrants agricoles, la création de variétés de blé qui utilisent l’azote de manière plus efficiente est aujourd’hui nécessaire. Cette thèse, issue d'un partenariat public-privé entre l'Institut National de la Recherche Agronomique et Biogemma, avait pour but d'apporter des outils nécessaires à la création de variétés répondant à cette exigence. Pour ce faire, nous avons analysé 225 variétés commerciales génotypées avec 24K SNP et testées dans huit combinaisons d’année, lieu et régime azoté. Nous avons montré que même si la sélection a amélioré l’efficience d’utilisation de l’azote en condition optimale et sub-optimale, ce progrès génétique doit être accéléré et mieux réparti entre les différents traits. Nous proposons pour cela de mixer sélection phénotypique et sélection assistée par marqueurs. Dans ce sens, nous avons développé une méthode pour définir les régions chromosomiques associées à nos 28 traits. Parmi les 333 régions identifiées, nous avons notamment localisé le gène NAM-A1 et avons pu caractériser ses variants naturels. Nous avons aussi montré que la sélection génomique pourrait être plus efficace si les SNP étaient présélectionnés en fonction de leurs significativités en génétique d’association multi-environnementale. Les réseaux d’interactions épistatiques furent aussi étudiés, mettant en évidence un sous-réseau particulièrement intéressant. Nos résultats et méthodes sont discutés au regard des stratégies d’amélioration variétale et de découverte de gènes. Des pistes de recherche complémentaires et des améliorations ont aussi été suggérées. / In a context of fertiliser reduction, breeding for enhanced nitrogen use efficiency in bread wheat is necessary. This PhD thesis resulting from private-public collaboration between the French National Institute for Agricultural Research and Biogemma aimed providing necessary tools. Analyses were conducted using a dataset of 225 commercial varieties genotyped with 24K SNP and tested in eight combinations of year, location, and nitrogen regimes. We showed that even if past selection increased nitrogen use efficiency at high and moderate nitrogen regimes, genetic progresses need to be accelerated and better balanced between traits. This could be achieved by mixing phenotypic and marker assisted selections. In this sense, we developed a method to define quantitative trait locus from genome-wide association study: 333 chromosomal regions involved in 28 NUE-related traits have been identified. The NAM-A1 gene was located in one of these regions and its natural variants were characterized. We also showed that genomic selection could be improved by pre-selecting SNP based on their significance in a multi-environmental genome-wide association study. Networks of epistasis interactions were also studied and an interesting sub-network was identified. Results and methods are discussed regarding breeding and gene discovery strategy. Further investigations and improvements are suggested.

This study was developed in order to explore chromosomal regions associated with carcass and meat traits in Nellore cattle breed, identifying metabolic and genetic pathways related to its characteristics expression, as well as generate additional phenotypes for future genome association studies, in order to fully describe parameters related to final product quality. Thereunto, 995 bulls were genotyped for more than 770,000 single nucleotide polymorphisms (SNPs), were evaluated for body weight at birth, weight gain at weaning and yearling, conformation, finishing precocity and muscling at weaning and yearling. These traits are correlated, therefore, genomic mapping method were applied in order to identify pleiotropic regions. Results highlighted previously described genomic regions associated to beef cattle weight gain and growth traits, particularly PLAG1 gene, sheltered by the most significantly associated marker region, which in other studies were associated to weight, height and sexual precocity in Nellore breed. To evaluate carcass and meat quality traits, 576 young bulls were evaluated for hot carcass weight, ribeye area, fat thickness, pH 24 hours after slaughter and color parameters (L*, a*, b*), for shearing force, dripping and cooking loss, evaluations were performed for different maturation times (7, 14 and 21 days). Animals were genotyped on two platforms, Illumina&reg; BovineHD BeadChip (HD) and Bovine GeneSeek&reg; Genomic Profiler &trade; HD Illumina Infinium&reg; (GGP). Animals genotyped at a lower density (GGP) were imputed to high density chip (HD). Shear force, dripping and cooking loss measures which relates to meat tenderness, were associated to cytoskeleton structure and proteolytic enzymes activity, pointing to serine/serpin enzyme complex as main candidates for regulate proteolysis and muscle fiber structure degradation. Were performed an evaluation of Longissimus thoracis et lumborum intramuscular fat content of 148 animals. It was approached by a human health perspective where samples received a classification regarding fatty acids effects on human organism (\"beneficial\", \"evil\" or \"neutral\"), as well as provided phenotypic information for future genome association studies. The identification of 42 fatty acids and 16 indexes, generated detailed information on these animals\' meat fat composition. Principal component analysis (PCA) results showed that large variation proportion between samples fat composition occurs due to expression differences among desaturase and elongase enzymes. Thus, it is expected that generated data, information and knowledge hereby, can assist animal breeding programs to improve Brazilian herds according meat chain interests. / O presente trabalho foi desenvolvido com o objetivo de explorar regiões cromossômicas associadas à características de carcaça e carne em bovinos da raça Nelore, explorar suas funções em vias metabólicas e gênicas relacionadas às manifestações dessas características, assim como gerar novos fenótipos para futuros estudos de associação genômica, com vistas a descrever, de forma completa, as características relacionadas à qualidade do produto final. Para isso, 995 animais machos não castrados, genotipados para mais de 770.000 marcadores de polimorfismos de nucleotídeo único (SNP), foram avaliados quanto ao peso corporal ao nascimento, ganho de peso à desmama e ao sobre ano, conformação, precocidade de terminação e musculosidade à desmama e ao sobre ano. Como estas características são correlacionadas, foram aplicadas metodologias de mapeamento genômico com o objetivo de identificar regiões pleiotrópicas. Os resultados destacaram regiões do genoma bovino que contêm genes descritos por influenciarem em características de crescimento e ganho de peso nestes animais, com destaque para o gene PLAG1, pertencente à região do marcador mais significativo associado aos fenótipos, anteriormente associado ao peso, altura e precocidade sexual em animais dessa raça. Para acessar atributos de qualidade de carcaça e carne, 576 machos não castrados foram avaliados quanto ao peso de carcaça quente, área de lombo, espessura de gordura subcutânea, pH após 24 horas do abate, cor (L*, a*, b*) e perdas de peso por exsudação e cozimento e força de cisalhamento em diferentes tempos de maturação (7, 14 e 21 dias). Os animais foram genotipados em duas plataformas, Illumina&reg; BovineHD BeadChip (HD) e GeneSeek&reg; Genomic Profiler Bovine HD&trade; Illumina Infinium&reg; (GGP), sendo os genótipos deste último imputados para o conjunto de maior densidade. As avaliações de perdas de peso por exsudação e cozimento e força de cisalhamento, utilizada para mensurar maciez, revelam a influencia da estrutura do citoesqueleto e da ação das enzimas proteolíticas, apontando o complexo enzimático serinas/serpinas como candidato na regulação do processo de proteólise e degradação da estrutura da fibra muscular. Foi realizada avaliação dos ácidos graxos no músculo Longissimus thoracis et lumborum de 148 animais com vistas à classificação das amostras quanto aos efeitos esperados no organismo humano (\"benéfico\", \"maléfico\" ou \"neutro\"), assim como prover informação fenotípica para futuros estudos de associação genômica. A identificação de 42 ácidos graxos e 16 índices gerou informação detalhada sobre a gordura presente na carne destes animais, sendo observado, por análise de componentes principais (PCA), que a maior variação entre a composição das amostras avaliadas parece ser em decorrência da diferença de expressão das enzimas elongases e dessaturases. Dessa forma, espera-se que os dados, informações e conhecimento gerados por este trabalho, possam auxiliar os programas de melhoramento genético animal a aprimorar o rebanho brasileiro segundo características de interesse da cadeia produtiva de carne.

Introduction: The continual increase of type 2 diabetes (T2D) prevalence is a global public health concern. The aetiology of T2D has not been fully elucidated and this is hampering the development of effective preventative and curative interventions to curb the T2D burden. Although much has been done to elucidate the environmental risk factors associated with T2D, little is known about the precise genetic risk factors that predispose people to it. There is limited knowledge about the common variants associated with T2D risk in the black South African population. However, evidence of shared common variants associated with T2D among people of different ethnicities has been documented. Nonetheless, the majority of the common variants that have been reported to be associated with T2D in other ethnicities are still yet to be evaluated in the black South African population. Objectives: The aim of this study was to evaluate the association of previously reported common genetic variants with T2D susceptibility, as indicated by impaired glucose tolerance (IGT), in a black South African population of Tswana descent. Methods: This study was a case-control study of 180 cases and 180 controls nested in the Prospective Urban Rural Epidemiology (PURE) study baseline data, which was collected in 2005. The DNA samples of the participants were genotyped for 77 single nucleotide polymorphisms (SNPs), using Illumina® VeraCode technology on the BeadXpress® platform. The gPlink software was used to evaluate the standard genetic models of disease penetrance for the association of the common variants with impaired glucose tolerance (IGT) while adjusting for age, sex and body mass index. Results: Four out of the 66 SNPs that were evaluated through the genetic association tests in this study were noted to be significantly associated with IGT (p< 0.05). Of the four SNPs, only rs1436955 was associated with an increase in T2D risk, while the other three variants, rs831571, rs8050136 and rs7542900, were noted to be associated with a decreased risk of T2D. However, none of the four SNPs was significantly associated with IGT after correcting for multiple testing (p <0.05). Conclusions: Black South Africans of Tswana descent might not share common variants associated with T2D risk, as indicated by IGT in other ethnicities. Wellpowered studies are required to evaluate the association of common variants with T2D risk in this population group. The results from this study emphasise the need for population-specific variants to assess the genetic susceptibility of complex diseases such as T2D in the black South African population. / MSc (Nutrition), North-West University, Potchefstroom Campus, 2014

Introduction: The continual increase of type 2 diabetes (T2D) prevalence is a global public health concern. The aetiology of T2D has not been fully elucidated and this is hampering the development of effective preventative and curative interventions to curb the T2D burden. Although much has been done to elucidate the environmental risk factors associated with T2D, little is known about the precise genetic risk factors that predispose people to it. There is limited knowledge about the common variants associated with T2D risk in the black South African population. However, evidence of shared common variants associated with T2D among people of different ethnicities has been documented. Nonetheless, the majority of the common variants that have been reported to be associated with T2D in other ethnicities are still yet to be evaluated in the black South African population. Objectives: The aim of this study was to evaluate the association of previously reported common genetic variants with T2D susceptibility, as indicated by impaired glucose tolerance (IGT), in a black South African population of Tswana descent. Methods: This study was a case-control study of 180 cases and 180 controls nested in the Prospective Urban Rural Epidemiology (PURE) study baseline data, which was collected in 2005. The DNA samples of the participants were genotyped for 77 single nucleotide polymorphisms (SNPs), using Illumina® VeraCode technology on the BeadXpress® platform. The gPlink software was used to evaluate the standard genetic models of disease penetrance for the association of the common variants with impaired glucose tolerance (IGT) while adjusting for age, sex and body mass index. Results: Four out of the 66 SNPs that were evaluated through the genetic association tests in this study were noted to be significantly associated with IGT (p< 0.05). Of the four SNPs, only rs1436955 was associated with an increase in T2D risk, while the other three variants, rs831571, rs8050136 and rs7542900, were noted to be associated with a decreased risk of T2D. However, none of the four SNPs was significantly associated with IGT after correcting for multiple testing (p <0.05). Conclusions: Black South Africans of Tswana descent might not share common variants associated with T2D risk, as indicated by IGT in other ethnicities. Wellpowered studies are required to evaluate the association of common variants with T2D risk in this population group. The results from this study emphasise the need for population-specific variants to assess the genetic susceptibility of complex diseases such as T2D in the black South African population. / MSc (Nutrition), North-West University, Potchefstroom Campus, 2014