The Nelore breed represents the vast majority of Brazilian Zebuine cattle (Bos taurus indicus). The great adaptability of the Nelore breed to Brazilian tropical climate, however, is not associated with meat tenderness (MT). It is known that MT is influenced by several environmental factors, but also genetic composition. In the first chapter, we report a genome-wide analysis of copy number variation (CNV) inferred from Illumina® Bovine High Density SNP-chip data for a Nelore population of 723 males including 30 sires. We detected >2600 CNV regions (CNVRs) representing ≈6.5% of the Bos taurus genome. The CNVR size was 65 kb on average, ranging from 5 kb to 4.3 Mb. A total of 1155 CNVRs (43.6%) overlapped 2750 genes. They are enriched for important functions such as immune response, olfactory reception and processes involving guanosine triphosphate (GTP). The GTP processes have known influence in skeletal muscle physiology and morphology. Quantitative trait loci for MT, partly specific for Nelore, overlapped a substantial fraction of CNVRs and two CNVRs were found proximal to glutathione metabolism genes that are associated with MT as well. Comparing our results with previous studies revealed an overlap in ≈1400 CNVRs (>50%). We selected 9 CNVRs that overlapped regions associated with MT and we validated them in all 30 sires by qPCR. There was identified many genomic regions of structural variation in Nelore with important implications on the MT phenotype. In the second chapter, a total of 34 animals of the population were subjected to transcriptome analysis and meat tenderness (MT) phenotyping. We identified 170 CNV fragments (CNVFs) residing in 20 CNVRs, which occurred in different frequencies between animals with tougher and softer meat genetic potential. A considerable fraction of the identified CNVFs affected gene expression of the MT genes, which play important roles in glycogen metabolism, connective tissue turnover, membrane transporters and glutathione pathways. We also detected that several CNVRs substantially influenced the expression of overlapped and nearby genes, where the increase or decrease of copy number correlated well with the change in gene expression. Among them are two CNVRs at chromosomes 12 and 23, which are in the vicinity of previously described QTLs for MT in Nelore breed. Several CNVFs, which are more frequent in animals with genetic potential for softer or tougher MT, showed significant differences in gene expression. Those regions are linked to important biological functions with highly relevant influences on MT and skeletal muscle physiology. / A raça Nelore é predominante no rebanho zebuíno brasileiro (Bos taurus indicus). A grande adaptabilidade da raça Nelore ao clima tropical brasileiro, no entanto, não está associada à maciez de carne (MT). Sabe-se que MT é influenciada por vários fatores ambientais e pela composição genética. Foi realizada uma análise de todo o genoma para inferir Variação no Número de Cópias de Segmentos Genômicos (Copy Number Variation - CNV) a partir de dados oriundos de chip de SNP (Illumina® Bovine High Density), para uma população de 723 machos Nelore, incluindo 30 ancentrais da população. Foram detectadas >2600 regiões de CNV (CNVRs) representando ≈6.5% do genoma bovino. O tamanho médio do CNVR foi de 65 kb, variando de 5 kb até 43 Mb. Um total de 1155 CNVRs (43.6%) obtiveram sobreposição com 2750 genes. Estes genes foram enriquecidos para as funções importantes, tais como resposta imunológica, recepção olfativa e processos que envolvem o trifosfato de guanosina (GTP). As vias metabólicas do GTP conhecidamente influenciam a fisiologia e a morfologia do músculo esquelético. Loci de características quantitativas (QTLs) para MT, alguns específicos para Nelore, sobrepuseram uma fração substancial das CNVRs encontradas. Dois CNVRs foram encontrados em região proximal à genes do metabolismo da glutationa os quais também são associados com MT. Comparando os resultados com estudos anteriores ≈1400 CNVRs (>50%) foram sobrepostos. Nove CNVRs em regiões associadas com MT foram validados nos 30 ancentrais por qPCR. Em conclusão, foram identificadas regiões genômicas de variação estrutural no Nelore, com potenciais implicações sobre o fenótipo MT. No segundo capítulo, um total de 34 animais da população foi submetido à análise do transcriptoma e análise de potencial genético para MT. Foram identificados 170 fragmentos de CNV (CNVFs) mapeados em 20 CNVRs, os quais mostraram frequências significativamente diferentes entre animais com potencial genético para carne mais dura ou mais macia. Uma fração considerável dos CNVFs identificados afetaram a expressão gênica de genes MT (anteriormente descritos como associados à MT ou fisiologia do músculo esquelético), os quais desempenham um papel importante no metabolismo de glicogênio, volume do tecido conjuntivo, transportadores de membrana e vias metabólicas da glutationa. Um número considerável de CNVRs foram associados à expressão de genes sobrepostos e nas proximidades, onde o aumento ou diminuição do número de cópias foi associado com a mudança na expressão gênica. Dois CNVRs associados foram mapeados para os cromossomo 12 e 23, estando próximos a QTLs anteriormente descritos para MT na raça Nelore. Vários CNVFs, entre animais com potencial genético para carne mais macia ou dura, mostraram diferenças significativas na expressão gênica. Essas regiões estão ligadas a importantes funções biológicas com influências altamente relevantes para MT e para a fisiologia do músculo esquelético.

The interdisciplinary field of systems biology has evolved rapidly over the last few years. Different disciplines have contributed to the development of both its experimental and theoretical branches.Although computational biology has been an increasing activity in computer science for more than a two decades, it has been only in the past few years that optimization models have been increasingly developed and analyzed by researchers whose primary background is Operations Research(OR). This dissertation aims at contributing to the field of computational biology by applying mathematical programming to certain problems in molecular biology.Specifically, we address three problems in the domain of Genome Wide Association Studies}:(i) the Pure Parsimony Haplotyping Under uncertatind Data Problem that consists in finding the minimum number of haplotypes necessary to explain a given set of genotypes containing possible reading errors; (ii) the Parsimonious Loss Of Heterozygosity Problem that consists of partitioning suspected polymorphisms from a set of individuals into a minimum number of deletion areas; (iii) and the Multiple Individuals Polymorphic Alu Insertion Recognition Problem that consists of finding the set of locations in the genome where ALU sequences are inserted in some individual(s).All three problems are NP-hard combinatorial optimization problems. Therefore, we analyse their combinatorial structure and we propose an exact approach to solution for each of them. The proposed models are efficient, accurate, compact, polynomial-sized and usable in all those cases for which the parsimony criterion is well suited for estimation. / Option Informatique du Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Les variétés modernes de canne à sucre sont d'origine bispécifique et possèdent une structure génétique complexe, aneuploïde et hautement polyploïde rendant difficile les études de résistance génétique. La feuille jaune de la canne a sucre est une maladie dont l'agent causal est le sugarcane yellow leaf virus (scylv). Ce virus a une large diversité. Seuls trois génotypes viraux, différenciables par rtpcr, ont été trouves en Guadeloupe. Les objectifs de l'étude sont d'évaluer: l/la possibilité de marquer la résistance de la plante au scylv grâce a une étude d'association pan-génomique 2/l'impact de la diversité de l'agent pathogène sur la résistance de la canne a sucre au scylv. Les études d'association ont été menées avec plus de 4000 marqueurs aflp et d'art sur quatre types de données phénotypiques (intensité et densité virale dans les feuilles et les tiges). Les phénotypes ont été mesures sur 189 variétés de cannes à sucre dans deux essais successifs dans un dispositif en trois blocs randomises. De ces variétés, 40 ont été sélectionnées et ont permis d'obtenir 10 croisements biparentaux. Les descendances obtenues ont été suivies sur deux essais. L'incidence et la diversité du scylv ont été évaluées pour les 40 variétés et les descendances. L'héritabilité au sens strict de la résistance aux scylv a été déterminée. Six marqueurs de résistance au scylv ont été identifies ainsi que deux gènes ayant potentiellement un rôle dans la résistance au virus. L'étude montre également que la résistance de la plante est variable en fonction du génotype du scylv et que cette résistance est en partie transmise aux descendances. Créer des variétés résistantes au scylv est donc possible. / Modern varieties of sugarcane have a bispecific origin and a complex genetic structure, aneuploid and highly polyploid, maklng genetic resistance study uneasy to perform. Yellow leaf of sugarcane is a viral disease whose causal agent is the sugarcane yellow leaf virus (scylv). This virus has a wide range of diversity. Only three viral genotypes, distinguishable by rt-pcr, were found in guadeloupe. The objectives of this srudy are to assess: l/the possibility to find markers associated with plant resistance to scylv through a genome wide association study 2 1 the impact of the pathogen diversity on the resistance of sugarcane to scylv. Association studies have been conducted with more than 4000 aflp and dart markers on four types of phenotypic data (virus intensity and density in leaves and canes). Phenotypes were measured on 189 varieties of sugarcane in two successive trials in a three randomized complete block design. From these varieties, 40 were selected and allowed to obtain 10 biparental crosses. The offspring were followed during two trials. The incidence and the diversity of scylv were evaluated in the 40 varieties and the offspring. The narrow sense heritability of the resistance to the scylvs was determined. Six markers of the resistance to the scylv and two genes, with potential contribution in virus resistance, have been identified. The study also shows that the resistance of the plant is variable depending on the scylv genotype and that this resistance is partly transmitted to the offspring. Breeding for scylv resistance is practicable.

Un objectif central en biologie est de comprendre la relation entre le génotype et le phénotype. Afin de disséquer les bases génétiques de la diversité phénotypique, il est nécessaire de disposer d’une collection de données génomiques d’un grand nombre d’individus d’une même espèce. Dans ce but, mes travaux de thèse se basent sur l’étude des séquences génomiques ainsi que des données phénotypiques de 1011 isolats naturels de la levure Saccharomyces cerevisiae. Dans un premier temps, je me suis intéressé à la description de la variation génétique et phénotypique pour dresser un portrait précis de l’histoire évolutive de cette espèce. Les données de phénotypage nous ont permis de réaliser des études pangénomiques d’association génotype-phénotype avec une puissance jusque là inégalée chez Saccharomyces cerevisiae. Je me suis par la suite penché sur l’évaluation des paramètres influençant le pouvoir de détection d’une telle approche, d’en apprécier limites pour tenter de les contourner. / Elucidating the genetic origin of phenotypic diversity among individuals within the same species is essential to understand evolution. Using whole genome sequences of 1,011 Saccharomyces cerevisiae isolates, my work sought to describe intraspecific genetic variation and investigate of its phenotypic consequences. Doing so, I obtained a precise view of the evolutionary history of S. cerevisiae. Phenotypic characterization provided the opportunity to perform genotype-phenotype genome-wide association studies with unprecedented power. I then focused on the evaluation of the parameters influencing genome-wide association studies, the appreciation of the limits of such an approach, and ways to circumvent them.

The cell differentiation process is associated with activation and repression of different genes, whereby the formation of heterochromatin is mediated by spreading of repressor proteins along large chromatin domains. Some of these proteins are methyltransferases, including GLP and G9a that are implicated in the addition of mono- and dimethyl groups to lysine 9 at Histone 3. Despite extensive research the exact mechanism of binding and spreading of G9a and GLP is unclear. To better understand the molecular mechanisms through which G9a and GLP bind to chromatin we tested the in vivo binding of a mutant G9a that is unable to bind to H3K9me2 histone marks via its Ankyrin domain. Murine erythroleukemia (MEL) cell line with expression of mutant G9a was generated using recombinant DNA technologies; G9a binding targets genome-wide were detected by the analysis of ChIP-sequencing data. We validated ChIP-sequencing data providing a reliable tool to visualize G9a targets in MEL cells. We also found that G9a Ankyrin mutant bound to all tested regions suggesting that the Ankyrin domain is not the only factor that contributes to the binding of G9a on chromatin in vivo.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第22344号 / 医博第4585号 / 新制||医||1042(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 藤渕 航, 教授 渡邊 直樹, 教授 玉木 敬二 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第22852号 / 農博第2435号 / 新制||農||1082(附属図書館) / 学位論文||R2||N5312(農学部図書室) / 京都大学大学院農学研究科応用生物科学専攻 / (主査)教授 寺内 良平, 准教授 三瀬 和之, 教授 那須田 周平 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

京都大学 / 0048 / 新制・課程博士 / 博士(人間・環境学) / 甲第22791号 / 人博第962号 / 新制||人||228(附属図書館) / 2020||人博||962(吉田南総合図書館) / 京都大学大学院人間・環境学研究科相関環境学専攻 / (主査)教授 瀬戸口 浩彰, 教授 市岡 孝朗, 教授 宮下 英明 / 学位規則第4条第1項該当 / Doctor of Human and Environmental Studies / Kyoto University / DFAM

Fusarium head blight (FHB) is a major challenge in global wheat production. In the United States, the disease is predominantly caused by the fungus Fusarium graminearum. Utilization of FHB-resistant wheat cultivars integrated with other measures such as fungicide application is the most effective approach for the management of this disease. This study aimed to 1) identify novel quantitative trait loci (QTL) for resistance to FHB in a Brazilian spring wheat cultivar ‘Surpresa’ through bi-parental mapping, 2) detect QTL for FHB resistance in a global panel of 233 spring wheat accessions by genome-wide association analysis (GWAS), and 3) localize genomic regions governing traits associated with virulence in Fusarium graminearum. Using phenotypic and genotypic data from 187 recombinant inbred lines derived from the cross between Surpresa and a susceptible spring wheat cultivar ‘Wheaton’, four QTL (Qfhb.ndwp-2AS, Qfhb.ndwp-2AL, Qfhb.ndwp-3B, and Qfhb.ndwp-4D) were mapped on chromosomes 2A, 3B, and 4D of Surpresa, respectively. Qfhb.ndwp-2AS, Qfhb.ndwp-2AL, and Qfhb.ndwp-3B were found to be novel based on physical locations of the markers tightly linked to these QTL. Two significant marker-trait associations (Qfhb.ndwp-3A and Qfhb.ndwp-2BL) were detected by GWAS of 233 spring wheat accessions, which conferred type II and type III FHB resistance and mapped on chromosomes 3A and 2B, respectively. Both QTL were novel based on the physical locations of tightly linked markers. GWAS of virulence and fungicide sensitivity using 183 F. graminearum isolates collected from North Dakota identified two significant marker-trait associations in chromosomes 1 and 3 for virulence, and two for fungicide sensitivity. The genes associated with virulence that were detected in this study were not previously reported. Identification of these novel genes in metabolic pathways of F. graminearum could help to develop new strategies for the management FHB.

Background and aims: Carotid artery plaque is an established marker of subclinical atherosclerosis and common patho-mechanisms with coronary artery disease (CAD) are hypothesized. We aimed to identify genetic variants associated with carotid plaque and examine the potential shared genetic basis with CAD. Methods: After investigating the reliability of plaque detection, we performed a genome-wide metaassociation study in two independent cohorts (LIFE-Adult, n=4,037 and LIFE-Heart, n=3,152) for carotid plaque score (PS), defined as the sum of the plaque load of common carotid artery and carotid bulb. Further, we analyzed whether previously reported CAD and stroke loci were also associated with PS. Results: We identified two loci with genome-wide significance for PS. One locus is the known CADlocus at chromosome 9p21 (lead SNP rs9644862, p=8.73x10-12). We also describe a novel locus at on chromosome 10q24 within the SFXN2 gene as the most probable candidate (lead SNP rs2902548, p=1.97x10-8). In addition, 17 out of 58 known CAD loci and six of 17 known stroke loci were associated with PS at a nominal level of significance. Conclusion: We showed that PS is a reliable trait to analyze genetics of atherosclerosis. Two new loci of genome-wide significant association with PS were found. The observed non-random overlap of CAD and PS associations strengthens the hypothesis of a shared genetic basis for these atherosclerotic manifestations.