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Family, twin and adoption studies consistently suggest that genetic factors strongly influence the risk for alcohol dependence (AD). Although the literature supports the role of genetics in AD, identification of specific genes contributing to the etiology of AD has proven difficult. These difficulties are due in part to the complex set of risk factors contributing to the development of AD. These risk factors include comorbidities with other clinical diagnoses and behavioral phenotypes (e.g., major depression), physiological differences that contribute to the differences between people in their level of response to ethanol (e.g., initial sensitivity) and finally the large number of biological pathways targeted by and involved in the processing of ethanol. These complexities have probably contributed to the limited success of linkage and candidate gene association studies in finding genes underlying AD. The powerful and unbiased genome-wide association study (GWAS) offers promise in the study of complex diseases. However, due to the complexities of known risk factors, GWAS data has yet to provide consistent, replicable results. In light of these difficulties, this dissertation has five specific aims which attempt to investigate genetic risk loci for AD and related phenotypes through improved methods for candidate gene selection, analysis of a pooled genome-wide association study, genome-wide analyses of initial sensitivity and maximum alcohol consumption in a twenty-four hour period and finally, creation of a multivariate AD/internalizing phenotype.

PROX1 étant un facteur de susceptibilité au diabète de type 2 (DT2), nousavons réalisé des études génétiques et moléculaires afin de comprendre son rôledans l’étiologie du DT2.Nous avons analysé l’impact de 80 SNPs de PROX1 sur des phénotypescliniques associés au DT2 dans l’étude HELENA (n=1155 adolescents) et montréque trois SNPs (rs340838, rs340837 et rs340836) sont associés à l’insulinémie àjeun. Nous avons évalué la fonctionnalité de 9 SNPs (les 3 SNPs associés et 6 SNPsen déséquilibre de liaison) en utilisant un gène rapporteur Luciférase dans descellules HepG2 et MIN6. Les allèles associés à la diminution de l’insulinémie desSNPs rs340874, rs340873 et rs340835 sont associés à une diminution del’expression du gène rapporteur Luciférase, suggérant que l’expression de PROX1est diminuée chez les individus porteurs des allèles à risque.Nous avons aussi montré que l’inhibition de l’expression de Prox1 par siRNAsdans les cellules INS-1E engendrait une diminution de 1,7 fois de la sécrétiond’insuline en réponse au glucose et qu’une concentration élevée en glucose modulaitpositivement l’expression de la protéine Prox1.Des analyses transcriptomiques réalisées dans les cellules INS-1E ont permisde montrer que certains des gènes cibles de PROX1 dans les cellules bêta sont desgènes impliqués dans des voies de sécrétion d’insuline.Enfin, nous avons également observé que l’agoniste de PPARgamma, latroglitazone, diminuait l’expression de Prox1 dans les cellules INS-1E.Ces résultats suggèrent qu’une altération de l’expression de Prox1 par desvariants cis-régulateurs pourrait conduire à une sécrétion d’insuline en réponse auglucose altérée des cellules bêta, conférant ainsi une susceptibilité au DT2. / As PROX1 is a susceptibility factor for type 2 diabetes (T2D), we conductedgenetic and molecular studies to better understand the role of PROX1 in the etiology of T2D. We assessed the impact of 80 PROX1 SNPs on T2D-related biochemical traits in the HELENA study (n=1155 adolescents) and showed that 3 SNPs (rs340838, rs340837 and rs340836) were significantly associated with fasting plasma insulin levels. We evaluated the functional impact of 9 SNPs (the 3 insulin-associated SNPs plus 6 SNPs in linkage disequilibrium) using a Luciferase reporter gene expression in HepG2 and MIN6 cells. The insulin-lowering alleles of the rs340874, rs340873 and rs340835 SNPs were associated with lower Luciferase gene expression, suggesting that PROX1 expression may be lower in individuals carrying the insulin-lowering alleles. We also showed that the knock-down of Prox1 expression by siRNA in INS-1E cells resulted in a 1.7 fold reduced glucose-stimulated insulin secretion and that high concentrations of glucose positively modulated Prox1 protein expression. Then, microarray analyses performed in INS-1E cells showed that some PROX1 target genes in the _cells are implicated in insulin secretion pathways. Finally, we observed that the PPARgamma agonist, the troglitazone, decreased Prox1 expression in INS-1E cells. Altogether, these results suggest that an altered expression of Prox1 bys cisregulators variants results in an altered -cell glucose-stimulated insulin secretion andthereby confers susceptibility to T2D.

Genome-wide association studies (GWAS) have delivered many novel insights about the etiology of many common heritable diseases. However, in most disorders studied by GWAS, the known single nucleotide polymorphisms (SNPs) associated with the disease do not account for a large portion of the genetic factors underlying the condition. This suggests that many of the undiscovered variants contributing to the risk of common diseases have weak effects or are relatively rare. This thesis introduces novel adaptations of techniques for improving detection power for both of these types of risk variants, and reports the results of analyses applying these methods to real datasets for common diseases. Chapter 2 describes a novel approach to improve the detection of weak-effect risk variants that is based on an adaptive sampling technique known as Distilled Sensing (DS). This procedure entails utilization of a portion of the total sample to exclude from consideration regions of the genome where there is no evidence of genetic association, and then testing for association with a greatly reduced number of variants in the remaining sample. Application of the method to simulated data sets and GWAS data from studies of age-related macular degeneration (AMD) demonstrated that, in many situations, DS can have superior power over traditional meta-analysis techniques to detect weak-effect loci. Chapter 3 describes an innovative pipeline to screen for rare variants in next generation sequencing (NGS) data. Since rare variants, by definition, are likely to be present in only a few individuals even in large samples, efficient methods to screen for rare causal variants are critical for advancing the utility of NGS technology. Application of our approach, which uses family-based data to identify candidate rare variants that could explain aggregation of disease in some pedigrees, resulted in the discovery of novel protein-coding variants linked to increased risk for Alzheimer's disease (AD) in African Americans. The techniques presented in this thesis address different aspects of the "missing heritability" problem and offer efficient approaches to discover novel risk variants, and thereby facilitate development of a more complete picture of genetic risk for common diseases.

Osteoarthritis (OA) is a common disease with a strong genetic component. Despite this, previous attempts to identify genetic variants that predispose to OA have met with limited success. Recently, the results of a large genome wide association study in OA has identified a novel susceptibility locus on chromosome 3 tagged by two SNPs, rs11177 (p=1.25x10-10) which lies within the coding region of GNL3 and rs6976 (p=7.24x10-11) situated in the 3’UTR of GLT8D1. The GNL3 gene encodes the protein nucleostemin which is found within the nucleolus of stem cells and tumour cells. It functions to regulate cell cycle progression, embryogenesis, tumorigenesis, tissue regeneration and ribosome biogenesis but its role in the joint is unknown. In an attempt to identify the causal variant(s) at locus 3p21.1 I conducted a mutation screen of GNL3 which identified a common non-synonymous coding variant, rs2289247, which was in strong LD (r2=0.92) with rs11177, as well as several other variants. Localisation studies showed that GNL3 was expressed at the mRNA and protein level in several joint tissues. While levels of mRNA expression were found to be significantly higher in human articular chondrocytes from OA patients as compared with controls, levels of GNL3 protein were significantly lower in OA chondrocytes than controls. Further studies showed that cytokines which have been implicated in the pathogenesis of OA such as IL1β, IL13, TNFα and FGF2 had no effect on GNL3 mRNA in cartilage. Knockdown of GNL3 using siRNA in articular chondrocytes and the chondrosarcoma cell line, JJ012, did not alter the mRNA expression of chondrogenic markers; COL2A, ACAN, MMP3, MMP13, RUNX2 and SOX9. Cultures of mesenchymal stem cells and articular chondrocytes from patients of different rs11177 genotypes, showed no difference in chondrogenic potential. Furthermore, genotypes at rs11177 and rs2289247 did not influence the expression of p53, MDM2 or GNL3 in response to stressful stimuli, including cisplatin and hypoxia, when cloned into a melanoma cell line. Studies of zebrafish carrying a loss of function mutation in gnl3 revealed a significant reduction in cartilage volume and an alteration in cartilage structure, as evident by a reduced number of chondrocytes, disorganised stacking and an increase in cartilage extracellular matrix in the mutant fish. This research has shown that gnl3 plays a vital role in chondrogenesis in zebrafish and has shown evidence of dysregulation of GNL3 expression in OA human articular chondrocytes. The in vitro studies failed to identify any specific effects of the variants rs11177 and rs2289247 on GNL3 expression, chondrogenesis or p53 stress response although, it remains possible that the variants may have modest effects that were not detected by the assays used. The zebrafish studies illustrate that gnl3 plays a critical role in normal cartilage development however further studies on GNL3 in OA would be of interest.

Submitted by DIEGO GABRIEL TORRES DINI null (diego.torres.dini@gmail.com) on 2017-02-25T21:08:29Z No. of bitstreams: 1 Diego Torres Dini Tese Doutoral.pdf: 1232376 bytes, checksum: dc45dfe7c23a8fd647db24acb963c71c (MD5) / Approved for entry into archive by Juliano Benedito Ferreira (julianoferreira@reitoria.unesp.br) on 2017-03-07T13:42:52Z (GMT) No. of bitstreams: 1 torresdini_dg_dr_ilha.pdf: 1232376 bytes, checksum: dc45dfe7c23a8fd647db24acb963c71c (MD5) / Made available in DSpace on 2017-03-07T13:42:52Z (GMT). No. of bitstreams: 1 torresdini_dg_dr_ilha.pdf: 1232376 bytes, checksum: dc45dfe7c23a8fd647db24acb963c71c (MD5) Previous issue date: 2017-02-03 / Outra / In Uruguay, reforestation with Eucalyptus sp. is of fundamental importance to produce paper, pulp and wood. The productivity of these continually grows due to application of breeding techniques, such as hybridization. This study aimed to investigate genetic parameters, productivity, stability, adaptability and to identify SNP markers associated with the diameter breast height (DBH) for to select Eucalypts grandis x Eucalyptus globulus full-sibs hybrid clones. The study was conducted in a clonal test, repeated at two different soils, in the state of Rio Negro, Uruguay. The population was phenotypically characterized to the DBH at 48 months of age and cambium tissues of each individual were sampled for genotyping with EuCHIP60K chip. The mean growth in DBH was similar between both places. The genotype-environment interaction was the simple type, with high genotype correlation in clones’ performance between environments (0.708), indicating the possibility of the same clones being selected for both places. Mean heritability between clones (0.724), coefficient of individual genetic variation (10.9%) and relative variation (0.916), showed the possibility of obtaining gains by selecting clones with higher growth, which was estimated in 3.1% for both sites together. A total of 15,196 markers SNPs were used in the genomic selection for the DBH, but after cleaning of SNPs data, the number was reduced for 15,196 (23.5%). The predictive capacity was expected to be low or negative (-0.15) for this population given the population size (78 individuals). We used the model rrBLUP with a validation of Jackknife. The model do not showed precision to predict the DBH. These results were consistent with theoretical expectations, which indicate that it is necessary to have an improvement population of at least 1,000 phenotyped and genotyped individuals. The DBH is the most important trait in the breeding of the genus Eucalyptus. However its quantitative nature added to the time necessary for this phenotype to develop makes the early detection of this trait are difficult. The identification of molecular markers associated with quantitative phenotypes is a good choice for the identification of QTLs that will help the early detection of individuals with high DBH. Significant markers associated to DBH , were indentificated into the chromosome 6, suggesting the presence of a QTL in this chromosome. Since they are clones originated from vegetative propagation and a full-sibs single-progeny, they should preferably be used for reforestation based on their cloning, since mating between clones can generate endogamy by biparental inbreeding. The utilization of SNPs helped to confirm the degree of parentage between the clones as well as clonal identity control.

The publication of a draft equine genome sequence and the release by Illumina of a 50,000 marker single-nucleotide polymorphism (SNP) genotyping chip has provided equine researchers with the opportunity to use new approaches to study the relationships between genotype and phenotype. In particular, it is hoped that the use of high-density markers applied to population samples will enable progress to be made with regard to more complex diseases. The first objective of this thesis is to explore the potential for the equine SNP chip to enable such studies to be performed in the horse. The second objective is to investigate the genetic background of osteochondrosis (OC) in the horse. These objectives have been tackled using 348 Thoroughbreds from the US, divided into cases and controls, and a further 836 UK Thoroughbreds, the majority with no phenotype data. All horses had been genotyped with the Illumina Equine SNP50 BeadChip. Linkage disequilibrium (LD) is the non-random association of alleles at neighbouring loci. The reliance of many genomic methodologies on LD between neutral markers and causal variants makes it an important characteristic of genome structure. In this thesis, the genomic data has been used to study the extent of LD in the Thoroughbred and the results considered in terms of genome coverage. Results suggest that the SNP chip offers good coverage of the genome. Published theoretical relationships between LD and historical effective population size (Ne) were exploited to enable accuracy predictions for genome-wide evaluation (GWE) to be made. A subsequent in-depth exploration of this theory cast some doubt on the reliability of this approach in the estimation of Ne, but the general conclusion that the Thoroughbred population has a small Ne which should enable GWE to be carried out efficiently in this population, remains valid. In the course of these studies, possible errors embedded within the current sequence assembly were identified using empirical approaches. Osteochondrosis is a developmental orthopaedic disease which affects the joints of young horses. Osteochondrosis is considered multifactorial in origin with a variety of environmental factors and heredity having been implicated. In this thesis, a genome-wide association study was carried out to identify quantitative trait loci (QTL) associated with OC. A single SNP was found to be significantly associated with OC. The low heritability of OC combined with the apparent lack of major QTL suggests GWE as an alternative approach to tackle this disease. A GWE analysis was carried out on the same dataset but the resulting genomic breeding values had no predictive ability for OC status. This, combined with the small number of significant QTL, indicates a lack of power which could be addressed in the future by increasing sample size. An alternative to genotyping more horses for the 50K SNP chip would be to use a low-density SNP panel and impute remaining genotypes. The final chapter of this thesis examines the feasibility of this approach in the Thoroughbred. Results suggest that genotyping only a subset of samples at high density and the remainder at lower density could be an effective strategy to enable greater progress to be made in the arena of equine genomics. Finally, this thesis provides an outlook on the future for genomics in the horse.

Family and twin studies have shown a heritable component to seasonal affective disorder (SAD). While a few studies have examined individual genetic variants in SAD, many methodological issues exist in the current literature. First, most studies combined major depression (MDD) and bipolar (BD) cases in the genetic analysis of SAD. This makes it difficult to differentiate the effect from MDD and BD. Second, most studies adopted a candidate gene approach and used fairly small sample sizes. This does not allow for testing across a wide variety of genes, and it yields less robust P-values. Third, healthy controls have been used, but not case comparisons, which makes it difficult to differentiate the effects of seasonality from that of the primary illness (MDD and BD). To overcome these issues, seasonal MDD and BD cases were separated into two different studies in this thesis; sample sizes for both studies are the largest in the current SAD molecular genetics literature; GWAS was used to test for potential risk loci in a hypothesis-free fashion; case comparisons were incorporated to exclude potential genetic contributions related generally to the primary diseases themselves (MDD and BD). For MDD, we performed a GWAS with 562 seasonal MDD cases and 1,225 comparison cases with non-seasonal MDD. Subjects were drawn from two iterations of the Genetics of Recurrent Early Onset Depression (GenRED) study. Seasonal cases were those whose depressive episodes typically started in fall or winter. A mega-analysis of the two GWAS datasets was done using SNPTEST. We found that two single nucleotide polymorphisms (SNPs), rs149882931 and rs77073398, on chromosome 16p12.1 were associated with seasonal depression, at a genome-wide significant level (OR= 1.66, P= 3.59 x 10-8 and OR=1.62, 4.76 x 10-8, respectively). Since SAD is more prevalent in females, a female-specific analysis was carried out. The two variants were more significant in this analysis: P=2.18x10-9 (OR=1.89) and P=2.79x10-9 (OR=1.82), respectively, and a significant sex-by-SNP interaction was observed. These SNPs are located in a conserved intergenic region between the genes HS3ST4 and C16orf82. The protein product of HS3ST4 modifies the side chains of heparan sulfate proteoglycans. We therefore tested the hypothesis that the heparan sulfate biosynthesis pathway would be enriched in nominally significant SNPs using the SNP ratio test, and found evidence for such enrichment (P=0.008, SNP ratio test, P=0.027, SKAT). For BD, the GWAS analysis of 818 seasonal BD cases and 1,515 healthy controls showed that BD-S is most strongly associated with two SNPs within the ZBTB20 genes. BD subjects were drawn from NIMH Bipolar Genetics Study (BIGS), and seasonal cases were defined as those with depressive episodes starting in fall or winter. An association study was carried out with SNPTEST, and we found two single nucleotide polymorphisms (SNPs) in the intronic region of ZBTB20 gene to be associated with BD-S (rs7646282, OR=2.34, P= 7.23 x 10-8 and rs139459337, OR=2.37, 8.05 x 10-8). A similar case-only study was carried out with 818 BD-S cases and 1239 cases without seasonal depressive symptoms (non-BDS), though no SNP was found to be significantly associated in this analysis. rs7646282 is the strongest SNP in cis-association with ZBTB20 gene expression, and ZBTB20 has been shown to affect the neural development of the hippocampus, a brain region implicated in the pathophysiology of BD. Finally, we sought to determine whether there is a role for circadian rhythm genes in BD susceptibility. In this study, we used a discovery set of 189 exome-sequenced BD patients and 105 healthy controls to look for circadian genes associated with BD. We found the DRD2 gene to be the circadian gene most strongly associated with BD. Among the rare damaging variants in the DRD2 gene, the S311C variant was the predominant SNP. To test whether this variant segregates in family members with BD, we genotyped the family members of probands from the discovery sample. This data was used for a linkage and family-based association study. Even though the linkage analysis was only very weakly positive, the family-based association study showed significant segregation of the variant in family members with BD (P< 0.05). To follow up on this finding, we further genotyped 2,185 unrelated BD cases and 1,982 healthy controls. We found no support for the S311C variant in this replication dataset. Sub-phenotype study of psychotic features and mood-incongruence also did not show significant association. Meta-analysis with 2,994 BD cases and 3,661 controls, however, revealed no association between the S311C variant and BD.

Alzheimer's disease (AD) is the most common neurodegenerative disease, characterized by progressive amyloid plaque aggregation, neurofibrillary tangles, and cortical tissue death. As the prevalence of AD is projected to climb in coming years, there is a vested interest in identifying endophenotypes by which to improve diagnostics and direct clinical interventions. The risk for complex disorders, such as AD, is influenced by multiple genetic, environmental, and lifestyle factors. Significant strides have been made in identifying genetic variants linked to AD through the genome-wide association study (GWAS). It has been estimated in more recent years, however, that GWAS-identified variants account for limited AD heritability, suggesting the role of non-sequence genetic mechanisms, such as epigenetic moderators. By influencing gene expression, epigenetic markers have been linked to age- associated decline through modulation of chromatin architecture and global genome instability, though such mechanisms are also involved with a number of normal biological processes, including neurogenesis. As the strategies of clinical genetics shift to include a heavier focus on epigenetic contributors, altered adult neurogenesis presents itself as a strong candidate for an endophenotype of AD development. This thesis proposes that, due to neuropathological dysfunction of epigenetic mechanisms in AD, new generations of neurons fail to proliferate, differentiate, and mature correctly, resulting in the larger loss of neurons and cognitive deficits characteristic to neurodegenerative disease. The plasticity of the epigenome and the role of epigenetic factors as mediators of the genome and the environment make such alterations attractive in AD research and implies the potential for therapeutic interventions. The present review submits neurogenesis as a viable target of epigenetic research in AD, highlights shared loci between neurogenesis and AD in the epigenome, and considers the promises and limitations of the neurogenic endophenotype.

Fusarium head blight (FHB) is a serious disease of wheat (Triticum aestivum) and other small grains; disease severity is affected by temperature and rainfall. This research comprised three studies: an artificially warmed experiment during 2016-2017, a morphology study and an FHB resistance screening study in 2015-2016, using approximately 250 wheat cultivars and breeding lines from programs in the eastern US. The location was the University of Kentucky Spindletop Research Farm in Lexington, KY. Higher levels of Fusarium damaged kernels and the toxin deoxynivalenol (DON) were observed in the warmed treatment compared to the control, and plant development was accelerated. In the FHB resistance screen, significant (p < 0.05) genotype differences for all traits were observed. A GWAS identified 16 SNPs associated with resistance and susceptibility, ranging from -2.14 to 4.01%. Three DON-associated SNPs reduced toxin levels by 3.2, 2.1, and 1.5 ppm. In the morphology study, negative correlations were observed among morphological and disease traits. Small effect SNPs were identified for all morphological traits, which might be useful in genomic selection; traits like spike length, spikelet number and inclination could be used in phenotyping. Response to warming indicates that existing resistance sources may be less effective in a warming climate.