Cranberry common bean (Phaseolus vulgaris L.) is planted worldwide and consumed as a critical food source of human protein, fibre, carbohydrates, and minerals. Marsh spot (MS) is a physiogenic disorder which severely impacts seed quality in common beans. Previous studies indicate that MS involves a nutritional disorder caused by Mn deficiency. However, the inheritance and genetic mechanism of MS resistance are still not fully understood. To investigate the genetics of MS resistance, a population of 138 recombinant inbred lines (RILs) was developed from a bi-parental cross between a susceptible cultivar Messina and a resistant cultivar Cran09. The population and its two parents were evaluated for MS resistance during five consecutive years from 2015 to 2019 in both sandy and heavy clay soils in Morden, Manitoba, Canada. The severities of MS were rated and subsequently converted to MS resistance index (MSRI) and MS incidence (MSI). Statistical analyses indicated that MSI and MSRI were highly correlated (r = 0.96-0.99) and had high broad-sense heritability (H²) of 86.5% and 83.2%, respectively. Joint segregation analysis (JSA) of 18 phenotypic datasets from five years and two soil types showed that MS resistance was controlled by four major genes with genetic interactions - one of which may suppress the additive effect of the other three genes. To identify the quantitative trait loci (QTL) and the candidate genes associated with the MS resistance, the 138 RILs and the two parents were sequenced using genotyping by sequencing approach. A total of 52,676 SNPs were detected. After further filtering with a threshold of minor allele frequency > 0.01 and call rate > 20%, 2,061 SNPs were retained and then imputed for genetic map construction and QTL mapping. A genetic map consisting of 2,058 SNP markers on 11 linkage groups or chromosomes was constructed, which covered 1,004 recombination blocks with a total length of 6,449 cM and an average block of 6.42 cM. Three linkage map-based QTL-mapping models ICIM-ADD, ICIM-EPI, and GCIM and one genome-wide association study (GWAS) model RTM-GWAS for 18 phenotypic datasets from different years and soil types were used for identification of QTL. A total of 36 QTL, including 21 of additive and 15 of epistatic effects, were identified. Functional gene annotation analysis revealed 151 Mn-related candidate genes across the common bean reference genome and 17 of them harbored the six QTL discovered in this study. In conclusion, MS resistance in common bean is a highly heritable trait and controlled by several major and minor genes. The results of JSA and QTL mapping advance the current understanding of the genetic mechanisms of MS resistance in cranberry common bean, and provide additional resources for application in genomics-assisted breeding and potential isolation and functional characterization of the candidate genes.

Genome-wide association studies (GWASs) have reported numerous associations between risk variants and major psychiatric disorders (MPDs) including schizophrenia (SCZ), bipolar disorder (BPD), major depressive disorder (MDD) and others. We reviewed all of the published GWASs, and extracted the genome-wide significant (p<10) and replicated associations between risk SNPs and MPDs. We found the associations of 6 variants located in 6 genes, including L type voltage-gated calcium channel (LTCCs) subunit alpha1 C gene (), that were genome-wide significant ( ) and replicated at single-point level across at least two GWASs. Among them, the associations between MPDs and rs1006737 within are most robust. Thus, as a next step, the expression of the replicated risk genes in human hippocampus was analyzed. We found had significant mRNA expression in human hippocampus in two independent cohorts. Finally, we tried to elucidate the roles of venlafaxine and ω-3 PUFAs in the mRNA expression regulation of the replicated risk genes in hippocampus. We used cDNA chip-based microarray profiling to explore the transcriptome-wide mRNA expression regulation by ω-3 PUFAs (0.72/kg/d) and venlafaxine (0.25/kg/d) treatment in chronic mild stress (CMS) rats. ω-3 PUFAs and venlafaxine treatment elicited significant up-regulation. We concluded that might confer the genetic vulnerability to the shared depressive symptoms across MPDs and CACNA1C might be the therapeutic target for depressive endophenotype as well.

Steroid hormones act as important regulators of physiological processes including gene expression. They provide possible mechanistic explanations of observed sex-dimorphisms in obesity and coronary artery disease (CAD). Here, we aim to unravel causal relationships between steroid hormones, obesity, and CAD in a sex-specific manner. In genome-wide meta-analyses of four steroid hormone levels and one hormone ratio, we identified 17 genome-wide significant loci of which 11 were novel. Among loci, seven were female-specific, four male-specific, and one was sex-related (stronger effects in females). As one of the loci was the human leukocyte antigen (HLA) region, we analyzed HLA allele counts and found four HLA subtypes linked to 17-OH-progesterone (17-OHP), including HLA-B*14*02. Using Mendelian randomization approaches with four additional hormones as exposure, we detected causal effects of dehydroepiandrosterone sulfate (DHEA-S) and 17-OHP on body mass index (BMI) and waist-to-hip ratio (WHR). The DHEA-S effect was stronger in males. Additionally, we observed the causal effects of testosterone, estradiol, and their ratio on WHR. By mediation analysis, we found a direct sex-unspecific effect of 17-OHP on CAD while the other four hormone effects on CAD were mediated by BMI or WHR. In conclusion, we identified the sex-specific causal networks of steroid hormones, obesity-related traits, and CAD.

京都大学 / 新制・課程博士 / 博士(農学) / 甲第24654号 / 農博第2537号 / 新制||農||1097(附属図書館) / 学位論文||R5||N5435(農学部図書室) / 京都大学大学院農学研究科農学専攻 / (主査)教授 田尾 龍太郎, 教授 土井 元章, 准教授 中野 龍平 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

Peripheral blood biomarkers can inform clinical care and drug development. Establishing causality between biomarker and disease is often critical for such applications, but epidemiological studies are limited due to biases from confounding and reverse causation. Mendelian randomization analysis leverages random inheritance of genetic variants at conception to mimic properties of randomized studies and estimate unconfounded effects between biomarker and disease, or vice-versa. This thesis demonstrates the utility of Mendelian randomization as a complementary tool to elucidate observational studies, predict drug safety and repurposing opportunities, and improve diagnostic biomarkers for cardiometabolic diseases. First, we characterized the hypothesized relationship between lipoprotein(a) and atrial fibrillation. We demonstrated both observed and genetically predicted lipoprotein(a) levels were associated with higher risk of atrial fibrillation across multiple independent cohorts. Importantly, risk was partly mediated independent of atherosclerotic cardiovascular disease, a known consequence of elevated lipoprotein(a) and itself a risk factor for atrial fibrillation. Next, we explored the lifelong effects of endogenous testosterone across a comprehensive set of 461 health outcomes in 161,268 males from the UK Biobank cohort. Using Mendelian randomization analysis, we found higher testosterone had beneficial effects on body composition and bone mineral density but adverse effects on prostate cancer, androgenic alopecia, spinal stenosis, and hypertension. Finally, we applied Mendelian randomization with the intention of discovering biomarkers caused by disease, which are expected to represent markers of early disease. As a proof-of-concept, we applied this framework to identify biomarkers associated with genetic predisposition to kidney function among 238 biomarkers measured in the ORIGIN trial. We discovered reduced kidney function caused increased trefoil factor 3 and showed its addition to models with known risk factors improved discrimination of incident early-stage chronic kidney disease. Taken together, Mendelian randomization identified biomarkers that warrant further study, with promising implications for screening, prevention, and treatment of different cardiometabolic diseases. / Thesis / Doctor of Philosophy (PhD) / Biological markers associated with disease can inform novel therapeutics or diagnostics but distinguishing causation from correlation is challenging. Mendelian randomization – a technique that leverages random inheritance of genetic variation to infer causality – was used to examine the role of biomarkers in cardiometabolic diseases. First, we implicated lipoprotein(a) as a risk factor for atrial fibrillation that acts independent of atherosclerotic cardiovascular disease. Second, we comprehensively characterized the lifelong effects of testosterone on health outcomes in males, where we found evidence of both beneficial and adverse effects on disease. Finally, we discovered trefoil factor 3 as a diagnostic marker for early-stage chronic kidney disease. Altogether, this thesis demonstrated different applications of Mendelian randomization that showcase its utility as a complementary tool to reveal causal biomarkers, and served to identify biomarkers for cardiometabolic diseases that merit further studies to evaluate their potential benefit on patient care.

No description available.

No description available.

No description available.

No description available.

<p>Gene expression is a complex process by which genetic information flow from genes to proteins. Factors regulating gene expression are diverse ranging from sequence elements on DNA, to various types of RNA, to proteins. These factors are categorized into two main categories, <em>cis</em>-acting elements and <em>trans</em>-acting elements. <em>PHO84</em> is a budding yeast gene that was previously reported to be regulated by its cognate antisense transcripts both in <em>cis</em> and in <em>trans</em>. The antisense transcripts of <em>PHO84</em> are a group of long non-coding RNAs (lncRNAs). In my project, I performed RNA-seq and TT-seq analysis to investigate the global correlation of sense/antisense pairs, which showed that the model of sense/antisense negative correlation is not always true for <em>PHO84</em> locus as well as others. I conducted a series of gene expression analysis experiments to decipher the mechanisms regulating <em>PHO84</em> gene, which showed that the 3’ untranslated region (3’UTR) of <em>PHO84</em> plays a regulatory role in the sense expression, an activity not linked to the antisense transcript levels. I also performed a genetic screen to identify <em>trans</em>-acting protein factors that promote the 3’UTR-dependent regulation at <em>PHO84</em> locus.</p> <p>Taken together, I provided insights on both <em>cis</em>- and <em>trans</em>-acting elements controlling the expression of the model gene <em>PHO84</em>. Such information can be taken further and be applied to other higher organisms, with possible implication in the identification of key players in human diseases arising from gene expression dysregulation. </p>