Saudi Cultural Missions Theses & Dissertations
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Item Restricted Evaluation of Salt Tolerance at the Seedling Stage and Genetic Diversity in USDA Tomato (Solanum lycopersicum) Germplasm, and Genomic Insights into Leafminer Resistance and Tallness in Spinach (Spinacia oleracea) through Genome-Wide Association Studies (GWAS) and Genomic Prediction Approaches(University of Arkansas, 2024-12) Alatawi, Ibtisam; Ainong, ShiGenetic diversity and stress tolerance mechanisms in tomato (Solanum lycopersicum) and spinach (Spinacia oleracea) were explored through advanced genomic tools, focusing on salt tolerance in tomato and leafminer resistance and plant height in spinach. Using genome-wide association studies (GWAS) and genomic prediction (GP), this research uncovers key insights into the genetic architecture of these traits, paving the way for improving crop resilience. In tomato, the evaluation of 71 and 280 USDA accessions under saline stress identified genotypes with significant salt tolerance. Population structure analysis revealed three genetic groups, emphasizing the influence of domestication on diversity. These findings provide a strong foundation for breeding salt-tolerant tomato varieties tailored to regions affected by salinity. For spinach, GWAS identified significant single nucleotide polymorphism (SNP) markers associated with leafminer resistance and tallness. Candidate genes related to pest resistance and height were identified, offering valuable targets for breeding programs. Genomic prediction models showed high accuracy in selecting resistant and optimized genotypes, supporting the acceleration of spinach breeding efforts. The integration of genomic technologies with traditional breeding approaches enhances the ability to develop more resilient and productive crop varieties. These findings offer critical contributions to sustainable agriculture, particularly in addressing challenges posed by salinity stress and pest infestations.24 0Item Restricted REPURPOSING DRUGS FOR HYPERCOAGULABLE CONDITIONS: A PRECISION MEDICINE APPROACH TO ADVANCE THERAPEUTIC DISCOVERY(Virginia Commonwealth University, 2024-12) Alghubayshi, Ali; Wijesinghe, Dayanjan SBackground: Sickle Cell Disease (SCD) and related hypercoagulable conditions, particularly those associated with elevated von Willebrand factor (vWF) levels, pose significant health challenges globally, with a notable burden in Saudi Arabia. Despite known genetic factors influencing these conditions, effective treatment options remain limited. This dissertation aims to leverage genomic data and bioinformatic techniques to identify novel therapeutic targets and drug repurposing opportunities for SCD and vWF-linked hypercoagulability. Methods: This research comprises three interconnected studies. First, a case-control Genome-Wide Association Study (GWAS) was conducted comparing Saudi SCD patients with healthy controls. The second study utilized bioinformatic pipelines to analyze the druggability of the identified genes that characterize Saudi SCD patients. The interaction of these genes with the currently approved medications was estimated. The third study extended this approach to vWF-linked hypercoagulability, utilizing publicly available GWAS data. These analyses integrated data from various sources, including databases of drug-gene interaction and protein structures, to identify potential drug repurposing candidates and novel drug targets. Results: The initial GWAS identified numerous significant genetic variants characterizing SCD cases in the Saudi population. Building on these findings, the second study revealed several approved medications showing potential for repurposing in SCD. Notably, drugs such as simvastatin, allopurinol, and specific immunomodulators have emerged as promising candidates. The analysis also identified novel drug targets with high druggability scores, in particular, the olfactory receptor gene clusters. The third study, focusing on vWF-linked hypercoagulability, identified additional potential candidates, including nebivolol, pravastatin, riociguat, candesartan, and acetylcysteine. This study also revealed several novel, highly druggable targets implicated in key processes related to blood coagulation and vascular function, such as CLEC4M and SLC44A2. Conclusion: This research provides a comprehensive framework for drug repurposing and novel drug discovery in SCD and related hypercoagulable conditions. The findings underscore the potential of leveraging genetic data to identify targeted therapies, offering a pathway to more personalized and likely effective treatments. While promising, these computational predictions require further validation through conducting clinical studies to be translated into clinical practice.16 0Item Restricted Genetics of Heat Tolerance in the Bengal and Assam Aus Panel of Rice(University of Aberdeen, 2024-07) Alonazy, Dalal; Price, Adam; Norton, Gareth; Barker, MartinRice (Oryza sativa L.) is considered as the main stable food and largest grain crop in many Asian countries since they rely on it for basic nutrition. During the past few years, the temperature in rice-growing regions has been rising, and extreme high temperature events are increasingly frequent, potentially causing crop damage. Heat stress caused by rising temperature over the optimal range is a significant abiotic stress affecting rice production. Heat stress can negatively affect plant growth, development and productivity, causing a loss of yield. Therefore, developing heat tolerant rice varieties is essential. In this work, heat tolerance was evaluated in 204 rice cultivars, mostly from Bengal and Assam Aus Panel (BAAP). High heat tolerant genotypes were identified using two approaches: spikelet fertility and chlorophyll fluorescence. For spikelet fertility, the heat tolerant genotypes identified were ARC 14965, ARC 10392 and Goria. For chlorophyll fluorescence, the genotypes identified were KALI AUS, Code No BI 93 and AUS 130. Genome-wide association (GWA) mapping was conducted on the heat tolerance trait with two million SNPs using an efficient mixed model (EMMA). The total number of QTLs associated with traits related to heat tolerance identified were 23 in fertility trait and 10 QTLs in photosynthetic trait. A number of these QTLs contained functional candidate genes. A total of seven candidate genes were identified for control/treatment ratio; SEC14, Hsp20, AP2/ERF, WRKY28, miRNA156, OsDjC56 and ZOS6-06 and three for QY trait after 60 minutes; PHD13, OsSTA65 and CGN. Additionally, RNA-sequencing analysis (RNA-seq) was conducted on spikelet fertility trait and well-known heat tolerant genes were detected such as (OsMYB55, OsHTASb and OsHSFC1b). Through the combination of GWA and transcriptomic analysis two excellent candidate genes associated with heat tolerance in rice were identified, namely; miRNA156 and OsDjC56. In addition, the candidate gene CGN in the leave study differentially expressed in the RNA-seq. In conclusion, the heat tolerant genotypes and QTLs and candidate genes identified in this study could be serve as valuable resource for further advanced research in rice heat tolerance and for breeding programs aimed at enhancing sustainable rice production. Such work could make an important contribution in supporting global food security worldwide.26 0Item Restricted Genetic and phenotypic investigation of nitrogen use efficiency in Rice(University of Aberdeen, 2024-03-15) Hazzazi, Yehia Abdulrahman Ali; Price, Adam; Norton, GarethRice is an important staple crop, serving as a primary food source for more than half of the global population. Its production depends upon rice cultivars and applied fertilisers, and nitrogen (N) is an essential nutrient for rice plants. Nitrogen plays a crucial role in the growth and development of rice plants and in the production of high-quality grains. It is a key component of chlorophyll, the pigment responsible for photosynthesis and impacts other phenotype expression of plants. Among different rice populations, aus rice has rich genetic diversity with wide variation in nitrogen use efficiency (NUE). This work evaluated NUE in the Bengal and Assam Aus Panel (BAAP, 266 out of 300 are aus rice), quantitative trait loci (QTLs), candidate genes were identified, and RNA-seq was evaluated. Two Preliminary experiments were conducted in different N levels to identify suitable N conditions and associated phenotype expression for screening the large rice BAAP sub-population. Six N treatments applied were selected as a screening method for subsequent experiments. The N response at the rice seedling stage was evaluated in a subset of BAAP grown in mixed (50%/50%) agricultural topsoil and sand under controlled conditions and different levels of N treatments using 15 rice cultivars in the first experiment (these cultivars have been used in the previous studies and some of them are my favorite) and 12 rice cultivars in the second experiment (the best 12 cultivars of 15 from the first experiment in terms of the result). Then, another experiment tested the effect of below-ground competition between 12 rice cultivars with and without bags under controlled greenhouse conditions at three N levels (0%,50% and 100% RDN). I used two nitrogen scales (one scale starting from 0 to 150 N% this was not too much high than optimum dose of nitrogen and the second sacle was taken lower dose as well as the higher that was much more doses than the optimum level of nitrogen which was 120 kg/ha). The main reason to select these levels of nitrogen only to know NUE threshold of plants. For that, I use the higher scale to find if plants grow similarly as they were growing in the first experiment. But I found that, the plants have stopped their growth at 150kg/ha. In the first experiment, various traits related to plant growth and nitrogen utilisation were investigated across different levels of nitrogen applications. The traits examined included plant height, nitrogen balance index (NBI), biomass production, shoot nitrogen percentage, and nitrogen uptake per plant. The results demonstrated a wide range of responses among the tested cultivars—Lemont, BRRI Dhan 28, IR 64, Nipponbare, Black Gora, and BJ1—indicating diverse reactions to varying nitrogen levels. Specifically, the phenotypic response to nitrogen was comparatively lower in Lemont, BRRI Dhan 28, IR 64, and Nipponbare, while it was xix higher in Black Gora and BJ1. These findings suggest distinct variations in how these cultivars express their phenotypic traits in response to nitrogen availability, providing valuable insights into their phenotypic responses under different nitrogen conditions. In the second experiment, the focus was on identifying cultivars that exhibited distinct responses to low and high nitrogen (N) conditions. Among the cultivars studied, N22 and BRRI Dhan 28 were identified as low nitrogen-responsive cultivars, indicating that these varieties demonstrated notable changes or adaptations in their traits under conditions of limited nitrogen availability. On the other hand, BJ1 and Niyan Wee were identified as high nitrogen-responsive cultivars, suggesting that these varieties displayed significant alterations in their characteristics or performance in response to ample nitrogen supply. These findings highlight the variability among different rice cultivars in their sensitivity and adaptation to nitrogen levels, providing valuable information for understanding and optimsing their growth under varying nutrient conditions. The notable genetic variation observed in shoot biomass among the tested rice cultivars within the same nitrogen treatment underscores the inherent diversity in their responses to environmental conditions. Specifically, the lower shoot biomass values observed in cultivars N22, IR 64, and BRRI 28 indicate that these varieties exhibit a tendency toward reduced above-ground plant material production under the specified nitrogen treatment. This may suggest that these cultivars are less efficient or responsive in utilizing nitrogen for shoot growth. On the contrary, the higher shoot biomass values observed in BJ1, Black Gora, and Niyan Wee signify that these particular cultivars have a genetic predisposition for enhanced above-ground biomass production under similar nitrogen conditions. This variability in shoot biomass responses highlights the intricate interplay between genetic factors and environmental cues, providing valuable insights for crop management strategies and genetic improvement programs aimed at tailoring rice varieties to specific nitrogen regimes for optimal agricultural productivity. Genome-wide association (GWA) mapping was conducted on nitrogen use efficiency associated traits with 2 million SNPs on a large BAAP population (230 rice cultivars) at two N levels (0% and 100% RDN). The total number of QTLs associated with traits related to NUE identified was 26 at N0, 48 at N100, and 30 of the ratio of N0/N100. A total of 109 candidate genes were found, including well-known genes OsNAR2.1, OsAAP, and OsbZIP59. Among identified QTLs, four notable QTLs on several chromosomes of different traits were selected for haplotyping. The haplotype variants of three candidate genes (OsbZIP59, OsNAR2.1, and OsCDKD-1) are discussed. xx N-responsive and unresponsive genotypes selected from large experiment for RNA-seq were used to identify differential expression of candidate genes for NUE in rice. This study categorised six rice genotypes into responsive and unresponsive groups based on their trait performance under the two nitrogen treatments. To investigate the transcriptomic differences, RNA was sequenced from shoots to gain insights into the gene expression patterns related to nitrogen treatments. Transcriptomics revealed the gene expression patterns and levels of RNA transcripts in a given sample, providing insights into which genes are active and to what extent they are being expressed for NUE relevant to GWAS. The N efficient accessions, QTLs and candidate genes identified in this work will be important resources for further research in rice NUE and breeding programs for sustainable rice production.38 0