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Item The Genomic Alteration Landscape of Pancreatic Duct Adenocarcinoma(North Dakota State University, 2022) Adeleke, DavidBy 2030, PDAC is projected to be the second leading cause of cancer-related death in the US. PDAC is a multifactorial disease driven by genomic alterations. Understanding this alteration landscape will both refine the knowledge of disease etiology and enhance disease stratifications, drug design, and targeted treatment. This study aimed to identify novel genetic alterations that are associated with pancreatic cancer biology and prognosis to further refine the genetic focus for therapy development, disease subtyping, and risk assessment in PDAC. To this end, SNV, CNV, and clinical data for PDAC patients were downloaded from the ICGC data portal and analyzed for somatic mutations and recurrent copy number variations. This study showed that KRAS, TP53, and TTN are not only highly mutated but also associated with poor survival in PDAC. Also, this study showed that CN-LOH TP53, KRAS, SMAD4, and RYR3 were associated with reduced risk of death from PDAC.Item Comparative Analysis of Zinc Oxide Nanoparticles Induced Transcriptomic Responses in Arabidopsis(North Dakota State University, 2019) Alasvand Zarasvand, AzitaThe impact that zinc oxide nanoparticles (ZnONP) have on plant physiological responses was evaluated by comparing gene expression changes after Arabidopsis thaliana plants were exposed to ZnONP, in comparison with ionic Zn2+ (ZnSO4) and non-treated controls. After treatment with ZnONP (concentration10 μg L−1), ionic Zn2+ (applied as ZnSO4 at a concentration of 19.7 μg/ L −1), expression analyses via RNA sequencing revealed that 369 genes were down regulated and 249 were upregulated (p < [FDR] 0.05, expression difference < 3). The downregulated genes in ZnONP treated seedlings compared to the Zn +2 ion and untreated controls were mainly abiotic stress (oxidative stress, low temperature) and biotic stress such as defense responsive genes based on the gene ontology analysis. The upregulated genes in response to ZnONP treated plants compared to the Zn +2 ion control plants were mainly photosynthesis, light harvesting complex, and hormone responsive genes such as abscisic acid.Item Variation in Core and Accessory Parts of Genome of Escherichia Coli Isolated from Soil from Riparian Areas in New York State(North Dakota State University, 2016) Maistrenko, OleksandrEscherichia coli is commensal bacteria and is a symbiont of the digestive system of vertebrates. Due to frequent deposition of E. coli into extrahost habitats (soil, water), approximately half of its population exists as free living organisms. It is unclear what genome-wide variation stands behind adaptation for extrahost habitat. This thesis applies a genome-wide association study approach to find genetic variation in core and accessory parts of genome of E. coli that is associated with 1) forest or agricultural field soil habitats and 2) with survival phenotype in soil microcosm. Gene composition analysis suggests that pan-genome of environmental E. coli is unlimited. Core and accessory genome contained variation associated with survival phenotype and with forest or field habitat.Item Validation of the Pyrenophora teres f. teres PttBee1 Region and Mapping of Resistance to P. teres f. maculata in Durum(North Dakota State University, 2021) Skiba, Ryan MichaelPyrenophora teres is a fungal pathogen of barley and other closely related grass species. Two forms of the pathogen, P. teres f. teres and P. teres f. maculata, are the causative agents of net form net blotch and spot form net blotch of barley, respectively. Genetic and bioinformatic approaches were used to identify eight candidate effectors in the P. teres f. teres PttBee1 region. Genes were validated using CRISPR-Cas9 mediated gene disruptions. As no transformants displayed alterations in virulence, additional markers were implemented into a P. teres f. teres genetic map to refine the locus. As P. teres f. maculata has recently emerged as a pathogen of wheat, a quantitative trait loci analysis and genome wide association study were performed with this pathogen using a durum wheat biparental mapping population and a subset of the Global Durum Wheat Panel, respectively, both showing an association with resistance/susceptibility on chromosome 2A.Item Identification of Stem Rust Resistance Quantitative Trait Loci in Durum Wheat Populations(North Dakota State University, 2022) Lund, KennedyStem rust (Puccinia graminis f. sp. tritici) negatively impacts durum wheat production worldwide. Resistance loci from four resistant landrace durum wheat lines were identified in biparental F¬5¬ recombinant inbred line (RIL) populations after crossing with the susceptible line ‘Rusty’. The populations were tested with foreign race of stem rust from Eastern Africa and Europe (JRCQC, TRTTF, TTRTF, and TTKSK) and local races from United States Upper Midwest (MCCF and RKQQ), followed by genotyping and linkage map construction to identify stem rust resistant quantitative trait loci (QTLs). At least one stem rust resistance QTL was identified in each population with a total of twelve QTLs identified overall. Seven of the identified QTL regions validated previously published stem rust resistance genes and the other five identified potentially novel stem rust resistance genes. Various resistance mechanisms were determined from QTL regions that provide stem rust resistance to the four durum wheat RIL populations.Item Genome-wide Scan for Loci Affecting Iron Deficieny Chlorosis in Soybean.(North Dakota State University, 2010) Chikara, ShireenIron deficiency results in iron deficiency chlorosis (IDC) in soybean grown in the north central regions of the United States. Soybean plants display a variety of symptoms, ranging from slight yellowing of the leaves to interveinal chlorosis, and sometimes IDC is followed by stunted growth. In severe cases IDC may even lead to cell death. The objective of this project was to employ a whole genome association mapping approach to uncover the genomic regions associated with the iron deficiency trait in soybean. Golden gate assay technology was applied to expedite the screening of 1,536 single nucleotide polymorphisms in two different sets of soybean populations belonging to the year 2005 and 2006. The two soybean populations were screened for IDC at multiple locations in replicated field trials. The experiment only considered marker loci with a minor allele frequency greater than 0.1. Probability-probability plot helped in selecting the appropriate general linear models, which controlled for only population structure, and mixed linear models, which controlled for both the population structure and the ancestry. For the 2005 population, three statistical approaches (PCA, PCA+K and PCA+K*) identified twelve marker/trait associations, and for the 2006 population, five statistical models (Q, PCA, Q+K, Q+K * and PCA+K*) resulted in the discovery of twenty-two such associations. Although none of the markers significantly associated with JDC was common to both the populations under study, similar regions of significance were observed between the two years. When the phenotypic and the genotypic data of the two populations were combined, 10 markers were significantly (pFDR < 0.01) associated with the IDC trait using the PCA and PCA+K* statistical models. Out of the 10 markers, six selected markers showed a significant phenotypic mean difference for the tolerant and susceptible alleles. A detailed analysis revealed that using a smaller set of combinations from these six markers can effectively identify IDC tolerant genotypes. The next step would be to verify the reproducibility of the selected set of marker combinations in another set of populations.Item Bioinformatic Analysis to Identify and Understand Aberrant DNA Methylation Pattern Associated with Pancreatic Cancer(North Dakota State University, 2021) Zamani, MariamIn this study, we searched for significant hypo and hyper methylation CpG (5'-C-phosphate-G-3') probes from The Cancer Genome Atlas (TCGA) datasets. First, the relationship between hypo and hypermethylation pattern in significantly expressed genes associated in pancreatic ductal adenocarcinoma (PDAC) was analyzed using computational methodologies in R package. This was done by combining DNA methylation (DM) and gene expression (GE) information, and their corresponding metadata (i.e., clinical data and molecular subtypes) and saved as R files. Next, examination of differentially methylated CpG sites (DMCs) between two groups (normal vs tumor) was identified gene sets. From this analysis, we found nine (09) overexpressed hypomethylated and six (06) under expressed hypermethylated genes near significant CpG probes. Results from this work will shed light on the relationship between CpG methylation and gene expression associated with PDAC.Item Mapping Ur-6, a Bean Rust Resistance Gene in Common Bean(North Dakota State University, 2020) Beerbower, Peter EdwardBean rust, caused by the fungus Uromyces appendiculatus (Pers.:Pers) Unger, is a disease of common bean (Phaseolus vulgaris) prevalent in the Americas and Africa. The most cost-effective countermeasure to bean rust is genetic resistance. While 17 dominant rust resistance genes (named with Ur- symbol) have been identified in common bean, not all of these genes have been genetically fine-mapped. To expand our knowledge of rust resistance genes in common bean, Ur-6 was mapped in the common bean genome. A GWAS analyses suggested that Ur-6 is present on chromosome Pv07 of P. vulgaris. Two InDel markers tightly linked to Ur-6 were developed by F2 bi-parental mapping and may prove effective for marker-assisted selection in bean breeding programs in the future. Further, 25 candidate genes were identified and are the potential focus of future gene validation research.