Genomics & Bioinformatics Masters Theses

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Browsing Genomics & Bioinformatics Masters Theses by browse.metadata.department "Genomics, Phenomics, and Bioinformatics"

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    Genome-wide Scan for Loci Affecting Iron Deficieny Chlorosis in Soybean.
    (North Dakota State University, 2010) Chikara, Shireen
    Iron 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.
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    The Genomic Alteration Landscape of Pancreatic Duct Adenocarcinoma
    (North Dakota State University, 2022) Adeleke, David
    By 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.
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    Identification of Stem Rust Resistance Quantitative Trait Loci in Durum Wheat Populations
    (North Dakota State University, 2022) Lund, Kennedy
    Stem 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.