Plant Sciences Masters Theses

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Browsing Plant Sciences Masters Theses by browse.metadata.program "Genomics and Bioinformatics"

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    Ascochyta Rabiei in North Dakota: Characterization of the Secreted Proteome and Population Genetics
    (North Dakota State University, 2011) Mittal, Nitin
    Chickpea is one of the most important leguminous crops grown in regions of southern Europe, Asia, the Middle East, and the United States. Ascochyta blight, caused by Ascochyta rabiei, is the most important foliar disease of chickpea. In favorable conditions, this disease can destroy the entire chickpea field within a few days. In this project the secreted proteins of Ascochyta rabiei have been characterized through one and two-dimensional polyacrylamide gel electrophoresis. This is the first proteomic study of the A. rabiei secretome, and a standardized technique to study the secreted proteome has been developed. A common set of proteins secreted by this pathogen and two isolates that exhibit the maximum and minimum number of secreted proteins when grown in modified Fries and Czapek Dox media have been identified. Population genetic studies of Ascochyta rabiei populations in North Dakota have been conducted using microsatellites and AFLP markers. Population genetic studies have shown that the ascochyta population in North Dakota has not changed genetically in the years 2005, 2006 and 2007, but the North Dakota population is different from the baseline population from the Pacific Northwest. The ascochyta population in North Dakota is a randomly mating population, as shown by the mating type ratio.
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    Biotic and Abiotic Factors Affecting the Survival of Listeria Monocytogenes in Prairie Pothole Soils and Sediments
    (North Dakota State University, 2017) Dusek, Nicholas Stephen
    The diversity-invasion relationship states that more diverse communities are more resistant to invasion. Listeria monocytogenes – a gram-positive facultative anaerobe, soil saprotroph, and opportunistic human pathogen – is capable of surviving in a diverse range of habitats, including soil, and several recent studies have shown that the prevalence of L. monocytogenes in soil increases with proximity to surface water. In addition, L. monocytogenes resides frequently in the guts of ruminants and poultry, creating many opportunities for deposition in soil. However, little work has been done to examine the effects of native soil microbiota on the survival of the pathogen. This thesis builds on previous work by examining microbial community diversity in the prairie pothole ecosystem and how it impacts the survival of L. monocytogenes. Results indicate that survival of L. monocytogenes does not seem to differ greatly as an effect of community diversity.
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    Development of a Molecular Marker to Track APA G40199 Introgression in Common Bean for Bruchid Resistance
    (North Dakota State University, 2018) Mazaheri, Lucy
    In common bean (Phaseolus vulgaris), the main seed storage pests are the bruchid beetles. Damage done to the seed by the larvae has a large impact on seed quality and yield. Arcelin (ARC), phytohaemagglutinin (PHA), and α-amylase inhibitor (α-AI) are linked seed storage proteins that form the APA locus on chromosome Pv04 and are associated with resistance. A major breeding objective is to introduce bruchid resistance into common bean from a resistant tepary genotype, G40199, by introgressing the resistant APA locus into susceptible common bean backgrounds. Here we developed a molecular marker that tracks the introgression. A set of PCR primers to the α-amylase inhibitor locus amplified a DNA fragment that showed a 45 base pair insertion in the middle of a lectin Leg_b domain. This enhanced locus characterization and insertion/deletion marker may preclude the need for bruchid resistance screening early in the breeding.
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    Genetic Investigation of Wild Oat with Acetyl-Coa Carboxylase Gene Sequence Variation
    (North Dakota State University, 2013) Mehta, Sonali
    Wild oat (Avena fatua) is a grass weed species that infests cropland. Common post-emergent herbicides for controlling wild oat are those that inhibit acetyl-CoA carboxylase (ACCase) and acetolactate synthase (ALS). Variation among plastidic ACCase gene sequences of herbicide-susceptible wild oat biotypes USDA96 and KYN119 revealed ACCase gene diversity consistent with possible separate diploid ancestry, with KYN119 more likely to share diploid ancestry with herbicide-resistant UM1. USDA96 wild oat shows low-level tolerance to the ALS-inhibiting herbicide flucarbazone, and the inheritance of this tolerance was studied among F3 families generated from KYN119 and USDA96 reciprocal crosses. Quantitative inheritance was observed at the below-label flucarbazone rate of 1.81 g ai/ha. Some F3 families had higher post-treatment main shoot dry weights than either parent, which may be due to heterosis and/or genetic contributions from both parents. No evidence for association between the Acc1;1 ACCase gene and low-level tolerance to flucarbazone was observed.
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    Genetics of Wheat Domestication and Septoria Nodorum Blotch Susceptibility in Wheat
    (North Dakota State University, 2019) Sharma, Sapna
    T. aestivum ssp. spelta Iranian type has long been thought to potentially be the direct non-free threshing hexaploid progenitor. I evaluated a RIL population derived from a cross between CS and Iranian spelta accession P503 to identify loci suppressing free-threshabilty in P503. Identification of QTL associated with threshability in region known to harbor the Tg2A gene, and an inactive tg2D allele supported the hypothesis of Iranian spelta being derived from a more recent hybridization between free-threshing hexaploid and emmer wheat. Parastagonospora nodorum is an important fungal pathogen and secretes necrotrophic effectors that evoke cell death. In this research, a DH population segregating for Snn5 was used to saturate Snn5 region of chromosome 4B with molecular markers. The physical distance between Snn5 flanking markers was narrowed to 1.38 Mb with genetic distance of 2.8 cM. The markers developed in this study will provide a strong foundation for map-based cloning of Snn5.
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    Protein-ligand Docking Application and Comparison using Discovery Studio and AutoDock
    (North Dakota State University, 2017) Wang, Qi
    Protein-ligand docking is a structure-based computational method, which is used to predict the small molecule binding modes and binding affinities with protein receptors. The goals of this study are to compare the docking performances of different software and apply the docking method to predict how protein fatty acid desaturase 1 (FADS1) interact with ligands. Two docking software, Discovery Studio and AutoDock, are used for docking comparison of 195 protein-ligand complexes from PDBind dataset. AutoDock performs a little bit better than Discovery Studio on the docking percentage, which is the percent of the docked complexes out of 195. On the other hand, Discovery Studio has a higher accuracy (successfully docked complexes, within 5 RMSD of the native complex structures) than AutoDock. The interaction between FADS1 and Sesamin shows a similar pattern comparing to the interaction between a homolog of FADS1 and a ligand shown in a PDB structure (PDB id 1EUE).
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    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, Oleksandr
    Escherichia 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.