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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 Unraveling the Genetic Architecture of Agronomic Traits and Developing a Genome Wide InDel Panel in Common Bean (Phaseolus vulgaris)(North Dakota State University, 2015) Mafimoghaddam, SamiraCommon bean (Phaseolus vulgaris) is an economically important legume. The agronomic characteristics of this crop such as days to flower, growth habit and seed yield affect breeding strategies. However, little is known about the genomic regions controlling these traits. Therefore, discovering the genetic architecture underlying important agronomic traits can accelerate breeding via marker assisted selection (MAS) in addition to providing genomic and biological information. Genome wide association studies (GWAS) are currently the method of choice to find the genomic regions associated with traits of interest using a population of unrelated individuals. It takes advantage of the historic recombinations that exist in the population to map the traits at a higher resolution. The availability of a reference genome in common bean has paved the way for higher throughput and more accurate genomic research including the discovery of new knowledge and development of new tools. In the first experiment we conducted GWAS using a panel of 280 diverse genotypes from the Middle American gene pool and about 15,000 SNPS with minor allele frequency of 5% and greater to map seven important agronomic traits in common bean. We were able to detect known and new genomic regions with strong candidate genes associated with these traits. In the second experiment we used sequence data from 19 genotypes from different bean market classes to develop a panel of insertion-deletion (InDel) markers that can be used for MAS as well as other genetic and genomic studies. These user-friendly, cost-effective, and co-dominant markers were tested for their efficiency and application. They demonstrated utility in a medium throughput genetic map construction and diversity analysis.Item Genome-Wide Association Mapping of Host Resistance to Stem Rust, Leaf Rust, Tan Spot, and Septoria Nodorum Blotch in Cultivated Emmer Wheat(North Dakota State University, 2015) Sun, QunCultivated emmer wheat (Triticum turgidum ssp. dicoccum) is a good source of genes for resistance to several major diseases of wheat. The objectives of this study were to use genome-wide association analysis to detect genomic regions in cultivated emmer germplasm harboring novel resistance genes to four wheat diseases: stem rust, leaf rust, tan spot, and Septoria nodorum blotch (SNB). A natural population including 180 cultivated emmer accessions with a high level of geographic diversity was assembled as the association-mapping panel. This cultivated emmer panel was evaluated phenotypically by scoring reactions to stem rust, leaf rust, tan spot, and SNB and was genotyped using a 9K SNP Infinium array. After filtering for missing data points and minor allele frequency (MAF), 4,134 SNPs were used for association analysis using 178 emmer accessions. Based on principle component (PC) analysis, five subpopulations strongly associated with geographic origins were suggested by the first three PCs. Genome-wide association analysis revealed that 222, 42, 146, and 42 SNPs were significantly associated with resistance to stem rust, leaf rust, tan spot, and SNB, respectively, at the significant level of 1 percentile. Among the significant SNPs at the significant level of 0.1 percentile, ten, one, nine, and one co-located with known genes or QTL associated with resistance to the four diseases, respectively. The remaining significant SNPs were located in the genomic regions where no known resistance genes have been identified for the four diseases. This evidence suggests that some of the emmer wheat accessions carry novel genes conferring resistance to the four diseases. Additionally, 14, three, eight, and five LD blocks harboring at least one significant SNP were identified and might harbor putative QTL related to resistance to the four diseases, respectively. These studies provide information about the genomic regions in cultivated emmer that are associated with resistance to stem rust, leaf rust, tan spot, and SNB. Results from these studies provide guidance for selecting emmer accessions when decisions are being made about the parents that will be used for the development of new resistant germplasm and mapping populations for identifying novel genes conferring resistance to major wheat diseases.Item Genomic Analysis of Domestication-Related Traits and Stem Rust Resistance in Tetraploid Wheat(North Dakota State University, 2017) Saini, JyotiModern durum and common wheat cultivars were developed from ancient wheat ancestors by natural and artificial selection of agronomic and domestication traits, which ultimatey decreased their genetic diversity and made them more susceptible to various biotic and abiotic stresses. At present, new sources of resistance need to be introgressed into future wheat cultivars to combat the effect of the disease stem rust caused by the biotrophic fungal pathogen Puccinia graminis f.sp. tritici (Pgt). In this dissertation, I first analyzed the domestication-related traits in a tetraploid recombinant inbred line (RIL) population developed from a cross between the durum wheat line Rusty and the cultivated emmer accession PI 193883 (referred to as the RP883 population). Second, the RP883 population and a double haploid (DH) population (referred to as the LP749 population) derived from a cross between the durum cultivar Lebsock and the Triticum. turgidium ssp. carthlicum accession PI 94749, and nine durum wheat cultivars were screened with Pgt races TMLKC, TTKSK, TRTTF, and TTTTF. Domestication-related trait analysis in the RP883 population showed vernalization (Vrn-A1) and domestication (Q) genes had a pleiotrophic effect on spike length, spikelet per spike, spike compactness, and threshability. Additionally, an interaction and dosage effect of three free-threshing trait governing loci, teneacious glume Tg2A and Tg2B, and q, revealed that mutation in all three loci are required to attain complete free threshability. The stem rust analysis done in the RP883 population showed two Sr gene regions conferring resistance against TMLKC, TTKSK, and TRTTF: one novel gene region on chromosome 2BL (Sr883) and likely a new allele or gene residing in close proximity to the Sr13 gene on 6AL. The second stem rust study using the LP749 population and nine durum wheat cultivars showed that most likely the U.S. durum germplasm carries the four major Sr genes, Sr7a (4AL), Sr8155B1 (6AS), Sr13 (6AL), and likely Sr9e (2BL) against TTKSK, TRTTF, and TTTTF. In conclusion, results obtained from this domestication study provide knowledge about different stages in wheat evolution. Both stem rust studies revealed genetic diversity in the tetraploid wheat gene pool and indicate their utility in future breeding programs.