Plant Sciences Doctoral Work
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Item A multi-omics multi-environment prediction in pulse crop(North Dakota State University, 2024) Saludares, RicaUnderstanding the genetic bases underlying seed yield and protein, and eventually recombining them in desired genetic backgrounds, continues to be a challenge to pulse crop breeders. Phenotypic selection for seed yield and protein in preliminary yield trials is hindered by the need to phenotype a large number of early-generation lines (>10,000) with limited seeds, resulting to trials with few replications and limited environments. In this study, we evaluated and applied a multi-trait multi-environment (MTME) and a multi-omics prediction framework to address phenotyping bottleneck and the complexities underlying negatively correlated traits, and maximize connectivity among genotypes for predicting performance of untested genotypes in diverse set of environments. Using over 200 NDSU modern advanced breeding lines and 300 USDA diverse accessions, our findings demonstrated that MTME prediction significantly enhanced predictive ability by 1.3 and 1.8-fold for yield and protein, respectively. For the environments with low heritability of tested trait, however, using the MTME prediction led to small increases in prediction accuracy. To further maximize connectivity among genotypes and environments, a subset of individuals was included from the testing population that led to 1.6 and 1.2-fold improvement for yield and protein, respectively. Incorporating additional orthogonal information such as gene expression (RNA) into the prediction framework showed potential for further increasing prediction accuracy. Using ~300 USDA diverse accessions assessed in two environments, integrating genotypic and expression data (DNA+RNA) resulted to higher predictive ability (0.48-0.55) over using DNA only (0.42) or RNA only (0.43-0.53). Overall, we found that maximizing the relationship among genotypes and environments, along with integration of additional orthogonal information (e.g. RNA) into genomic prediction framework can further enhance predicting performance of untested genotypes in diverse environments.Item Combining metabolite breeding with good agronomic performance in dry bean (Phaseolus vulgaris L.)(North Dakota State University, 2024) Rodriguez, OscarGrowth habit is one of the most important domestication traits in dry bean (Phaseolus vulgaris L.). In the U.S., Type II indeterminate upright varieties have helped farmers to switch from historic two-pass harvest to one-pass in direct harvest. Previous work suggested a stem diameter of 5.6 mm as threshold to select Type II architecture plants suitable for direct combining. In addition, the metabolic profile of indeterminate plants in dry bean is of great interest not only to define differences in seed coat color but to observe relationships with other traits, plant growth one of them. This study aimed to validate the correlation between stem diameter and other agronomic traits using breeding lines from a commercial program; further, this study investigates stem diameter as selection criteria to select genotypes that combine high seed yield and upright architecture, and to find genetic regions related to plant height, stem diameter and metabolic profile using a GWAS. Overall, mean stem diameter values were above 7.5 mm, higher than the proposed threshold of 5.6 mm. Stem diameter, showed no significant GxE interactions and the highest broad-sense heritabilities for pinto and slow darkening pinto. In market classes black, great northern, and navy plant height was the most relevant trait for seed yield variation, while stem diameter had low effect. In contrast, plant height and stem diameter are required to explain part of seed yield variability and continue selecting upright plants for pinto, red/pink, and SD-pinto. According to the GWAS, a region on chromosome Pv07 (40 Mb), was shared between plant height and stem diameter. Genes found in this region relate to plant growth and disease avoidance, which makes this region interesting to continue with further studies for plant architecture. Regarding metabolic studies GWAS identified a very interesting region on chromosome Pv01 (61.4 Mb), related to the enzyme Flavonoid 3'-monooxygenase / Flavonoid 3'-hydroxylase. This enzyme is present in the flavonoid biosynthesis pathway. However, it could also have relationship to plant growth. Further cloning of this region would be ideal to confirm differences in seed coat color and plant growth.Item Improvement of Organoleptic Attributes of Yellow Pea Flour Through An Emerging Green Technology: Supercritical Carbon Dioxide + Ethanol Extraction(North Dakota State University, 2020) Vatansever, SerapAn increasing demand for following healthier eating pattern has created a rapidly growing food market, including more nutrient dense and healthier plant-based foods. Nutrient-dense yellow pea flour is ideal for addressing these new-generation foods. However, its utilization in foods is limited due to its unpleasant flavor. Therefore, an eco-friendly deflavoring method has recently been found effective to improve sensory quality of pulse ingredients. Supercritical carbon dioxide + ethanol (SC-CO2+EtOH) extraction was applied as deflavoring method. The goals of this research were to evaluate (1) the applicability of this extraction at optimized conditions to reduce off-flavor compounds of pea flour, and (2) interaction effect of extraction and particle size on flavor profile, physicochemical properties, particle size distribution, moisture sorption isotherms of deflavored pea flours. Findings of this study showed that operating conditions of SC-CO2+EtOH extraction significantly (p<0.05) optimized using a central composite rotatable design under response surface methodology to ethanol (22%), temperature (86 C), and pressure (42.71 MPa). Extraction at optimum conditions reduced total volatile (TV) content (0.55 µg/g) and improved sensory attributes of pea flour. TV contents of non-deflavored and deflavored whole pea flour and its fractions ranged from 7.1 to 18.1 µg/g and 0.4 to 2.7 µg/g, respectively. Similarly, the total volatile intensity of deflavored pea flours were significantly lower than non-deflavored flours as detected by the GC-Olfactory system. The extraction decreased moisture, resistant starch, damage starch, and lipid content of pea flours. Flours with coarse particles had lower protein, total starch, and starch damage than other flours. Medium and fine fractions had greater protein and total starch, respectively. Deflavored pea flours had lower viscosity parameters and water solubility index depending on particle size. Water sorption capacity of deflavored pea flours decreased with increased water activity. SC-CO2+EtOH extraction and particle size had a significant interaction effect for most response variables.Item Genome-Wide Association Mapping and Genomic Prediction for Resistance to Sclerotinia Stem Rot in Rapeseed/Canola (Brassica napus L.) Germplasm Collections(North Dakota State University, 2021) Roy, JayantaSclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum, is a devastating disease of rapeseed/canola that causes significant seed yield loss, reduced oil content, and quality. Lack of complete immune genotypes and polygenic resistance between host and pathogen often impedes the development of functional molecular markers and gene identification to enable SSR resistance breeding. However, genomics-assisted breeding approaches such as genome-wide association (GWA) mapping and genomic prediction (GP) are considered most promising for the genetic improvement of complex traits over classical breeding. Therefore, the objective of this study was to perform GWA mapping and GP in a diverse rapeseed/canola panel using ~24,000 to ~28,000 single nucleotide polymorphisms (SNPs) under field and greenhouse environments. Extensive phenotyping against S. sclerotiorum infection revealed few lines had promising resistance at seedling and adult stages in both environments. Adult plant resistance (APR) was characterized in four field environments by recording four traits and found strong associations among them. GWA models using the four traits identified 133 SNPs and 69 putative candidate genes associated with APR. The predictive ability (PA) ranged from 0.41-0.64 depending on trait specifications. For seedling resistance (SR) under a greenhouse environment, multiple GWA models using multiple traits detected 219 SNPs. Multiple GP models resulted in 0.45-0.68 PA for these traits. Association analyses for APR under controlled environments using five traits identified 37 and 50 significant SNPs in spring (SP) and semi-winter & winter populations (SWP), respectively. GP analyses revealed 0.48-0.60 and 0.10-0.19 PA in SP and SWP, respectively. Based on the GWA results collected from all experiments, we detected previously mapped overlapping genomic regions as well as new regions on chromosome A09 (33.34-39.13 Mb), C02 (59.17-62.79 Mb), and C6 (32.24-37.67 Mb). These findings would provide exciting opportunities to narrow the genomic regions to guide map-based cloning of SSR resistance genes to assist in future marker-assisted selection. Moreover, we have achieved a medium to high PA by implementing GP. Our study concludes that GWA mapping and GP hold promise to lead a step forward towards the genomics-assisted SSR resistance rapeseed/canola breeding that would help to achieve rapid gains from the selection.Item Optimizing Glufosinate for Weed Control in Agricultural Systems(North Dakota State University, 2021) Kazmierczak, AngelaWeed management is an essential component of production agriculture. While many weed management methods exist today, chemical practices have proven to be the most efficient and are the most widely adopted methods. The objectives of this research were to: 1) maintain glufosinate weed control activity using a larger than recommended ultra-coarse spray droplet spectrum through utilizing commercially available adjuvants and 2) improve the activity of commercial glufosinate formulations in terms of increased weed control and shortened rainfast interval. Field trials were conducted to identify adjuvants that would maintain glufosinate weed control activity at an ultra coarse spray quality. Commercially available adjuvants representing acidic ammonium sulfate (AMS) replacements, deposition aids, and organosilicone surfactants were applied with a medium and ultra coarse spray quality. The negative impact of an ultra coarse spray quality on glufosinate activity was only observed when utilizing only AMS in the spray solution, and these impacts were dependent on the treated species. While there were individual additives that provided enhanced weed control of certain species, no specific adjuvant class improved Liberty 280 SL efficacy consistently throughout the tested species. To determine which adjuvants enhanced glufosinate weed control efficacy and rainfastness in a commercial formulation, trials were conducted with sublethal rates using a simplified glufosinate formulation (GFA 196 SL), which contained a lower adjuvant load. Candidates of three adjuvant classes, polymers, surfactants, and oils, were tested. The additives were evaluated for effect on efficacy in field trials, and their effect on uptake and rainfastness were evaluated in radiolabeled laboratory work, as well as in simulated rainfall environments in both the field and greenhouse. Overall, the polymer Kuraray provided the best enhancement of glufosinate activity for both efficacy and rainfast characteristics. Oils were the only class of adjuvant to consistently improve glufosinate activity in these trials. The included oils provided the most consistent enhancement of glufosinate in the greenhouse rainfast trial by reducing the rainfast period by over 50% compared to GFA 196 SL alone and improving glufosinate uptake into common lambsquarters. Further research is needed to consider the feasibility of directly formulating these additives into a future glufosinate formulation.Item Identification of Genomic Regions Associated With Color-Related Traits in Durum Wheat(North Dakota State University, 2022) Hosseinirad, SeyedaliDurum wheat (Triticum turgidum L. ssp. durum Desf.) is one of the main crops for human consumption, and it is an essential ingredient for pasta production. The color of pasta can range from bright yellow to dim brown. Pasta brightness and yellowness are important quality indicators for producers and customers. Releasing durum wheat cultivars capable of producing pasta products with high yellow color can be an important goal for breeders. Yellow pigment content (YPC) is one of the important components that affect pasta color. The yellow color of pasta is not necessarily dictated by the presence of YPC; soluble brown pigment (SBP) and enzymes such as polyphenol oxidase (PPO) and peroxide (POD) are other factors that contribute to pasta color. Marker-assisted selection (MAS) can accelerate the selection process for breeding programs that develop new durum wheat cultivars with high yellow color. This dissertation used quantitative trait loci (QTL) mapping to identify QTL for these color-related traits. Two populations, each with 192 recombinant inbred lines (RILs), were developed from crosses between Joppa and D12118 (Population one [POP1]) and Mountrail and Carpio (Population two [POP2]). The phenotyping of these traits was carried out in two locations in North Dakota, USA. Genotyping of the RIL populations was conducted using the wheat Illumina iSelect 90K SNP assay. There were significant phenotypic differences among the genotypes for all traits. In POP1, entry lines 32 and 78 with both high YPC and low SBP, and in POP 2 entry lines 1, 82, and 101 with high YPC could be excellent sources for improving the yellow color in durum wheat. In this study, 31 Additive QTL (A-QTL) and 370 minor digenic epistatic QTL (DE-QTL) associated with all four traits were identified. In Pop1, the most significant A-QTL were detected on Chromosomes 5A (D1.SBP5A.ndsu) for SBP and 5B (D1.YPC5B.ndsu) and 6B (D1.YPC6B.ndsu) for YPC. In POP2, major A-QTL were found on chromosomes 7A (D2.YPC7A.ndsu), 2A (D2.PPO2A.ndsu), and 3A (D2.POD3A.ndsu) for YPC, PPO, and POD, respectively. The information provided in the current study could be employed with MAS to increase selection efficiency and improve the color of durum wheat.Item Genetic Dissection and Improvement of Fusarium Head Blight Resistance in Durum Wheat(North Dakota State University, 2022) Wang, RunhaoFusarium Head Blight (FHB) is a destructive and complex fungal disease in wheat. Durum wheat, an economically important crop for pasta production, is under the severe impact of FHB. While numerous favorable QTL/genes have been identified in common wheat, there are fewer resistance resources found in durum wheat. An interspecific cross between FHB resistant hard red spring wheat (HRSW) and durum wheat cultivar ‘Riveland’ has been conducted for the introgression of resistance resources to durum wheat. Given the complex quantitative trait of FHB resistance in wheat, a recurrent selection population was constructed by crossing durum wheat cultivars and durum breeding lines deviated from resistant tetraploid wheat and common wheat. Several FHB resistant breeding lines with lower FHB severity, lower plant height, and shorter flowering date than ‘Riveland’ were obtained from interspecies crosses and recurrent selection populations. These breeding lines can be used for the development of new durum wheat cultivars with high resistance to FHB. To explore the implementation of genome-wide markers to screen FHB resistance in the durum wheat breeding program, a genomic prediction model was built using breeding lines from 2012-2018 advanced yield trials (AYT) evaluated in multiple environments of scab nurseries. The genomic prediction accuracies were 0.53 and 0.47, respectively, based on ten-fold cross-validation and forward prediction to untested breeding lines. The results indicated that genomic selection could enhance FHB resistance improvement in the durum wheat breeding program.Item Understanding the Mode of Action of Essential Oil Nanoemulsions to Inhibit Fusarium Growth and Mycotoxin Production in Cereal(North Dakota State University, 2022) Jiang, HaiyangDeoxynivalenol (DON) is a commonly occurred mycotoxin in cereal-based food, which is mainly produced by Fusarium spp. in the field. It is unfeasible to entirely avoid DON contamination in cereal grains with good agricultural practices. Therefore, it is of great importance to have a strategy for preventing DON contamination in our final food products. In recent years, utilization of plant extracts such as essential oils (EOs) as antifungal and mycotoxin inhibitory agents in foods have gained popularity. Depending on the EO type and chemical composition of EOs, the antifungal and mycotoxin inhibitory efficacies of different EOs might be varied. In addition, their antifungal mode of actions (MOA) against Fusarium spp. growth remains unknown. Therefore, the overall objectives of this project were to understand how different type of clove EOs (clove bud EO and clove leave EO), hop essential oil (HEO) impact their antifungal and mycotoxin inhibitory efficacies, and their corresponding antifungal MOA. Finally, HEO in nanoemulsion form was applied to evaluate their application during micro malting process using naturally Fusarium infected barley grains. Results denoted that physically stable 5 wt% EO in-water nanoemulsions with the mean particle sizes less than 170 nm can be built by blending either corn oil or medium chain triglyceride (MCT) with EOs. The largest percentage of chemical constituent in clove essential oils (CO) and HEO was eugenol (phenol type) and β-myrcene (monoterpene type), respectively. In terms of their application as antifungal agents, CO had better antifungal and mycotoxin inhibitory efficacy against Fusarium graminearum growth and DON production in vitro as compared to HEO because of their high percentage of eugenol content. The major antifungal MOA of EO nanoemulsions included altering total lipid content in cell, chitin content in outer spore cell membrane, and damaging cytoplasmic membrane. In the application case study, results indicated that Fusarium biomass (Tri 5 DNA) and DON contents were reduced at each malting stage with the treatments of HEO nanoemulsion by malting Fusarium infected barley. This study provided the valuable information on utilization of EO nanoemulsions as natural antifungal agents during food processing.Item Cover Crops Benefits, Nitrogen Credits, and Yield Effects in Maize and Sugarbeet in the Northern Great Plains(North Dakota State University, 2021) Cabello Leiva, SergioFall-seeded cover crops (CC) provide soil coverage that prevents soil erosion and reduces NO3-N leaching. It is believed N accumulated in CC biomass is available to the next crop. The main objective of this research is to determine if N in the CC biomass provides N to the next crop of maize (Zea mays L.) and sugarbeet (Beta vulgaris L.). Two experiments were conducted in Hickson and Prosper, ND from 2017-2019. Maize grain yield and quality and sugarbeet root yield and chemical composition of the root were evaluated after fall-seeded cover crops. Fall biomass was greater in radish (Raphanus sativus L.) and oat (Avena sativa L.) than the other cover crops evaluated. Likewise, in the sugarbeet experiment, the check treatment (no CC) contained greater soil NO3-N concentrations compared with all CC. Winter-hardy CC survived the winter and reduced gravimetric water content in the soil profile in comparison with winter-killed CC and the check. Winter camelina [Camelina sativa (L.) Crantz] and winter rye (Secale cereale L.) reduced maize grain yield compared with the check and other cover crop treatments. Winter camelina and winter wheat (Triticum aestivum L.) decreased sugarbeet stand establishment and root yield in Prosper and Hickson in 2018. The yield of both crops increased with increased N rate, but the N accumulated in the cover crops biomass did not make a difference in grain or root yield of either maize or sugarbeet, indicating there was no N cycling to the following crop in these experiments.Item Improved Viability of Lactobacillus rhamnosus GG During Storage and Simulated Gastrointestinal Digestion by Encapsulation(North Dakota State University, 2021) Qi, XiaoxiProbiotics are “live microorganisms which when administered in adequate amounts confer a health benefit on the host”. However, the current techniques are still struggling with delivering enough live probiotics into the designated site of action. This project aimed to improve the viability of the probiotic Lactobacillus rhamnosus GG (LGG) under adverse conditions by encapsulation. Properties of the formed microcapsules such as particle size, morphology, mechanical properties, and rheological properties were examined by corresponding methods and equipment, and the viability of LGG under storage and simulated gastrointestinal (GI) digestion was evaluated.First, two modified alginate-based hydrogel bead systems were established on the basis of the reaction between sodium alginate (ALG) and Ca2+ by 1) adding an additional layer of chitosan with three different molecular weights was formed on the surface of alginate particles; 2) partially substituting ALG with low methoxyl pectin (LMP) or κ-carrageenan (KC) to form a double-network since pectin and carrageenan can interact with Ca2+ as well. In the first system, I found that the chitosan oligosaccharide (COS) improved the viability of LGG during storage by reinforcing the mechanical properties. However, no significant improvement on the viability of LGG during GI digestion was observed. In the second hydrogel bead systems, the ALG to LMP ratio of 8:2 in hydrogel provided the stronger inner structure and showed a better protective effect on the viability of LGG during GI digestion. Furthermore, I studied the complex coacervates formed from sugar beet pectin (SBP) and sodium caseinate (SC) or pea protein isolates (PPI) to be as encapsulation wall material for improving the viability of LGG during digestion. The impact of protein type, protein to sugar beet pectin mixing ratio (5:1 or 2:1), as well as the finishing technology (freeze-drying and spray-drying) on the viability of LGG were examined. Spray-dried samples, especially spray-dried PPI‒SBP microcapsules, demonstrated superior performance against cell loss and maintained more than 7.5 Log CFU/g viable cells after simulated GI digestion. Overall, the project demonstrated a great potential for improving the viability of probiotics by encapsulation.Item Dual Role of Phenolic Bioactives in Improving Functional Health Benefits and Abiotic Stress Resilience in Barley(North Dakota State University, 2021) Ramakrishna, RamnarainFood insecurity, climate change, and public health challenges are interconnected and pressing issues facing humanity in the 21st century. Therefore, it is imperative to address key obstacles underlying food and nutritional insecurity by developing strategies to concurrently improve the nutritional benefits and environmental stress resilience of food crops. The metabolic and physiological roles of plant-derived phenolic compounds are particularly relevant in addressing these challenges. Phenolic compounds are an integral part of plant adaptive defense responses against biotic and abiotic stresses. When consumed as part of diet, certain phenolic compounds from plant-based foods also provide wider protection against metabolic breakdowns and related health risks associated with non-communicable chronic diseases (NCDs). Therefore, the central theme of this dissertation is to delineate the dual protective roles of phenolic compounds in improving crop stress resilience and their human health protective functions, specifically antioxidant and anti-hyperglycemic benefits supporting management of early stages of type 2 diabetes. Barley was used as a model crop; initially several malting barley samples were screened based on their phenolic-linked antioxidant and anti-hyperglycemic functions using in vitro assay models. Following metabolically driven screening, novel bioprocessed elicitor treatments such as marine protein hydrolysates and chitosan oligosaccharides were used as seed and foliar treatments to improve type 2 diabetes supporting dietary functions through upregulation of proline-associated pentose phosphate pathway (PAPPP), which is linked to the biosynthesis of phenolic metabolites. Improvement of phenolic biosynthesis and type 2 diabetes related benefits were observed in grains and sprouts with targeted elicitor treatments. Further, elicitor treatments were also found to positively improve PAPPP-linked metabolic responses under abiotic stresses, such as high soil salinity and water logging stress. From a human health perspective, food barley tea and coffee were found to have significant phenolic-linked antioxidant, and anti-hyperglycemic benefits. Additionally, integrated bioprocessing strategy by combining sprouting with mixed Kefir culture-mediated fermentation was found to improve phenolic-linked antioxidant, anti-hyperglycemic, and human gut health benefits relevant functionalities in pigmented and unpigmented food barley substrates. Therefore, these metabolically driven strategies can be targeted to screen both abiotic stress resilience and human health protective functions in malting and food barley varieties.Item Genotype and Environmental Effects on Quality Traits of Durum Wheat Grown in North Dakota(North Dakota State University, 2020) Moayedi, SaraVariation in grain, semolina, dough strength, and pasta quality traits were evaluated using the effect of genotype and weather factors (air temperature, rainfall, and relative humidity). In addition, size exclusion high performance liquid chromatography (SE-HPLC) was applied to determine the correlation between quality traits and protein molecular weight distribution (MWD) with cooked firmness and cooked weight of fresh pasta made from four durum wheat genotypes. Results indicated that the environment was a great source of variation in the majority of quality traits such as test weight, 1000-kernel weight, grain protein content, vitreous kernel content, falling number, semolina protein content, semolina extraction rate, pasta color, and pasta cooking quality traits. However, grain yellow pigment content, semolina yellowness (b* value), gluten index, and mixogram time-to-peak were mainly affected by genotype. High air temperature and days with temperature ≥ 30 °C were desirable for high protein content and high pasta cooking quality. Ideal growing locations to achieve the greatest falling number, vitreous kernel content, gluten index, and high pasta color were favored by low relative humidity and low rainfall. Days with temperature ≤ 13 °C favored high 1000-kernel weight and test weight. In addition, damp conditions such as high relative humidity favored 1000-kernel weight and semolina extraction rate. Protein content and its fractions had a predominant role on the variation of fresh pasta cooked firmness and cooked weight, while gluten index did not relate to cooking quality. The quantitative increase in extractable monomeric protein (gliadins) was associated with a decline in cooked firmness, while it enhanced cooked weight. The possible gel forming properties of some protein fractions, including albumin + globulin during cooking were associated with high cooked firmness, low cooked weight, and low cooking loss in fresh pasta. Genotypes differed in their genetic potential for quality traits evaluated and in the magnitude of their response to the environment. A trait is defined as stable when it is not greatly affected by the environment. Stable traits are necessary in order to have consistency in crop quality across years and growing locations.Item Strategies for Improving Wheat and Soybean Production Systems in North Dakota(North Dakota State University, 2021) Schmitz, Peder E. KennethPlanting date (PD), seeding rate (SR), genotype, and row spacing (RS) influence hard red spring wheat (HRSW, Triticum aestivum L. emend. Thell.) and soybean [Glycine max (L.) Merr.] yield. Evaluating HRSW economic optimum seeding rates (EOSR) is needed as modern hybrids may improve performance and have different SR requirements than cultivars. Two cultivars and five hybrids were evaluated in five North Dakota environments at two PDs and five SRs ranging from 2.22-5.19 million live seeds ha-1 in 2019-2020. Planting date, SR, and genotypes have unique yield responses across environments. Hybrid yield was the most associated with kernels spike-1 (r=0.17 to 0.43). The best hybrid yielded greater than cultivars in three environments. The EOSR ranged from 4.08-4.15 and 3.67-3.85 million seeds ha-1 for cultivars and hybrids, respectively. Hybrids are economical if seed prices are within $0.18 kg-1 of cultivars. In soybean, individual and synergistic effects of PD, SR, genotype relative maturity (RM), and RS on seed yield and agronomic characteristics, and how well canopy measurements can predict seed yield in North Dakota were investigated. Early and late PD, early and late RM, and two SRs (457 000 and 408 000 seed ha-1) were evaluated in 14 environments and two RS (30.5 and 61 cm) were included in four environments in 2019-2020. Individual factors resulted in 245 and 189 kg ha-1 more yield for early PD and late RM, respectively. The improved treatment of early PD, late RM, and high SR factors had 16% yield and $140 ha-1 more partial profit greater than the control. When including RS, 30.5 cm RS had 7% more yield than 61 cm RS. Adding 30.5 cm RS to the improved treatment in four environments resulted in 26% yield and $291 ha-1 more partial net profit compared to the control. A normalized difference vegetative index (NDVI) at R5 was the single best yield predictor, and stepwise regression using canopy measurements explained 69% of yield variation. North Dakota farmers are recommended to combine early PDs, late RM cultivars, 457 000 seed ha-1 SR, and 30.5 cm RS to improve soybean yield and profit compared to current management trends.Item Characterization of Genetic Resistance to Sclerotinia sclerotiorum and Epidemiology of the Disease in Brassica napus L.(North Dakota State University, 2020) Shahoveisi, FereshtehThis dissertation contains three research chapters conducted on Sclerotinia stem rot (SSR) of canola (Brassica napus L.). This disease is caused by the fungus Sclerotinia sclerotiorum and is considered endemic in canola-producing areas of North Dakota. The first research chapter presents results of a study that evaluated the role of eight phenotyping scoring systems and nine variant calling and filtering methods in detection of QTL associated with response to SSR. The study, conducted on two doubled-haploid mapping populations, showed that using multiple phenotypic data sets derived from lesion length and plant mortality and imputing missing genotypic data increased the number of QTL detected without negatively affecting the effect (R2) of QTL. Nineteen QTL were detected on chromosomes A02, A07, A09, C01, and C03 in this study. The second research chapter presents results of a work that assessed the role of temperature regimes and wetness duration on S. sclerotiorum ascospore germination and ascosporic infection efficiency. This study showed that optimum ascospore germination occurred at 21 °C while it significantly decreased at 10 and 30 °C. Infection efficacy experiments indicated that extreme temperatures and interrupting wet periods were detrimental for the disease development. A logistic regression model with 75% accuracy was developed for the disease perdition. The third research chapter presents results of a study that evaluated the role of temperature on mycelial growth of 19 S. sclerotiorum isolates collected from different geographical regions and on SSR development on plant introduction (PI) lines with different levels of resistance. Mycelial growth and disease development peaked at 25 °C. While lesion expansion on resistant cultivars and the susceptible check was negatively affected at 30 °C, the disease developed significantly on the PI with a high level of susceptibility. Results of these studies provide insights into integrated management strategies of SSR.Item The Molecular Basis of Demethylation Inhibitor Fungicide Resistance in Cercospora beticola and the Role of Seed Inoculum in Cercospora Leaf Spot Disease of Sugar Beet(North Dakota State University, 2020) Spanner, Rebecca EllenCercospora leaf spot (CLS) is the most destructive foliar disease of sugar beet worldwide. CLS is caused by the filamentous fungus Cercospora beticola. Disease management currently relies upon timely application of fungicides, but reliance on certain chemical classes has led to the development of resistance in multiple C. beticola populations. One such class is the demethylation inhibitor (DMI) fungicides of which the genetic basis of resistance has been unclear. Therefore, the first objective of this PhD research was to perform a genome-wide association study on 190 C. beticola isolates to identify mutations associated with tetraconazole (a common DMI) fungicide resistance. Whole genome resequencing identified multiple novel loci associated with sensitivity to tetraconazole including a pleiotropic drug resistance ATP-binding cassette transporter, a regulator of G-protein signaling domain (RGD) protein, a DYRK protein kinase and mutations within and upstream of the gene encoding the DMI target Cytochrome P450 51 (CYP51). This demonstrated the genetic complexity in resistance to DMIs and suggested the involvement of cellular signaling and multidrug resistance as well as target site mutations. The second objective of this research was to investigate the potential of seedborne C. beticola to initiate CLS disease in sugar beet. We showed that viable C. beticola was present in commercial sugar beet seed lots and could function as primary inoculum to cause CLS symptoms in seedlings. All strains identified were resistance to QoI fungicide chemistries and most were also resistant to DMI fungicides. Detection of C. beticola DNA in xylem sap suggested that the fungus may be systemically colonizing the plant via the vascular system. Long-read nanopore sequencing detected other potential pathogenic fungi in seed DNA (e.g. Fusarium and Alternaria spp.) that may also act as primary inoculum sources for important sugar beet diseases. This PhD research has improved our understanding of the development of DMI fungicide resistance in C. beticola, as well as highlighted the importance of seed inoculum in the manifestation of CLS in sugar beet, both of which could improve CLS disease management in the future.Item Altering Grapevine Crop-load and Canopy Architecture Through Cultural and Genetic Methods(North Dakota State University, 2020) Svyantek, Andrej WilliamNorth Dakota's extremely short growing season leads to premature harvest of unripe, high acid grapes with atypical fruit chemistry. To combat the short growing season, grape growers utilize labor intensive grapevine canopy management practices to expose grape clusters to sunshine for enhanced ripening potential. This research examined leaf removal and shoot-thinning, two widely utilized canopy management practices, for their effect on fruit chemistry of two regionally important, cold-hardy grapevines, ‘Frontenac’ and ‘Marquette’. These management techniques were effective at altering fruit chemistry as measured by sugar; however, they are costly to employ commercially due to yield reduction and labor requirements. Furthermore, they rarely impacted the targeted fruit component, acidity of grape must. Ultimately, we sought to mitigate labor expenses associated with on-farm canopy management practices by breeding cold-hardy grapevines with reduced single leaf area. To accomplish this goal, we utilized a novel mutant grapevine with highly dissected, technically compound leaves, ‘Chasselas Cioutat’. After crossing ‘Chasselas Cioutat’ with native, North Dakota isolated, wild riverbank grapes (V. riparia) and two interspecific breeding parents (‘Frontenac gris’ and ‘E.S. 5-8-17’), we observed developmental transitions within leaf shape of young seedling grapevines. Newly emerged leaves became progressively more lobed between main veins as seedlings exited juvenility. However, the targeted compound leaf form was not observed in outcrossed progeny, with one rare exception. For these reasons, grapevines were maintained under greenhouse conditions and advanced to the next generation. Within the first generation of inbreeding, segregation was observed for the distinct compound leaf trait. On-going work to isolate quantitative trait loci is merging genetic maps from multiple sequencing technologies with image analysis to create the first high-resolution understanding of genetic control of compound leaf shape in grapevines. Overall, these efforts have provided the foundation for future breeding aimed at incorporating functional leaf shapes (compound leaf morphology) in the vineyard. Future work in North Dakota grapevine management may need to focus on techniques that promote winter survival and early ripening. Future breeding efforts should continue to focus on the use of novel germplasm material to overcome biotic stresses, improve fruit quality, and increase environmental resistance.Item Functional Bioactive Compounds from Sweet Potatoes for Human Health Benefits(North Dakota State University, 2020) Chintha, PradeepikaGlobal food and nutritional insecurities, public health challenges of diet-linked non-communicable chronic diseases (NCDs), and rapid climate change-linked agricultural production challenges are interconnected and require urgent attention. Therefore, to address these complex and interconnected challenges, it is essential to advance robust and resilient strategies based on sustainable agricultural production practices, wider integration of nutritionally-balanced plant-based foods in the diet, improvement of human health-targeted nutritional qualities, post-harvest preservation qualities and food processing optimization. Therefore, food plants that are climate resilient and rich source of human health protective nutritional bioactives, such as sweet potato are ideal dietary targets for advancing global food and nutritional security solutions, while also addressing emerging NCD-linked health challenges. Sweet potatoes are rich source of stress protective phenolic bioactives with dual functional benefits relevant for resilience to climate change and countering diet-linked NCD challenges. However, the phenolic bioactive compounds and associated health protective functionalities of sweet potatoes vary widely between different flesh color and cultivars, due to different pre-harvest production practices, post-harvest storage conditions, and with different food processing strategies. Therefore, the aim of this dissertation was to screen sweet potato cultivars of different flesh color (off-white, orange, purple) and optimizing different food processing strategies based on optimum phenolic bioactive-linked antioxidant, anti-diabetic and anti-hypertensive properties using metabolically-targeted in vitro assay models. Overall, high soluble phenolic-linked antioxidant activity was observed in purple-fleshed cultivar, while high type 2 diabetes relevant anti-hyperglycemic and anti-hypertensive properties were observed in orange and white-fleshed sweet potatoes. Additionally, improvement in stability and retention of phenolic bioactives and associated functionalities were present in bio-transformed sweet potatoes after fermentation with beneficial lactic acid bacteria (LAB). Furthermore, food processing (deep-frying, baking, steaming, and boiling) optimization studies revealed optimum food processing conditions (cooking temperature, cooking time, and sweet potato sample size) based on higher retention of phenolics and associated antioxidant and anti-hyperglycemic functionalities. We also advanced metabolically-driven elicitation strategy based on the conceptual foundation of dual functional benefits of phenolic compounds to improve wound-healing in bruised potato tubers through stimulation of redox-linked pathway (pentose phosphate pathway) regulation associated with stress-protective phenolic biosynthesis and antioxidant enzyme responses.Item Structure Modification to Enhance Pulse Protein Functions and Flavor Profile Opportunities in Saccharide Mediated Glycation via Maillard-Driven Chemistry(North Dakota State University, 2020) Zha, FengchaoOwing to the combined characteristics of low allergens and lipids, as well as high versatility and abundance, eco-friendly pulse-based protein has served as a critical contender to supplement animal protein. The inferior solubility and off-flavor, however, place a practical restriction on its application. Glycation via Maillard-driven reaction is a potential green chemistry to modulate protein structure and functions. The various types of protein, saccharides with different molecular mass and structural characteristics, and two reaction systems (dry and wet heating) were applied to synthesize protein-saccharides conjugates. The aims were to investigate (i) the effect of glycation on functionalities and flavor of pulse-based protein using above-mentioned elements, and (ii) mechanisms by which glycation affects the protein architectures and modulates its functionalities. SDS-PAGE, SEM and FTIR-ATR were applied to confirm the successful development of protein-saccharide conjugates. The extent of glycation was time-dependent, and 11S and 7S globulin were mainly responsible for conjugation with gum Arabic (GA) under dry heating conditions (60°C, 79% relative humidity, pH 7.0). Glycation significantly improved protein solubility at neutral pH, whereas such effect varied depending on the protein source and reaction time. The stability of emulsion against environment stress and lipid oxidation gained a significant improvement, which was attributed to electrostatic interactions and stronger steric hindrance of protein-GA conjugates. HS-SPME-GC-MS analysis indicated glycation is a promising approach to mitigate the beany flavor, presumably because of the alterations in protein structure resulting in release of unpleasant odorants. The solubility of pea protein was sufficiently improved after glycation, while its thermal stability was remarkably lowered under wet heating conditions (80°C, pH 10.0). The proposed principle involved glycation via Maillard-driven chemistry enhanced the surface hydrophilicity of protein and unfolded its spatial architectures.Item Black Bean Milling and Flour Functionality(North Dakota State University, 2020) Fernando, Hettige Supun SandaruDry bean utilization by the food industry can be increased by developing value-added processing applications. The goals of this research were to evaluate (1) the effect of milling method on the physical, chemical and functional properties of whole black bean flour and its fractions and (2) the effect of removing soluble phenolic compounds on the functional and rheological properties of black bean protein isolates. Black bean was milled with five laboratory mills [cyclone mill, hammer mill, stone mill (fine, medium, coarse), disc mill (fine, coarse), and centrifugal mill (10,000 or 12,000 rpm and 250, 500, 1000 μm aperture screen)] and the resulting flours were evaluated for their physical, chemical and flow properties of bulk samples and particle size fractions. Whole black bean flour and cotyledon flour were subjected to phenolic extraction and protein isolation, resulting in protein isolates with and without soluble phenolics. Solubility, wettability, dispersibility, water binding capacity, foam capacity and stability, emulsification capacity, and gelation properties of protein isolates were evaluated. Variation in milling method produced flours with significantly different flour characteristics. Geometric mean size of whole bean flour was negatively correlated with starch damage (r = -0.92), L* (r = -0.94), angle of repose (r = -0.94), and angle of slide (r = -0.80 to -0.90) and positively correlated with moisture (r = 0.72), and loose bulk density (r = 0.72). Milling method and particle size interaction was significant on characteristics of black bean flour fractions. Particle circularity of flour fractions had a negative correlation of r = -0.93, r = -0.81, r ≈ -0.95, and r = -0.94 with L*, angle of repose, angle of slide and compact density, respectively. Particle circularity had a positive correlation of r = 0.93 and r = 0.89 with average minimum particle size and loose bulk density, respectively. The removal of soluble phenolic compounds improved the brightness, solubility, wettability, dispersibility, foaming capacity, foaming stability, emulsion capacity, emulsion stability and gelling properties of protein isolates. These findings will help food manufacturers to process black bean ingredients using different mill settings to achieve different functionalities depending on the consumer requirements.Item Developing a New SNP Chip for Genomic Selection in the North Dakota State University Barley-Breeding Program(North Dakota State University, 2020) Dompenciel, Jose Antonio RiveraThe use of Genomic Selection has become popular due to its wide success in private and public breeding programs. The current dissertation aims to derive information that will be used to produce a single nucleotide polymorphisms (SNP) chip that can be used to successfully predict traits of economic importance for the North Dakota State University (NDSU) barley breeding program. Three training populations were tested to determine which should be used for predictive modeling. Multiple predictive models were employed to verify the most effective method for each individual trait. Through this research, four major findings were concluded: the successful identification of (i) the traits that are candidates for prediction, (ii) the most successful models for each trait, (iii) the minimum number of markers required to predict a trait, and (iv) the markers that should be included on NDSU barley breeding program’s new SNP chip for genomic selection.