Browsing by Subject "Soybean"
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Item Evaluating the Utility and Causative Genetics of Soybean Mutants(2016-03) Campbell, BenjaminSoybean (Glycine max (L.) Merr.) is the second most widely planted crop in the United States by acreage, but yet its genetic resources, mapping methodologies, and breeding improvements lag behind those of other major crop species. In the 20th century, soybean researchers gathered a wealth of natural soybean genetic diversity in the forms of soybean’s wild relative G. soja, soybean landraces, soybean elite lines, and spontaneous mutants. Starting in that same century, researchers began inducing soybean mutations through chemical or irradiation mutagenesis to generate new phenotypes. In the 21st century, these mutagenesis efforts have expanded and have been coupled with new genomics tools to enhance soybean functional genomics. These new mutagenesis efforts and genomics tools will be discussed in chapter one. One of the challenges facing soybean is the difficulties in gene mapping, cloning, and validation. A major focus of this dissertation is the adaptation of new genomics tools and mapping methodologies to soybean in order to facilitate the identification of causative mutants in soybean. Chapter two demonstrates a more classical approach to gene mapping and soybean whole plant transformation to identify the causative loci for three spontaneous chlorophyll deficient mutants. In contrast, chapter three utilizes a combination of new genomics approaches to map and clone a fast neutron induced mutant and validates the result using both a second mutant allele from a historic soybean mutant and transformation of an Arabidopsis mutant. Chapter four builds off of the results of chapter three in leveraging the genomic mapping approach to clone a spontaneous canopy architecture mutant. Several unexpected results and conclusions are reported in the following chapters. Chapter two provides evidence to challenge the widely held idea of gene redundancy in soybean provides an effective buffer against mutations. Additionally, to our knowledge, the research of chapter two reports the first instance of identical mutations affecting two different paralogs resulting in nearly identical phenotypes. Chapter three demonstrates that array comparative genomic hybridization technology and whole genome sequencing of mutant and wild-type bulks can be effectively combined to map and clone a fast neutron mutant from a small F2 population. The chapter also provides an example of the high complexity of mutations that can result from fast neutron irradiation. Chapter four describes the mapping and characterizing a short petiole mutant. The research identifies that the short petiole trait (lps1) is due to a three base-pair in frame insertion in an uncharacterized gene. It was found that the mutation decreases petiole length primarily by decreased cell length and that the short petiole trait could be agronomically beneficial through improved harvest index. The results from chapter four suggest that there is the capacity to improve soybean’s productivity and agronomics through modifications to canopy architecture, as has been demonstrated in other major crop species. The fifth and final chapter discusses potential future directions for soybean genomics research. New population designs with improved efficiency are described. Additionally, suggestions are made for how to utilize current technologies to improve next generation population designs.Item Fine-Mapping, Physiological Evaluation, and Candidate Gene Exploration of an Iron Deficiency Chlorosis Tolerance Locus in Soybean(2020-07) Merry, RyanIron Deficiency Chlorosis (IDC) can be a significant yield limiting nutrient stress in soybean. IDC most frequently occurs in high pH soils that are rich in calcium carbonates, as is common in areas of the Midwestern United States. While several agronomic solutions exist to combat IDC, such as the application of iron chelates at planting, the use of tolerant soybean genotypes remains the most effective method of controlling IDC stress. Breeding for IDC tolerance is common, however little about the genetics of IDC is understood, aside from a major tolerance locus located on Gm03. A tolerance locus was previously discovered through bi-parental and association mapping on Gm05 to a 1.5 megabase region, which in this study was found to be important in elite soybean germplasm and warranted further investigation. Fine-mapping was conducted using heterogeneous inbred families, narrowing the interval to 137 kilobases and 17 genes. A controlled environment assay was developed to analyze the effect of nodulation, pH, and calcium carbonates on soybean genotypes and to assess the expression of Glyma.05g001700, a gene candidate in the fine-mapped region. Glyma.05g001700 was further explored using protein modeling, domain classification, gene homology, haplotype diversity, and overexpression in soybean hairy roots to assess gene function. It was concluded that Glyma.05g001700 is likely involved in iron homeostasis through changes in gene expression driven by a putative TATA box present in the tolerant genotype ‘Fiskeby III’.Item Fusarium and Phytophthora Species associated with root rot of soybean (Glycine max)(2011-01) Bienapfl, John ChristopherRoot diseases of soybean cause substantial yield reduction in the United States. Fusarium and Phytophthora represent groups of fungal pathogens commonly associated with root rot of soybean. Little is known regarding their distribution, etiology, and how they may interact in causing root rot on soybean. Additionally, diagnostic tools that allow for rapid and accurate detection of these pathogens are essential for disease management, but need to be developed and validated. Furthermore, fungicidal compounds that potentially affect root infection by these fungal pathogens are being studied to minimize yield losses due to root diseases of soybean and improve crop productivity.Item Genetic Analysis Of Whole-Plant Leaf Area, Leaf Shape, And Leaf Venation Branching In Soybean(2020-04) McCoy, ErikIncreasing soybean production to meet growing demand requires closing the current yield gap, and approaching the yield potential through genetic improvement and optimization of cultivars for specific growth conditions. Leaf traits are important targets for improvement and play key roles in the capture and usage and storage of the resources needed for yield production. Leaf area has been shown to be associated with yield through its effect on transpiration and interception of photosynthetically active radiation (PAR). Leaf shape has similar effects on transpiration through boundary layer effects, and also controls the amount of intercepted PAR by altering the canopy structure and the amount of light that penetrates through the canopy. Leaf venation determines the rate of water flow through the plant, and the geometry of vein topology likely has a significant effect on this rate, and therefore the total water transpired by the plant as a whole. Vein branching angles are thought to play a role in hydraulic conductance, and may also act as a structural constraint to leaf area development. While leaf shape in soybean is known to be controlled by the Ln locus, which in addition pleiotropically affects seed size and number, the genetic basis of whole-plant leaf area and venation topology traits are yet to be discovered. Leaf area, shape, and venation topology are closely linked during leaf development, so an understanding of their genetic basis and relationship to one another is critical to the optimization of leaf type for a target environment. The goals of this study are to identify QTL for whole-plant leaf area, leaf shape, and vein branching angle, as well as to quantify and compare the relationships between these traits. A bi-parental SoyNAM population (IA3023 x LG94-1906) consisting of 136 genotypes was grown twice over two years and measurements were taken for whole-plant leaf area, whole-plant dry mass, specific leaf area, leaflet length, leaflet width, leaflet shape, vein branching angle, and leaflet area. QTL mapping and correlation analyses were performed for all of these leaf traits. Novel QTL were identified for whole-plant leaf area and vein branching angle that co-localized with the Ln locus. QTL identified for leaflet length, leaflet width, and leaflet shape also co-localized with the Ln locus as expected, however a second, novel QTL was identified for leaflet length. These results suggest that the Ln locus may contribute to leaf area and vein branching angle determination in addition to leaf shape and seed size/number. Further investigation into the genetic basis of these traits and their interactions will help in developing cultivars with ideal leaf types. A negative correlation between vein branching angle and whole-plant leaf area was found, supporting the hypothesis that larger branching angles constrain leaf area development. Additional study on this relationship in soybean and other crops may prove this connection spans across species, and can be a useful target in breeding for ideal leaf types.Item Improving Stink Bug Management in The Midwest: Understanding Dispersal Capacity and Developing Sampling Plans(2020-12) Carlesso Aita, RafaelStink bugs are an emerging threat for horticultural and field crops in the North Central Region of the United States. This threat can be attributed to the increase in abundance of Pentatomidae species native to North America over the years, and to the spread of invasive stink bugs throughout this region, in particular, the brown marmorated stink bug, (Halyomorpha halys). There is a lack of decision-making frameworks that provide more efficient sampling for stink bugs in soybean for this region, and there is a need to understand the dispersal capacities of laboratory-reared H. halys. Therefore, my research developed more efficient sampling for herbivorous stink bugs in this region and assessed the dispersal capacity of H. halys under laboratory conditions. First, I developed a binomial or decision-making sequential sampling plan for herbivorous stink bugs by using data from 11 states of the North Central Region. Results showed that using a tally threshold of 3 stink bugs per 25 sweeps for action thresholds corresponding to the current action thresholds of 5 (soybean grown for seeds) and 10 (soybean grown for grain) stink bugs per 25 sweeps, provided the best sampling outcomes in terms of efficiency and accuracy. In addition, we showed that 18 and 12 sample units, for action thresholds of 5 and 10 stink bugs per 25 sweeps respectively, would be needed for reliable decision-making sampling. The development of a binomial sequential sampling plan for stink bugs in soybean should provide increased efficiency with regards to the number of sample units required to reach a management decision. Secondly, I assessed the effects of starvation, age, mating status, and pre-flight weight on flight parameters of laboratory-reared H. halys using flight mills. Although some statistical differences were observed across the experiments, these differences represented minimum ecological significance. These results could reflect the resilience of H. halys as a successive invasive species to North America and could help predict the dispersal potential of this species in Minnesota. The results of my thesis will provide valuable information to fine-tune integrated pest management strategies for stink bugs in the North Central Region, enabling more efficient scouting for growers and consultants as well as better forecasting the dispersal capacity of an important invasive species to the region.Item Interaction of temperature, soil moisture, seed treatment, cultivar, and soybean cyst nematode in root rot of soybean.(2011-04) Meyer, Paul WellsThe root rot complex comprised of Fusarium species, Rhizoctonia solani, Phytophthora sojae, and Pythium species is a major contributor to yield loss in soybean. Due to its wide distribution, Fusarium solani is possibly the most important contributor to losses caused by this complex in Minnesota. Heterodera glycines, commonly known as soybean cyst nematode (SCN), is the most destructive soilborne pathogen of soybean. Yield losses to Fusarium root rot and SCN for 2005 in Minnesota were estimated to be 85,000 tons and 250,000 tons, respectively. The etiology of seed, seedling, and root rots of soybean in Minnesota is poorly understood, and the interactions between the major root infecting pathogens of soybean are even less well understood. Root rot of soybean during germination and emergence is a major cause of stand establishment problems. Seed treatment fungicides have provided inconsistent control of pre-emergence seed, seedling, and root rot during field trials in Minnesota, and cultivars resistant to native isolates of F. solani are not available. Previous studies have investigated the interaction between SCN and Fusarium virguliforme, but not between SCN and F. solani. This is important, since SCN is prevalent in agricultural soils in Minnesota. My objectives were to (1) determine the relationship between soil temperature and moisture in root infection by Fusarium spp., Pythium spp., P. sojae, and Rhizoctonia spp. in natural soil samples taken from soybean fields in Minnesota, (2) determine the frequency of root infection as a function of seed treatment and sampling time after planting in natural soil, and the soil temperature and moisture conditions at which seed treatments are effective (or not effective), (3) determine the predominant native Fusarium species infecting soybean in Minnesota soil as a function of temperature and soil moisture, (4) screen soybean varieties in maturity group 2 and earlier for partial resistance to Fusarium spp. naturally present in soil, and for partial resistance to an isolate of F. solani artificially inoculated in sterile sand, and (5) determine the effect of soybean taproot infection by an isolate of F. solani on secondary root tip infection by SCN, and vice versa.Item Interactions of Fusarium virguliforme with Other Common Soybean Root Pathogens and the Soybean Aphid(2020-08) Geske, AlissaMany diseases reduce soybean (Glycine max) yield every year, with root diseases often having the greatest impacts on yield in the Midwestern U.S. One important root pathogen of soybean is Fusarium virguliforme (Fv), the causal agent of sudden death syndrome (SDS). Even though soybean plants displaying SDS symptoms are commonly attacked by multiple fungal pathogens and insects, it is unknown how interactions between Fv and other attackers may alter SDS disease development and soybean growth. In our first study, we examined potential interactions between Fv and other common soybean root pathogens including F. acuminatum, F. oxysporum, F. solani, and Clonostachys rosea. Interactions were assessed in vitro and in soybean plants to evaluate their effect on SDS disease development and soybean growth. Results from the in vitro studies suggest that the growth of Fv was not affected by any of these fungi, but the growth of F. acuminatum and F. oxysporum isolates was reduced in the presence of Fv. Further results suggest that coinfection of soybean with Fv and C. rosea and Fv and F. solani can reduce SDS foliar disease severity and that coinfection of soybean with Fv and F. oxysporum and Fv and F. acuminatum can increase SDS foliar severity compared to the Fv-only treatment under growth chamber conditions. Coinfections of soybean with Fv and all eight fungal test isolates individually did not increase or decrease levels of root rot or plant biomass compared to infection by Fv alone. In our second study, we examined potential interactions between Fv and the soybean aphid, Aphis glycines, in greenhouse, growth chamber, and field experiments to evaluate their effect on SDS disease development, aphid growth, and soybean growth. Overall, the results suggest that Fv and soybean aphids have minimal to no interaction with one another while co-occurring on soybean when SDS develops to low levels, as was the case in these studies. There was no clear effect of soybean aphid herbivory on SDS foliar or root disease development in these studies nor did we detect a clear effect of combined soybean aphid herbivory and Fv infection on soybean growth. To our knowledge this is the first investigation into potential interactions between Fv and other common root pathogens and Fv and the soybean aphid.Item QTL mapping and GWAS identify sources of iron deficiency chlorosis and canopy Wilt Tolerance in the Fiskeby III X Mandarin (Ottawa) soybean population(2015-01) Butenhoff, Karl JosephAbiotic stresses are a major yield limiting component in soybean production that producers cannot directly control. Therefore, an increase in the understanding of how different abiotic stresses affect soybean, and the identification of sources of tolerance to these stresses will be critical for the continued increase of soybean productivity well into the future. Here I present three separate, but related, studies analyzing iron deficiency chlorosis and drought tolerance in several soybean populations. For the first and second studies, the objectives were to (i) characterize the Fiskeby III X Mandarin (Ottawa) recombinant inbred line (RIL) population for its tolerance to iron deficiency chlorosis (IDC) and drought; (ii) identify quantitative trait loci (QTL) via composite interval mapping for iron deficiency chlorosis and canopy wilt in the RIL population; and (iii) identify co-localization of abiotic stress QTL and putative candidate genes for iron deficiency chlorosis tolerance and delayed canopy wilt. Iron chlorosis and canopy wilt scores were significantly different across the three years tested between the RILs as well as the parents of the population. Fiskeby III consistently scored better than Mandarin (Ottawa) for tolerance to iron chlorosis and canopy wilt in all three years. Two QTL were discovered, one on chromosome five and one on chromosome six, that together accounted for approximately 25 percent of the phenotypic variation for IDC. Two QTL were also identified for canopy wilt, one on chromosome six and one on chromosome 12, that together accounted for approximately 13 percent of the phenotypic variation. The two QTL identified on chromosome six co-localized to the same confidence interval. Several previously identified QTL co-localized with the identified IDC and canopy wilt QTL in this study. In addition, a potential candidate gene was identified on chromosome five that may play a role in the soybean IDC response. The third study was undertaken to potentially validate the QTL identified for IDC in the first study in two independent soybean populations. The objectives of this study were to (i) utilize association mapping to detect markers significantly associated with IDC in two independent populations, (ii) compare significant identified markers with the QTL regions identified in the bi-parental RIL population, and (iii) validate the major QTL identified on chromosome five in the RIL population. Association mapping identified 12 significant markers that accounted for 27.2 percent and 8.9 percent of the phenotypic variation for IDC in the two populations, respectively. These markers co-localized with several known iron related QTL and genes. A significant cluster of 11 markers on chromosome five co-localized with the major IDC QTL identified in the bi-parental Fiskeby III X Mandarin (Ottawa) population. A second potential candidate gene was identified in this QTL region that may be related to IDC in soybean.Item QTL mapping of iron deficiency chlorosis tolerance in soybean using connected populations(2014-03) Jones, Ilene LouiseSoybean iron deficiency chlorosis or IDC is a yield limiting, abiotic stress condition common to calcareous soil types present in the Upper Midwest. Complex interactions among soil chemical and physical properties within these calcareous soils limit the amount of ferrous iron available to soybean plants. The subsequent nutrient deficiency leads to the classic chlorotic phenotype characterized by interveinal yellowing of new growth trifoliates. IDC is responsible for yield losses up to 0.8 Mg ha-1 amounting to an estimated economic loss of $120 million per annum. To mitigate yield losses, growers prefer to plant IDC tolerant cultivars; however, IDC tolerant cultivars have been known to yield less on non-chlorotic soils. In order to improve IDC tolerance without an associated reduction in yield, we evaluated yield and IDC performance using a network of 13 F4-derived recombinant inbred line (RIL) populations connected by common parents. Chlorosis severity was evaluated using two methods: visual chlorosis ratings and remote sensing via normalized difference vegetative index (NDVI) values collected from the GreenSeeker® RT100 System. NDVI values correlated strongly with visual chlorosis ratings with the largest negative Pearson's correlation coefficient of -0.89 (p-value < 0.0001) captured at the V4 growth stage. NDVI values collected at V4 were moderately correlated to yield with a Pearson's correlation coefficient of -0.61 (p-value < 0.0001), indicating that IDC tolerant lines yield less than IDC susceptible lines on non-chlorotic soils. Co-localization of IDC and yield QTL detected on linkage groups A1/5, J/16, and L/19 confirm that the correlations are in part due to genetically linked loci or pleiotropic effects of a single locus.Item The role of deleterious substitutions in crop genomes(2016-10) Kono, ThomasHistorically, it has been postulated that populations carry genetic variants with deleterious effects as segregating variation. Recent advances in DNA resequencing technology allow a new view on this topic, providing a way to identify segregating molecular sequence variants that alter sites that show constrained evolution. Targeted identification and removal of such segregating variants has been proposed as a novel path for improving agronomic performance in plant breeding programs. In this dissertation, I present a brief review of deleterious variation, and why it may be important to plant breeding. Then, I present a tool for classifying single nucleotide polymorphisms into functional classes using public sequence databases. Next, I present a survey of potentially deleterious alleles segregating in two crop species, and a software package that implements a likelihood ratio test for sequence constraint and deleterious prediction. Finally, I present an examination of the contribution of potentially deleterious alleles to yield in a barley breeding experimental population. While potentially deleterious alleles themselves do not explain a larger proportion of phenotypic variation than non- deleterious alleles, genomic prediction of phenotypes may be improved by examining informative subsets of sequence variants, rather than with genomewide markers.Item Toward “free trade” from Kant's cosmopolitan ideal(2012-09) Deng, YiMy dissertation aims to present a coherent Kantian justice in terms of Kant's publicity principle. The theoretical construction arises from inquiries about the case of China's soybean market shift after its accession to the WTO, and holds the practical aims of diagnosing injustices and prescribing individuals', states' and global institutions' responsibilities in rectifying injustices. Specifically, I advocate for publicity as negotiable consent, which could entail active citizenship and moral politicians. By appealing to publicity as negotiable consent, I argue that the Chinese soybean case involves injustice, and provide corresponding expansions of Kant's cosmopolitan right, republicanism, and a federalism of free states as conditions for justice. The puzzling relationship between the WTO and federalism of free states suggests the need to address connections between trade liberalization and cosmopolitan ideal. By appealing to the I-Ching, I present the dynamic balance of Yin and Yang as a model for the interaction between capital and labor in the context of global justice. The interdependent yin-yang indicates that the discrepancy between theoretical predictions from the WTO and empirical evidence in the Chinese soybean case has resulted from the WTO's neglect of mobility differentiations among the factors of production. At the end of my dissertation, an appropriate capital-labor relation prescribed by yin-yang leads to practical suggestions for the WTO. Emphasizing a mixture of bottom-up and top-down restrictions, both "publicity as negotiable consent" and yin-yang energize an account of Kantian justice as a dynamic theory which is continually responding to the uncertain, complicated, but practical issues.Item The Under-Explored Diversity of the Soybean Genome(2015-12) Anderson, JustinGenetic diversity is an important component to ongoing plant breeding. Understanding where it exists and what it comes from can influence the ability to search and detect valuable agronomic traits in the future. In this thesis I explore three avenues surrounding this topic. In the first chapter I explore the current literature and knowledge of structural variation, such as deletions and duplications, documented in the soybean germplasm. In the next chapter I describe detecting these unique genetic variants in a subset of 41 soybean breeding lines and interesting patterns shaping their frequencies. In the third chapter I explore the frequency at which these genetic variants are induced in fast neutron mutagenesis or plant genetic transformation and tissue culture. Finally, in my last chapter I explore the USDA germplasm diversity to analyze patterns of local adaptation and environmental association in Glycine soja, soybean’s crop wild relative.