Plant Science & Landscape Architecture Theses and Dissertations
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Item GENOMICS ENABLED GENE DISCOVERY IN DIPLOID AND POLYPLOID WHEAT(2024) Yadav, Inderjit Singh; Tiwari, Vijay; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Hexaploid bread wheat (Triticum aestivum) is one of the most important staple food crops for humans. Sustainable genetic improvement in wheat is critical for ensuring global food security and requires the introduction of new genes and alleles into elite wheat cultivars. The progenitor species and wild wheat relatives are a reservoir of genetic diversity for wheat improvement. This doctoral thesis demonstrates the application of genomic resources and bioinformatics pipelines to characterize the wild germplasm and to streamline the gene discovery pipeline using five diverse species involving wheat progenitor, wild, and related species. Genomics-assisted characterization of the genetic diversity present in gene banks is a major step towards the systematic utilization of unexploited germplasm to ensure the sustainable development of new varieties. Toward this end, we used genomics datasets to curate wild and related accessions of tetraploid wheat from two distinct species Triticum turgidum and Triticum timopheevii. Using Genotyping by sequencing (GBS) data and a unique similarity matrix and powercore analysis, a set of 102 accessions were identified as the core set accessions that represent 20 and 35 percent of the total accessions of the WGRC tetraploid wheat collection of T. turgidum and T. timopheevii, respectively. Further, three distinct centers of rich genetic diversity were identified for wild and domesticated emmer and T. timopheevii in the Fertile Crescent. GWAS analysis of the genotypic and phenotypic dataset identified a novel QTL for leaf rust resistance on chromosome 2B in T. timopheevii. Triticale is a man-made cereal derived from a cross between tetraploid and hexaploid wheat with diploid rye. There are large numbers of triticale germplasm available in different gene banks; however, in many cases, the ploidy information is not accurate and affects the quality of work with large triticale germplasm. In this work, using the low-cost GBS datasets, a pipeline was developed to detect contamination in the UMD triticale collection and facilitated the accurate classification of ploidy, ensuring the purity of the triticale germplasm. This approach identified contamination of 11 wheat accessions and enabled the correct classification of 236 hexaploid and 12 octoploid triticale, these results were further confirmed through GISH experiments. Wild and related germplasms are considered as the goldmine of genetic diversity for wheat improvement. The modern wheat cultivars have gone through several rounds of heavy selections for yield related traits and have lost the genetic diversity against several abiotic and biotic stresses. On the other hand, wild relatives of wheat have been growing naturally without any substantial artificial selection pressure and it allowed them to preserve their genetic diversity. This study investigates the genetic diversity of a selected set of genes to visualize the differences in wild wheat relatives and polyploid wheat cultivars. To study these differences, group 5 chromosome of Aegilops geniculata and Aegilops umbellulata, belonging to the tertiary gene pool, were assembled. Comparative analysis revealed a higher rate of pseudogenization in bread wheat compared to these two wild relatives, primarily due to the difference in exon/intron length between the genes, rendering these genes non-functional. Diploid einkorn wheat (Triticum monococcum), with inherent disease resistance, offers a valuable resource for wheat improvement. To facilitate its proper utilization, two of the reference genomes-one wild (T. monococcum ssp. aegilopoides) and one domesticated (T. monococcum ssp. monococcum) were assembled in the study. Kmer-GWAS identified seven novel QTLs associated with powdery mildew resistance, three for leaf rust resistance, and two for stem rust resistance. These QTLs harbor diverse gene classes encoding for resistance gene analogs, cysteine-rich receptor kinases, transcription factors, and G-type lectins. Overall, the knowledge and resources developed in this research would contribute to the characterization of vast germplasm and the development of climate-resilient wheat.Item DESIGNING AN ACCESSIBLE AGRICULTURAL GARDEN: CONNECTING SOLIDARITY & AGROECOLOGY(2024) Boyle, Patrick Robert; Ruggeri, Deni; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)This thesis explores the potential of agroecology as a transformative framework for guiding the transition of Bergamo's agricultural landscape toward sustainability, resilience, and community well-being. Grounded in the evolution of agroecology from farm-scale design to regional planning, the research investigates how this approach can integrate ecological methodologies and participatory action research in design to implement sustainable farming practices, rehabilitate landscapes, and cultivate solidarity-driven producer-consumer relationships. By emphasizing the interconnectedness of ecology, economy, and society, the study addresses whether agroecology can shape a district into a resilient landscape that enhances people's lives and promotes health and well-being.Through an interdisciplinary lens, the thesis also delves into the broader concept of landscape, highlighting its role in social well-being and advocating for the protection and responsible management of landscapes as a fundamental human right. It explores the principles of landscape democracy and solidarity, aiming to empower communities to reconnect with their environments and promote ecological restoration through collective action and ethical practices. Ultimately, the research strives to contribute to the discourse on agroecology and landscape planning, offering proposals and strategies for actionable change in regenerative and organic agricultural systems that prioritize the needs and values of local communities.Item INTEGRATING FORWARD AND REVERSE GENETIC TOOLS FOR FAST FORWARDING WHEAT IMPROVEMENT(2024) Schoen, Adam William; Tiwari, Vijay K; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Bread wheat (Triticum aestivum) provides roughly 20% of the human daily caloric intake and is an important crop for global food security. Changing climatic conditions as well as biotic and abiotic stresses are threatening wheat production worldwide. Sustainable and continuous improvement of wheat using novel genes and alleles is critical to tackle wheat’s imminent challenges. Recent advances in wheat genomics have allowed researchers now to fast-track gene discovery pipelines by implementing strategies first developed in less complex model species. This thesis explores the use of forward and reverse genetic approaches to efficiently discover, map, and validate genes controlling important agronomic traits in bread wheat as well as describes a robust protocol to reduce the generation time in winter wheat. Speed breeding is an important tool that utilizes an increased photoperiod and growing temperature to increase vegetative growth and reduce the time from sowing to harvest. Chapter 1 of this thesis outlines a reproducible method to significantly reduce the generation time in winter wheat from over 120 days based on what has been previously reported to 93 days regardless of vernalization requirements or photoperiod sensitivity and provide a useful tool to increase the pace of the genetic gains in the winter wheat breeding programs. Tillering in wheat directly influences the major yield-related trait, spikes per unit area. Using the forward genetics approach, chapter 2 of thesis reports the identification of a novel tiller inhibition gene (tin6) to a small physical region of 2.1 Mb region on chromosome 2DS. This was the first example of using a genome coming from the pan-genome of wheat to perform MutMap. Using reverse genetics also has the potential to improve the end-use properties of wheat by knocking out genes which result in an increase of the nutritional value of the flour. Chapter 3 of this thesis, TILLING was used to identify knockouts in all three homeologous copies of the starch synthase gene SSIIa, which has been shown to increase the amount resistant starch in the endosperm of wheat which is known to have health benefits in humans. The grains coming from triple knockouts of SSIIa contained 118% higher resistant starch, and though they showed a decrease in thousand kernel weight, they did not have a shriveled phenotype which had been seen in other ssiia mutants. Chapter 4 of the thesis demonstrate reference genome enabled positional cloning of a tiller inhibition gene (tin3) in diploid wheat species Triticum monococcum. A MutMap population generated from a cross between tin3 and wildtype T. monococcum resulted in the identification of a single candidate gene, encoding a BLADE-ON-PETIOLE-Like protein, containing a splice-variant mutation. To show the power of using a diploid species for translational research in hexaploid wheat, the reverse genetics approach TILLING (Targeting Induced Local Lesions IN Genomes) was used to identify mutations in all three homeologous copies of tin3 in the Jagger mutant population. The full null mutant for the tin3 locus in wheat showed significantly reduced tillering in comparison to wildtype providing concrete evidence that genetic discoveries that are found in diploid wheat can be effectively translated to hexaploid wheat. There are some genes and QTLs have been identified that increase spike length, spikelets per spike, and grain size, very few studies have focused on increasing the number of grains per floret. Chapter 5 of the thesis was focused on positional cloning of the Mov-1 locus which is the underlying gene responsible for the multiovary (MOV) phenotype. The Mov-1 locus dominantly expresses as three ovaries per wheat floret, each of which develop into a grain. Using high resolution genetic mapping with the MOV-reference genome and gene expression data, we identified a single candidate gene that was localized to a small 144kb region on the Mov-1 physical region. To validate the role of the Mov-1 candidate gene in the MOV phenotype, ethyl methanesulfonate (EMS) and gamma radiation mutagenesis was performed to create deleterious point and deletions mutations, respectively. Using 5 independent TILLING and 5 deletion mutants this study demonstrate that Mov-1 candidate gene is required for the MOV phenotype in wheat. It is an exciting time to work in wheat research as the growing wheat genomic toolbox allows for researchers to efficiently identify and validate genes that have potential to improve wheat performance. The methods and findings in this body of work provide a breadth of knowledge that can be implemented in additional genetic studies in wheat in order to fast-track gene and trait discovery for the benefit of wheat geneticists and breeders alike.Item INVESTIGATING THE RELATIONSHIPS BETWEEN BUILT AND NATURAL WINDOW VIEWS, AND STUDENTS PERCEIVED RESTORATION USING VRITUAL REALITY(2024) Esmaeili, Azadeh; Ellis, Christopher C.E; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)This thesis explores the concept of perceived restorativeness in virtual window views, which have significant contributions to the field of landscape architecture and environmental psychology. It begins with a comprehensive literature review to define perceived restorativeness which lies on Attention Restoration Theory(ART). The main emphasis in literature is on the importance of four restorative factors: fascination, being away, extent, and compatibility. All these four factors contribute to an environment’s restorative quality.This study acknowledges the existing gaps regarding the impact of virtual views both built and natural environments on perceived restoration within design studio , because the studio environments are critical in landscape architecture, architecture, and all the fields related to design. This study wants to fill this gap. In terms of research questions, all the research questions are designed to explore how different virtual window views affect perceived restoration, and whether variation in the natural and built environment affects that restorative quality. In the methodology chapter, the process of collecting data from participants for data analysis is described.45 participants responded to the perceived restorativeness scale (PRS-16), after displaying virtual window views from the School of Architecture Design Studio. All the responses were analyzed by using paired t-test and ANOVA to measure the restorative quality of different window views. Findings from data analysis indicate that not all virtual window views make the same restorative impact on participants. A significant variation was observed within and between categories of built and nature. Although all the nature views have significant restorative quality, the plaza as a virtual built window view perceived restorative benefit as well. This study makes an important contribution to investigating the restorative quality of virtual views in educational settings.Item Co-Creating the Yard: A study in defining dignity in the workplace for landscape labor(2024) McCormick, Katherine; Ruggeri, Deni; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Landscape architecture and landscape labor share a reciprocal relationship; one does not exist without the other. A landscape designer or architect produces a set of plants and a labor crew installs and maintains the work of the landscape designer or architect. This thesis project explores the definition of dignity as it pertains to landscape labor through participatory research methods: interviews, photovoice, vignettes, and co-design. The crew members of one landscape design/build and maintenance firm participated in the research. The research gathered informed the re-design of the Yard: the workspace where the landscape crew members report to work each morning and afternoon.Item INTEGRATED EDIBLE LANDSCAPES: CELEBRATING MULTICULTURALISM AT BROOKSIDE GARDENS(2024) Dirmeyer, Brandt; Ellis, Christopher; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Cultural diversity is an integral part of twenty-first century societies. The planet is interconnected now more than ever. The effects of climate change are forcing people to leave their homes in search of better living conditions. When people immigrate to a new place, they take with them their experiences, their traditions, and their identities, including their preferred foods, but the raw ingredients that one is accustomed to may be difficult to access. One way in which public spaces can help individuals adapt to their new environment is by making a place feel familiar through integrated edible landscape designs. By growing culturally relevant edible plants in a public space, the feeling of being at home can be cultivated while at the same time increasing the availability of culturally relevant crops to foreign born persons dealing with food insecurity.Item Spreading the Seeds of a Solidarity Landscape: Co-creating a Biophilic Landscape and Training Curriculum in Northern Italy(2024) Christensen, Mary Elizabeth; Ruggeri, Deni; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)A wealth of research explores the link between biophilia, access to nature, health, well-being, and quality of life (Wilson, 1984; Kellert, 1997; Louv, 2008; Kaplan & Kaplan, 1989; Cooper Marcus & Sachs, 2013). Drawing on this body of research, nature-based interventions employed by social work professionals promote positive connections to nature and improve health and well-being for vulnerable populations (Obeng et al., 2023; Overbey et al., 2021). This thesis explores a participatory action research project using the case study of Villaggio Solidale, a charitable co-housing community in Northern Italy. Following the use of participatory methods, including co-creation, listening, observation, and prototyping, researchers are co-designing a Solidarity Landscape and co-creating a training curriculum with community social workers and educators to integrate nature-based interventions, biophilia, and well-being into the larger ecosystem surrounding Villaggio Solidale, ensuring that the landscape will become a central tool to support community solidarity, health, and well-being.Item MAKING APPLES BLUSH: UNDERSTANDING HOW THE COMBINED USE OF REFLECTIVE GROUNDCOVERS AND PLANT GROWTH REGULATORS IMPACT RED SKIN COLORATION AND QUALITY OF ‘HONEYCRISP’ APPLES IN THE MID-ATLANTIC US(2024) Miah, Md Shipon; Farcuh, Macarena; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Apples are among the most valuable fruits globally, with 'Honeycrisp' ranking as the top sales-producing cultivar in the US. However, challenges such as insufficient red skin coloration and increased preharvest fruit drop significantly diminish their market value. Reflective groundcovers have been reported to enhance apple skin coloration, while the application of the plant growth regulator AVG reduces fruit drop but may negatively impact skin coloration. Research on the impacts of these practices in mid-Atlantic US-grown apples remains limited. In this two years study, our aims were 1) to evaluate the effect of reflective groundcovers on solar radiation (PPFD, UV) distribution; 2) to assess the combined effect of reflective groundcovers and ethylene inhibitor (AVG) on preharvest fruit drop, ethylene production, red blush percentage, and overall fruit quality; 3) to investigate the combined effect of reflective groundcovers and ethylene inhibitor (AVG) on expression level of key anthocyanin and ethylene biosynthesis related genes; 4) to determine the combined effect of reflective groundcovers and ethylene inhibitors (AVG) in the accumulation of total anthocyanin. Apples underwent four treatment combinations of reflective groundcover (Extenday) and AVG (130 mg L−1). Our findings revealed that Extenday significantly enhanced skin coloration (>75% blush) through increased reflectance of PPFD and UV radiation, along with increased IEC, while also accelerating fruit maturity, i.e., overripening. In fact, Extenday-only treated fruit exhibited the highest upregulation of ethylene and anthocyanin biosynthetic-related genes, as well as total anthocyanins. Conversely, AVG notably reduced fruit drop and decreased IEC, delaying fruit maturity while significantly diminishing red coloration (30–48% blush). AVG treated fruit significantly suppressed the expression of key ethylene and anthocyanin biosynthetic structural and regulatory genes, as well as total anthocyanins. The combined application of Extenday and AVG synergistically decreased fruit drop while enhancing skin coloration (>50% blush), but without inducing overripening. This combination fine-tuned the transcript accumulation of ethylene and anthocyanin biosynthetic-related genes, as well as total anthocyanins, enabling 'Honeycrisp' fruit to exceed 50% blush, while moderately increasing IEC (compared to Extenday-only and control fruit), thus enhancing fruit economic value. Therefore, combining Extenday and AVG can boost the market value for 'Honeycrisp' apples in the mid-Atlantic US.Item Refining the understanding of the crosstalk between auxin and indolic defense compound metabolism in Arabidopsis thaliana to improve transferability of the model system to major crops(2024) House, Lillyanna; Peer, Wendy A; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The main natural auxin, indole-3-acetic acid (IAA), modulates a diversity of plant growth and developmental responses through the tight regulation of auxin biosynthesis and inactivation, transport, and signaling. Evidence that analogous auxin metabolic pathways contributing to programmed and plastic development exist amongst different plant species, points to the necessity for refinement of the current understanding of auxin metabolism in Arabidopsis thaliana to improve its transferability as a model system to major crops. Evaluation of the current understanding of auxin biology in plants and analytical tools available for the visualization and quantification of auxin reveal several gaps of knowledge. This work seeks to address this by 1.) elucidating the specific roles of DIOXYGENASE FOR AUXIN OXIDATION 1 and 2 (DAO1 and DAO2) in the oxidative catabolism of IAA and IA-conjugates and functionality of oxidized IAA (oxIAA), 2.) clarifying the function of ATP-BINDING CASSETTE subfamily B (ABCB) transporters and the interplay of auxin, brassinolide, and ethylene in apical hook development and 3.) investigating the possibility of an analogous auxin metabolic pathway involving the natural auxin, phenylacetic acid (PAA), in Oryza sativa. Herein, it is shown that DAO2 activity is similar to DAO1 and assists in the regulation of auxin homeostasis under high auxin conditions and DAO1 is both soluble and plasma membrane associated. Additionally, oxIAA functions as a weak “anti-auxin” to modulate processes like apical hook development, where a subset of ABCB transporters is found to function in auxin mobilization downstream of ethylene signaling and brassinolide transport. The detection of PAA was achieved using LC-MS, however further method development is required for accurate quantification of PAA in rice tissue samples. Application of previous and new knowledge pertaining to the crosstalk between auxin and indolic defense metabolism in Arabidopsis revealed a seemingly analogous pathway in rice whereby phenyl acetonitrile (PAN) is converted to PAA, likely via nitrolases. The results presented herein, refine the understanding of auxin metabolism in Arabidopsis and exemplify the use of a model system in elucidating similar pathways in agriculturally significant crops.Item THE ECONOMIC EFFECTS OF STORMWATER BEST MANAGEMENT PRACTICES (BMPS) ON HOUSING SALE PRICES IN WASHINGTON, D.C.(2024) Park, Boyoung; Kweon, Byoung-Suk; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The aim of this dissertation seeks to investigate the economic effects of stormwater best management practices (BMPs) on housing sale prices in Washington, D.C. Stormwater best management practices (BMPs) were designed to address flooding and water quality issues that impact environmental, social, and economic effects. As awareness of the BMPs increased, municipalities and local governments developed regulations to require developers and property owners to implement BMPs. Effective stormwater management was not merely a matter of environmental responsibility but may create significant economic incentives. To study the economic effects of BMPs on housing prices, this study reviewed 32 years of research articles answering following questions: 1) How do BMPs affect housing prices? 2) What kinds of stormwater BMPs have been studied that affect housing prices? This review study used the PRISMA approach to conduct an in-depth systematic review. The search parameters included articles written in English and published between January 1990 and September 2022 using Google Scholar, ProQuest, and EBSCO host search engines. Initially, more than 20,000 studies were identified. Ultimately, 23 Studies were selected for inclusion with specific search terms. The results of this study show that many BMPs (trees, detention basins, retention basins, parks, etc.) use various measurements (e.g., percent coverages, proximity) to estimate the economic impacts on housing prices. Our robust findings address that BMPs have more substantially positive (82.6%) than negative effects (52.2%) on housing prices. Trees and parks had an impact that is more positive on housing prices than detention and retention basins. While studies on the economic value of BMPs were limited, literature found that the capitalization of real estate can be affected by nearby stormwater BMPs using the hedonic pricing method. To extend the economic effects of BMPs on housing sale prices in Washington, D.C., this study addresses research questions: Do stormwater BMPs positively impact housing sale prices? How do proximity and number or structural BMPs affect the housing sale prices? This study used the hedonic pricing method by applying hierarchical regression models to determine whether a set of independent variables significantly improved the models. The primary findings indicate that BMPs have positive, negative, or no effects on housing sale prices. Proximity to BMPs inside of parks increased housing sale prices in all buffers. In contrast, proximity to BMPs outside of parks and impervious roads decreased housing sale prices in all buffers. Percent tree canopy coverage negatively linked to a 50 m buffer and no relationship with other buffers on housing sale prices. This study implies that BMPs impact housing prices and can be improved by landscape architects, policy makers, and stakeholders. To compare the economic effects of BMPs on housing sale prices in high-income and low-income wards in Washington, D.C., this study addresses how environmental, structural, neighborhood and locational variables hierarchically affect housing sale prices in high-income and low-income wards. The robust findings of this study conclude that environmental variables (e.g., proximity of houses to parks with BMPs, house to BMPs inside of parks, and house to BMPs outside of parks, impervious surfaces, and impervious roads) can be attractive factors for purchasing homes, according to model 1 and model 3 in high-income ward. In contrast, there was no evidence of the economic effects of environmental variables on housing sale prices in low-income ward. All structural variables in the high-income ward were statistically significant on housing sale prices. In contrast, limited structural variables in low-income ward were statistically significant on housing sale prices. Several locational and neighborhood variables (e.g., population density, unemployment rate, and poverty rate) in the high-income ward were statistically significant on housing sale prices. These results contribute to property owners considering how environmental, structural and neighborhood and locational variables could be beneficial between high-income and low-income communities. However, such disproportionate economic effects of factors concern remain. The intervention of green gentrification should be considered between local government and disparate community groups by supporting financial incentives for homeownership or having an equity project for existing residents to improve their communities. This could change the neighborhood composition which is associated with the availability of stormwater BMPs as well as the involvement of these efforts from landscape architects, urban planners, stakeholders, and government is essential to accelerate the strategies to fair distribution and effects of stormwater BMPs on housing sale prices.