Plant Science & Landscape Architecture Theses and Dissertations
Permanent URI for this collectionhttp://hdl.handle.net/1903/2797
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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 TO WHAT EXTENT DO MODE OF REPRODUCTION, LEVELS OF GENOTYPIC DIVERSITY, AND CONNECTIVITY IN Vallisneria americana MICHX. CONFER RESILIENCE TO A CHANGING CLIMATE?(2023) Perkins, Carrie; Neel, Maile C.; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The macrophyte Vallisneria americana Michx. (Hydrocharitaceae) is a foundational submersed aquatic vegetation (SAV) species that provides valuable ecosystem services, such as nutrition for waterfowl and shelter for fish. When healthy, V. americana can absorb excess nutrients from the water and stabilize sediments, but many of its meadows, which span freshwater to oligohaline environments in eastern North America, have been declining since European settlers cleared the land. Declines only intensified in the 1950s due to chronic environmental stressors and major storm events. To determine the extent to which remaining populations can adapt through natural selection or acclimate to novel environmental conditions, I combined observational field data, greenhouse experiments, and spatial modeling to quantify V. americana reproduction at local to regional scales, evaluate evidence of local adaptation and acclimation to environmental stress, and assess the extent to which high levels of connectivity in a V. americana-dominated landscape can absorb environmental stress.I quantified reproduction at 15 sites in the Chesapeake Bay and 14 sites in the Hudson River, with sites in each geographic region spanning the portion of the salinity gradient in which V. americana grows (0-12 ppt). Numbers of inflorescences, sex ratios, and distances among male and female inflorescences varied greatly across latitude and along salinity gradients. Hudson V. americana had fewer inflorescences across two sampling seasons than Chesapeake Bay V. americana but delayed phenology, skewed sex ratios, and large distances among males and females relative to the Chesapeake Bay were more pronounced in 2018. In 2018, warmer spring and summer water temperatures in the Chesapeake coincided with our findings of higher flowering, fruiting, and potential for pollination at the three Chesapeake sites that served as means of comparison to the Hudson. By contrast, in 2020 Hudson plants were larger and produced more inflorescences in July than Chesapeake plants produced in June, indicating that the regional difference in phenology may be smaller than our hypothesis of approximately 23 days, although it is difficult to estimate how much smaller. We attribute this result to sites in the Hudson – mainly those in the tidal-fresh zone of the river – being highly responsive to unusually warm 2020 spring water temperatures. But not all sites experienced this warmth. The tidal-saline zone of the Hudson and the non-tidal zone of the Chesapeake had the fewest flowers and fruits of either region, likely due to the synergistic effects of cold temperatures and high salinity and turbidity in the former and fast currents in the latter inhibiting growth and reproduction. Through greenhouse experiments evaluating growth and reproduction of Chesapeake and Hudson V. americana grown in different salinity conditions, we found evidence of one-way local adaptation in plants sourced from brackish waters of both the Chesapeake and Hudson. In the first experiment (parental-generation), brackish-source plants demonstrated phenotypic buffering, a stress-induced version of phenotypic plasticity. When exposed to three salinity treatments (0 ppt, 6 ppt, and 12 ppt) applied after plants had sprouted, brackish-source plants buffered the effects of salt stress via increased vegetative growth in the form of many ramets and turions at the cost of small stature. By contrast, plants sourced from fresh waters of both regions grew tall in fresh water, but photosynthetic leaf material declined from the time of salt application (June) to the end of the experiment (September). The most severe salinity treatment, 18 ppt, was lethal to most individuals regardless of source habitat. Unfortunately, neither phenotypic buffering nor phenotypic plasticity sensu stricto was carried over via transgenerational plasticity (TGP), when turions were exposed to 12 ppt immediately upon planting (offspring generation). This early-development salt exposure proved lethal for some individuals and sublethal (had a negative effect on growth but did not result in mortality) for others, with turions either failing to sprout or growing a single shoot that was minuscule in stature. Parental-generation salt exposure only exacerbated these offspring effects, producing a non-adaptive TGP effect, resulting in even lower chance of sprouting, higher chance of mortality, and smaller stature. Evidence of local adaptation and acclimation to salinity only when exposure begins later in development suggests that populations have potential for resilience to saltwater intrusion (movement of saline water into fresh water) only if salinities do not remain elevated during the time of early plant development (spring/early summer) and across multiple seasons. In the event of prolonged salinity stress, much habitat (~10,000 hectares) that is currently mesohaline (5-12 ppt) but within the range of tolerance for V. americana will become unsuitable. In our spatial model of SAV persistence in the V. americana-dominated Upper Chesapeake Bay, high connectivity and high probability of SAV presence were found not only in the freshwater head of the Bay, but also in mesohaline (5-12 ppt) and oligohaline (0.5-5 ppt) waters near Middle River. Persistence of predominantly freshwater aquatic macrophytes in Middle River suggests that either 1) plants are locally adapted to brackish waters or 2) existing connectivity buffers the stress of low-quality habitat. Excess nitrogen, an anthropogenic environmental stressor that remains at high levels in Baltimore Harbor and other tributaries, was correlated with a decreased probability of SAV presence in the southern portion of our study area. As expected, low nitrogen, low salinity, and high landscape connectivity at the head of the Bay coincided with the highest predicted probabilities of SAV presence, particularly in the core of the one of the largest SAV beds in the entire Chesapeake Bay, the Susquehanna Flats.Item The MEIOTIC PROPHASE AMINOPEPTIDASE 1 regulates polyploidy in Arabidopsis thaliana(2017) Wattarantenne, Kasuni Vishwaprabha; Peer, Wendy A; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Growth and development in plants is dependent on cellular functions such as cell cycle progression. M1 aminopeptidases have been shown to regulate mitosis and meiosis in animals. MEIOTIC PROPHASE AMINOPEPTIDASE M1 (MPA1) in Arabidopsis thaliana was previously shown to regulate cell cycle progression during prophase I in meiosis I in both female and male gametophytes and be essential for homologous recombination. mpa1 homozygous embryos are lethal due to chromosome de-synapsis resulting in uneven distribution of chromosomes in daughter cells and massive decrease in homologous crossovers reduces independent assortment. Here, I show that MPA1 is a soluble protein and is expressed throughout the seedling: in the primary root, hypocotyl, cotyledons, petioles and root and shoot apical meristem. I isolated and characterized four mpa1 alleles, and I showed that MPA1 loss-of-function mutants exhibited three significant phenotypes corresponding to development in seedlings and adult plants in Arabidopsis: non-disjunction in mitotic cells, altered polyploidy, and temporary arrest of primary root growth during seedling establishment.Item Genetic Control of Flowering Time in a Soft Red Winter Wheat Doubled Haploid Population(2015) Miller, Daniela Michelle; Costa, Jose M; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Flowering time in wheat is regulated mainly by response to seasonal environmental cues and controlled by the photoperiod and vernalization pathways. Allelic diversity in genes controlling these pathways is used by breeders to adapt wheat for optimal yield in a broad range of environments. This study characterized genetic loci influencing heading date in a soft red winter wheat doubled haploid population. Two photoperiod insensitivity alleles, Ppd-A1a and Ppd-D1a, were found to have major effects in eight field locations. The Ppd-A1 locus explained up to 16.8% of variation in heading date, whereas the Ppd-D1 locus explained up to 39.7%. In reduced vernalization greenhouse experiments, a QTL in the same region as the VRN-A1 gene explained up to 42.4% of variation in heading date, suggesting that the population differed in this region. Assays for previously-described allelic diversity in the VRN-A1 gene, however, did not detect any polymorphism between parents of the population.Item Epidemiology and population structure of Xylella fastidiosa, the causal agent of bacterial leaf scorch, among urban trees in the District of Columbia(2014) Harris, Jordan Lee; Balci, Yilmaz; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)A survey of urban trees affected by bacterial leaf scorch caused by Xylella fastidiosa was conducted in the District of Columbia during 2012 and 2013. Disease occurred most frequently with Quercus palustris, Q. rubra, Ulmus americana, and Platanus occidentalis. Eight other symptomatic and five asymptomatic tree species were found infected. The bacterium was also detected on asymptomatic portion of seven tree species. The occurrence of crown dieback was found significantly associated with X. fastidiosa-infection on Q. palustris, Q. rubra, U. americana, and P. occidentalis. A multi-locus sequence typing analysis using 10 housekeeping loci for X. fastidiosa revealed five clonal strains among the urban trees. These strains were host specific, with only one clone being associated with members of the red oak family, American elm, American sycamore, and two clones being associated with mulberry. Long-term management strategies aimed at mitigating the occurrence of bacterial leaf scorch disease are discussed.