Browsing by Subject "Plant biological sciences"
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Item Characterization of maize genes that exhibit present-absent expression in different genotypes.(2010-12) Chakravartty, MoumitaMaize inbred lines exhibit high levels of gene expression diversity. Several hundred genes exhibit severe expression variation such that the transcript is detected only in one inbred and absent in another. However, the frequency, types of genes affected and potential causes for these “present-absent” (PA) expression patterns in maize inbred lines are not well characterized. Microarray analyses of gene expression patterns in 11-day old seedlings, ear, embryo, and endosperm tissues from two maize inbred lines, B73 and Mo17, identified 570 genes (out of 17000) with PA expression patterns in at least one tissue type. Over 55% of the PA genes exhibit “constitutively absent expression” in which one of the two genotypes exhibits lack of expression in all tissues tested. The remaining PA genes exhibit “tissue specific absent expression” where a gene exhibits present-absent expression in some tissues and present-present expression in at least one other tissue types studied. Many of the PA genes are maize-specific sequences that do not have orthologues in other plant species and the majority of the remaining PA genes are members of gene families. Using existing eQTL and aCGH datasets, we found that PA expression differences are primarily caused by differential regulation rather than by differences in gene content. Collectively, our analysis documented a high frequency of genes that are expressed in some maize lines but not others and suggests that many of these changes are due to trans-regulatory variation.Item Comparative analyses identify adaptive genetic variation in crops and crop wild relatives(2013-12) Fang, ZhouComparative population genetic analyses provide a means of identifying adaptive genetic variation. In this dissertation, I apply population genetic approaches to identify putatively adaptive variants in the genomes of crops and crop wild relatives. These approaches have the potential to identify genetic variants that are under selection and thus potentially contributing to local adaptation. As a background to the dissertation, I present in Chapter 1 the state of research in this field at the time I started my PhD and give a brief introduction to the projects described in this dissertation. In Chapter 2, I report a ~50-Mb chromosomal inversion in the wild ancestor of maize - teosinte (Zea mays ssp. parviglumis) and characterized its distribution and abundance in natural populations using population genetic approaches. This is also the first study in plants to apply population genetic approaches to identify chromosomal structural variation. In Chapter 3, I used a population genetic approach to identify genomic regions that contain adaptive mutations resistant to Fusarium head blight in a barley experimental breeding population. The successful application of comparative population genetic approaches in this study suggests this approach can also be used to identify genomic regions that are under selection in other breeding populations. In Chapter 4, I studied the geographic differentiation in wild barley (Hordeum vulgare ssp. spontaneum). I found two genomic regions contribute disproportionately to the population structure in wild barley. These same regions, with reduced evidence of recombination, are strongly associated with environmental variables. Population genetic evidence and previous cytological and genetic studies suggest these two genomic regions may be chromosomal structural rearrangements.Item Evaluating the chemical diversity and biological activity of plant extracts for commercialization(2014-11) Martin, Amanda C.Perennial plants are a manageable natural resource with the potential to provide both highly valuable biologically active chemicals and ecosystem services. Ecosystem services include various benefits that are provided by an ecosystem such as food, fuel, recreation, as well as water, air, and land quality for society. Biologically active chemicals from plants have a long history of use by humans in botanical medicines and pharmaceuticals, food and dietary supplements, agricultural inputs, and home and personal care products. There are different strategies that can be used to incorporate plants into an economic and ecosystem service role. Method development and application studies were used to facilitate use of plant derived bioactive compounds for commercial use. Methodological studies, using the technique of metabolic fingerprinting, resulted in the determination of extraction conditions that maximize chemical diversity and yield. Maximum chemical diversity in a plant extract was most efficiently approached if solvent partitioning was performed on an extract made with 70 percent ethanol. Additionally, strategies to integrate extract chemical analysis with information regarding extract quality, such as cytotoxicity measurements, were developed and used to evaluate commercial kava samples obtained from multiple sources. These approaches were then applied to two different perennial plant species (Comptonia peregrina, and (Glycyrrhiza lepidota,) with the aim of developing their commercial value based on their extractable chemical composition. These studies resulted in the isolation of two small molecules from (C. peregrina, with strong antimicrobial activity and the identification of two (G. lepidota, populations with the potential to be developed into a cultivar with optimal characteristics for the cultivation of biologically active compounds.Item Experimental warming: how temperature affects germination and survival of Minnesota tree species.(2012-01) Pinahs, Christopher A.Seed germination and survival were assessed for ten Minnesota tree species and Rhamnus cathartica, a Minnesota invasive, grown under three temperature treatments (ambient, +1.8 °C, +3.6 °C) and two canopy types (open, understory) at two study sites near the ecotonal boundary between southern boreal and northern temperate forest biomes. Initial germinant establishment, overall establishment, and survivorship were analyzed in response to temperature and canopy type. When it had an effect, elevated temperature negatively influenced all three life-history phases, but the effects were more prevalent for overall establishment and survivorship. Abies balsamea, P. glauca, P. banksiana, B. papyrifera, and A. rubrum all showed considerable negative effects to heating, while P. strobus and P. tremuloides showed moderately negative effects. Meanwhile, both Quercus species and R. cathartica appear relatively unaffected by heating. Thus, even moderate climate warming will likely influence the germination and survival of Minnesota boreal and temperate tree species.Item Item Identification and characterization of three Arabidopsis sugar insensitive genes(2008-10) Huang, YadongCarbohydrates have signaling functions in regulating gene expression, metabolic pathways and developmental processes. Eukaryotic organisms have evolved conserved and novel mechanisms for sensing and responding to sugars. Plant sugar response pathways are complex and exhibit cross-talk with other response pathways. Sugar responses and signaling pathways have been studied via physiological, biochemical and genetic approaches. Genetic screens have identified sugar response mutants with altered seedling growth phenotypes. The Gibson lab has isolated an array of sugar insensitive (sis) mutants by screening mutagenized Arabidopsis seeds on high concentrations of sugars. The identification and characterization of three of the SIS genes, SIS7, SIS3 and SIS8, are presented here. SIS7 is allelic to NCED3/STO1, an abscisic acid (ABA) biosynthetic gene, which is involved in drought and salt stress responses. Lateral root (LR) development of sis7 mutants is resistant to the inhibitory effects of osmotica. Transcriptomic analysis revealed that a set of auxin-related genes are expressed at lower levels in sis7 seeds than in wildtype seeds when incubated with glucose, suggesting that these genes may be involved in controlling LR development by both ABA and auxin. SIS3 encodes a RING finger protein that functions as an E3 ligase in in vitro ubiquitination assays. The sis3 seeds display wild-type germination responses to ABA and GA. However, the root growth of sis3 mutants has slightly reduced sensitivity to ABA. The sis8 mutants have decreased sensitivity to high sugars and hyperosmolarity. Positional cloning of sis8 revealed that the mutation is in a putative mitogen-activated protein kinase kinase kinase gene. Seed germination assays indicate that sis8 mutants have wild-type sensitivity to ABA and GA, whereas overexpression of SIS8 causes slight hypersensitive responses. Potential interaction partners of SIS8 have been identified via yeast two-hybrid screening. A T-DNA insertion in the gene encoding one potential SIS8- interacting protein, UGT72E1, causes a sis phenotype. Further studies of the SIS3 and SIS8 genes will provide more insight into the mechanisms of sugar signaling in plants.Item New analytical methodologies in the study of auxin biochemistry(2014-08) Yu, PengAuxin is the essential plant hormone that regulates many aspects of plant growth and development. Plants typically possess highly complex biochemical networks to regulate the homeostasis of the active hormone, through the regulation of biosynthesis, degradation, transport and conjugation. Biosynthesis, among other processes, has been of particular importance and warranted extensive studies over the decades of auxin research. A number of pathways were proposed and some enzymes potentially involved have been characterized. Stable isotope labeling and turnover studies have proven very useful in these investigative efforts. With the advancement of analytical and computational technologies, it is now feasible to concurrently analyze the turnover patterns of all the precursors in the entire auxin biosynthesis network. I devoted chapter two of the dissertation to establish LC-MS methods to concurrently quantify most of the auxin precursors and deployed different isotopic labeling strategies for turnover studies in Arabidopsis thaliana. Preliminary results showed that indole-3-pyruvate (IPyA) and indole-3-acetaldehyde (IAAld) were among the fastest to be labeled and a key regulatory step existed between IPyA and indole-3-acetic acid (IAA). Chapter three reported the discrepancy and the study of the amount of the total IAA determined by alkaline hydrolysis and that of the summation of all known forms of IAA conjugates in Arabidopsis. My results indicated that chemical artifacts induced by harsh chemical treatments were responsible for a significant portion of the unknown putative IAA conjugates. In chapter four, I described a facile way to directly survey a plant extract for its indole profile, notably IAA conjugates, based on high resolution and accurate mass (HR/AM) liquid chromatography-mass spectrometry (LC-MS). The method was successfully applied to Glycine max, Solanum lycopersicum, Cocos nucifera, and Ginkgo biloba. Together, these investigations and developments have led to an improved understanding of auxin metabolism and now provide useful tools for subsequent studies.