Plant Biology Commons^™

An Integrative Approach To Genomic Introgression Mapping, Andrew J. Severin, Gregory A. Peiffer, Wayne W. Xu, D. L. Hyten, Bruna Bucciarelli, Jamie A. O'Rourke, Yung-Tsi Bolon, David Grant, Andrew Farmer, Gregory D. May, Carroll P. Vance, Randy C. Shoemaker, Robert M. Stupar

Department of Agronomy and Horticulture: Faculty Publications

Near-isogenic lines (NILs) are valuable genetic resources for many crop species, including soybean (Glycine max). The development of new molecular platforms promises to accelerate the mapping of genetic introgressions in these materials. Here, we compare some existing and emerging methodologies for genetic introgression mapping: single-feature polymorphism analysis, Illumina GoldenGate single nucleotide polymorphism (SNP) genotyping, and de novo SNP discovery via RNA-Seq analysis of next-generation sequence data. We used these methods to map the introgressed regions in an iron-inefficient soybean NIL and found that the three mapping approaches are complementary when utilized in combination. The comparative RNA-Seq approach offers …

Soydb: A Knowledge Database Of Soybean Transcription Factors, Zheng Wang, Marc Libault, Trupti Joshi, Babu Valliyodan, Henry T. Nguyen, Dong Xu, Gary Stacey, Jianlin Cheng

Department of Agronomy and Horticulture: Faculty Publications

Background: Transcription factors play the crucial rule of regulating gene expression and influence almost all biological processes. Systematically identifying and annotating transcription factors can greatly aid further understanding their functions and mechanisms. In this article, we present SoyDB, a user friendly database containing comprehensive knowledge of soybean transcription factors.

Description: The soybean genome was recently sequenced by the Department of Energy-Joint Genome Institute (DOE-JGI) and is publicly available. Mining of this sequence identified 5,671 soybean genes as putative transcription factors. These genes were comprehensively annotated as an aid to the soybean research community. We developed SoyDB - a knowledge database …

Transgenic Maize Lines With Cell-Type Specific Expression Of Fluorescent Proteins In Plastids, Amir Sattarzadeh, Jonathan Fuller, Salvador Moguel, Katia Wostrikoff, Shirley Sato, Sarah Covshoff, Tom Clemente, Maureen Hanson, David Stern

Department of Agronomy and Horticulture: Faculty Publications

Plastid number and morphology vary dramatically between cell types and at different developmental stages. Furthermore, in C4 plants such as maize, chloroplast ultrastructure and biochemical functions are specialized in mesophyll and bundle sheath cells, which differentiate acropetally from the proplastid form in the leaf base. To develop visible markers for maize plastids, we have created a series of stable transgenics expressing fluorescent proteins fused to either the maize ubiquitin promoter, the mesophyll-specific phosphoenolpyruvate carboxylase (PepC) promoter, or the bundle sheath-specific Rubisco small subunit 1 (RbcS) promoter. Multiple independent events were examined and revealed that maize codon-optimized versions of YFP and …

Comparative Leaf Decomposition Rates Including A Non-Native Species In An Urban Ozark Stream, Sarah E. Lewis, Arthur V. Brown

Journal of the Arkansas Academy of Science

Leaf decomposition of three species of native Ozark vegetation was compared to that of one nonnative invasive species. Leaves were placed in an urban gravel-bed stream for 23 days. Changes in mass and condition of the leaves were assessed along with stream temperature, flow, width, depth and discharge. Species native to Eastern North American forests were sycamore (Platanus occidentalis), dogwood (Cornus florida), and redbud (Cercis canadensis). The nonnative species, Japanese (Amur) honeysuckle (Lonicera maackii) comprised approximately 80% of the understory vegetation within the riparian zone of the study reach. After 23 days, Sycamore lost 24.6% mass, dogwood lost 30%, redbud …

The Pathogenicity Determinant Of Citrus Tristeza Virus Causing The Seedling Yellows Syndrome Maps At The 3′-Terminal Region Of The Viral Genome, Maria R. Albiach-Marti, Cecile J. Robertson, Siddarame Gowda, Satyanarayana Tatineni, Belen Belliure, Stephen M. Garnsey, Svetlana Y. Folimonova, Pedro Moreno, William O. Dawson

Department of Plant Pathology: Faculty Publications

Citrus tristeza virus (CTV) (genus Closterovirus, family Closteroviridae) causes some of the more important viral diseases of citrus worldwide. The ability to map disease-inducing determinants of CTV is needed to develop better diagnostic and disease control procedures. A distinctive phenotype of some isolates of CTV is the ability to induce seedling yellows (SY) in sour orange, lemon and grapefruit seedlings. In Florida, the decline isolate of CTV, T36, induces SY, whereas a widely distributed mild isolate, T30, does not. To delimit the viral sequences associated with the SY syndrome, we created a number of T36/T30 hybrids by substituting T30 …

Heterologous Minor Coat Proteins Of Citrus Tristeza Virus Strains Affect Encapsidation, But The Coexpression Of Hsp70h And P61 Restores Encapsidation To Wild-Type Levels, Satyanarayana Tatineni, Siddarame Gowda, William O. Dawson

Department of Plant Pathology: Faculty Publications

The long flexuous bipolar virions of Citrus tristeza virus (CTV), a Closterovirus, are encapsidated with two capsid proteins at opposite ends: the minor coat protein (CPm) encapsidates the 5′ 630 nts of the genomic RNA and the major coat protein encapsidates the remainder of the genome. In this study, we found encapsidation of CTV CPm in the absence of other assembly-related proteins is highly specific in contrast to most plant viruses that allow virion assembly by a range of heterologous coat proteins. Heterologous CPms with 95–96% amino acid identity from related strains in CTV-CPm, a replicon with CPm as …

Soil And Root Populations Of Fluorescent Pseudomonas Spp. Associated With Seedlings And Field-Grown Plants Are Affected By Sorghum Genotype, Deanna L. Funnell-Harris, Jeffrey F. Pedersen, Scott E. Sattler

Department of Plant Pathology: Faculty Publications

Sorghum [Sorghum bicolor (L.) Moench] is valued for bioenergy, feed and food. Potential of sorghum genotypes to support differing populations of root- and soil-associated fluorescent Pseudomonas spp. or Fusarium spp., in two soils, was assessed. Culturable pseudomonads were enumerated from roots and soil of sorghum (Redlan and RTx433) and wheat (Lewjain) seedlings repeatedly grown in cycled soils in the growth chamber. Pseudomonads and Fusarium spp. were assessed from roots and soil of field-grown sorghum along with biological control traits hydrogen cyanide (HCN) and 2,4-diacetylphlorogluconol (phl) production. After four 4-week cycles, soil associated with Redlan seedlings had greater numbers …

Brown Midrib Mutations And Their Importance To The Utilization Of Maize, Sorghum, And Pearl Millet Lignocellulosic Tissues, Scott E. Sattler, Deanna L. Funnell-Harris, Jeffrey F. Pedersen

Department of Plant Pathology: Faculty Publications

Brown midrib mutants have been isolated in maize (Zea mays), sorghum (Sorghum bicolor) and pearl millet (Pennisetum glaucum) arising by either spontaneous or chemical mutagenesis. The characteristic brown coloration of the leaf mid veins is associated with reduced lignin content and altered lignin composition, traits useful to improve forage digestibility for livestock. Brown midrib phenotype is correlated with two homologous loci in maize (bm1 and bm3) and sorghum (bmr6 and bmr12), which encode cinnamyl alcohol dehydrogenase (CAD) and a caffeic O-methyl transferase (COMT). These enzymes are involved in the last …

Upper Canopy Collection And Identification Of Grapevines (Vitis) From Selected Forests In The Southeastern United States, Sydney E. Everhart

Department of Plant Pathology: Faculty Publications

Woody grapevines (Vitis spp.) are common in the deciduous forests of the southeastern United States. Their growth habit makes leaf collection challenging and polymorphic leaves make identification of species difficult. Mature grapevines can grow up to 48 cm in diameter at breast height and reach the upper canopy of trees more than 35 m in height. Leaf morphology is the most readily available character used for species identification. However, most mature grapevines do not produce leaves below the upper canopy and if they do, these leaves are morphologically indistinguishable from other species. In order to sample leaves from …

Regulation Of Septum Formation By The Bud3–Rho4 Gtpase Module In Aspergillus Nidulans, Haoyu Si, Daniela Justa-Schuch, Stephan Seiler, Steven D. Harris

Department of Plant Pathology: Faculty Publications

The ability of fungi to generate polarized cells with a variety of shapes likely reflects precise temporal and spatial control over the formation of polarity axes. The bud site selection system of Saccharomyces cerevisiae represents the best-understood example of such a morphogenetic regulatory system. However, the extent to which this system is conserved in the highly polarized filamentous fungi remains unknown. Here, we describe the functional characterization and localization of the Aspergillus nidulans homolog of the axial bud site marker Bud3. Our results show that AnBud3 is not required for polarized hyphal growth per se, but is involved in septum …

An In Vitro Method For The Analysis Of Infection-Related Morphogenesis In Fusarium Graminearum, William R. Rittenour, Steven D. Harris

Department of Plant Pathology: Faculty Publications

Fusarium graminearum is a significant pathogen of many cereal crops. With its genetic tractability, ease of culture, genome sequence availability and economic significance, F. graminearum has become the subject of intensive molecular research. Although molecular tools have been developed to enhance research into virulence determinants of F. graminearum, simple assays for infection-related development are lacking. As such, the objective of this study was to develop an in vitro protocol for the analysis of infection-related morphogenesis in F. graminearum. We demonstrate that two morphologically distinct hyphal structures are produced by F. graminearum during the invasion of detached wheat glumes: subcuticular hyphae …

Global Assessment Of Nitrogen Deposition Effects On Terrestrial Plant Diversity : A Synthesis, R. Bobbink, K. Hicks, J. Galloway, T. Spranger, R. Alkemade, M. Ashmore, M. Bustamante, S. Cinderby, E. Davidson, F. Dentener, B. Emmett, J. W. Erisman, M. Fenn, Frank S. Gilliam, A. Nordin, L. Pardo, W. Devries

Biological Sciences Faculty Research

Atmospheric nitrogen (N) deposition is a recognized threat to plant diversity in temperate and northern parts of Europe and North America. This paper assesses evidence from field experiments for N deposition effects and thresholds for terrestrial plant diversity protection across a latitudinal range of main categories of ecosystems, from arctic and boreal systems to tropical forests. Current thinking on the mechanisms of N deposition effects on plant diversity, the global distribution of G200 ecoregions, and current and future (2030) estimates of atmospheric N-deposition rates are then used to identify the risks to plant diversity in all major ecosystem types now …

The Role Of Taabf1 In Abscisic Acid-Mediated Suppression Of 𝒶-Amylase Gene Expression In Cereal Grains, Lauren J. Harris

Honors Theses

The phytohormones gibberellin (GA) and abscisic acid (ABA) regulate important developments events in germinating seeds. Specifically, GA induces the expression of hyrolase genes, like the α-amylase gene Amy32b, which mobilizes starch reserves to be used by the embryo, and ABA suppresses this induction. Recent advancements identified ABA and GA receptors and key components in the signaling pathways, however, the mechanism of crosstalk between the hormones remains largely unknown. To further elucidate the mechanism of ABA suppression of GA-induced genes, we focused on the transcription factor TaABF1, a member of the ABA response element binding factor family. TaABF1 has been shown …

Comparison Between In Vitro And In Vivo Antibacterial Activity Of Curcuma Zedoaria From Malaysia., Behrooz Banisalam

Student Works (2010-2019)

The rhizomes of the Zingiberaceae family are vegetables widely used in many Asian countries and their medicinal functions have been broadly discussed and accepted in many traditional recipes. In this study, the antimicrobial activity of extracts of Curcuma zedoaria from Malaysia was compared between two systems as in vitro and in vivo. The comparison was performed against four bacterial strains including two gram negative strains (E.coli and Pseudomonas aeruginosa) and two gram positive strains (Bacillus cereus and Staphylococcus aureus) using the agar well diffusion method. Extracts were made in three different solvents; petroleum ether, chloroform and methanol extracts exhibited antibacterial …

Development Of Protocols For Tissue Culture And Mutagenesis In Two Variegated Sansevieria Sp., Irmawati Akma Abdul Hapiz

Student Works (2010-2019)

Studies were conducted to develop the tissue culture protocol and mutagenesis through Gamma ray irradiation for two variegated Sansevieria species known as Sansevieria trifasciata var. Laurentii (goldband Sansevieria) and Sansevieria trifasciata var. Hahnii (birdnest Sansevieria). Seven combinations of BAP and NAA were chosen which are represented by letter A= 1.00 mg/I BAP, B = 1.00 mg/I BAP + 0.25 mg/I NAA, C = 2.00 mg/I BAP + 0.50 mg/I NAA, D = 2.00 mg/I BAP + 1.00 mg/I NAA, E = 3.00 mg/I BAP + 1.00 mg/I NAA, F = 4.00 mg/I BAP + 1.00 mg/I NAA and G = …

Structural And Functional Divergence Of A 1-Mb Duplicated Region In The Soybean (Glycine Max) Genome And Comparison To An Orthologous Region From Phaseolus Vulgaris, Jer-Young Lin, Robert M. Stupar, Christian Hans, D. L. Hyten, Scott A. Jackson

Department of Agronomy and Horticulture: Faculty Publications

Soybean (Glycine max) has undergone at least two rounds of polyploidization, resulting in a paleopolyploid genome that is a mosaic of homoeologous regions. To determine the structural and functional impact of these duplications, we sequenced two ~1-Mb homoeologous regions of soybean, Gm8 and Gm15, derived from the most recent ~13 million year duplication event and the orthologous region from common bean (Phaseolus vulgaris), Pv5. We observed inversions leading to major structural variation and a bias between the two chromosome segments as Gm15 experienced more gene movement (gene retention rate of 81% in Gm15 versus 91% in …

The Wheat Bzip Factor, Taabf1, Mediates Aba-Induced Gene Expression In Bombarded Barley Aleurone Layers, Benjamin R. Keyser

Honors Theses

The plant hormone Abscisic acid (ABA) plays a central role in maturation and germination in seeds, as well as mediating adaptive responses to abiotic environmental stresses. ABA induces the expression of many genes, including late-embryogenesis-abundant genes such as HVA1. To elucidate the ABA signaling pathway leading to HVA1 expression, we focus on the bZIP factor TaABF1. Analysis of the interplay between ABA and TaABF1 in the aleurone cells of imbibing cereal grains indicated that the two are not additive in their induction of the HVA1 promoter. A synthetic ABA analog, PBI-51, did not specifically inhibit the effect of exogenous ABA …

Functional Analysis Of B And C Class Floral Organ Genes In Spinach Demonstrates Their Role In Sexual Dimorphism, D Noah Sather, Maja Jovanovic, Edward M. Golenberg

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Evolution of unisexual flowers entails one of the most extreme changes in plant development. Cultivated spinach, Spinacia oleracea L., is uniquely suited for the study of unisexual flower development as it is dioecious and it achieves unisexually by the absence of organ development, rather than by organ abortion or suppression. Male staminate flowers lack fourth whorl primordia and female pistillate flowers lack third whorl primordia. Based on theoretical considerations, early inflorescence or floral organ identity genes would likely be directly involved in sex-determination in those species in which organ initiation rather than organ maturation is regulated. In this …

Molecular Studies Of 5-Azacytidine-Induced Early-Flowering Lines Of Flax, Megan A. House

Theses and Dissertations (Comprehensive)

Several early-flowering flax (Linum usitatissimum L.) lines were derived from treatment of germinating seeds with 5-azacytidine in 1990. These lines are also shorter, have fewer leaves, and their DNA is hypomethylated, relative to their corresponding controls. The work presented in this thesis used early-flowering and control lines of the Royal (R) flax genotype, and the Large (L) flax genotroph. Firstly, levels of cytosine methylation were measured over a 24-hour period in the early-flowering line RE2 and its control (RC), using an HPLC method. Secondly, to determine the response of the flax lines to short-day conditions, control and early-flowering …

Don't Judge A Book By Its Cover: The Curious Case Of Wild Ginger Pollination, W. John Hayden

Biology Faculty Publications

What pollinates wild ginger? This seems like an easy question. The inconspicuous little flowers are held close to the forest floor, often completely hidden by a dense canopy of ginger leaves above. Flower color is rather drab, dominated by brown and maroon hues. Wind pollination seems completely unlikely and flowers pollinated by bees, butterflies, moths, or hummingbirds are always much more showy and accessible to these flying creatures. Flies, however, given their natural inclination to seek carrion as a food source for their babies (i.e. maggots), are often attracted to brown and maroon flowers. And because their actual quarry, animal …

Morphogenesis And Tissue Culture Studies Of Gerbera Jamesonii Bolus Ex. Hook F., Nor Azlina Hasbullah

Student Works (2010-2019)

In vitro regeneration of Gerbera jamesonii Bolus ex. Hook f. was successfully carried out in this study. Petiole and leaf explants from 8-week-old aseptic seedlings were used as source of explants. Different response was observed when different explants were cultured on the culture media. MS (Murashige and Skoog, 1962) supplemented with 2.0 mg/l BAP and 0.5 mg/l NAA was identified as the optimum medium for shoot regeneration, while petiole explant was identified as the most responsive explant in this study. Petiole explants regenerated shoots (94.3 } 2.5 %) and produced 9.3 } 0.6 shoots per explant. MS basal medium was …

Studies Of Antioxidant And Angiotensin Converting Enzyme Inhibitory Activity Of Orthosiphon Stamineus (Misai Kucing)., Che Wan Imanina Che Wan Takwa

Student Works (2010-2019)

Abstract NA

Physiological And Biochemical Attributes Of Red-Fleshed Dragon Fruit, Hylocereus Polyrhizus., Punitha R. Vasanthan

Student Works (2010-2019)

An understanding of the postharvest parameters is essential for the successful market introduction of red-fleshed dragon fruit, Hylocereus polyrhizus, which has been recently developed as fruit crop. In this study, fruit at three different harvest maturities were evaluated in terms of physiological and biochemical aspects. Fruit which were harvested at complete red stage maintained their quality for up to one week. On the other hand, fruit harvested at early maturity attained the physical properties of fruit ripened on the plant (firmness reduced, peel colour changes, pH increased) but they contained noticeably lower concentrations of soluble sugars suggesting that fruit can …

Marine Algae As A Source Of Photosensitisers For Photodynamic Therapy Of Cancer., Tang Yee Voon

Student Works (2010-2019)

Photodynamic therapy (PDT) involves the intravenous administration of a photosensitiser that preferentially localises in cancerous tissues more than the surrounding normal tissues. Subsequent illumination of photosensitiser generates reactive oxygen species that cause irreversible photo-damage to the cancer cells. To date, most photosensitisers that have been approved for clinical use or are currently in clinical trials are cyclic tetrapyrroles which are derived or inspired by naturally occurring chlorophyll and its degradation products. Some non-tetrapyrrolic photosensitisers have also been found in nature suggesting that there are potential photosensitisers with interesting structures in nature. To this end, this thesis outlines the collection of …

Molecular Characterization And Expression Analysis Of Putative Rpk1 And Putative Clv1 In Malaysian Indica Rice (Oryza Sativa L.) Cv.Mr219 And Malaysian Wild Rice (Oryza Rufipogon) Irgc105491., Law Yee Song

Student Works (2010-2019)

Two candidate yield-related genes, putative Receptor-like Protein Kinase 1 (putative RPK1) and putative CLAVATA1 Receptor Kinase (putative CLV1), were selected for molecular characterization and expression analysis. This was carried out using in four rice lines comprising the parents and two BC₂F₇ lines from a local rice breeding program, with Malaysian rice variety, Oryza sativa ssp. indica cv. MR219 as recurrent parent, and Oryza rufipogon (IRGC105491) as donor parent. Approximately 2.8 kb and 2.6 kb putative RPK1 cDNA nucleotide sequences were obtained from Oryza rufipogon and Oryza sativa ssp. indica cv. MR219 respectively. However, only 402 …

Effects Of Plant Growth Regulators And Physiological Stresses On The Growth Of Bougainvillea Spp., Mohammed Saifuddin

Student Works (2010-2019)

This study was aimed to investigate the effects of physiological stresses such as pruning, shading, phloemic stress and plant hormones such as gibberellic acid (GA3) and naphthalene acetic acid (NAA) on the growth, development and flowering process of bougainvillea plants. The plants (Bougainvillea glabra and Bougainvillea spectabilis) were grown under prevailing conditions (temperature 21-32°C, maximum PAR 2100 μE m-2 s-1 and relative humidity of 60-90%) using completely randomized design. Field experiments as well as biochemical analysis were carried out at the Plant Physiology Garden and the Plant Physiology Laboratory, Institute of Biological Sciences, University of Malaya. Results on frequent pruning …

Characterization Of Microrna172 And Its Potential Target In Oil Palm (Elaeis Guineensis Jaq.), Fatemeh Mehrpooyan

Student Works (2010-2019)

Oil palm (Elaeis guineensis) is the world’s major perennial monocot crop and contributes highly to the economies of South East Asia. As the oil palm fruit is the source of the main economic output for this crop, floral development is a critical process related to oil palm productivity. miR172 has been shown to be an important regulator of the AP2 family transcription factors involved in floral timing in a number of plants and belongs to a group of highly conserved miRNA that can be identified based on sequence homology. Six oil palm miR172 paralogs, representing two distinct mature miR172 sequences, …

Phylogeographical Patterns Of Neobalanocarpus Heimii (Dipterocarpaceae) For The Evolutionary History And Chain Of Custody Certification., Tnah Lee Hong

Student Works (2010-2019)

Tectonic movement and climatic oscillations during the Cenozoic have had dramatic effect on the biota of the tropical rain forest. This study aims to reveal the phylogeography and evolutionary history of a Peninsular Malaysian endemic tropical timber, Neobalanocarpus heimii (Dipterocarpaceae), based on chloroplast DNA (cpDNA) variation. Fifteen haplotypes were identified from 10 intraspecific variable sites of five non-coding cpDNA regions: trnL intron, trnS-trnG spacer, trnG intron, trnK intron and psbK-trnS spacer. Two major genealogical cpDNA lineages of N. heimii were elucidated: a widespread southern and a northern region. The species is predicted to survive in multiple refugia during climatic oscillation: …

Studies Of Antioxidant Activity Of Bioactive Compounds Derived From Ardisia Crispa., Hassan Mahmood Kzar Jindal

Student Works (2010-2019)

In recent times, researches have focused on medicinal plants in order to extract natural and low cost antioxidants that can help protect the human body against oxidative stress, and replace the synthetic additives that might be carcinogenic. In present study, the crude extracts of leaves and fruits from Ardisia crispa were investigated for their chemical constituents and antioxidant activity. Preliminary phytochemical screening of the crude extracts via TLC analysis revealed the presence of several secondary compounds mainly, terpenoids and phenolic compounds in addition to alkaloids and saponins. HPLC analysis showed the possibility of presence of gallic acid in the fruits …

Studies On The Bioactive Properties Of Selected Plant And Fermented Extracts., Saravana Kumar Sinniah

Student Works (2010-2019)

The aim of this study was to isolate protein/peptide and secondary metabolites from plant and fermented sources. The extracts were used to test for antimicrobial and antioxidant properties. In the current study protein/peptide extracts of Allium sativum showed promising results with a 15mm inhibition zone against Escherichia coli, 28mm against Staphylococcus aureus, 16.3mm against Bacillus cereus and 9mm against Pseudomonas aeruginosa. The minimum bacteriocidal concentration (MBC) results showed that Allium sativum protein/peptide extract is only bacteriostatic and not bacteriocidal. Andrographis paniculata showed the most promising result for the ethanolic extracts with an inhibition zone of 14mm against B. cereus, 11.5mm …