Plant Biology Commons^™

A Dedicated Type Ii Nadph Dehydrogenase Performs The Penultimate Step In The Biosynthesis Of Vitamin K1 In Synechocystis And Arabidopsis, Abdelhak Fatihi, Scott Latimer, Stefan Schmollinger, Anna Block, Patrick Dussault, Wim F.J. Vermaas, Sabeeha S. Merchant, Gilles J. Basset

Department of Agronomy and Horticulture: Faculty Publications

Mutation of Arabidopsis thaliana NAD(P)H DEHYDROGENASE C1 (NDC1; At5g08740) results in the accumulation of demethylphylloquinone, a late biosynthetic intermediate of vitamin K₁. Gene coexpression and phylogenomics analyses showed that conserved functional associations occur between vitamin K biosynthesis and NDC1 homologs throughout the prokaryotic and eukaryotic lineages. Deletion of Synechocystis ndbB, which encodes for one such homolog, resulted in the same defects as those observed in the cyanobacterial demethylnaphthoquinone methyltransferase knockout. Chemical modeling and assay of purified demethylnaphthoquinone methyltransferase demonstrated that, by virtue of the strong electrophilic nature of S-adenosyl-Lmethionine, the transmethylation of the demethylated precursor …

Proteomic Profiling Of Maize Opaque Endosperm Mutants Reveals Selective Accumulation Of Lysine-Enriched Proteins, Kyla J. Morton, Shangang Jia, Chi Zhang, David R. Holding

Department of Agronomy and Horticulture: Faculty Publications

Reduced prolamin (zein) accumulation and defective endoplasmic reticulum (ER) body formation occurs in maize opaque endosperm mutants opaque2 (o2), floury2 (fl2), defective endosperm*B30 (DeB30), and Mucronate (Mc), whereas other opaque mutants such as opaque1 (o1) and floury1 (fl1) are normal in these regards. This suggests that other factors contribute to kernel texture. A liquid chromatography approach coupled with tandem mass spectrometry (LC-MS/MS) proteomics was used to compare non-zein proteins of nearly isogenic opaque endosperm mutants. In total, 2762 proteins were identified that were enriched for biological processes such as protein transport and folding, amino acid biosynthesis, …

Tonoplast Sugar Transporters (Sbtsts) Putatively Control Sucrose Accumulation In Sweet Sorghum Stems, Saadia Bihmidine, Benjamin T. Julius, Ismail M. Dweikat, David M. Braun

Department of Agronomy and Horticulture: Faculty Publications

Carbohydrates are differentially partitioned in sweet versus grain sorghums. While the latter preferentially accumulate starch in the grain, the former primarily store large amounts of sucrose in the stem. Previous work determined that neither sucrose metabolizing enzymes nor changes in Sucrose transporter (SUT) gene expression accounted for the carbohydrate partitioning differences. Recently, 2 additional classes of sucrose transport proteins, Tonoplast Sugar Transporters (TSTs) and SWEETs, were identified; thus, we examined whether their expression tracked sucrose accumulation in sweet sorghum stems. We determined 2 TSTs were differentially expressed in sweet vs. grain sorghum stems, likely underlying the massive difference in sucrose …

Selection For Silage Yield And Composition Did Not Affect Genomic Diversity Within The Wisconsin Quality Synthetic Maize Population, Aaron Lorenz, Timothy M. Beissinger, Renato Rodrigues Silva, Natalia De Leon

Department of Agronomy and Horticulture: Faculty Publications

Maize silage is forage of high quality and yield, and represents the second most important use of maize in the United States. The Wisconsin Quality Synthetic (WQS) maize population has undergone five cycles of recurrent selection for silage yield and composition, resulting in a genetically improved population. The application of high-density molecular markers allows breeders and geneticists to identify important loci through association analysis and selection mapping, as well as to monitor changes in the distribution of genetic diversity across the genome. The objectives of this study were to identify loci controlling variation for maize silage traits through association analysis …

A Roadmap For Functional Structural Variants In The Soybean Genome, Justin E. Anderson, Michael B. Kantar, Thomas Y. Kono, Fengli Fu, Adrian O. Stec, Qijian Song, Perry B. Cregan, James E. Specht, Brian W. Diers, Steven B. Cannon, Leah K. Mchale, Robert M. Stupar

Department of Agronomy and Horticulture: Faculty Publications

Gene structural variation (SV) has recently emerged as a key genetic mechanism underlying several important phenotypic traits in crop species. We screened a panel of 41 soybean (Glycine max) accessions serving as parents in a soybean nested association mapping population for deletions and duplications in more than 53,000 gene models. Array hybridization and whole genome resequencing methods were used as complementary technologies to identify SV in 1528 genes, or approximately 2.8%, of the soybean gene models. Although SV occurs throughout the genome, SV enrichment was noted in families of biotic defense response genes. Among accessions, SV was nearly eightfold less …

Overexpression Of The Transporters Atzip1 And Atmtp1 In Cassava Changes Zinc Accumulation And Partitioning, Eliana Gaitán-Solis, Nigel J. Taylor, Dimuth Siritunga, William Stevens, Daniel P. Schachtman

Department of Agronomy and Horticulture: Faculty Publications

Zinc deficiency in humans is a serious problem worldwide with an estimated one third of populations at risk for insufficient zinc in diet, which leads to impairment of cognitive abilities and immune system function. The goal of this research was to increase the bioavailable zinc in the edible portion of cassava roots to improve the overall zinc nutrition of populations that rely on cassava as a dietary staple. To increase zinc concentrations, two Arabidopsis thaliana genes coding for ZIP1 and MTP1 were overexpressed with a tuber-specific or constitutive promoter. Eighteen transgenic events from four constructs, out of a total of …

Genetic Control Of Morphometric Diversity In The Maize Shoot Apical Meristem, Samuel Leiboff, Xianran Li, Heng-Cheng Hu, Natalie Todt, Jinliang Yang, Xiao Li, Xiaoqing Yu, Gary J. Muehlbauer, Marja C.P. Timmermans, Jianming Yu, Patrick S. Schnable, Michael J. Scanlon

Department of Agronomy and Horticulture: Faculty Publications

The maize shoot apical meristem (SAM) comprises a small pool of stem cells that generate all above-ground organs. Although mutational studies have identified genetic networks regulating SAM function, little is known about SAM morphological variation in natural populations. Here we report the use of high-throughput image processing to capture rich SAM size variation within a diverse maize inbred panel. We demonstrate correlations between seedling SAM size and agronomically important adult traits such as flowering time, stem size and leaf node number. Combining SAM phenotypes with 1.2 million single nucleotide polymorphisms (SNPs) via genome-wide association study reveals unexpected SAM morphology candidate …

Differential Expression Analysis In Rna-Seq By A Naive Bayes Classifier With Local Normalization, Yongchao Dou, Xiaomei Guo, Lingling Yuan, David R. Holding, Chi Zhang

Department of Agronomy and Horticulture: Faculty Publications

To improve the applicability of RNA-seq technology, a large number of RNA-seq data analysis methods and correction algorithms have been developed. Although these new methods and algorithms have steadily improved transcriptome analysis, greater prediction accuracy is needed to better guide experimental designs with computational results. In this study, a new tool for the identification of differentially expressed genes with RNA-seq data, named GExposer, was developed. This tool introduces a local normalization algorithm to reduce the bias of nonrandomly positioned read depth. The naive Bayes classifier is employed to integrate fold change, transcript length, and GC content to identify differentially expressed …

Soil And Crop Response To Stover Removal From Rainfed And Irrigated Corn, Ian Kenney, Humberto Blanco-Canqui, Deann R. Presley, Charles W. Rice, Keith Janssen, Brian Olson

Department of Agronomy and Horticulture: Faculty Publications

Excessive corn (Zea mays L.) stover removal for biofuel and other uses may adversely impact soil and crop production. We assessed the effects of stover removal at 0, 25, 50, 75, and 100% from continuous corn on water erosion, corn yield, and related soil properties during a 3-year study under irrigated and no-tillage management practice on a Ulysses silt loam at Colby, irrigated and strip till management practice on a Hugoton loam at Hugoton, and rainfed and no-tillage management practice on a Woodson silt loam at Ottawa in Kansas, USA. The slope of each soil was <1%. One year after removal, complete (100%) stover removal resulted in increased losses of sediment by 0.36–0.47 Mg ha-1 at the irrigated sites, but, at the rainfed site, removal at rates as low as 50% resulted in increased sediment loss by 0.30 Mg ha-1 and sediment-associated carbon (C) by 0.29 kg ha-1. Complete stover removal reduced wet aggregate stability of the soil at the irrigated sites in the first year after removal, but, at the rainfed site, wet aggregate stability was reduced in all years. Stover removal at rates ≥ 50%resulted in reduced soil water content, increased soil temperature in summer by 3.5–6.8 °C, and reduced tem-perature in winter by about 0.5 °C. Soil C pool tended to decrease and crop yields tended to increase with an increase in stover removal, but 3 years after removal, differences were not significant. Overall, stover removal at rates ≥50% may enhance grain yield but may increase risks of water erosion and negatively affect soil water and temperature regimes in this region.

Engineering Triterpene Metabolism In Tobacco, Zuodong Jiang

Theses and Dissertations--Plant and Soil Sciences

Terpenes comprise a large diverse class of natural products and many of them attract interest because of their physiological function, therapeutic and industrial values. Triterpene oils including squalene (C30), botrycococcene (C30) and their methylated derivatives (C31-C37) generated by the green algae Botryococcus braunii race B, which have recently received significant attention because of their utility for advanced biofuels. However, the slow growth habit of B. braunii makes it impractical as a robust biofuel production system. In this thesis, we firstly evaluated the potential of generating high levels of triterpene (C30) production in tobacco plants by diverting carbon flux from cytosolic …

Unveiling Novel Aspects Of D-Amino Acid Metabolism In The Model Bacterium Pseudomonas Putida Kt2440, Atanas D. Radkov

Theses and Dissertations--Plant and Soil Sciences

D-amino acids (D-AAs) are the α-carbon enantiomers of L-amino acids (L- AAs), the building blocks of proteins in known organisms. It was largely believed that D-AAs are unnatural and must be toxic to most organisms, as they would compete with the L-counterparts for protein synthesis. Recently, new methods have been developed that allow scientists to chromatographically separate the two AA stereoisomers. Since that time, it has been discovered that D-AAs are vital molecules and they have been detected in many organisms. The work of this dissertation focuses on their place in bacterial metabolism. This specific area was selected due to …

2015 Virginia Wildflower Of The Year: Sweet Pepperbush, Clethra Alnifolia, W. John Hayden

Biology Faculty Publications

Clethra alnifolia is a rhizomatous shrub with aerial stems from 1 to 3 m tall. Leaves are simple, alternate, and bear stellate hairs; petioles are short, 5–10 mm long; leaf blades are obovate to oblong, 5–10 cm long, with relatively blunt apices, cuneate (wedgelike) bases, and margins that are entire toward the base but finely serrate above the middle; venation is pinnate with secondary veins that extend to leaf margins. Stipules are lacking. Flowers are borne on erect terminal racemes that may be solitary or accompanied by additional racemes terminating few-leaved branches arising from upper nodes. Raceme axes and pedicels …

The Functional Role Of Leaf Nutrients In An Old-Field Successional Community, Kirstin I. Duffin

Masters Theses

In functional ecology, traits that capture aspects of plant performance are used to understand how organisms interact with their environment. Leaf nutrients are an example of a functional trait that directly links to plant metabolic processes and therefore may describe plant assemblage dynamics. Multivariate leaf nutrient analyses may be used with other functional traits to understand ecological strategies because they are a direct measure of leaf metabolic processes and can describe nuances in plant allocation patterns. In this thesis, I explored (1) whether a suite of leaf nutrients (carbon, nitrogen, phosphorus, potassium, calcium, and magnesium) was related to plant growth …

Dispersal: A Multidisciplinary Investigation Of Plant Life, Alexandra E. Arzt

Theses and Dissertations

Using plants as a basis for exploring the interstices between the human and nonhuman, this thesis investigates ideas of awareness, intelligence, deep time, animism, and the fluctuating human perception of the agency of Nature. It outlines environmental art practices since the 1950s involving vegetal life. In addition, the paper provides a critical analysis of plant perception of Jakob von Uexküll’s work and theories of vital materialism and “critical plant studies” while noting recent studies in plant neurobiology. In my work, plants become active participants via their movement, seeding, and smell. This study takes the form of imitation, purposeful symbiosis, anthropomorphism, …

Predicting Carbon Isotope Discrimination In Eelgrass (Zostera Marina L.) From The Environmental Parameters- Light, Flow, And [Dic], Meredith L. Mcpherson, Richard C. Zimmerman, Victoria J. Hill

OES Faculty Publications

Isotopic discrimination against ¹³C during photosynthesis is determined by a combination of environmental conditions and physiological mechanisms that control delivery of CO₂ to RUBISCO. This study investigated the effects of light, flow, dissolved inorganic carbon (DIC) concentration, and its speciation, on photosynthetic carbon assimilation of Zostera marinaL. (eelgrass) using a combination of laboratory experiments and theoretical calculations leading to a mechanistic understanding of environmental conditions that influence leaf carbon uptake and determine leaf stable carbon isotope signatures δ¹³C. Photosynthesis was saturated with respect to flow at low velocity ~ 3 cm s^-1, but …

Linking Photosynthesis Physiology Of Upland Hardwood Reproduction To Ecology And Silviculture In The Arkansas Ozarks, Kutcher K. Cunningham

Theses and Dissertations

Oak (Quercus) forests in the Arkansas Ozarks have been important culturally, ecologically and environmentally for centuries. Historically these forests were fire dependent and dominated by oak species. In the past century, fire suppression and land management have caused these forests to densify. As a result, oaks are increasingly less abundant following disturbance in natural hardwood stands. Many applied ecological studies have explored methods and practices to maintain oak species in newly developing stands. This study attempted to link the mechanistic physiology of oak and non-oak reproduction to the applied ecological work. Varying stand conditions were generated in an undisturbed mature …

Metabolic Engineering Of Oilseed Crops To Produce High Levels Of Novel Acetyl Glyceride Oils With Reduced Viscosity, Freezing Point And Calorific Value, Jinjie Liu, Adam Rice, Kathleen Mcglew, Vincent Shaw, Hyunwoo Park, Thomas E. Clemente, Mike Pollard, John Ohlrogge, Timothy P. Durrett

Department of Agronomy and Horticulture: Faculty Publications

Seed oils have proved recalcitrant to modification for the production of industrially useful lipids. Here, we demonstrate the successful metabolic engineering and subsequent field production of an oilseed crop with the highest accumulation of unusual oil achieved so far in transgenic plants. Previously, expression of the Euonymus alatus diacylglycerol acetyltransferase (EaDAcT) gene in wild-type Arabidopsis seeds resulted in the accumulation of 45 mol% of unusual 3-acetyl-1,2- diacyl-sn-glycerols (acetyl-TAGs) in the seed oil (Durrett et al., 2010 PNAS 107:9464). Expression of EaDAcT in dgat1 mutants compromised in their ability to synthesize regular triacylglycerols increased acetyl-TAGs to 65 mol%. Camelina and soybean …

First Report Of Goss's Bacterial Leaf Blight And Wilt Of Corn Caused By Clavibacter Michiganensis Subsp. Nebraskensis In North Dakota, A. Friskop, K. Kinzer, M. Mcconnell, Z. Liu, K. A. Korus, A. Timmerman, T. Jackson

Department of Plant Pathology: Faculty Publications

In August of 2011, the North Dakota State University Plant Diagnostic Lab received a hybrid corn (Zea mays) leaf sample from Burleigh County in southcentral North Dakota (ND). The leaf had long, irregular, water-soaked lesions consistent with Goss's leaf blight of corn. Using a light microscope at 10× magnification, bacterial streaming was observed from the excised edge of leaf tissue. A bacterial suspension was created, streaked onto a semi-selective CNS medium (1), and incubated at 22°C. Dark yellow-orange colonies appeared on the medium after 5 days. Single colonies were subcultured onto additional CNS media. To verify the identity …

The Mechanism Of Lhcp Insertion Into Thylakoid Membranes, Larae Brown

Graduate Theses and Dissertations

The light harvesting chlorophyll a/b-binding proteins (LHCPs) are the most abundant membrane proteins. LHCP is a nuclear encoded protein which is targeted to the thylakoid membranes by chloroplast signal recognition particles (cpSRP). Insertion into thylakoid membranes is facilitated by the cpSRP receptor cpFtsY and the Alb3 translocase. Work here focused on understanding the molecular events of LHCP insertion into the thylakoid membranes. Specifically, we sought to develop a tool to detect the insertion of the lumen-localized loop of LHCP into thylakoid membranes, which relies on cleavage of the loop by a thylakoid lumen processing protease. We also sought to understand …

Functional Genomics And Microbiome Profiling Of The Asian Longhorned Beetle (Anoplophora Glabripennis) Reveal Insights Into The Digestive Physiology And Nutritional Ecology Of Wood Feeding Beetles, Erin D. Scully, Scott M. Geib, John E. Carlson, Ming Tien, Duane Mckenna, Kelli Hoover

Department of Agronomy and Horticulture: Faculty Publications

Background: Wood-feeding beetles harbor an ecologically rich and taxonomically diverse assemblage of gut microbes that appear to promote survival in woody tissue, which is devoid of nitrogen and essential nutrients. Nevertheless, the contributions of these apparent symbionts to digestive physiology and nutritional ecology remain uncharacterized in most beetle lineages.

Results: Through parallel transcriptome profiling of beetle- and microbial- derived mRNAs, we demonstrate that the midgut microbiome of the Asian longhorned beetle (Anoplophora glabripennis), a member of the beetle family Cerambycidae, is enriched in biosynthetic pathways for the synthesis of essential amino acids, vitamins, and sterols. Consequently, the midgut …