Plant Biology Commons^™

Inmut-Finder: A Software Tool For Insertion Identification In Mutagenesis Using Nanopore Long Reads, Rui Song, Ziyao Wang, Hui Wang, Han Zhang, Xuemeng Wang, Hanh Nguyen, David Holding, Bin Yu, Tom Clemente, Shangang Jia, Chi Zhang

Center for Plant Science Innovation: Faculty Publications

Background: Biological mutagens (such as transposon) with sequences inserted, play a crucial role to link observed phenotype and genotype in reverse genetic studies. For this reason, accurate and efficient software tools for identifying insertion sites based on the analysis of sequencing reads are desired. Results: We developed a bioinformatics tool, a Finder, to identify genome-wide Insertions in Mutagenesis (named as “InMut-Finder”), based on target sequences and flanking sequences from long reads, such as Oxford Nanopore Sequencing. InMut-Finder succeeded in identify > 100 insertion sites in Medicago truncatula and soybean mutants based on sequencing reads of whole-genome DNA or enriched …

3d Reconstruction Identifies Loci Linked To Variation In Angle Of Individual Sorghum Leaves, Michael C. Tross, Mathieu Gaillard, Mackenzie Zwiener, Chenyong Miao, Ryleigh J. Grove, Bosheng Li, Bedrich Benes, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

Selection for yield at high planting density has reshaped the leaf canopy of maize, improving photosynthetic productivity in high density settings. Further optimization of canopy architecture may be possible. However, measuring leaf angles, the widely studied component trait of leaf canopy architecture, by hand is a labor and time intensive process. Here, we use multiple, calibrated, 2D images to reconstruct the 3D geometry of individual sorghum plants using a voxel carving based algorithm. Automatic skeletonization and segmentation of these 3D geometries enable quan- tification of the angle of each leaf for each plant. The resulting measurements are both heritable and …

Somatic Variants For Seed And Fruit Set In Grapevine, Laura Costantini, Paula Moreno-Sanz, Chinedu Charles Nwafor, Silvia Lorenzi, Annarita Marrano, Fabiana Cristofolini, Elena Gottardini, Stefano Raimondi, Paola Ruffa, Ivana Gribaudo, Anna Schneider, Maria Stella Grando

Center for Plant Science Innovation: Faculty Publications

Background: Grapevine reproductive development has direct implications on yield. It also impacts on berry and wine quality by affecting traits like seedlessness, berry and bunch size, cluster compactness and berry skin to pulp ratio. Seasonal fluctuations in yield, fruit composition and wine attributes, which are largely driven by climatic factors, are major challenges for worldwide table grape and wine industry. Accordingly, a better understanding of reproductive processes such as gamete development, fertilization, seed and fruit set is of paramount relevance for managing yield and quality. With the aim of providing new insights into this field, we searched for clones with …

Grand Rapids Flora Then And Now: Emma Cole Project 2021, Haley Weesies, Zachary Hartwig, Lucas Walker, Natalie Vredevoogd, Garrett Crow, Dave Warners

Summer Research

In 1901, local botanist and teacher Emma Cole published Grand Rapids Flora: A Catalogue of the Flowering Plants and Ferns Growing Without Cultivation in the Grand Rapids Area. Despite immense changes in land use and development of Grand Rapids in the past 120 years, her work remains the most comprehensive floristic inventory of the area to date. • Develop floristic inventories of field sites. o Periodically visit each site May-August, documenting all plant species observed. o Make herbarium voucher specimens of all species in flower or in fruit to be pressed and dried. This is done in order to document …

Protein Prenylation In The Moss Physcomitrium Patens, Zayna H. Qaissi, Anam F. Ahmed, Katherine V. Brown, Mark P. Running

Undergraduate Arts and Research Showcase

Protein prenylation is the addition of a 15 or 20 carbon lipid to a cysteine near carboxyl terminus of target proteins. Prenylation increases hydrophobicity, which facilitates membrane associations and protein-protein interaction. Protein prenylation is generally conserved among eukaryotes, and mutations in genes that carry out prenylation are lethal in animals and yeast. In plants prenylation mutations are not always lethal, but they do affect development, disease resistance, biofuel production, and drought response, among other processes of agricultural interest. To understand the evolutionary and developmental implications of plant protein prenylation, we used the sequenced, annotated, and translated genome of the moss …

The Study Of Ppal And Its Role In The Development Of Physcomitrella Patens, Susana Perez-Martinez, Christine Chen, Mark P. Running

Undergraduate Arts and Research Showcase

Protein Prenylation is the addition of lipids to select proteins that play a key role during the development of plants. There are three enzymes that play a role in protein prenylation: protein farnesyltransferase (PFT), protein geranylgeranyl-transferase-I (PGGT), and Rab geranylgeranyltransferase (Rab-GGT). However, there is a protein called PPAL that has a similar alpha subunit of PFT, PGGT, and RAB-GGT but its biochemical function is unknown. Physconmitrella patens, a type of moss, was chosen to explore the role of PpPPAL in the development process. There are two copies of PPAL found in moss. PPAL1 and PPAL2. To study the role …

Examining Climate Change Effects On Flowering In Moss Campion, Mykaela Tanino-Springsteen, Olivia Dewitt, Anna Sher

DU Undergraduate Research Journal Archive

Examining the variation in the collection date of herbarium specimens is a common method for studying the phenological effects of climate change on a flowering plant species. We used herbarium data to examine how warming temperatures have affected flowering time in Silene acaulis in the state of Colorado. Silene acaulis, commonly known as moss campion and cushion pink, is an alpine tundra plant. Using ordinal date of collection as a proxy for flowering date and year collected as a proxy for increasing average temperature, a linear regression test found that there was no significant relationship between increasing temperatures and …

Seed-Shattering Phenology At Soybean Harvest Of Economically Important Weeds In Multiple Regions Of The United States. Part 2: Grass Species, Lauren M. Schwartz-Lazaro, Lovreet S. Shergill, Jeffrey A. Evans, Muthukumar V. Bagavathiannan, Shawn C. Beam, Mandy D. Bish, Jason A. Bond, Kevin W. Bradley, William S. Curran, Adam S. Davis, Wesley J. Everman, Michael L. Flessner, Steven C. Haring, Nicholas R. Jordan, Nicholas E. Korres, John L. Lindquist, Jason K. Norsworthy, Tameka L. Sanders, Larry E. Steckel, Mark J. Vangessel, Blake Young, Steven B. Mirsky

Department of Agronomy and Horticulture: Faculty Publications

Seed shatter is an important weediness trait on which the efficacy of harvest weed seed control (HWSC) depends. The level of seed shatter in a species is likely influenced by agroecological and environmental factors. In 2016 and 2017, we assessed seed shatter of eight economically important grass weed species in soybean [Glycine max (L.) Merr.] from crop physiological maturity to 4 wk after maturity at multiple sites spread across 11 states in the southern, northern, and mid-Atlantic United States. From soybean maturity to 4 wk after maturity, cumulative percent seed shatter was lowest in the southern U.S. regions and increased …

Coal Char Effects On Soil Chemical Properties And Maize Yields In Semi-Arid Region, Dinesh Panday, Maysoon M. Mikha, Xiaocun Sun, Bijesh Maharjan

Department of Agronomy and Horticulture: Faculty Publications

Soil amendments with high carbon (C) content can be effective in semi-arid regions where soils are characterized by low C. A field study was conducted in 2016–2018 to evaluate the effect of char on soil chemical properties and irrigated maize (Zea mays L.) yields in sandy loam fertilized with urea or composted manure. Carbon-rich char used was a product of coal combustion residue from a local factory in western Nebraska. The experiment was arranged in a split-plot randomized complete block design in four replications with char (0, 6.7, 13.4, 20.1, and 26.8Mg C ha⁻¹) as main and …

A Comparison Of Media To Determine Optimal Growth In Aquaponics: Prg Virtual Showcase January 2021, Rachel L. Fogle, Andrea Nagy, Claribel Asare, Steven Berry, Jordan Brown, Aquila Durham-Lewis

Harrisburg University Presidential Research Grants

No abstract provided.

Identification Of Loci Influencing Teosinte Crossing Barrier 1 (Tcb1) Efficacy In Maize By Quantitative Trait Loci (Qtl) Mapping And Genome-Wide Association Study (Gwas), Namrata Maharjan

Electronic Theses and Dissertations

Pollen cross-contamination has been a major problem for maize breeders. Various mechanical methods applied to avoid the contaminations are ineffective. The genetic factors related to maize fertilization can be used to develop an effective method to prevent pollen contamination. Pollen rejection ability controlled by Teosinte crossing barrier 1 (Tcb1) is such a genetic system. Silks possessing dominant Tcb1-s reject pollen possessing the recessive allele (tcb1). Successful fertilization occurs when Tcb1-s pollen falls upon tcb1 silks. The efficacy of dominant Tcb1-s was, however, reduced when repeatedly backcross with maize inbred lines, which suggests that there are modifiers to Tcb1-s. To find …

A Biocontrol Pesticide Derived From Mycovirus-Infected Sclerotinia Sclerotiorum Can Induce Plant Resistance, Connor Pedersen

Electronic Theses and Dissertations

Soybean leaf-associated gemycircularvirus-1 (SlaGemV-1) is a novel mycovirus discovered through the metagenomic sequencing of soybean leaves which is capable of inducing hypovirulence in the highly pathogenic fungus Sclerotinia sclerotiorum. RNASeq analysis techniques were used to determine the transcriptional changes caused by the infection of virus in S. sclerotiorum, as well as the transcriptional changes in Glycine max caused by the colonization of hypovirulent, SlaGemV-1-infected S. sclerotiorum. RNASeq results indicate that viral infection leading to hypovirulence may attenuate expression of genes relating to cell wall synthesis, microtubule formation, and metabolism of steroids and natural antibiotics. Cytochrome P450-related genes, kinesin domain genes, …

Transcriptomics Reveals The Putative Mycoparasitic Strategy Of The Mushroom Entoloma Abortivum On Species Of The Mushroom Genus Armillaria, Rachel A. Koch, Joshua R. Herr

Department of Plant Pathology: Faculty Publications

During mycoparasitism, a fungus—the host—is parasitized by another fungus—the mycoparasite. The genetic underpinnings of these relationships have been best characterized in ascomycete fungi. However, within basidiomycete fungi, there are rare instances of mushroom-forming species parasitizing the reproductive structures, or sporocarps, of other mushroom-forming species, which have been rarely investigated on a genetic level. One of the most enigmatic of these occurs between Entoloma abortivum and species of Armillaria, where hyphae of E. abortivum are hypothesized to disrupt the development of Armillaria sporocarps, resulting in the formation of carpophoroids. However, it remains unknown whether carpophoroids are the direct result of …

Genetic (Co)Variation And Accuracy Of Selection For Resistance To Viral Mosaic Disease And Production Traits In An Inter-Ecotypic Switchgrass Breeding Population, Serge J. Edmé, Gautam Sarath, Nathan Palmer, Gary Y. Yuen, Anthony A. Muhle, Rob Mitchell, Satyanarayana Tatineni, Christian Tobias

Department of Plant Pathology: Faculty Publications

Obtaining good accuracy and reliability of estimated breeding values is essential to increase the efficiency of a plant breeding program. Genetic variation was assessed for categorical (Virc) and binary (Virb) mosaic (caused by Panicum mosaic virus), dry matter (DMY) and predicted ethanol (Etoh) yields, and lignin content (Klason or KL, and acid-detergent or ADL) in a Summer–Kanlow switchgrass (Panicum virgatum L.) population. Breeding values were predicted with the restricted maximum likelihood–best linear unbiased prediction (REML-BLUP) approaches using a multivariate phenotypic (PBLUP) and animal (ABLUP) models, integrating a three-generation pedigree (1,622 half-sibs) in ABLUP and not in PBLUP. Models …

Poplar Allene Oxide Synthase 1 Gene Promoter Drives Rapid And Localized Expression By Wounding, Bin Lei, Christopher J. Frost, Tao Xu, Joshua Herr, John E. Carlson, Haiying Liang

Department of Plant Pathology: Faculty Publications

Promoters play critical roles in controlling the transcription of genes and are important as tools to drive heterologous expression for biotechnological applications. In addition to core transcription factor-binding motifs that assist in the binding of RNA polymerases, there are specific nucleotide sequences in a promoter region to allow regulation of gene expression. The allene oxide synthase (AOS) gene family are cytochrome P450s that are responsive to a variety of environmental stress, making them good candidates for the discovery of inducible promoters. Populus AOS homologs separate phylogenetically into two clades. Based on the 19 promoter motifs with significant abundance differences between …

Pratylenchus Smoliki, A New Nematode Species (Pratylenchidae: Tylenchomorpha) From The Great Plains Region Of North America, Thomas Powers, Timothy Todd, Tim Harris, Rebecca Higgins, Ann Macguidwin, Peter Mullin, Mehmet Ozbayrak, Kirsten Powers, Kanan Sakai

Department of Plant Pathology: Faculty Publications

Pratylenchus smoliki is a new species of root-lesion nematode described from corn-soybean production fields in the Central Great Plains of North America. It is characterized by populations with relatively abundant males, two lip annuli, females with a round functional spermatheca and a conoid to subcylindrical tail with a non-crenate, smooth terminus. In host preference tests, corn and wheat produce the largest nematode populations, whereas sorghum and soybeans produce less than 20% the numbers observed on corn. Scanning electron microscopy reveals that the en face patterns compare to those seen in Pratylenchus pseudocoffeae, P. scribneri, P. hexincisus, and …

Studying Morphological, Physiological, And Molecular Regulation Of Stomatal Conductance And Its Relationship To Water Use Efficiency In Alfalfa, Surbhi Gupta

Electronic Theses and Dissertations

Alfalfa (Medicago sativa), being a leguminous, highly fibrous, and proteinaceous plant has always been one of the top choices for the forage production but has high cost of irrigation in many dry and warm areas such as California and Arizona. Thus, a reduction of irrigation by using the higher water use efficiency (WUE) varieties can help the growers in reducing the cost and is critical for sustainable agriculture production. WUE is closely related to water loss through transpiring stomata. A study in our lab reported that Riverside (RS) an alfalfa genotype that has naturized in the national grassland in South …

That Code-Switching Switchgrass - A Root Analysis Of Two Ecotypes Of P. Virgatum Under Temperture Variations, Hannah Johnson

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

Impact Of Arbuscular Mycorrhizal Fungi On Conyza Canadensis Drought Responses And Possible Mechanisms, Kian G.M. Speck, Ylva Lekberg, Anna Sala

Undergraduate Theses, Professional Papers, and Capstone Artifacts

• Arbuscular mycorrhizal fungi (AMF) are important plant mutualists that can facilitate plant responses to various environmental stressors, such as drought. A plant that may benefit from AMF-induced drought tolerance is Conyza canadensis due to its ability to thrive in dry conditions and its high colonization rate. However, no studies have researched C. canadensis in this context and the exact mechanisms of AMF-induced drought tolerance are still unknown.
• To better understand if and how AMF facilitate drought response in C. canadensis, we conducted a greenhouse experiment comparing the response of mycorrhizal and non-mycorrhizal plants to three watering levels. We measured …

James B Beard: The Father Of Contemporary Turfgrass Science, G.K. Stahnke, P.E. Rieke, Robert C. Shearman, Roch E. Gaussoin, David Kopec

Department of Agronomy and Horticulture: Faculty Publications

James B Beard (24 Sept 1935 to 8 May 2018) can rightly be considered the “Father” of contemporary turfgrass science. During his career, he was known for setting a standard that provided the foundation for turfgrass science through his thorough approach to research, teaching, mentoring and communications. The books he published outlined a vision for an evolving scientific discipline. He trained and mentored >45 domestic and international doctoral and master students and numerous post-doctoral trainees, who in turn continued to raise the quality of contemporary turfgrass science in the USA and internationally. He led the effort to change the name …