Genetics and Genomics Commons^™

Herbicide-Resistant Risk Assessment: Response Of Common Nebraska Weeds To Dicamba Dose, Roberto J. Crespo

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Dicamba-resistant soybeans are being developed to provide an additional herbicide mechanism of action that can be used in soybean, and to provide a tool to help manage or mitigate the evolution of other herbicide-resistant weed populations. The objectives of this thesis were to assess the risk of common Nebraska weeds developing resistance to dicamba, quantify baseline dose-response to dicamba of high-risk weed species, and survey the variability in dicamba dose-response among populations of those species. Twenty-five weed scientists were asked to estimate the risk likelihood of ten weed species evolving resistance to dicamba following the commercialization of dicamba-resistant soybean. Palmer …

Oral Presentation: Plant Genes And Drought Tolerance, Norris Lam

Festival of Communities: UG Symposium (Posters)

Research has shown that a gene from C3 xerophyte Larrea tridentata (creosote bush), LtWRKY21, is involved in pathways governing creosote bush’s high tolerance to environmental stress. By understanding the way in which creosote bush adapts to drought, crop plants can be engineered to be more drought tolerant during times of imminent global climate change. To study the underlying mechanisms of creosote bush drought response, the LtWRKY21 gene was mobilized into the model organism Arabidopsis thaliana. Chlorophyll degradation, cellular electrolyte leakage, and water content in leaves will serve as indicators of drought tolerance in LtWRKY21-transgenic A. thaliana after treatment in chemically …

Screening Synteny Blocks In Pairwise Genome Comparisons Through Integer Programming, Haibao Tang, Eric Lyons, Brent S. Pedersen, James C. Schnable, Andrew H. Paterson, Michael Freeling

Department of Agronomy and Horticulture: Faculty Publications

Background:

It is difficult to accurately interpret chromosomal correspondences such as true orthology and paralogy due to significant divergence of genomes from a common ancestor. Analyses are particularly problematic among lineages that have repeatedly experienced whole genome duplication (WGD) events. To compare multiple “subgenomes” derived from genome duplications, we need to relax the traditional requirements of “one-to-one” syntenic matchings of genomic regions in order to reflect “one-to-many” or more generally “many-to-many” matchings. However this relaxation may result in the identification of synteny blocks that are derived from ancient shared WGDs that are not of interest. For many downstream analyses, we …

Leaf Number Indicates Salt Tolerance Of Young Seedling Families Of European Aspen (Populus Tremula L.) Growing In Different Soils, Lu-Min Vaario, Kim Yrjälä, Matti Rousi, Timo Sipila, Pertti Pulkkinen

Aspen Bibliography

Soil salinity limits plant productivity and quality. We evaluated the response of 12 aspen (Populus tremula) families to salt stress in two different soils irrigated for 4-weeks with 0, 80 or 160 mM saline solution. Easily measurable characteristics such as shoot height, leaf number, dry mass as well as the distribution of sodium (Na+) ions were measured in 5-month-old aspen seedlings raised in controlled greenhouse conditions on two different soils. Growth among families varied significantly, and the interaction between family and soil type was significant. From 2–5 months, leaf number correlated with that of the first month and salin-ity tolerance. …

Genes Identified By Visible Mutant Phenotypes Show Increased Bias Toward One Of Two Subgenomes Of Maize, James C. Schnable, Michael Freeling

Department of Agronomy and Horticulture: Faculty Publications

Not all genes are created equal. Despite being supported by sequence conservation and expression data, knockout homozygotes of many genes show no visible effects, at least under laboratory conditions. We have identified a set of maize (Zea mays L.) genes which have been the subject of a disproportionate share of publications recorded at MaizeGDB. We manually anchored these ‘‘classical’’ maize genes to gene models in the B73 reference genome, and identified syntenic orthologs in other grass genomes. In addition to proofing the most recent version 2 maize gene models, we show that a subset of these genes, those that …

Dose–Sensitivity, Conserved Non-Coding Sequences, And Duplicate Gene Retention Through Multiple Tetraploidies In The Grasses, James C. Schnable, Brent S. Pedersen, Sabarinath Subramaniam, Michael Freeling

Department of Agronomy and Horticulture: Faculty Publications

Whole genome duplications, or tetraploidies, are an important source of increased gene content. Following whole genome duplication, duplicate copies of many genes are lost from the genome. This loss of genes is biased both in the classes of genes deleted and the subgenome from which they are lost. Many or all classes are genes preferentially retained as duplicate copies are engaged in dose sensitive protein–protein interactions, such that deletion of any one duplicate upsets the status quo of subunit concentrations, and presumably lowers fitness as a result. Transcription factors are also preferentially retained following every whole genome duplications studied. This …

Adventures In The Enormous: A 1.8 Million Clone Bac Library For The 21.7 Gb Genome Of Loblolly Pine., Zenaida V. Magbanua, Seval Ozkan, Benjamin D. Bartlett, Philippe Chouvarine, Christopher A. Saski, Aaron Liston, Richard C. Cronn, C. Dana Nelson, Daniel G. Peterson

CALS Publications

Loblolly pine (LP; Pinus taeda L.) is the most economically important tree in the U.S. and a cornerstone species in southeastern forests. However, genomics research on LP and other conifers has lagged behind studies on flowering plants due, in part, to the large size of conifer genomes. As a means to accelerate conifer genome research, we constructed a BAC library for the LP genotype 7-56. The LP BAC library consists of 1,824,768 individually-archived clones making it the largest single BAC library constructed to date, has a mean insert size of 96 kb, and affords 7.6X coverage of the 21.7 Gb …

Minimal Art: Or Why Small Viral K+ Channels Are Good Tools For Understanding Basic Structure And Function Relations, Gerhard Thiel, Dirk Baumeister, Indra Schroeder, Stefan M. Kast, James L. Van Etten, Anna Moroni

James Van Etten Publications

Some algal viruses contain genes that encode proteins with the hallmarks of K+ channels. One feature of these proteins is that they are less than 100 amino acids in size, which make them truly minimal for a K+ channel protein. That is, they consist of only the pore module present in more complex K+ channels. The combination of miniature size and the functional robustness of the viral K+ channels make them ideal model systems for studying how K+ channels work. Here we summarize recent structure/function correlates from these channels, which provide insight into functional properties such as gating, pharmacology and …

Functional Hak/Kup/Kt-Like Potassium Transporter Encoded By Chlorella Viruses, Timo Greiner, José Ramos, Maria C. Alvarez, James Gurnon, Ming Kang, James L. Van Etten, Anna Moroni, Gerhard Thiel

James Van Etten Publications

Chlorella viruses are a source of interesting membrane transport proteins. Here we examine a putative K+ transporter encoded by virus FR483 and related chlorella viruses. The protein shares sequence and structural features with HAK/KUP/KT-like K+ transporters from plants, bacteria and fungi. Yeast complementation assays and Rb+ uptake experiments show that the viral protein, termed HAKCV (high-affinity K+ transporter of chlorella virus), is functional, with transport characteristics that are similar to those of known K+ transporters. Expression studies revealed that the protein is expressed as an early gene during viral replication, and proteomics data indicate that it is not packaged in …

Multicentury Fire And Forest Histories At 19 Sites In Utah And Eastern Nevada, Emily K. Heyerdahl, Peter M. Brown, Stanley G. Kitchen, Marc H. Weber

Aspen Bibliography

Our objective is to provide site-specific fire and forest histories from Utah and eastern Nevada that can be used for land management or additional research. We systematically sampled fire scars and tree-recruitment dates across broad gradients in elevation and forest type at 13 sites in Utah and 1 in eastern Nevada to characterize spatial and temporal variation in historical fire regimes as well as forest structure and composition. We collected similar data non-systematically at five additional sites in Utah. These 19 sites include a broad range of forest types (from pinyon-juniper woodlands to spruce-fir forests) and fire regime types. In …

Giant Viruses, James L. Van Etten

James Van Etten Publications

The common view of viruses, mostly true, is of tiny burglars that sneak into cells, grab the biosynthetic controls and compel the cell to make huge numbers of progeny that break out of the cell and keep the replication cycle going. Viruses are supposed to be diminutive even compared to cells that are just a micrometer (1,000 nanometers) in diameter. They are supposed to travel light, making do with just a few well-adapted genes.

In 1992, a new microorganism was isolated from a power-plant cooling tower in Bradford, England, where Timothy Robotham, a microbiologist at Leeds Public Health Laboratory, was …

A Novel Gene Silencing Vector For Plant Genomics And Biotechnology, Dustin Hoover, Scott Nicholson, Vibha Srivastava

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

Gene silencing is a process of suppressing activity of specific genes by producing “interfering” RNA encoded by foreign genes. This process serves as the principle of genetic modification in plants and animals, which is an important tool in genomics and biotechnology, allowing scientists to manipulate organisms to better meet human demands. New approaches of gene silencing may enable improvements on current practices of genetic modification, and broaden the application and impact of gene silencing in biotechnology. Recently, a novel vector design consisting of the transcription of short gene fragments lacking transcription termination signals was demonstrated to be effective in partial …

The Arabidopsis Trithorax-Like Factor Atx1 Functions In Dehydration Stress Responses Via Aba-Dependent And Aba-Independent Pathways, Yong Ding, Zoya Avramova, Michael Fromm

School of Biological Sciences: Faculty Publications

Emerging evidence suggests that the molecular mechanisms driving the responses of plants to environmental stresses are associated with specific chromatin modifications. Here, we demonstrate that the Arabidopsis trithorax-like factor ATX1, which trimethylates histone H3 at lysine 4 (H3K4me3), is involved in dehydration stress signaling in both abscisic acid (ABA)-dependent and ABA-independent pathways. The loss of function of ATX1 results in decreased germination rates, larger stomatal apertures, more rapid transpiration and decreased tolerance to dehydration stress in atx1 plants. This deficiency is caused in part by reduced ABA biosynthesis in atx1 plants resulting from decreased transcript levels from NCED3, which …

Oregon Aspen Project, Forest Restoration Partnership

Aspen Bibliography

The Oregon Aspen Project was initiated in response to the decline of aspen groves in Oregon and throughout the Western United States, and the lack of information to guide managers interested in stewardship to enhance this resource. There were three central goals and accompanying objectives for this project which are listed below. The project accomplishments are provided below each bulleted objective

Phenotypic And Genetic Characterization Of Wildland Collections Of Western And Searls Prairie Clovers For Rangeland Revegetation In The Western Usa, Kishor Bhattarai

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Western prairie clover [Dalea ornata (Douglas ex Hook.) Eaton & J. Wright] is a perennial legume that occurs in the northern Great Basin, Snake River Basin, and southern Columbia Plateau, whereas Searls prairie clover [Dalea searlsiae (A. Gray) Barneby], also a perennial legume, occurs in the southern Great Basin and surrounding areas. Understanding the genetic and ecotypic variation of these prairie clovers is a prerequisite for developing populations suitable for rangeland revegetation in the western USA. DNA sequences of internal transcribed spacer (ITS/5.8S) and trnK/matK were used to study the phylogeny of these species. The species were distinguished …

Quantitative Trait Loci For Agronomic And End-Use Quality Performance And The Effect Of Soilborne Wheat Mosaic Virus In A Hard Winter Wheat Population In Nebraska, Nicholas A. Crowley

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

To better understand agronomic and end-use quality in wheat (Triticum aestivum L.) we developed a population containing 154 F6:8 recombinant inbred lines (RILs) from the cross TAM107-R7/Arlin. The parental lines and RILs were phenotyped at six environments in Nebraska and differed for resistance to Wheat soilborne mosaic virus (WSBMV), morphological, agronomic, and end-use quality traits. Additionally, a 2300 cM genome-wide linkage map was created for quantitative trait loci (QTL) analysis. Based on our results across multiple environments, the best RILs could be used for cultivar improvement. The population and marker data are publicly available for interested researchers for future research. …

Determining The Fate Of Hybridized Genomes In The Allopolyploid Brassica Napus, Tina Y. Wang

Master's Theses

Polyploidy is widely acknowledged as a widespread mechanism in the evolution and speciation of the majority of flowering plants. Allopolyploid forms through interspecific hybridization and whole genome duplication. While allopolyploids may display increased vigor relative to their progenitors, they can also face challenges to fertility following hybridization. Genetic changes in allopolyploids result from recombination between the hybridized subgenomes, which can influence phenotype and ultimately determine fitness of future generations. To study dynamic changes that follow allopolyploid formation, Brassica napus lineages were derived by hybridizing Brassica oleracea and Brassica rapa. Two lineages of B. napus were analyzed for genetic and phenotypic …

Following Tetraploidy In Maize, A Short Deletion Mechanism Removed Genes Preferentially From One Of The Two Homeologs, Margaret R. Woodhouse, James C. Schnable, Brent S. Pedersen, Eric Lyons, Damon Lisch, Shabarinath Subramaniam, Michael Freeling

Department of Agronomy and Horticulture: Faculty Publications

Previous work in Arabidopsis showed that after an ancient tetraploidy event, genes were preferentially removed from one of the two homeologs, a process known as fractionation. The mechanism of fractionation is unknown. We sought to determine whether such preferential, or biased, fractionation exists in maize and, if so, whether a specific mechanism could be implicated in this process. We studied the process of fractionation using two recently sequenced grass species: sorghum and maize. The maize lineage has experienced a tetraploidy since its divergence from sorghum approximately 12 million years ago, and fragments of many knocked-out genes retain enough sequence similarity …

A Functional Calcium-Transporting Atpase Encoded By Chlorella Viruses, Maria Cristina Bonza, Holger Martin, Ming Kang, Gentry L. Lewis, Timo Greiner, Sonia Giacometti, James L. Van Etten, Maria Ida De Michelis, Gerhard Thiel, Anna Moroni

James Van Etten Publications

Calcium-transporting ATPases (Ca²⁺ pumps) are major players in maintaining calcium homeostasis in the cell and have been detected in all cellular organisms. Here, we report the identification of two putative Ca²⁺ pumps, M535L and C785L, encoded by chlorella viruses MT325 and AR158, respectively, and the functional characterization of M535L. Phylogenetic and sequence analyses place the viral proteins in group IIB of P-type ATPases even though they lack a typical feature of this class, a calmodulin-binding domain. A Ca²⁺ pump gene is present in 45 of 47 viruses tested and is transcribed during virus infection. Complementation analysis of …

Identification Of An L-Rhamnose Synthetic Pathway In Two Nucleocytoplasmic Large Dna Viruses, Madhu Parakkottil Chothi, Garry A. Duncan, Andrea Armirotti, Chantal Abergel, James R. Gurnon, James L. Van Etten, Cinzia Bernardi, Gianluca Damonte, Michela Tonetti

James Van Etten Publications

Nucleocytoplasmic large DNA viruses (NCLDVs) are characterized by large genomes that often encode proteins not commonly found in viruses. Two species in this group are Acanthocystis turfacea chlorella virus 1 (ATCV-1) (family Phycodnaviridae, genus Chlorovirus) and Acanthamoeba polyphaga mimivirus (family Mimiviridae), commonly known as mimivirus. ATCV-1 and other chlorovirus members encode enzymes involved in the synthesis and glycosylation of their structural proteins. In this study, we identified and characterized three enzymes responsible for the synthesis of the sugar L-rhamnose: two UDP-D-glucose 4,6-dehydratases (UGDs) encoded by ATCV-1 and mimivirus and a bifunctional UDP-4-keto-6-deoxy-D-glucose epimerase/reductase (UGER) from mimivirus. Phylogenetic …

Genomic Perspectives On Evolution In Bracken Fern, Joshua P. Der

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The fern genus Pteridium comprises a number of closely related species distributed throughout the world. Collectively they are called bracken ferns and have historically been treated as a single species, Pteridium aquilinum. Bracken is notorious as a toxic weed that colonizes open fields and poisons livestock. Bracken is also easily cultured and has become one of the most intensively studied ferns. Bracken has been used as a model system for the study of the fern life cycle, fern gametophyte development, the pheromonal mechanism of sex determination, toxicology, invasion ecology, and climate change. This dissertation places bracken within a global …

Damage Agents And Condition Of Mature Aspen Stands In Montana And Northern Idaho, Brytten E. Steed, Holly S.J. Kearns

Aspen Bibliography

No abstract provided.

Implications Of The Plastid Genome Sequence Of Typha (Typhaceae, Poales) For Understanding Genome Evolution In Poaceae, Mary M. Guisinger, Timothy W. Chumley, Jennifer V. Kuehl, Jeffrey L. Boore, Robert K. Jansen

All Faculty Scholarship for the College of the Sciences

Plastid genomes of the grasses (Poaceae) are unusual in their organization and rates of sequence evolution. There has been a recent surge in the availability of grass plastid genome sequences, but a comprehensive comparative analysis of genome evolution has not been performed that includes any related families in the Poales. We report on the plastid genome of Typha latifolia, the first non-grass Poales sequenced to date, and we present comparisons of genome organization and sequence evolution within Poales. Our results confirm that grass plastid genomes exhibit acceleration in both genomic rearrangements and nucleotide substitutions. Poaceae have multiple structural rearrangements, including …

Genetic Variation At Nuclear Loci Fails To Distinguish Two Morphologically Distinct Species Of Aquilegia, Elizabeth A. Cooper, Justen B. Whittall, Scott A. Hodges, Magnus Nordborg

Biology

Aquilegia formosa and pubescens are two closely related species belonging to the columbine genus. Despite their morphological and ecological differences, previous studies have revealed a large degree of intercompatibility, as well as little sequence divergence between these two taxa [1,2]. We compared the inter- and intraspecific patterns of variation for 9 nuclear loci, and found that the two species were practically indistinguishable at the level of DNA sequence polymorphism, indicating either very recent speciation or continued gene flow. As a comparison, we also analyzed variation at two loci across 30 other Aquilegia taxa; this revealed slightly more differentiation among taxa, …

Genetic Variation In Past And Current Landscapes: Conservation Implications Based On Six Endemic Florida Scrub Plants, Eric S. Menges, Rebecca W. Dolan, Robert Pickert, Rebecca Yahr, Doria R. Gordon

Scholarship and Professional Work - LAS

If genetic variation is often positively correlated with population sizes and the presence of nearby populations and suitable habitats, landscape proxies could inform conservation decisions without genetic analyses. For six Florida scrub endemic plants (Dicerandra frutescens, Eryngium cuneifolium, Hypericum cumulicola, Liatris ohlingerae, Nolina brittoniana, and Warea carteri), we relate two measures of genetic variation, expected heterozygosity and alleles per polymorphic locus (APL), to population size and landscape variables. Presettlement areas were estimated based on soil preferences and GIS soils maps. Four species showed no genetic patterns related to population or landscape factors. The …

Crystal Structure Of A Virus-Encoded Putative Glycosyltransferase, Yi Xiang, Ulrich Baxa, Ying Zhang, Alasdair C. Steven, Gentry L. Lewis, James L. Van Etten, Michael G. Rossmann

James Van Etten Publications

The chloroviruses (family Phycodnaviridae), unlike most viruses, encode some, if not most, of the enzymes involved in the glycosylation of their structural proteins. Annotation of the gene product B736L from chlorovirus NY-2A suggests that it is a glycosyltransferase. The structure of the recombinantly expressed B736L protein was determined by X-ray crystallography to 2.3-Å resolution, and the protein was shown to have two nucleotide-binding folds like other glycosyltransferase type B enzymes. This is the second structure of a chlorovirus-encoded glycosyltransferase and the first structure of a chlorovirus type B enzyme to be determined. B736L is a retaining enzyme and belongs …

The Role Of Cuticle, Fatty Acids, And Lipid Signaling In Plant Defense, Ye Xia

Theses and Dissertations--Plant Pathology

Systemic acquired resistance (SAR) is initiated upon recognition of specific microbial effectors by cognate plant resistance proteins and immunizes distal tissues of plants against secondary infections. SAR involves the generation of a mobile signal at the site of primary infection, which then translocates to and activates defense responses in the distal tissues via some unknown mechanism(s). This study shows that an ACYL CARRIER PROTEIN 4 (ACP4), GLABRA1 (GL1) and ACYL CARRIER BINDING PROTEINS (ACBP) are required for the processing of the mobile SAR signal in distal tissues of Arabidopsis. Although acp4, gl1 and acbp plants generate the mobile signal, …

Microarray Analysis Of Paramecium Bursaria Chlorella Virus 1 Transcription, Giane M. Yanai-Balser, Garry A. Duncan, James D. Eudy, Dong Wang, Xiao Li, Irina V. Agarkova, David D. Dunigan, James L. Van Etten

James Van Etten Publications

Paramecium bursaria chlorella virus 1 (PBCV-1), a member of the family Phycodnaviridae, is a large doublestranded DNA, plaque-forming virus that infects the unicellular green alga Chlorella sp. strain NC64A. The 330-kb PBCV-1 genome is predicted to encode 365 proteins and 11 tRNAs. To monitor global transcription during PBCV-1 replication, a microarray containing 50-mer probes to the PBCV-1 365 protein-encoding genes (CDSs) was constructed. Competitive hybridization experiments were conducted by using cDNAs from poly(A)- containing RNAs obtained from cells at seven time points after virus infection. The results led to the following conclusions: (i) the PBCV-1 replication cycle is temporally …

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 = …

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 …