Genetics and Genomics Commons^™

Ploidy Number For Panicum Virgatum (Switchgrass) From The Long Island Sound Coastal Lowland Compared To Upland And Lowland Cultivars., Tanisha Williams, Carol Auer

Plant Science Articles

Panicum virgatum L. (switchgrass) is a native, perennial grass in North America with important ecological function in ecoregions including the Long Island Sound Coastal Lowland in the Northeastern United States. In recent decades, switchgrass has become a model lignocellulosic bioenergy crop with a large research portfolio describing its distribution, genetics, genomics, phenology, traits, gene flow, and cultivation. Switchgrass has been divided into two ecotypes, the Lowland ecotype which is tetraploid (2n= 4x= 36 chromosomes) and the Upland ecotype which is tetraploid or octaploid (2n= 8x= 72). While most switchgrass research has focused on genotypes from the Midwest or Southeastern regions, …

Chlorovirus Atcv-1 Is Part Of The Human Oropharyngeal Virome And Is Associated With Changes In Cognitive Functions In Humans And Mice, Robert H. Yolken, Lorraine Jones-Brando, David D. Dunigan, Geetha Kannan, Faith Dickerson, Emily Severance, Sarven Sabunciyan, C. Conover Talbot Jr., Emese Prandovszky, James R. Gurnon, Irina V. Agarkova, Flora Leister, Kristin L. Gressitt, Ou Chen, Bryan Deuber, Fangrui Ma, Mikhail V. Pletnikov, James L. Van Etten

James Van Etten Publications

Chloroviruses (family Phycodnaviridae) are large DNA viruses known to infect certain eukaryotic green algae and have not been previously shown to infect humans or to be part of the human virome. We unexpectedly found sequences homologous to the chlorovirus Acanthocystis turfacea chlorella virus 1 (ATCV-1) in a metagenomic analysis of DNA extracted from human oropharyngeal samples. These samples were obtained by throat swabs of adults without a psychiatric disorder or serious physical illness who were participating in a study that included measures of cognitive functioning. The presence of ATCV-1 DNA was confirmed by quantitative PCR with ATCV-1 DNA being …

Legume Crops Phylogeny And Genetic Diversity For Science And Breeding, Petr Smýkal, Clarice J. Coyne, Mike J. Ambrose, Nigel Maxted, Hanno Schaefer, Matthew W. Blair

Agricultural and Environmental Sciences Faculty Research

Economically, legumes (Fabaceae) represent the second most important family of crop plants after the grass family, Poaceae. Grain legumes account for 27% of world crop production and provide 33% of the dietary protein consumed by humans, while pasture and forage legumes provide vital part of animal feed. Fabaceae, the third largest family of flowering plants, has traditionally been divided into the following three subfamilies: Caesalpinioideae, Mimosoideae, and Papilionoideae, all together with 800 genera and 20,000 species. The latter subfamily contains most of the major cultivated food and feed crops. Among the grain legumes are some of mankind's earliest crop plants, …

Chlorovirus Skp1-Binding Ankyrin Repeat Protein Interplay And Mimicry Of Cellular Ubiquitin Ligase Machinery, Eric A. Noel, Ming Kang, Jiri Adamec, James L. Van Etten, George A. Oyler

James Van Etten Publications

The ubiquitin-proteasome system is targeted by many viruses that have evolved strategies to redirect host ubiquitination machinery. Members of the genus Chlorovirus are proposed to share an ancestral lineage with a broader group of related viruses, nucleo-cytoplasmic large DNA viruses (NCLDV). Chloroviruses encode an Skp1 homolog and ankyrin repeat (ANK) proteins. Several chlorovirus-encoded ANK repeats contain C-terminal domains characteristic of cellular F-boxes or related NCLDV chordopox PRANC (pox protein repeats of ankyrin at C-terminal) domains. These observations suggested that this unique combination of Skp1 and ANK repeat proteins might form complexes analogous to the cellular Skp1-Cul1-F-box (SCF) ubiquitin ligase complex. …

The Trehalose Pathway In Maize: Conservation And Gene Regulation In Response To The Diurnal Cycle And Extended Darkness, Clémence Henry, Samuel W. Bledsoe, Allison Siekman, Alec Kollman, Brian M. Waters, Regina Feil, Mark Stitt, L. Mark Lagrimini

Department of Agronomy and Horticulture: Faculty Publications

Energy resources in plants are managed in continuously changing environments, such as changes occurring during the day/night cycle. Shading is an environmental disruption that decreases photosynthesis, compromises energy status, and impacts on crop productivity. The trehalose pathway plays a central but not well-defined role in maintaining energy balance. Here, we characterized the maize trehalose pathway genes and deciphered the impacts of the diurnal cycle and disruption of the day/night cycle on trehalose pathway gene expression and sugar metabolism. The maize genome encodes 14 trehalose-6-phosphate synthase (TPS) genes, 11 trehalose-6-phosphate phosphatase (TPP) genes, and one trehalase gene. Transcript abundance of most …

Chlorovirus Pbcv-1 Encodes An Active Copper-Zinc Superoxide Dismutase, Ming Kang, Garry A. Duncan, Charles Kuszynski, George Oyler, Jiayin Zheng, Donald F. Becker, James L. Van Etten

James Van Etten Publications

Superoxide dismutases (SODs) are metalloproteins that protect organisms from toxic reactive oxygen species by catalyzing the conversion of superoxide anion to hydrogen peroxide and molecular oxygen. Chlorovirus PBCV-1 encodes a 187-amino-acid protein that resembles a Cu-Zn SOD with all of the conserved amino acid residues for binding copper and zinc (named cvSOD). cvSOD has an internal Met that results in a 165-amino-acid protein (named tcvSOD). Both cvSOD and tcvSOD recombinant proteins inhibited nitroblue tetrazolium reduction of superoxide anion generated in a xanthine-xanthine oxidase system in solution. tcvSOD was chosen for further characterization because it was easier to produce. Recombinant tcvSOD …

Expression Of Chlorovirus Mt325 Aquaglyceroporin (Aqpv1) In Tobacco And Its Role In Mitigating Drought Stress, Saadia Bihmidine, Mingxia Cao, Ming Kang, Tala Awada, James L. Van Etten, David Dunigan, Thomas E. Clemente

James Van Etten Publications

Main conclusions A Chlorovirus aquaglyceroporin expressed in tobacco is localized to the plastid and plasma membranes. Transgenic events display improved response to water deficit. Necrosis in adult stage plants is observed.

Aquaglyceroporins are a subclass of the water channel aquaporin proteins (AQPs) that transport glycerol along with other small molecules transcellular in addition to water. In the studies communicated herein, we analyzed the expression of the aquaglyceroporin gene designated, aqpv1, from Chlorovirus MT325, in tobacco (Nicotiana tabacum), along with phenotypic changes induced by aqpv1 expression in planta. Interestingly, aqpv1 expression under control of either a constitutive or …

Functional Genomics Of Maize Endosperm Maturation And Protein Quality, Lingling Yuan

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

Maize is one of the most important cereal crops and widely cultivated throughout the world. The study on maize kernel development including protein quality improvement is essential for removing dietary protein deficiency because of the lack of essential amino acids, especially lysine and tryptophan, in maize kernel. Quality Protein Maize (QPM) is a hard kernel variant of the high-lysine mutant, opaque-2. We created opaque QPM variants to identify opaque-2 modifier genes and to investigate deletion mutagenesis combined with Illumina sequencing as a maize functional genomics tool. A K0326Y-QPM deletion mutant, line 107, was null for the 27- and 50-kD …

Genome-Wide Analysis And Expression Profile Of The Bzip Transcription Factor Gene Family In Grapevine (Vitis Vinifera), Jinyi Liu, Nana Chen, Fei Chen, Bin Cai, Silvia Dal Santo, Tornielli Battista Tornielli, Mario Pezzoti, Zong-Ming Cheng

Plant Sciences Publications and Other Works

Background

Basic leucine zipper (bZIP) transcription factor gene family is one of the largest and most diverse families in plants. Current studies have shown that the bZIP proteins regulate numerous growth and developmental processes and biotic and abiotic stress responses. Nonetheless, knowledge concerning the specific expression patterns and evolutionary history of plant bZIP family members remains very limited.

Results

We identified 55 bZIP transcription factor-encoding genes in the grapevine (Vitis vinifera) genome, and divided them into 10 groups according to the phylogenetic relationship with those in Arabidopsis. The chromosome distribution and the collinearity analyses suggest that expansion of …

Development Of A Quantitative Real-Time Polymerase Chain Reaction (Rt-Pcr) Assay For Plant Species, Kayla Curtis, Heather Miller Coyle

Forensic Science Publications

In order to facilitate optimal plant DNA quantitation and identification, an assay has been developed that uses generic plant PCR primers that amplify a region in the chloroplast genome of plant samples. The assay uses the SYBR green detection dye to detect the PCR product with a universal PCR primer set to the large subunit of ribulose bisphosphate carboxylase, rbcL, but can be used with any of the universal barcode primers for land plants (rbcL, matK, trnH, psbA). Standard dilutions of control wheat DNA of varying concentrations were tested to create a standard curve. Several plant DNA extractions of different …

Ficotylus Laselvae N. Sp. (Tylenchomorpha: Anguinidae) Associated With Ficus Colubrinae In Costa Rica, Robin M. Giblin-Davis, Natsumi Kanzaki, Kerrie A. Davies, Weimin Ye, Yongsan Zeng, Barbara J. Center, Alejandro Esquivel, Thomas O. Powers

Department of Plant Pathology: Faculty Publications

Ficotylus laselvae n. sp. was recovered from under the bracts of figs (syconia) of Ficus colubrinae from La Selva, Costa Rica, during a survey of nematode rainforest biodiversity and is described herein. This is only the second report of an association between the nematode suborder Tylenchina and the sycones of figs. Previous reports of most nematode associates of the sycones of figs have been from the lumen and involved transmission by female fig wasp pollinators (Agaonidae) during pollination/oviposition (e.g., Schistonchus and Parasitodiplogaster spp.). The association between F. laselvae n. sp. and Ficus colubrinae may involve an invertebrate host, …

Studies On Sensitivity Reduction In Solo And Mixture Treatments And Fungicide-Induced Mutagenesis In Monilinia Fructicola, Guido Schnabel, F. Chen, Sydney E. Everhart, W. C. Bridges, X. Liu

Department of Plant Pathology: Faculty Publications

Three fungicide-sensitive Monilinia fructicola isolates were exposed in weekly transfers of mycelia to a dose gradient of a DMI and a QoI fungicide (azoxystrobin) in solo or mixture treatments and fungicide sensitivity as well as genetic changes were assessed. Isolates showed a faster reduction in sensitivity (higher resistance factors) to azoxystrobin than to SYP-Z048; this process was slower in the mixture treatment. The decrease of fungicide sensitivity was not a heritable trait. Genomic mutagenesis at 8 of 15 microsatellite loci was evidenced in one of three isolates tested after exposure to azoxystrobin. These non-coding regions of the genome either showed …

Viruses As Nanoparticles: Structure Versus Collective Dynamics, S. Sirotkin, A. Mermet, M. Bergoin, V. Ward, James L. Van Etten

James Van Etten Publications

In order to test the application of the “nanoparticle” concept to viruses in terms of low-frequency dynamics, large viruses (140–190 nm) were compared to similar-sized polymer colloids using ultra-small-angle x-ray scattering and very-low-frequency Raman or Brillouin scattering. While both viruses and polymer colloids show comparable highly defined morphologies, with comparable abilities of forming self-assembled structures, their respective abilities to confine detectable acoustic vibrations, as expected for such monodisperse systems, differed. Possible reasons for these different behaviors are discussed.

Viruses Infecting Marine Picoplancton Encode Functional Potassium Ion Channels, Fenja Siotto, Corinna Martin, Oliver Rauh, James L. Van Etten, Indra Schroeder, Anna Moroni, Gerhard Thiel

James Van Etten Publications

Phycodnaviruses are dsDNA viruses, which infect algae. Their large genomes encode many gene products, like small K+ channels, with homologs in prokaryotes and eukaryotes. Screening for K+ channels revealed their abundance in viruses from fresh-water habitats. Recent sequencing of viruses from marine algae or from salt water in Antarctica revealed sequences with the predicted characteristics of K+ channels but with some unexpected features. Two genes encode either 78 or 79 amino acid proteins, which are the smallest known K+ channels. Also of interest is an unusual sequence in the canonical α-helixes in K+ channels. Structural prediction algorithms indicate that the …

Aba Signaling Is Necessary But Not Sufficient For Rd29b Transcriptional Memory During Successive Dehydration Stresses In Arabidopsis Thaliana, Laetitia Virlouvet, Yong Ding, Hiroaki Fujii, Zoya Avramova, Michael Fromm

School of Biological Sciences: Faculty Publications

Plants subjected to a prior dehydration stress were seen to have altered transcriptional responses during a subsequent dehydration stress for up to 5 days after the initial stress. The abscisic acid (ABA) inducible RD29B gene of Arabidopsis thaliana was strongly induced after the first stress and displayed transcriptional memory with transcript levels nine-fold higher during the second dehydration stress. These increased transcript levels were due to an increased rate of transcription and are associated with an altered chromatin template during the recovery interval between the dehydration stresses. Here we use a combination of promoter deletion/substitutions, mutants in the trans-acting …

H3k27me3 And H3k4me3 Chromatin Environment At Super-Induced Dehydration Stress Memory Genes Of Arabidopsis Thaliana, Ning Liu, Zoya Avramova, Michael Fromm

School of Biological Sciences: Faculty Publications

Pre-exposure to a stress may alter the plant’s cellular, biochemical, and/or transcriptional responses during future encounters as a “memory” from the previous stress. Genes increasing transcription in response to a first dehydration stress, but producing much higher transcript levels in a subsequent stress, represent the super-induced “transcription memory” genes in Arabidopsis thaliana. The chromatin environment (histone H3 tri-methylations of Lys 4 and Lys 27, H3K4me3, and H3K27me3) studied at five dehydration stress memory genes revealed existence of distinct memory-response subclasses that responded differently to CLF deficiency and displayed different transcriptional activities during the watered recovery periods. Among the most …

Sudden Aspen Decline Report For Spruce Beetle Epidemic And Aspen Decline Management Response Eis, Jim Worrall, Suzanne Marchetti, Gerald E. Rehfeldt

Aspen Bibliography

Aspen is an important component of GMUG’s forests. Over 288,000 ha (712,000 acres) of aspendominated forest type (TAA) occur across the GMUG (Table 1). Just over half (55%) of the aspen forest type is outside wilderness and roadless areas.

Global Changes In Mineral Transporters In Tetraploid Switchgrasses (Panicum Virgatum L.), Nathan A. Palmer, Aaron J. Saathoff, Brian M. Waters, Teresa Donze, Tiffany M. Heng-Moss, Paul Twigg, Christian M. Tobias, Gautam Sarath

Department of Agronomy and Horticulture: Faculty Publications

Switchgrass (Panicum virgatum L) is a perennial, C4 grass with great potential as a biofuel crop. An in-depth understanding of the mechanisms that control mineral uptake, distribution, and remobilization will benefit sustainable production. Nutrients are mobilized from aerial portions to below-ground crowns and rhizomes as a natural accompaniment to above-ground senescence post seed-set. Mineral uptake and remobilization is dependent on transporters, however, little if any information is available about the specific transporters that are needed and how their relative expression changes over a growing season.Using well-defined classes of mineral transporters, we identified 520 genes belonging to 40 different transporter …

Switchgrass (Panicum Virgatum L) Flag Leaf Transcriptomes Reveal Molecular Signatures Of Leaf Development, Senescence, And Mineral Dynamics, Nathan A. Palmer, Teresa Donze-Reiner, David Horvath, Tiffany Heng-Moss, Brian M. Waters, Christian M. Tobias, Gautam Sarath

Department of Agronomy and Horticulture: Faculty Publications

Switchgrass flag leaves can be expected to be a source of carbon to the plant, and its senescence is likely to impact the remobilization of nutrients from the shoots to the rhizomes. However, many genes have not been assigned a function in specific stages of leaf development. Here, we characterized gene expression in flag leaves over their development. By merging changes in leaf chlorophyll and the expression of genes for chlorophyll biosynthesis and degradation, a four-phase molecular roadmap for switchgrass flag leaf ontogeny was developed. Genes associated with early leaf development were up-regulated in phase 1. Phase 2 leaves had …