Life Sciences Commons^™

Nebline, Nov./Dec. 2011

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Feature: Avoid Guessing About Holiday Food Safety

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Heritable Epigenetic Variation Among Maize Inbreds, Steve R. Eichten, Ruth A. Swanson, James C. Schnable, Amanda J. Waters, Peter J. Hermanson, Sanzhen Liu, Cheng-Ting Yeh, Yi Jia, Karla Gendler, Michael Freeling, Patrick S. Schnable, Matthew W. Vaughn, Nathan M. Springer

Department of Agronomy and Horticulture: Faculty Publications

Epigenetic variation describes heritable differences that are not attributable to changes in DNA sequence. There is the potential for pure epigenetic variation that occurs in the absence of any genetic change or for more complex situations that involve both genetic and epigenetic differences. Methylation of cytosine residues provides one mechanism for the inheritance of epigenetic information. A genome-wide profiling of DNA methylation in two different genotypes of Zea mays (ssp. mays), an organism with a complex genome of interspersed genes and repetitive elements, allowed the identification and characterization of examples of natural epigenetic variation. The distribution of DNA methylation …

Nebline, October 2011

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Feature: What is Your Energy IQ?

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Miscanthus 3 Giganteus Productivity: The Effects Of Management In Different Environments, Matt Maughan, German Bollero, D.K. Lee, Robert Darmody, Stacy Bonos, Laura Cortese, James Murphy, Roch E. Gaussoin, Matthew Sousek, David Williams, Linda Williams, Fernando Miguez, Thomas Voigt

Department of Agronomy and Horticulture: Faculty Publications

Miscanthus 9 giganteus is a C4 perennial grass that shows great potential as a high-yielding biomass crop. Scant research has been published that reports M. 9 giganteus growth and biomass yields in different environments in the United States. This study investigated the establishment success, plant growth, and dry biomass yield of M. 9 giganteus during its first three seasons at four locations (Urbana, IL; Lexington, KY; Mead, NE; Adelphia, NJ) in the United States. Three nitrogen rates (0, 60, and 120 kg ha -1) were applied at each location each year. Good survival of M. 9 giganteus during its first …

Nebline, September 2011

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Feature: 4-H Helps Build Successful Scientists

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Nebline, August 2011

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Feature: For Many 4-H Families, County Fair is Quality Time Together

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Lancaster County Super Fair Schedule & Map Special Pullout Section

Hydrologic Effectiveness And Plant Survivability In The Holmes Lake Rain Garden Pilot Program: Year Three, Marilyn K. Liebsch

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

Rain gardens are increasingly being used as small scale stormwater best management practices (BMPs) to reduce stormwater runoff through infiltration and to remove pollutants through filtration. In 2007, as part of a comprehensive water quality restoration process of Holmes Lake in Lincoln, Nebraska, 20 pilot rain gardens were installed in residential and school properties in the watershed. Currently, assessment and monitoring has been limited to participant surveys and cannot be used to determine if hydraulic or vegetative problems exist within the garden area. In this study, visual inspections were conducted to establish a database standard for successful rain gardens, hydraulic …

Nebline, July 2011

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Feature: Urban Agriculture is a Growing Trend

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Biology, Systematics, Phylogenetic Analysis And Dna Character-Based Species Diagnosis Of The False Root-Knot Nematode Nacobbus Aberrans (Thorne, 1935) Thorne & Allen 1944 (Nemata:Pratylenchidae), Angel Ramirez-Suarez

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

The False Root-Knot nematode Nacobbus aberrans is a plant parasitic nematode that causes yield losses in several crops and plant protection agencies have established regulations to prevent infestations from spreading to new agricultural areas. The taxonomic status of the nematode has been the subject of controversy due to wide degree of variation exhibited by the species. This variability has led to the suggestion that N. aberrans is actually a species complex rather than a single species. In order to test this hypothesis, we compared twelve N. aberrans populations, which include isolates from western Nebraska, two distinct regions of Mexico and …

Nebline, June 2011

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Feature: Lower Platte South Natural Resources District Trails in Lancaster County Offer Recreation & Education

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Nebline, May 2011

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Feature: Nature, Gardening & Science Come Together in the Butterfly Garden

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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 …

Nebline, April 2011

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Feature: Supplemental Kits Make Learning Nutrition Fun

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Characterizing The Chemoprevention Potential Of Amenity Grass Phenolic Extracts In Vitro And The Corresponding Nutraceutical Targets Within Hepg2 Carcinoma Cells, Casey J. Wegner

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

This research has revealed significant chemopreventive potential belonging to the planet’s most renewable and abundant plant source: amenity grasses. The characterization results from Chapter 1 demonstrated the potential chemoprevention attributes of supina bluegrass and bermudagrass crude extracts linked to the extensive phenolic acid profiles of these amenity grasses. In contrast to cereals, amenity grass phenolic extracts (AGPE) offer appreciable amounts of unbound/free ferulic acid that would be available for rapid in vivo absorption. The literature has shown ferulic acid to be a highly available and health benefitting phenolic compound. Chapter 1 in vitro studies demonstrated AGPE-induced antiproliferation and apoptotic induction …

A First Insight Into Population Structure And Linkage Disequilibrium In The U.S. Peanut Minicore Collection, Vikas Belamkar, Michael Gomez Selvaraj, Jamie L. Ayers, Paxton R. Payton, Naveen Puppala, Mark D. Burow

Department of Agronomy and Horticulture: Faculty Publications

Knowledge of genetic diversity, population structure, and degree of linkage disequilibrium (LD) in target association mapping populations is of great importance and is a prerequisite for LD-based mapping. In the present study, 96 genotypes comprising 92 accessions of the US peanut minicore collection, a component line of the tetraploid variety Florunner, diploid progenitors A. duranensis (AA) and A. ipaënsis (BB), and synthetic amphidiploid accession TxAG-6 were investigated with 392 simple sequence repeat (SSR) marker bands amplified using 32 highly-polymorphic SSR primer pairs. Both distance- and model-based (Bayesian) cluster analysis revealed the presence of structured diversity. In general, the wild-species accessions …

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 …

Nebline, March 2011

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Feature: Connect, Learn, and Share With Extension

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Weed Awareness Insert

Nebline, February 2011

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Feature: Got Bed Bugs? Don't Panic! There are Steps You Can Take

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The Composition And Origins Of Genomic Variation Among Individuals Of The Soybean Reference Cultivar Williams 82, William J. Haun, D. L. Hyten, Wayne W. Xu, Daniel J. Gerhardt, Thomas J. Albert, Todd Richmond, Jeffrey A. Jeddeloh, Gaofeng Jia, Nathan M. Springer, Carroll P. Vance, Robert M. Stupar

Department of Agronomy and Horticulture: Faculty Publications

Soybean (Glycine max) is a self-pollinating species that has relatively low nucleotide polymorphism rates compared with other crop species. Despite the low rate of nucleotide polymorphisms, a wide range of heritable phenotypic variation exists. There is even evidence for heritable phenotypic variation among individuals within some cultivars. Williams 82, the soybean cultivar used to produce the reference genome sequence, was derived from backcrossing a Phytophthora root rot resistance locus from the donor parent Kingwa into the recurrent parent Williams. To explore the genetic basis of intracultivar variation, we investigated the nucleotide, structural, and gene content variation of different …

Nebline, January 2011

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Feature: Tightening Your Belt in Tough Times

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Annual Report Special Pullout Section

Soil Fertility And Crop Yields In Long-Term Organic And Conventional Cropping Systems In Eastern Nebraska, Samuel E. Wortman, Tomie D. Galusha, Stephen C. Mason, Charles A. Francis

Department of Agronomy and Horticulture: Faculty Publications

Organic agriculture aims to build soil quality and provide long-term benefits to people and the environment; however, organic practices may reduce crop yields. This long-term study near Mead, NE was conducted to determine differences in soil fertility and crop yields among conventional and organic cropping systems between 1996 and 2007. The conventional system (CR) consisted of corn (Zea mays L.) or sorghum (Sorghum bicolor (L.) Moench)–soybean (Glycine max (L.) Merr.)–sorghum or corn–soybean, whereas the diversified conventional system (DIR) consisted of corn or sorghum– sorghum or corn–soybean–winter wheat (wheat, Triticum aestivum L.). The animal manure-based organic system (OAM) …

Stacking Resistance Alleles From Wild And Domestic Soybean Sources Improves Soybean Cyst Nematode Resistance, Myungsik Kim, D. L. Hyten, Terry L. Niblack, Brian W. Diers

Department of Agronomy and Horticulture: Faculty Publications

The soybean cyst nematode (SCN; Heterodera glycines Ichinohe) is the most economically important soybean [Glycine max (L.) Merr.] pathogen in the United States. Field SCN populations are adapting to the narrowly based SCN resistance currently deployed in soybean cultivars. The objective of our research was to measure the effects of combinations of SCN resistance genes or quantitative trait loci (QTL) from the wild soybean (Glycine soja Siebold & Zucc.) PI 468916 and the domesticated soybean accessions PI 88788 and PI 437654. Two populations were developed to test the combinations of QTL and genes. Both populations segregated for the …

Identification Of A Second Asian Soybean Rust Resistance Gene In Hyuuga Soybean, Mandy D. Kendrick, Donna K. Harris, Bo-Keun Ha, D. L. Hyten, P. B. Cregan, Reid D. Frederick, H. Roger Boerma, Kerry F. Pedley

Department of Agronomy and Horticulture: Faculty Publications

Asian soybean rust (ASR) is an economically significant disease caused by the fungus Phakopsora pachyrhizi. The soybean genes Rpp3 and Rpp?(Hyuuga) confer resistance to specific isolates of the pathogen. Both genes map to chromosome 6 (Gm06) (linkage group [LG] C2). We recently identified 12 additional soybean accessions that harbor ASR resistance mapping to Gm06, within 5 centimorgans of Rpp3 and Rpp?(Hyuuga). To further characterize genotypes with resistance on Gm06, we used a set of eight P. pachyrhizi isolates collected from geographically diverse areas to inoculate plants and evaluate them for differential phenotypic responses. …

Cytokinin-Mediated Source ⁄Sink Modifications Improve Drought Tolerance And Increase Grain Yield In Rice Under Water-Stress, Zvi Peleg, Maria Reguera, Ellen Tumimbang, Harkamal Walia, Eduardo Blumwald

Department of Agronomy and Horticulture: Faculty Publications

Drought is the major environmental factor limiting crop productivity worldwide. We hypothesized that it is possible to enhance drought tolerance by delaying stress-induced senescence through the stress-induced synthesis of cytokinins in crop-plants. We generated transgenic rice (Oryza sativa) plants expressing an isopentenyltransferase (IPT) gene driven by PSARK, a stress- and maturation-induced promoter. Plants were tested for drought tolerance at two yield-sensitive developmental stages: pre- and post-anthesis. Under both treatments, the transgenic rice plants exhibited delayed response to stress with significantly higher grain yield (GY) when compared to wild-type plants. Gene expression analysis revealed a significant shift in expression of hormone-associated …

Registration Of Seven Winter Wheat Germplasm Lines Carrying The Wsm1 Gene For Wheat Streak Mosaic Virus Resistance, Jasdeep S. Mutti, P. Stephen Baenziger, Robert A. Graybosch, Roy French, Kulvinder S. Gill

Department of Agronomy and Horticulture: Faculty Publications

Seven winter wheat (Triticum aestivum L.) germplasm lines carrying the Wsm1 gene conferring resistance to Wheat streak mosaic virus (WSMV)—Alliance-Wsm1 (Reg. No. GP-858, PI 653710), Arrowsmith-Wsm1 (Reg. No. GP-859, PI 653711), Goodstreak-Wsm1 (Reg. No. GP-860, PI 653712), Harry-Wsm1 (Reg. No. GP-861, PI 653713), Millennium-Wsm1 (Reg. No. GP-862, PI 653714), Wahoo-Wsm1 (Reg. No. GP-863, PI 653715), and Wesley-Wsm1 (Reg. No. GP-864, PI 653716)—were codeveloped by Washington State University, Pullman, WA; the University of Nebraska, Lincoln, NE; and the USDA-ARS. These seven different winter wheat cultivars were selected to provide more sources of effective …

Estimation Of Surface Soil Organic Matter Using A Ground-Based Active Sensor And Aerial Imagery, D. F. Roberts, V. I. Adamchuk, J. F. Shanahan, R. B. Ferguson, J. S. Schepers

Department of Agronomy and Horticulture: Faculty Publications

Active canopy sensors are currently being studied as a tool to assess crop N status and direct in-season N applications. The objective of this study was to use a variety of strategies to evaluate the capability of an active sensor and a wide-band aerial image to estimate surface soil organic matter (OM). Grid soil samples, active sensor reflectance and bare soil aerial images were obtained from six fields in central Nebraska before the 2007 and 2008 growing seasons. Six different strategies to predict OM were developed and tested by dividing samples randomly into calibration and validation datasets. Strategies included uniform, …

Switchgrass Contains Two Cinnamyl Alcohol Dehydrogenases Involved In Lignin Formation, Aaron J. Saathoff, Christian M. Tobias, Scott E. Sattler, Eric J. Haas, Paul Twigg, Gautam Sarath

Department of Agronomy and Horticulture: Faculty Publications

Lignin content of switchgrass (Panicum virgatum L.), a bioenergy species, is a critical determinant of biomass quality since it can negatively impact conversion of biomass into liquid fuels via biochemical platforms. Cinnamyl alcohol dehydrogenase (CAD) is a key enzyme in lignin biosynthesis. Here, we have shown that cv. Kanlow switchgrass contains at least two closely related CAD genes (PviCAD1 and PviCAD2) that code for proteins containing highly conserved domains and residues that identify them as bona fide CADs. Both recombinant proteins displayed substrate kinetics consistent with their presumed role in cell wall lignification. Proteomic and immunoblotting detected …

Mutational Analysis Of The Major Soybean Uref Paralogue Involved In Urease Activation, Joe C. Polacco, D. L. Hyten, Mônica Medeiros-Silva, David A. Sleper, Kristin D. Bilyeu

Department of Agronomy and Horticulture: Faculty Publications

The soybean genome duplicated ~14 and 45 million years ago and has many paralogous genes, including those in urease activation (emplacement of Ni and CO₂ in the active site). Activation requires the UreD and UreF proteins, each encoded by two paralogues. UreG, a third essential activation protein, is encoded by the single-copy Eu3, and eu3 mutants lack activity of both urease isozymes. eu2 has the same urease-negative phenotype, consistent with Eu2 being a single-copy gene, possibly encoding a Ni carrier. Unexpectedly, two eu2 alleles co-segregated with missense mutations in the chromosome 2 UreF paralogue (Ch02UreF), suggesting …

Genome-Wide Association Analysis Identifies Candidate Genes Associated With Iron Deficiency Chlorosis In Soybean, Sujan Mamidi, Shireen Chikara, R. Jay Goos, D. L. Hyten, Deepti Annam, Samira Mafi Moghaddam, Rian K. Lee, P. B. Cregan, Phillip E. Mcclean

Department of Agronomy and Horticulture: Faculty Publications

Iron deficiency chlorosis (IDC) is a significant yield-limiting problem in several major soybean [Glycine max (L.) Merr.] production regions in the United States. Soybean plants display a variety of symptoms that range from a slight yellowing of the leaf to interveinal chlorosis, to stunted growth that reduces yield. The objective of this analysis was to employ single nucleotide polymorphism (SNP)-based genome-wide association mapping to uncover genomic regions associated with IDC tolerance. Two populations [2005 (n = 143) and 2006 (n = 141)] were evaluated in replicated, multilocation IDC trials. After controlling for population structure and individual relatedness, and selecting …