Life Sciences Commons^™

Adding Value To Graduate Education: The Comprehensive Examination, John L. Lindquist, Samuel E. Wortman, Charles A. Francis

Department of Agronomy and Horticulture: Faculty Publications

Virtually all graduate study requirements for MS or PhD degrees include a written comprehensive and an oral exam, the latter most often a presentation of thesis or dissertation results. The written exam takes many forms, but the goals are to test the candidate for technical competence and affirm that the prior program course work has been effective in bringing the candidate to an acceptable level of understanding of the discipline in which she or he has been immersed. Although long accepted as a useful hurdle on the path to a degree, for some exceptional students who have already demonstrated competence …

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 …

Use Of Natural Variation Reveals Core Genes In The Transcriptome Of Iron-Deficient Arabidopsis Thaliana Roots, Ricardo J. Stein, Brian M. Waters

Department of Agronomy and Horticulture: Faculty Publications

Iron (Fe) is an essential mineral micronutrient for plants and animals. Plants respond to Fe deficiency by increasing root uptake capacity. Identification of gene networks for Fe uptake and homeostasis could result in improved crop growth and nutritional value. Previous studies have used microarrays to identify a large number of genes regulated by Fe deficiency in roots of three Arabidopsis ecotypes. However, a large proportion of these genes may be involved in secondary or genotype-influenced responses rather than in a universal role in Fe uptake or homeostasis. Here we show that a small percentage of the Fe deficiency transcriptome of …

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 …

Integrated Soil–Crop System Management For Food Security, Xin-Ping Chen, Zhen-Ling Cui, Peter M. Vitousek, Kenneth Cassman, Pamela A. Matson, Jin-Shun Bai, Qing-Feng Meng, Peng Hou, Shan-Chao Yue, Volker Römheld, Fu-Suo Zhang

Department of Agronomy and Horticulture: Faculty Publications

China and other rapidly developing economies face the dual challenge of substantially increasing yields of cereal grains while at the same time reducing the very substantial environmental impacts of intensive agriculture. We used a model-driven integrated soil–crop system management approach to develop a maize production system that achieved mean maize yields of 13.0 t ha−1 on 66 on-farm experimental plots—nearly twice the yield of current farmers’ practices—with no increase in N fertilizer use. Such integrated soil–crop system management systems represent a priority for agricultural research and implementation, especially in rapidly growing economies.

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 …

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 …

What Is The Potential Of Substituting Legumes For Synthetic Nitrogen In Warm Season Perennial Grasses Used For Stocker Cattle Grazing?, J. Biermacher, John A. Guretzky, Ryan Reuter, Maru Kering, Twain Butler, Job Springer, James Rogers, John Blanton, Joe Bouton

Department of Agronomy and Horticulture: Faculty Publications

Stocker cattle grazing warm season perennial grasses is an important economic activity in the southern Great Plains. Substantial increases in the price of nitrogen fertilizer is negatively affecting forage producers’ profitability. Two alternative nitrogen management systems that use annual and perennial legumes have been developed for bermudagrass pastures. The goal of the study is to determine if the legumes systems are more profitable than the conventional practice of applying synthetic sources of nitrogen. Enterprise budgeting techniques were employed to compare the economics of the legume systems relative to the common practice. Results of the two-year grazing study show that the …

Structuring An Efficient Organic Wheat Breeding Program, P. Stephen Baenziger, Ibrahim Salah, Richard S. Little, Dipak K. Santra, Teshome Regassa, Meng Yuan Wang

Department of Agronomy and Horticulture: Faculty Publications

Our long-term goal is to develop wheat cultivars that will improve the profitability and competitiveness of organic producers in Nebraska and the Northern Great Plains. Our approach is to select in early generations for highly heritable traits that are needed for both organic and conventional production (another breeding goal), followed by a targeted organic breeding effort with testing at two organic locations (each in a different ecological region) beginning with the F₆ generation. Yield analyses from replicated trials at two organic breeding sites and 7 conventional breeding sites from F₆ through F₁₂ nurseries revealed, using analyses of …

Effect Of Nitrogen Fertilizer Rate And Harvest Season On Forage Yield, Quality, And Macronutrient Concentrations In Midland Bermuda Grass, Maru K. Kering, John A. Guretzky, Eddie Funderburg, Jagadeesh Mosali

Department of Agronomy and Horticulture: Faculty Publications

Bermuda grass [Cynodon dactylon (L.) Pers.] is a major forage for grazing and hay production in the southern United States. The objectives of this study were to determine effects of nitrogen (N) fertilization rate (0, 112, 224, 336, and 448 kg ha⁻¹), split spring and summer applications of N at the 224 and 448 kg ha⁻¹ rates, and harvest periods (spring and summer) on forage yield, crude protein (CP), acid detergent fiber (ADF), neutral detergent fiber (NDF), total digestible nutrients (TDN), and concentrations of phosphorus (P), potassium (K), magnesium (Mg), and calcium (Ca) in Midland Bermuda …

Learning Gains And Response To Digital Lessons On Soil Genesis And Development, Martha Mamo, James A. Ippolito, Timothy A. Kettler, Ronald Reuter, Dennis L. Mccallister, Patricia Morner, Dann E. Husmann, Erin E. Blankenship

Department of Agronomy and Horticulture: Faculty Publications

Evolving computer technology is offering opportunities for new online approaches in teaching methods and delivery. Well-designed web-based (online) lessons should reinforce the critical need of the soil science discipline in today's food, energy, and environmental issues, as well as meet the needs of the diverse clientele with interest in agricultural and/ or environmental disciplines. The objectives of the project were to: (1) develop web-based lessons in soil genesis and development and (2) evaluate context-based case studies or application lessons (agronomic, environmental, and ecological situations) to teach soil genesis and development. Six principles lessons, along with three applications lessons, were developed …

High-Yield Irrigated Maize In The Western U.S. Corn Belt: I. On-Farm Yield, Yield Potential, And Impact Of Agronomic Practices, Patricio Grassini, John Thorburn, Charles Burr, Kenneth Cassman

Department of Agronomy and Horticulture: Faculty Publications

Quantifying the exploitable gap between average farmer yields and yield potential (Y_P) is essential to prioritize research and formulate policies for food security at national and international levels. While irrigated maize accounts for 58% of total annual maize production in the Western U.S. Corn Belt, current yield gap in these systems has not been quantified. Our objectives were to quantify Y_P, yield gaps, and the impact of agronomic practices on both parameters in irrigated maize systems of central Nebraska. The analysis was based on a 3-y database with field-specific values for yield, applied irrigation, and N …

No-Tillage Increases Soil Profile Carbon And Nitrogen Under Long-Term Rainfed Cropping Systems, Gary E. Varvel, Wallace Wilhelm

Department of Agronomy and Horticulture: Faculty Publications

Emphasis and interest in carbon (C) and nitrogen (N) storage (sequestration) in soils has greatly increased in the last few years, especially C with its’ potential to help alleviate or offset some of the negative effects of the increase in greenhouse gases in the atmosphere. Several questions still exist with regard to what management practices optimize C storage in the soil profile. A long-term rainfed study conducted in eastern Nebraska provided the opportunity to determine both the effects of different tillage treatments and cropping systems on soil N and soil organic C (SOC) levels throughout the soil profile. The study …

Volume, Texture, And Molecular Mechanism Behind The Collapse Of Bread Made With Different Levels Of Hard Waxy Wheat Flours, Shivananda K. Garimella Purna, Rebecca A. Miller, Paul A. Seib, Robert A. Graybosch, Yong-Cheng Shi

Department of Agronomy and Horticulture: Faculty Publications

Physico-chemical properties of bread baked by partially replacing normal wheat (Triticum aestivum L.) flour (15, 30, and 45%) with two hard waxy wheat flours were investigated. Substitution with waxy wheat flour resulted in higher loaf volume and softer loaves. However, substitution at >30% resulted in excessive post-bake shrinkage and a ‘key-hole’ shape with an open crumb structure. Bread crumb microstructure indicated a loss of starch granule rigidity and fusing of starch granules. The cells in the interior of the bread did not become gas-continuous and as a result, shrunk as the loaf cooled. Soluble starch content was significantly higher in …

Biological Suppression Of Velvetleaf (Abutilon Theophrasti ) In An Eastern Nebraska Soil, Jane Okalebo, Gary Y. Yuen, Rhae A. Drijber, Erin E. Blankenship, Cafer Eken, John L. Lindquist

Department of Agronomy and Horticulture: Faculty Publications

Weed-suppressive soils contain naturally occurring microorganisms that suppress a weed by inhibiting its growth, development, and reproductive potential. Increased knowledge of microbe–weed interactions in such soils could lead to the identification of management practices that create or enhance soil suppressiveness to weeds. Velvetleaf death and growth suppression was observed in a research field (fieldA) that was planted with high populations of velvetleaf, which may have developed via microbial mediated plant–soil feedback. Greenhouse studies were conducted with soil collected from fieldA (soilA) to determine if it was biologically suppressive to velvetleaf. In one study, mortality of velvetleaf …

Switchgrass, Kenneth P. Vogel, Gautam Sarath, Aaron J. Saathoff, Robert B. Mitchell

Department of Agronomy and Horticulture: Faculty Publications

17.1 Introduction

Switchgrass (Panicum virgatum L.) is a warm-season perennial grass that is native to North America that is being developed into a biomass energy crop. It has been used in pastures and for conservation purposes in the Great Plains and the Midwest, USA, for over 70 years.1 The research supporting its use as a pasture and conservation species was largely conducted by US Department of Agriculture (USDA) research programs, most notably the Agricultural Research Service (ARS) project located at the University of Nebraska-Lincoln and USDA Plant Materials Centers that are located throughout the United States. In this report, …

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) …

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 …

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. …

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 …

Moving Magnesium In Plant Cells, Brian M. Waters

Department of Agronomy and Horticulture: Faculty Publications

Magnesium (Mg) is among the most abundant mineral elements in plants, yet the knowledge of which genes control its accumulation in specific tissues and organelles lags behind that of many other mineral elements. Only in recent years has identification of important molecular players begun to take shape. In this issue of New Phytologist, Conn et al. (pp. 583–594) shed additional light on two Mg transporters that play important roles in accumulation of Mg in leaf cell vacuoles. Using subcellular-level ion measurements on leaves, gene expression measurements after single-cell sampling, a genetic approach, and clever use of calcium (Ca) and …

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 …

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 …

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 …

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 …

Moving Micronutrients From The Soil To The Seeds: Genes And Physiological Processes From A Biofortification Perspective, Brian M. Waters, Renuka P. Sankaran

Department of Agronomy and Horticulture: Faculty Publications

The micronutrients iron (Fe), zinc (Zn), and copper (Cu) are essential for plants and the humans and animals that consume plants. Increasing the micronutrient density of staple crops, or biofortification, will greatly improve human nutrition on a global scale. This review discusses the processes and genes needed to translocate micronutrients through the plant to the developing seeds, and potential strategies for developing biofortified crops.

The Role Of Transition Metal Homeostasis In Plant Seed Development, Elsbeth L. Walker, Brian M. Waters

Department of Agronomy and Horticulture: Faculty Publications

Copyright © 2011 Elsevier Ltd. Used by permission.

Switchgrass For Forage And Bioenergy: Harvest And Nitrogen Rate Effects On Biomass Yields And Nutrient Composition, John A. Guretzky, Jon T. Biermacher, Billy Cook, Maru K. Kering, Jagadeesh Mosali

Department of Agronomy and Horticulture: Faculty Publications

Switchgrass (Panicum virgatum L.) may have value as forage and a bioenergy feedstock. Our objective was to evaluate how harvest system and N fertilizer rates affected biomass yield and nutrient composition of young stands of switchgrass (cv. Alamo) in the southern Great Plains, USA. Nitrogen fertilization increased biomass yields from 10.4, 10.8, and 12.2 Mg ha⁻¹ at 0 kg N ha⁻¹ to 13.7, 14.6, and 21.0 Mg ha⁻¹ at 225 kg N ha⁻¹ when harvested after seed set (October), after frost (December), and twice per year after boot stage (July) and frost, respectively. Nutrient concentrations …