Agronomy and Crop Sciences Commons^™

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 …

Wayne E. Sabbe Arkansas Soil Fertility Studies 2010, Nathan A. Slaton

Arkansas Agricultural Experiment Station Research Series

Rapid technological changes in crop management and production require that the research efforts be presented in an expeditious manner. The contributions of soil fertility and fertilizers are major production factors in all Arkansas crops.

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, …

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. …

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 …

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 …

Contents, Discovery Editors

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

No abstract provided.

Instructions For Authors, Discovery Editors

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

No abstract provided.

Comparison Of Growing Media For Container Grown Plants, Paul Harris, David Longer, Derrick Oosterhuis, Dimitra Loka

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

Greenhouse and growth chamber experiments are conducted worldwide in efforts to produce solutions that would increase yields of agronomic crops. However, the results of those experiments vary due to the many growth media being used. An experiment was conducted in the fall of 2010 to identify a broadly acceptable growth media that would produce uniform stands and optimum results in greenhouse and growth chamber settings. A total of six growth media were tested on cotton (Gossypium hirsutum) at the Arkansas Agricutural Research and Extension Center’s Altheimer Lab in Fayetteville. The plants grown in each medium were harvested six weeks after …

Letter From The Dean, Michael Vayda

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

No abstract provided.

Discovery: The Student Journal Of Dale Bumpers College Of Agricultural, Food And Life Sciences - Volume 12 2011, Several Authors

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

No abstract provided.

Arkansas Cotton Variety Test 2010, Fred M. Bourland, A. B. Beach, D. P. Roberts Jr.

Arkansas Agricultural Experiment Station Research Series

The primary goal of the Arkansas Cotton Variety Test is to provide unbiased data regarding the agronomic performance of cotton varieties and advanced breeding lines in the major cotton-growing areas of Arkansas. This information helps seed companies establish marketing strategies and assists producers in choosing varieties to plant.

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, …

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 …

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.

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 …

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 …

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 …

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.

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 …

Arkansas Soybean Performance Tests 2010, R. D. Bond, D. G. Dombek, J. A. Still, R. M. Pryor

Arkansas Agricultural Experiment Station Research Series

Soybean variety and strain performance tests are conducted each year in Arkansas by the University of Arkansas Division of Agriculture Arkansas Crop Variety Improvement Program.

Arkansas Corn And Grain Sorghum Performance Tests 2010, R. D. Bond, D. G. Dombek, J. A. Still, R. M. Pryor

Arkansas Agricultural Experiment Station Research Series

Corn and grain sorghum performance tests are conducted each year in Arkansas by the University of Arkansas Division of Agriculture. The tests provide information to companies marketing seed within the state and aid the Arkansas Cooperative Extension Service in formulating recommendations for producers.

Arkansas Wheat Cultivar Performance Tests 2009-2010, J. T. Kelly, R. G. Miller, R. D. Bond, E. A. Milus, R. K. Bacon

Arkansas Agricultural Experiment Station Research Series

Wheat cultivar performance tests are conducted each year in Arkansas by the Arkansas Agricultural Experiment Station, Department of Crop, Soil and Environmental Sciences. The tests provide information to companies developing cultivars and/or marketing seed within the state and aid the Arkansas Cooperative Extension Service in formulating cultivar recommendations for small-grain producers.

Summaries Of Arkansas Cotton Research 2009, Derrick M. Oosterhuis

Arkansas Agricultural Experiment Station Research Series

No abstract provided.

B. R. Wells Rice Research Studies 2009, R. J. Norman, K. A. K. Moldenhauer

Arkansas Agricultural Experiment Station Research Series

No abstract provided.

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 …

Environmental Variables Influencing The Severity Of Pierce's Disease In California Grapevines, Christopher James Boisseranc

Master's Theses

This project was designed to correlate environmental variables with the development of Pierce’s Disease (PD), an infection caused by the gram negative bacterium Xylella fastidiosa (Xf), in grapes (Hopkins et al. 2002). PD is one of the most difficult crop pathogens to manage because it is vectored by insects and its continued presence in the vine is usually fatal. PD is influenced by the interaction of host, disease and vector, and probably many other environmental variables. The general objective was to study and identify the most important variables involved in the expression of Pierce’s Disease.

Over a two year period, …