Plant Biology 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 …

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 …

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. …

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 …

Intermediate Steps Of Loline Alkaloid Biosynthesis, Jerome Ralph Faulkner

University of Kentucky Doctoral Dissertations

Epichloë species and their anamorphs, Neotyphodium species, are fungal endophytes that inhabit cool-season grasses and often produce bioprotective alkaloids. These alkaloids include lolines, which are insecticidal and insect feeding deterrents. Lolines are exo-1-aminopyrrolizidines with an oxygen bridge between carbons 2 and 7, and are usually methylated and formylated or acetylated on the 1-amine. In previously published studies lolines were shown to be derived from the amino acids L-proline and L-homoserine. In addition the gene cluster involved in loline-alkaloid biosynthesis has also been characterized. In this dissertation a survey of plant-endophyte symbioses revealed a phenotype with only N-acetylnorloline. This …

Restoration Of Tall Fescue Pastures To Native Warm Season Grasslands: Does A Fungal Endophyte Symbiosis Play A Role In Restoration Success?, Sarah Lynn Hall

University of Kentucky Doctoral Dissertations

Tall fescue, a cool-season grass native to Europe, central Asia, and northern Africa, has been widely distributed throughout the U.S. for use as turf and forage. Following its widespread planting, its ability to associate with a toxic fungal endophyte, Neotyphodium coenophialum, was discovered. Research has linked this fescue-endophyte association with increased biotic and abiotic stress resistance in endophyte-infected (E+) versus endophyte-free (E-) plants, and these differences may affect the ability of land managers to eradicate tall fescue and restore native grasslands. I conducted three studies to examine whether E+ tall fescue plants respond differently to management than E- plants, …

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 …

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 …

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.

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 …

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.

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 …

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 …

Effects Of Mulching, Fertilizer, Seeding And Seedling Treatments On Plant Species Recovery In Kondoa Irangi Hills, Tanzania, H. V. M. Lyaruu

Tanzania Journal of Science

Fertilization, mulching, imported seed bank seeding and seedlings were applied to triplicates of 1m x1m plots at Chakwe and Gubali sites in Kondoa Irangi Hills, Tanzania. Responses tested were seedling recruitment, species turnover, species’ biomass, mortality of seedlings, total number of perennial and woody species recruited and leguminous species. There were high significant correlations of 0.85 and 0.87 between seedling recruitment and mortality in both sites, indicating that other factors, probably aridity, rather than prevailing site conditions were likely to be important determinants of mortality. Inorganic fertilization was not an efficient means of improving short-term productivity, seedling recruitment or increased …

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 …

Good Agricultural Practices For Food Safety Of Fresh Produce, Laurie Hodges

Department of Agronomy and Horticulture: Faculty Publications

What are the guiding principles of food safety for fresh produce?

• Once contaminated, removing or killing pathogens on produce is very difficult.

• Preventing microbial contamination at all steps, from production to distribution, is strongly favored over treatments to eliminate contamination that may have occurred.

• Document the implementation of prevention programs, and educate workers at all levels of the agricultural and packing environments on food safety.

Key Signatures of a Credible Food Safety Program

The following is a condensed checklist of practices and conditions that reduce the potential for fresh produce to be exposed to pathogenic microbes. Review …

Soydb: A Knowledge Database Of Soybean Transcription Factors, Zheng Wang, Marc Libault, Trupti Joshi, Babu Valliyodan, Henry T. Nguyen, Dong Xu, Gary Stacey, Jianlin Cheng

Department of Agronomy and Horticulture: Faculty Publications

Background: Transcription factors play the crucial rule of regulating gene expression and influence almost all biological processes. Systematically identifying and annotating transcription factors can greatly aid further understanding their functions and mechanisms. In this article, we present SoyDB, a user friendly database containing comprehensive knowledge of soybean transcription factors.

Description: The soybean genome was recently sequenced by the Department of Energy-Joint Genome Institute (DOE-JGI) and is publicly available. Mining of this sequence identified 5,671 soybean genes as putative transcription factors. These genes were comprehensively annotated as an aid to the soybean research community. We developed SoyDB - a knowledge database …

A High Density Integrated Genetic Linkage Map Of Soybean And The Development Of A 1536 Universal Soy Linkage Panel For Quantitative Trait Locus Mapping, D. L. Hyten, Ik-Young Choi, Qijian Song, James E. Specht, Thomas E. Carter Jr., Randy C. Shoemaker, Eun-Young Hwang, Lakshmi K. Matukumalli, P. B. Cregan

Department of Agronomy and Horticulture: Faculty Publications

Single nucleotide polymorphisms (SNPs) are the marker of choice for many researchers due to their abundance and the high-throughput methods available for their multiplex analysis. Only recently have SNP markers been available to researchers in soybean [Glycine max (L.) Merr.] with the release of the third version of the consensus genetic linkage map that added 1141 SNP markers to the map. Our objectives were to add 2500 additional SNP markers to the soybean integrated map and select a set of 1536 SNPs to create a universal linkage panel for high-throughput soybean quantitative trait locus (QTL) mapping. The GoldenGate assay …

Structural And Functional Divergence Of A 1-Mb Duplicated Region In The Soybean (Glycine Max) Genome And Comparison To An Orthologous Region From Phaseolus Vulgaris, Jer-Young Lin, Robert M. Stupar, Christian Hans, D. L. Hyten, Scott A. Jackson

Department of Agronomy and Horticulture: Faculty Publications

Soybean (Glycine max) has undergone at least two rounds of polyploidization, resulting in a paleopolyploid genome that is a mosaic of homoeologous regions. To determine the structural and functional impact of these duplications, we sequenced two ~1-Mb homoeologous regions of soybean, Gm8 and Gm15, derived from the most recent ~13 million year duplication event and the orthologous region from common bean (Phaseolus vulgaris), Pv5. We observed inversions leading to major structural variation and a bias between the two chromosome segments as Gm15 experienced more gene movement (gene retention rate of 81% in Gm15 versus 91% in …

Fine Mapping The Soybean Aphid Resistance Gene Rag1 In Soybean, Ki-Seung Kim, Stephanie Bellendir, Karen A. Hudson, Curtis B. Hill, Glen L. Hartman, D. L. Hyten, Matthew E. Hudson, Brian W. Diers

Department of Agronomy and Horticulture: Faculty Publications

The soybean aphid (Aphis glycines Matsumura) is an important soybean [Glycine max (L.) Merr.] pest in North America. The dominant aphid resistance gene Rag1 was previously mapped from the cultivar ‘Dowling’ to a 12 cM marker interval on soybean chromosome 7 (formerly linkage group M). The development of additional genetic markers mapping closer to Rag1 was needed to accurately position the gene to improve the effectiveness of markerassisted selection (MAS) and to eventually clone it. The objectives of this study were to identify single nucleotide polymorphisms (SNPs) near Rag1 and to position these SNPs relative to Rag1. …

Fine Mapping Of The Soybean Aphid-Resistance Gene Rag2 In Soybean Pi 200538, Ki-Seung Kim, Curtis B. Hill, Glen L. Hartman, D. L. Hyten, Matthew E. Hudson, Brian W. Diers

Department of Agronomy and Horticulture: Faculty Publications

The discovery of biotype diversity of soybean aphid (SA: Aphis glycines Matsumura) in North America emphasizes the necessity to identify new aphid-resistance genes. The soybean [Glycine max (L.) Merr.] plant introduction (PI) 200538 is a promising source of SA resistance because it shows a high level of resistance to a SA biotype that can overcome the SA-resistance gene Rag1 from ‘Dowling’. The SA-resistance gene Rag2 was previously mapped from PI 200538 to a 10-cM marker interval on soybean chromosome 13 [formerly linkage group (LG) F]. The objective of this study was to fine map Rag2. This fine mapping …

Abundance Of Ssr Motifs And Development Of Candidate Polymorphic Ssr Markers (Barcsoyssr_1.0) In Soybean, Qijian Song, Gaofeng Jia, Youlin Zhu, David Grant, Rex T. Nelson, Eun-Young Hwang, D. L. Hyten, P. B. Cregan

Department of Agronomy and Horticulture: Faculty Publications

Simple sequence repeat (SSR) genetic markers, also referred to as microsatellites, function in map-based cloning and for marker-assisted selection in plant breeding. The objectives of this study were to determine the abundance of SSRs in the soybean genome and to develop and test soybean SSR markers to create a database of locus-specific markers with a high likelihood of polymorphism. A total of 210,990 SSRs with di-, tri-, and tetranucleotide repeats of five or more were identified in the soybean whole genome sequence (WGS) which included 61,458 SSRs consisting of repeat units of di- (≥10), tri- (≥8), and tetranucleotide (≥7). Among …

Inoculation With Arbuscular Mycorrhizal Fungi Or Crop Rotation With Mycorrhizal Plants Improves The Growth Of Maize In Limed Acid Sulfate Soil, Hasao Higo, Katsunori Isobe, Dong-Jin Kang, Kazuhiro Ujie, Rhae A. Drijber, Ryuichi Ishii

Department of Agronomy and Horticulture: Faculty Publications

Arbuscular mycorrhizal fungi (AMF) improve the uptake of immobile mineral nutrients such as phosphate, thereby improving plant growth. In acid sulfate soil (ASS), AMF spore density is generally low which impacts root colonization and phosphate uptake. Thus, inoculation may help increase AMF colonization of crops grown in ASS. AMF spore density decreases after cultivation of a non-host crop or bare fallow. In addition, preceding crops affect the growth and yield of subsequent crops. The production of AMF inocula requires AMF-compatible plants. The objective of the present study is to elucidate the effect of preceding crops on the persistence of inoculated …