Agricultural Science Commons^™

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 …

Crop Registration: The Pathway To Public Access Of Plant Genetic Materials To Build Crops For The Future, D. D. Ellis, K. A. Garland-Campbell, J. A. Grotenhuis, M. M. Jenderek, Jeffrey F. Pedersen

Department of Agronomy and Horticulture: Faculty Publications

Starting in 1926 and continuing for 80+ yr, 11,241 crop genetic materials have been registered as of 31 Dec. 2008. The crop registration process is an important pathway to publically describe and document new and useful genetic materials and to incorporate these into the public domain via the National Plant Germplasm System (NPGS). Crop Registration materials are now searchable via the Germplasm Resources Information Network (GRIN) and demand for registered materials remains strong with more than 9150 registered accessions distributed in the past 26 yr by the NPGS. Guidelines continue to evolve to accommodate global factors effecting germplasm exchange such …

Efficacy Of Singular And Stacked Brown Midrib 6 And 12 In The Modification Of Lignocellulose And Grain Chemistry, Scott E. Sattler, Deanna L. Funnell-Harris, Jeffrey F. Pedersen

Department of Agronomy and Horticulture: Faculty Publications

In sorghum, brown midrib (bmr) 6 and 12 impair the last two steps of monolignol synthesis. bmr genes were introduced into grain sorghum to improve the digestibility of lignocellulosic tissues for grazing or bioenergy uses following grain harvest. Near-isogenic grain sorghum hybrids (AWheatland X RTx430) were developed containing bmr6, bmr12, and the bmr6 bmr12 double mutant (stacked), and their impacts were assessed in a two-year field study. The bmr genes did not significantly impact grain or lignocellulosic tissue yield. Lignocellulosic tissue from bmr6, bmr12, and stacked hybrids had reduced lignin content and increased in …

Heterosis In Sweet Sorghum And Selection Of A New Sweet Sorghum Hybrid For Use In Syrup Production In Appalachia, T. W. Pfeiffer, M. J. Bitzer, J. J. Toy, Jeffrey F. Pedersen

Department of Agronomy and Horticulture: Faculty Publications

Although heterosis is well established in grain and forage sorghum [Sorghum bicolor (L.) Moench], reports of heterosis in sweet sorghum are limited to results from grain sorghum × sweet sorghum hybrids. Recent development of cytoplasmic male-sterile sweet sorghum lines allows creation of sweet sorghum hybrids for research and industry. Male sterility may also affect allocation of photosynthate to plant parts, creating the potential to increase sugar content in stems by eliminating seed as a sink. The objectives of this study were to compare performance of A₃ cytoplasmic male-sterile lines and A₃ cytoplasmic male-sterile hybrids to fertile B …

Influences Of Wind And Sandblasting On The Endangered Blowout Penstemon, James Stubbendieck, Cheryl D. Dunn, Heidi L. Hillhouse, L. M. Landholt

Department of Agronomy and Horticulture: Faculty Publications

Blowout penstemon Penstemon haydenii is a federally endangered species growing only in areas with active wind erosion in sand dunes of the central United States. This early seral species declines as the blowout habitat stabilizes, allowing later seral species to increase. Blowout penstemon populations and plant size declined in the 1990s when precipitation was higher than normal, resulting in reduced sand movement. We conducted a greenhouse experiment to determine whether blowing sand influenced vigor and persistence of blowout penstemon seedlings. Treatments were wind, sandblasting, wind with sandblasting, and a control. The wind treatment was a constant 14 km h^{–1 …}

Fine Mapping Of The Scn Resistance Locus Rhg1-B From Pi 88788, Myungsik Kim, David L. Hyten, Andrew F. Bent, Brian W. Diers

Department of Agronomy and Horticulture: Faculty Publications

Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is the most economically damaging soybean [Glycine max (L.) Merr.] pest in the USA and genetic resistance is a key component for its control. Although SCN resistance is quantitative, the rhg1 locus on chromosome 18 (formerly known as Linkage Group G) confers a high level of resistance. The objective of this study was to fi ne-map the rhg1-b allele that is derived from plant introduction (PI) 88788. F₂ and F₃ plants and F_3:4 lines from crosses between SCN resistant and susceptible genotypes were tested with genetic markers to …

High-Throughput Snp Discovery And Assay Development In Common Bean, David L. Hyten, Qijian Song, Edward W. Fickus, Charles V. Quigley, Jong-Sung Lim, Ik-Young Choi, Eun-Young Hwang, Marcial Pastor-Corrales, Perry B. Cregan

Department of Agronomy and Horticulture: Faculty Publications

Background: Next generation sequencing has significantly increased the speed at which single nucleotide polymorphisms (SNPs) can be discovered and subsequently used as molecular markers for research. Unfortunately, for species such as common bean (Phaseolus vulgaris L.) which do not have a whole genome sequence available, the use of next generation sequencing for SNP discovery is much more difficult and costly. To this end we developed a method which couples sequences obtained from the Roche 454-FLX system (454) with the Illumina Genome Analyzer (GA) for high-throughput SNP discovery. Results: Using a multi-tier reduced representation library we discovered a total of …

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 …

Elevated Co2 Effects On Semi-Arid Grassland Plants In Relation To Water Availability And Competition, Feike A. Dijkstra, Dana Blumenthal, Jack A. Morgan, Daniel R. Lecain, Ronald F. Follett

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

1. It has been suggested that much of the elevated CO₂ effect on plant productivity and N cycling in semi-arid grasslands is related to a CO₂-induced increase in soil moisture, but the relative importance of moisture-mediated and direct effects of CO₂ remain unclear.

2. We grew five grassland species common to the semi-arid grasslands of northern Colorado, USA, as monocultures and as mixtures of all five species in pots. We examined the effects of atmospheric CO₂ concentration (ambient vs. 780 p.p.m.) and soil moisture (15 vs. 20% m⁄m) on plant biomass and plant N uptake. …

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 …

Tcjp An Improved Method To Quantify Puccinia Coronata F. Sp. Avenae Dna In The Host Avena Sativa, M. Acevedo, E. W. Jackson, A. Sturbaum, H. W. Ohm, J. M. Bonman

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Identification and genetic mapping of loci conferring resistance to polycyclic pathogens such as the rust fungi depends on accurate measurement of disease resistance. We converted an absolute quantification assay of Puccinia coronata DNA to a relative assay by adding a TaqMan^® primers/probe set specific to the oat β-actin gene to simplify and improve quantification of fungal infection. The new multiplex assay estimates the amount of fungal DNA in a sample relative to the amount of host DNA and requires fewer and less labour-intensive steps than previous assays. The relative fungal DNA assay (RFDNA) reliably detected and quantified both host …

Weed Genomics Advance: A Commentary, Stephen O. Duke, Jonathan Gressel

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

A recent book edited by Neal Stewart summarized the salient information about the genomics of weeds. It is a relatively slim volume, in part because so little is known of weed genomics. The rapidly evolving weeds of modern agriculture cry out for understanding their evolution at the genomic level. Still, granting agencies have been reluctant to fund weed genomics in the past, stating that it was enough to support the sequencing of economically important plants (crops), and forgetting that there may be use to sequencing plants that have extremely negative economicimpactsonthose crops. This attitude hasbeenchanging, and the costs have come …

Horticulture Of Ribes, K. E. Hummer, A. Dale

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

The genus Ribes L., known as currants and gooseberries, contains more than 150 diverse species indigenous throughout the northern hemisphere and along the Rocky Mountain, Sierra Nevada and Sierra Madres in North America through mountain ranges of Central America to the Andes in South America. Beginning in the 1400s, four main crop types, black currants (Ribes, subgenus: Ribes, section: Botrycarpum), red and white currants (Ribes, subgenus: Ribes, section: Ribes) and gooseberries (Ribes, subgenus: Grossularia) were domesticated from European species. American and Eurasian species were selected and combined into …

Yeasts Associated With Nectarines And Their Potential For Biological Control Of Brown Rot, W. J. Janisiewicz, C. P. Kurtzman, J. S. Buyer

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Resident fruit microflora has been the source of biocontrol agents for the control of postharvest decay of fruits and the active ingredient in commercialized biocontrol products. With the exception of grapes and apples, information on the resident microflora of other fruits is only fragmentary, but greater knowledge in this area can be very helpful in developing biocontrol strategies. We characterized the yeast microflora of nectarines (‘Croce del Sud’) from the early stages of fruit development until harvest. The fruit samples were collected from trees in an unmanaged orchard. The resident fruit microflora was separated from the occasionally deposited microorganisms by …

Comparison Of Percent Hatch And Fungal Infestation In Channel Catfish Eggs After Copper Sulfate, Diquat Bromide, Formalin, And Hydrogen Peroxide Treatment, Andrew J. Mitchell, David L. Straus, Bradley Farmer, Ray Carter

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Reduced survival of fish eggs is often a result of infestation with fungi Saprolegnia spp. However, timely chemical treatments often limit these infestations and increase survival. The effect of copper sulfate pentahydrate (CSP; 10 mg of CSP/L of water), diquat bromide (25 mg of diquat cation/L), formalin (433 mg/L), and hydrogen peroxide (H₂O₂; 250 mg/L) on percent hatch and fungal infestation in eggs of channel catfish Ictalurus punctatus was compared in two identical trials (five replicates for each chemical treatment per trial). The percent hatch in all chemical treatments was significantly better than percent hatch of …

Role Of The Oviduct In Maintaining Sustained Fertility In Hens, M. R. Bakst

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

In poultry, sperm transferred by natural mating or AI into the distal end of the vagina immediately begin their ascent to the utero-vaginal junction (UVJ) at the anterior end of the vagina. However, due to an intense selection process in the vagina, less than 1% of the sperm transferred actually reach the UVJ. Those sperm that do reach the UVJ enter numerous tubular invaginations of the vagina’s surface epithelium located in the UVJ mucosa, collectively referred to as the sperm-storage tubules (SST). Sperm residing in the SST lumen are capable of surviving up to several weeks while retaining their fertilizing …

Restoration Of Spermatogenesis After Transplantation Of C-Kit Positive Testicular Cells In The Fowl, Pavel Trefil, Murray R. Bakst, Haifen Yan, Jiří Hejnar, Jiří Kalina, Jitka Mucksová

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Transplantation of male germ line cells into sterilized recipients has been used in mammals for conventional breeding as well as for transgenesis. We have previously adapted this approach for the domestic chicken and we present now an improvement of the germ cell transplantation technique by using an enriched subpopulation of c-Kit-positive spermatogonia as donor cells. Dispersed c-Kit positive testicular cells from 16 to 17 week-old pubertal donors were transplanted by injection directly into the testes of recipient males sterilized by repeated gamma irradiation. We describe the repopulation of the recipient’s testes with c-Kit positive donor testicular cells, which resulted in …

Proteomic Analysis Of The Major Cellular Proteins Of Bovine Trophectoderm Cell Lines Derived From Ivp, Parthenogenetic And Nuclear Transfer Embryos: Reduced Expression Of Annexins I And Ii In Nuclear Transfer-Derived Cell Lines, Neil C. Talbot, Anne M. Powell, Thomas J. Caperna, Wesley M. Garrett

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Trophectoderm cell lines were established from 8-day in vitro-cultured embryos of cattle derived from fertilization (IVF), somatic cell nuclear transfer (NT), or parthenogenetic activation (P) of in vitro-matured oocytes and from five 8-day-old in vivo (V) embryos. The most abundant cellular proteins of 5 V-, 16 NT-, 12 P-, and 16 IVF-derived cell lines were compared by 2D-gel electrophoresis and mass spectrometry; that is, the unaltered thiourea/urea extract of each cell culture was analyzed. Common protein spots (n = 118) were examined, and 95% were identified with significant scores from protein and gene database searches. Of the proteins …

Field Applications Of Entomopathogenic Fungi Beauveria Bassiana And Metarhizium Anisopliae F52 (Hypocreales: Clavicipitaceae) For The Control Of Ixodes Scapularis (Acari: Ixodidae), Kirby C. Stafford Iii, Sandra A. Allan

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Two commercial formulations of Beauveria bassiana (Balsamo-Crivelli) Vuillemin were applied to residential sites in Old Lyme, CT, for the control of nymphs of the blacklegged tick, Ixodes scapularis, in 1999 and 2000. The pyrethroid bifenthrin was applied to other premises for comparison with B. bassiana. A wood chip barrier was installed and maintained at six of the treated properties. In 1999, control of I. scapularis nymphs ranged from 74.5 to 83.0% on lawns without wood chips and from 88.9 to 90% on lawns with wood chip barriers. As a control check, no ticks (n= 23) collected …

Herbicides For Establishing Switchgrass In The Central And Northern Great Plains, Robert B. Mitchell, Kenneth P. Vogel, John Berdahl, Robert A. Masters

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Weed interference limits switchgrass (Panicum virgatum L.) establishment from seed. Our objectives were to determine the effect of selected post-plant, preemergence herbicides on stand establishment and subsequent biomass yields of adapted upland switchgrass cultivars grown in three environments in the Central and Northern Great Plains. A separate experiment was conducted in eastern Nebraska to determine if there were any differences among switchgrass ecotypes for herbicide tolerance to the optimal herbicide combination. Herbicides applied immediately after planting were different concentrations of atrazine [Aatrex 4L^®; 6- chloro-N-ethyl-N′-(1-methylethyl)-1,3,5-triazine-2,4-diamine], quinclorac (Paramount^®; 3,7-Dichloro-8-quinolinecarboxylic acid), atrazine+quinclorac, imazapic …

Soil Water And Crop Growth Processes In A Farmer's Field, Susmitha Surendran Nambuthiri

University of Kentucky Doctoral Dissertations

The study was aimed to provide information on local biomass development during crop growth using ground based optical sensors and to incorporate the local crop status to a crop growth simulation model to improve understanding on inherent variability of crop field. The experiment was conducted in a farmer’s field located near Princeton in Caldwell County, Western Kentucky. Data collection on soil, crop and weather variables was carried out in the farm from 2006 December to 2008 October. During this period corn (Zea mays L.) and winter wheat (Triticum sp) were grown in the field. A 450 m …

Tillage Depth Effects On Soil Physical Properties, Sugarbeet Yield, And Sugarbeet Quality, J. D. Jabro, W. B. Stevens, W. M. Iversen, R. G. Evans

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Tillage depth influences the soil–water–plant ecosystem, thereby affecting crop yield and quality. The effects of tillage depth on soil physical properties and sugarbeet (Beta vulgaris L.) yield and quality were evaluated. A field study composed of two tillage depths [10 cm, referred to as shallow (ST), and 20 cm, referred to as deep (DT)] was conducted on a Lihen sandy loam soil in spring 2007 at the Agricultural Research Service (ARS) irrigated research farm near Williston, North Dakota. Soil bulk density (ρb), gravimetric water content (θw), and saturated hydraulic conductivity (Ks) were measured three times during the growing season …

Permanent Genetic Resources Added To The Molecular Ecology Resources Database 1 February 2010–31 March 2010, D. Aurelle, M. R. Pooler, T. A. Rinehart, B. E. Scheffler, Molecular Ecology Resources Primer Development Consortium

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

This article documents the addition of 228 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Anser cygnoides, Apodemus flavicollis, Athene noctua, Cercis canadensis, Glis glis, Gubernatrix cristata, Haliotis tuberculata, Helianthus maximiliani, Laricobius nigrinus, Laricobius rubidus, Neoheligmonella granjoni, Nephrops norvegicus, Oenanthe javanica, Paramuricea clavata, Pyrrhura orcesi and Samanea saman. These loci were cross-tested on the following species: Apodemus sylvaticus, Laricobius laticollis and Laricobius osakensis (a proposed new species currently being described).

Soybase, The Usda-Ars Soybean Genetics And Genomics Database, David Grant, Rex T. Nelson, Steven B. Connon, Randy C. Shoemaker

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

SoyBase, the USDA-ARS soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics and related data resources for soybean. SoyBase contains the most current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. The quantitative trait loci (QTL) represent more than 18 years of QTL mapping of more than 90 unique traits. SoyBase also contains the wellannotated ‘Williams 82’ genomic sequence and associated data mining tools. The genetic and sequence views of the soybean chromosomes and the extensive data on traits and phenotypes are extensively interlinked. This allows entry to the database using almost any …

Eupatorium Capillifolium Essential Oil: Chemical Composition, Antifungal Activity, And Insecticidal Activity, Nurhayat Tabanca, Ulrich R. Bernier, Maia Tsikolia, James Becnel, Blair Sampson, Chris Werle, Betül Demirci, Kemal Hüsnü Can Başer, Eugene K. Blythe, Cecil Pounders, David E. Wedge

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Natural plant extracts often contain compounds that are useful in pest management applications. The essential oil of Eupatorium capillifolium (dog-fennel) was investigated for antifungal and insecticidal activities. Essential oil obtained by hydrodistillation of aerial parts was analyzed by gas chromatography (GC) and gas chromatography–mass spectrometry (GC/MS). The major components were determined to be thymol methyl ether (=methyl thymol) (36.3%), 2,5-dimethoxy-p-cymene (20.8%) and myrcene (15.7%). Antifungal activity of the essential oil was weak against the plant pathogens Colletotrichum acutatum, C. fragariae, and C. gloeosporioides in direct bioautography assay. The E. capillifolium oil showed promising repellent activity against …

Arkansas Soybean Performance Tests 2009, D. G. Dombeck, R. D. Bond, I. L. Eldridge, 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. The tests provide information to companies developing varieties and/or marketing seed within the state, and aid the Arkansas Cooperative Extension Service in formulating variety recommendations for soybean producers.

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 …