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Evidence From Micromorphology And Gross Morphology Of The Genus Loranthus (Loranthaceae) In Iran, Robabeh Shahi Shavvon, Shahryar Saeidi Mehrvarz, Narges Golmohammadi Jan 2012

Evidence From Micromorphology And Gross Morphology Of The Genus Loranthus (Loranthaceae) In Iran, Robabeh Shahi Shavvon, Shahryar Saeidi Mehrvarz, Narges Golmohammadi

Turkish Journal of Botany

The genus Loranthus L. (Loranthaceae) is represented in Iran by 2 species: Loranthus europaeus Jacq. and L. grewingkii Boiss. & Buhse; the latter species is endemic to the area of Flora Iranica. The plants of Loranthus are hemiparasites growing on various host trees such as Quercus infectoria Oliv., Acer monspessulanum L., and Armeniaca vulgaris Lam. In order to investigate the range of morphological variation in different populations of these species, an inclusive gross morphological and micromorphological study was conducted. For this purpose, the anatomical characteristics of the stem, leaf, petiole, and fruit were also investigated. The most prominent features were …


Reproductive Success Of The Rare Endemic Orchis Galilaea (Orchidaceae) In Lebanon, Nisrine Machaka Houri, Mohammad Souheil Al-Zein, Duncan Brian Westbury, Salma Nashabe Talhouk Jan 2012

Reproductive Success Of The Rare Endemic Orchis Galilaea (Orchidaceae) In Lebanon, Nisrine Machaka Houri, Mohammad Souheil Al-Zein, Duncan Brian Westbury, Salma Nashabe Talhouk

Turkish Journal of Botany

The biology and ecology of Orchis galilaea Schltr., a species endemic to Lebanon, Palestine, and Jordan, is poorly studied, a fact that hinders present and future management and conservation efforts concerning this species. In this paper, we report findings of a field investigation that assessed the impact of altitude, population density, and plant size on the reproductive success of O. galilaea. The results revealed that plant size and population density were significantly correlated with reproductive success while altitude was not. This study is part of ongoing research on the ecological responses of O. galilaea and provides a baseline for understanding …


Leaf And Anatomical Traits In Relation To Physiological Characteristics In Mulberry (Morus Sp.) Cultivars, Vineet Kumar, Javuli Kodandaramaiah, Mala Vati Rajan Jan 2012

Leaf And Anatomical Traits In Relation To Physiological Characteristics In Mulberry (Morus Sp.) Cultivars, Vineet Kumar, Javuli Kodandaramaiah, Mala Vati Rajan

Turkish Journal of Botany

Micromorphological and anatomical traits in relation to physiological characteristics were studied in the leaves of 4 mulberry (Morus sp.) cultivars (V_1, TR_{10}, S_{34}, and Mysore local) by scanning electron microscope. The results revealed that leaf thickness was lowest (124.42 ± 2.21 µm) in the TR_{10} genotype and highest in V_1 (263.77 ± 5.17 µm). Cultivar S_{34} ranked second in respect to leaf thickness (203.57 ± 1.98 µm), followed by Mysore local (127.94 ± 2.19 µm). The thickness of palisade parenchyma was 143.66 ± 2.42 µm in V_1, 64.95 ± 1.60 µm in TR_{10}, 83.92 ± 1.43 µm in S_{34}, and …


Using Sex Pheromone Traps In The Decision-Making Process For Pesticide Application Against Fall Armyworm (Spodoptera Frugiperda [Smith] [Lepidoptera: Noctuidae]) Larvae In Maize, Ivan Cruz, Maria De Lourdes Corrêa Figueiredo, Rafael Braga Da Silva, Ivana Fernandes Da Silva, Cristiane De Souza Paula, John E. Foster Jan 2012

Using Sex Pheromone Traps In The Decision-Making Process For Pesticide Application Against Fall Armyworm (Spodoptera Frugiperda [Smith] [Lepidoptera: Noctuidae]) Larvae In Maize, Ivan Cruz, Maria De Lourdes Corrêa Figueiredo, Rafael Braga Da Silva, Ivana Fernandes Da Silva, Cristiane De Souza Paula, John E. Foster

Department of Entomology: Faculty Publications

The fall armyworm, Spodoptera frugiperda (Smith) (Lepidoptera: Noctuidae), is a major pest of maize and frequently demands control measures. The timing of insecticide application is a key factor in determining its efficiency, so an experiment was designed to investigate this. Application of insecticide was based on three criteria: (i) the number of trap-caught moths in a Delta-type trap with a commercial sex pheromone lure placed in the center of the target area, soon after plant emergence; (ii) the percentage of plants exhibiting pinhole-type damage (10% or 20%), and (iii) the percentage of plants exhibiting shot hole–type damage (10% or 20%) …


Spatial Patterns Of Brown Rot Epidemics And Development Of Microsatellite Markers For Analyzing Fine-Scale Genetic Structure Of Monilinia Fructicola Populations Within Peach Tree Canopies, Sydney E. Everhart, A. Askew, L. Seymour, T. C. Glenn, H. Scherm Jan 2012

Spatial Patterns Of Brown Rot Epidemics And Development Of Microsatellite Markers For Analyzing Fine-Scale Genetic Structure Of Monilinia Fructicola Populations Within Peach Tree Canopies, Sydney E. Everhart, A. Askew, L. Seymour, T. C. Glenn, H. Scherm

Department of Plant Pathology: Faculty Publications

To better understand the fine-scale spatial dynamics of brown rot disease and corresponding fungal genotypes, we analyzed three-dimensional spatial patterns of pre-harvest fruit rot caused by Monilinia fructicola in individual peach tree canopies and developed microsatellite markers for canopy-level population genetics analyses. Using a magnetic digitizer, high-resolution maps of fruit rot development in five representative trees were generated, and M. fructicola was isolated from each affected fruit. To characterize disease aggregation, nearest-neighbor distances among symptomatic fruit were calculated and compared with appropriate random simulations. Within-canopy disease aggregation correlated negatively with the number of diseased fruit per tree (r = −0.827, …


Prothioconazole Tolerant Cryptococcus Flavescens Strains For Biological Control Of Fusarium Head Blight, David A. Schisler, Michael J. Boehm Jan 2012

Prothioconazole Tolerant Cryptococcus Flavescens Strains For Biological Control Of Fusarium Head Blight, David A. Schisler, Michael J. Boehm

Department of Plant Pathology: Faculty Publications

Strains of Cryptococcus flavescens which are superior antagonists of F. graminearum for suppression and control of FHB in cereals, particularly in wheat and barley, are described. The strains are prothioconazole tolerant variants of previously described C. flavescens OH 182.9 (NRRL Y-30216). Moreover, these prothioconazole tolerant variants exhibit significantly increased efficacy against F. graminearum in comparison to the parent strain OH 182.9.


Product Comparison Of Foliar Fungicide Efficacy On Diseases Of Field Corn In Nebraska, 2011, C. M. Schleicher, T. A. Jackson Jan 2012

Product Comparison Of Foliar Fungicide Efficacy On Diseases Of Field Corn In Nebraska, 2011, C. M. Schleicher, T. A. Jackson

Department of Plant Pathology: Faculty Publications

foliar fungicide efficacy trial was conducted at the University of Nebraska-Lincoln South Central Agricultural Laboratory near Clay Center, NE. Dekalb corn hybrid DKC 62-54, rating of “good” (6 out of 9) for gray leaf spot (GLS) and “excellent” (2 out of 9) for common rust (CR), was planted on 3 May in 30-in. rows with a target population of 32,000 plants/A. The trial area was disked with soybean as the previous year’s crop. On 9 May before plant emergence, a herbicide program of Roundup (1 pt/A), Verdict (16 fl oz/A) and Atrazine (1 lb/A) was applied to the trial site. …


Efficacy Evaluation Of Foliar Fungicide Application Timing On Diseases Of Field Corn In Nebraska, 2011, C. M. Schleicher, T. A. Jackson Jan 2012

Efficacy Evaluation Of Foliar Fungicide Application Timing On Diseases Of Field Corn In Nebraska, 2011, C. M. Schleicher, T. A. Jackson

Department of Plant Pathology: Faculty Publications

foliar fungicide efficacy timing trial was conducted at the University of Nebraska-Lincoln South Central Agricultural Laboratory near Clay Center, NE. Dekalb corn hybrid DKC 62-54, rating of “good” (6 out of 9) for gray leaf spot (GLS) and “excellent” (2 out of 9) for common rust (CR), was planted on 3 May in 30-in. rows with a target population of 32,000 plants/A. The trial area was disked with soybean as the previous year’s crop. On 9 May before plant emergence, a herbicide program of Roundup (1 pt/A), Verdict (16 fl oz/A) and Atrazine (1 lb/A) was applied to the trial …


Evaluation Of Foliar Fungicide Efficacy On Sorghum In Nebraska, 2011, C. M. Schleicher, T. A. Jackson-Ziems Jan 2012

Evaluation Of Foliar Fungicide Efficacy On Sorghum In Nebraska, 2011, C. M. Schleicher, T. A. Jackson-Ziems

Department of Plant Pathology: Faculty Publications

A foliar fungicide efficacy trial was conducted at the University of Nebraska-Lincoln South Central Agricultural Laboratory near Clay Center, NE. DeKalb sorghum hybrid DKS 36-06 was planted on 23 May in 30-in. rows with a target population of approximately 120,000 plants/A. The trial area was disked with soybean as the previous year’s crop. Four treatments and a nontreated control were replicated six times in a randomized complete block design. Each plot was four rows (10 ft) wide by 40 ft in length. . . . There were significant differences in GLS AUDPC among treatments. The nontreated control exhibited the largest …


Application Timing On Foliar Fungicide Efficacy On Sorghum In Nebraska, 2009, C. M. Schleicher, T. A. Jackson Jan 2012

Application Timing On Foliar Fungicide Efficacy On Sorghum In Nebraska, 2009, C. M. Schleicher, T. A. Jackson

Department of Plant Pathology: Faculty Publications

A foliar fungicide efficacy trial was established at the University of Nebraska-Lincoln South Central Agricultural Laboratory near Clay Center, NE. Grain sorghum hybrid NC+ 7R83 was planted on 18 May in 30-in. rows with a target population of 90,000 plants/A. The trial area was disked with a crop history of five years of continuous corn. Eight treatments and a non-treated control were replicated six times in a randomized complete block design. Each plot was four rows (10 ft) wide by 40 ft in length. . . . There were no significant differences in stay green. Stay green percentages ranged from …


Effects Of Crop Injury On Disease Development, Tamra A. Jackson, Loren J. Giesler, Robert M. Harveson Jan 2012

Effects Of Crop Injury On Disease Development, Tamra A. Jackson, Loren J. Giesler, Robert M. Harveson

Department of Plant Pathology: Faculty Publications

The effect of damage caused by blowing soil and leaf contact with high speed winds and hail will all create a similar level of wounding that is often sufficient for pathogens that require wounds to enter (infect) plants. As we look at the level of disease and crop damage we can identify several examples in the corn and soybean disease systems when this can be a factor that could lead to significant disease development and possibly trigger a disease management action.

Hail and wind damage can result in an open canopy which can affect the microclimate and impact disease development. …


What's New In Plant Pathology: Resistance: Mystery And Misunderstandings, Amy D. Timmerman, Loren J. Giesler, Robert M. Harveson, Tamra Jackson-Ziems, Stephen N. Wegulo Jan 2012

What's New In Plant Pathology: Resistance: Mystery And Misunderstandings, Amy D. Timmerman, Loren J. Giesler, Robert M. Harveson, Tamra Jackson-Ziems, Stephen N. Wegulo

Department of Plant Pathology: Faculty Publications

One of the most common management recommendations for plant diseases is the use of resistant or tolerant varieties/hybrids in your production system. However, there is common confusion on the definition and differentiation of susceptible, tolerant, and resistant varieties/hybrids from a plant pathology viewpoint. A susceptible variety/hybrid allows the pathogen to reproduce and causes significant disease development and in turn compromises the productivity of the plant (i.e., yield). A tolerant variety/hybrid allows the pathogen to reproduce and cause disease at the same or at a slightly reduced rate as a susceptible variety/cultivar; however, there is no noticeable reduction in the plant’s …


Crop Management Of Switchgrass, Matt A. Sanderson, Marty R. Schmer, Vance Owens, Pat Keyser, Wolter Elbersen Jan 2012

Crop Management Of Switchgrass, Matt A. Sanderson, Marty R. Schmer, Vance Owens, Pat Keyser, Wolter Elbersen

Department of Agronomy and Horticulture: Faculty Publications

Management of switchgrass for bioenergy and forage share some commonalities, of particular interest in bioenergy crop production is: (1) rapid establishment of switchgrass to generate harvestable biomass in the seeding year, (2) highly efficient management of soil and fertilizer N to minimize external energy inputs, and (3) harvest management to maximize yields of lignocellulose. Bioenergy cropping may entail management for multiple services in addition to biomass yield including soil C sequestration, wildlife habitat, landscape management, and water quality protection. Management is a critical factor especially as land classified as marginal or idle land will be emphasized for bioenergy production to …


Auxin Controls Arabidopsis Adventitious Root Initiation By Regulating Jasmonic Acid Homeostasis, Laurent Gutierrez, Gaëlle Mongelard, Kristýna Floková, Daniel I. Păcurar, Ondrej Novák, Paul E. Staswick, Mariusz Kowalczyk, Monica Păcurar, Gaia Geiss, Catherine Bellini Jan 2012

Auxin Controls Arabidopsis Adventitious Root Initiation By Regulating Jasmonic Acid Homeostasis, Laurent Gutierrez, Gaëlle Mongelard, Kristýna Floková, Daniel I. Păcurar, Ondrej Novák, Paul E. Staswick, Mariusz Kowalczyk, Monica Păcurar, Gaia Geiss, Catherine Bellini

Department of Agronomy and Horticulture: Faculty Publications

Vegetative shoot-based propagation of plants, including mass propagation of elite genotypes, is dependent on the development of shoot-borne roots, which are also called adventitious roots. Multiple endogenous and environmental factors control the complex process of adventitious rooting. In the past few years, we have shown that the auxin response factors ARF6 and ARF8, targets of the microRNA miR167, are positive regulators of adventitious rooting, whereas ARF17, a target of miR160, is a negative regulator. We showed that these genes have overlapping expression profiles during adventitious rooting and that they regulate each other’s expression at the transcriptional …


Modulation Of Kernel Storage Proteins In Grain Sorghum (Sorghum Bicolor (L.) Moench), Tejinder Kumar, Ismail M. Dweikat, Shirley Sato, Zhengxiang Ge, Natalya Nersesian, Han Chen, Thomas Elthon, Scott Bean, Brian P. Ioerger, Mike Tilley, Thomas E. Clemente Jan 2012

Modulation Of Kernel Storage Proteins In Grain Sorghum (Sorghum Bicolor (L.) Moench), Tejinder Kumar, Ismail M. Dweikat, Shirley Sato, Zhengxiang Ge, Natalya Nersesian, Han Chen, Thomas Elthon, Scott Bean, Brian P. Ioerger, Mike Tilley, Thomas E. Clemente

Department of Agronomy and Horticulture: Faculty Publications

Sorghum prolamins, termed kafirins, are categorized into subgroups α, β, and γ. The kafirins are co-translationally translocated to the endoplasmic reticulum (ER) where they are assembled into discrete protein bodies that tend to be poorly digestible with low functionality in food and feed applications. As a means to address the issues surrounding functionality and digestibility in sorghum, we employed a biotechnology approach that is designed to alter protein body structure, with the concomitant synthesis of a co-protein in the endosperm fraction of the grain. Wherein perturbation of protein body architecture may provide a route to impact digestibility by reducing disulphide …


Cover Crop Mixtures For The Western Corn Belt: Opportunities For Increased Productivity And Stability, Samuel E. Wortman, Charles A. Francis, John L. Lindquist Jan 2012

Cover Crop Mixtures For The Western Corn Belt: Opportunities For Increased Productivity And Stability, Samuel E. Wortman, Charles A. Francis, John L. Lindquist

Department of Agronomy and Horticulture: Faculty Publications

Achieving agronomic and environmental benefits associated with cover crops oft en depends on reliable establishment of a highly productive cover crop community. The objective of this study was to determine if cover crop mixtures can increase productivity and stability compared to single species cover crops, and to identify those components most active in contributing to or detracting from mixture productivity. A rainfed field experiment was conducted near Mead, Nebraska, United States, in 2010 and 2011. Eight individual cover crop species (in either the Brassicaceae [mustard] or Fabaceae [legume] family) and four mixtures of these species (two, four, six, and eight …


Local Conditions, Not Regional Gradients, Drive Demographic Variation Of Giant Ragweed (Ambrosia Trifida) And Common Sunflower (Helianthus Annuus) Across Northern U.S. Maize Belt, Samuel E. Wortman, Adam Davis, Brian J. Schutte, John L. Lindquist, John Cardina, Joel Felix, Christy L. Sprague, J. Anita Dille, Analiza H. M. Ramirez, Graig Reicks, Sharon A. Clay Jan 2012

Local Conditions, Not Regional Gradients, Drive Demographic Variation Of Giant Ragweed (Ambrosia Trifida) And Common Sunflower (Helianthus Annuus) Across Northern U.S. Maize Belt, Samuel E. Wortman, Adam Davis, Brian J. Schutte, John L. Lindquist, John Cardina, Joel Felix, Christy L. Sprague, J. Anita Dille, Analiza H. M. Ramirez, Graig Reicks, Sharon A. Clay

Department of Agronomy and Horticulture: Faculty Publications

Knowledge of environmental factors influencing demography of weed species will improve understanding of current and future weed invasions. The objective of this study was to quantify regional-scale variation in vital rates of giant ragweed and common sunflower . To accomplish this objective, a common field experiment was conducted across seven sites between 2006 and 2008 throughout the north central U.S. maize belt. Demographic parameters of both weed species were measured in intra- and interspecific competitive environments, and environmental data were collected within site-years. Site was the strongest predictor of below ground vital rates (summer and winter seed survival and seedling …


An Investigation Of Reflective Mulches For Use Over Capillary Mat Systems For Winter-Time Greenhouse Strawberry Production, George E. Meyer, Ellen T. Paparozzi, Elizabeth Walter-Shea, Erin E. Blankenship, Stacy A. Adams Jan 2012

An Investigation Of Reflective Mulches For Use Over Capillary Mat Systems For Winter-Time Greenhouse Strawberry Production, George E. Meyer, Ellen T. Paparozzi, Elizabeth Walter-Shea, Erin E. Blankenship, Stacy A. Adams

Department of Agronomy and Horticulture: Faculty Publications

Photosynthethically active radiation (PAR) is a principle environmental variable used by horticultural specialists, agronomists and ecosystem modelers to characterize the quantity and quality of light conducive to plant growth and development. Spatial distribution of PAR in a greenhouse can be quite variable and diffuse throughout the day time photoperiod, especially at low sun angles in northern regions of the United States. Four colors of reflective plastic mulches (white, red, olive, and black) were evaluated for winter-time strawberry (Fragaria × ananassa Duch.) production based on their reflectance and transmittance properties in a double-polyethylene, plastic-glazed Quonset greenhouse inNebraska. The spectral properties …


Inheritance Of Grain Polyphenol Oxidase (Ppo) Activity In Multiple Wheat (Triticum Aestivum L.) Genetic Backgrounds, Somrudee Nilthong, Robert A. Graybosch, P. Stephen Baenziger Jan 2012

Inheritance Of Grain Polyphenol Oxidase (Ppo) Activity In Multiple Wheat (Triticum Aestivum L.) Genetic Backgrounds, Somrudee Nilthong, Robert A. Graybosch, P. Stephen Baenziger

Department of Agronomy and Horticulture: Faculty Publications

Grain polyphenol oxidase (PPO) activity can cause discoloration of wheat (Triticum aestivum L.) food products. Five crosses (PI 117635/Antelope; Fielder/ NW03681; Fielder/Antelope; NW07OR1070/Antelope; NW07OR1066/OR2050272H) were selected to study the genetic inheritance of PPO activity. STS markers, PPO18, PPO29 and STS01, were used to identify lines with putative alleles at the Ppo-A1 and Ppo-D1 loci conditioning low or high PPO activity. ANOVA showed significant genotypic effects on PPO activity (P\0.0001) in all populations. The generations and generation 9 genotype effects were not significant in any population. A putative third (null) genotype at Ppo-A1 (no PCR fragments for PPO18) was discovered …


Identification And Characterization Of Four Missense Mutations In Brown Midrib 12 (Bmr12), The Caffeic O-Methyltranferase (Comt) Of Sorghum, Scott E. Sattler, Nathan A. Palmer, Ana Saballos, Ann M. Greene, Zhanguo Xin, Gautam Sarath, Wilfred Vermerris, Jeffrey F. Pedersen Jan 2012

Identification And Characterization Of Four Missense Mutations In Brown Midrib 12 (Bmr12), The Caffeic O-Methyltranferase (Comt) Of Sorghum, Scott E. Sattler, Nathan A. Palmer, Ana Saballos, Ann M. Greene, Zhanguo Xin, Gautam Sarath, Wilfred Vermerris, Jeffrey F. Pedersen

Department of Agronomy and Horticulture: Faculty Publications

Modifying lignin content and composition are targets to improve bioenergy crops for cellulosic conversion to biofuels. In sorghum and other C4 grasses, the brown midrib mutants have been shown to reduce lignin content and alter its composition. Bmr12 encodes the sorghum caffeic O-methyltransferase, which catalyzes the penultimate step in monolignol biosynthesis. From an EMS-mutagenized TILLING population, four bmr12 mutants were isolated. DNA sequencing identified the four missense mutations in the Bmr12 coding region, which changed evolutionarily conserved amino acids Ala71Val, Pro150Leu, Gly225Asp, and Gly325Ser. The previously characterized bmr12 mutants all contain premature stop codons. These newly identified mutants, along …


Agriculture And Food In Crisis: Conflict, Resistance, And Renewal [Book Review], Charles A. Francis Jan 2012

Agriculture And Food In Crisis: Conflict, Resistance, And Renewal [Book Review], Charles A. Francis

Department of Agronomy and Horticulture: Faculty Publications

Edited by Fred Magdoff and Brian Tokar. 2010. Monthly Review Press, New York, New York, United States. 348 p. Paperback, cloth US$ 75.00, paper US$ 18.95, ISBN-13 978-1-58367-226-6.

That doubling of food production over the next four decades will be needed to adequately nourish our human population is not news, but the incredible steps essential to achieve that goal and their political and social implications are less well reported. In this series of 16 essays edited by Fred Magdoff and Brian Tokar, several thoughtful specialists in global food issues explore the historical, biological, economic, energy, political and social dimensions of …


Estimating Construction Costs For A Low-Cost Quonset-Style Greenhouse, David P. Lambe, Stacy A. Adams, Ellen T. Paparozzi Jan 2012

Estimating Construction Costs For A Low-Cost Quonset-Style Greenhouse, David P. Lambe, Stacy A. Adams, Ellen T. Paparozzi

Department of Agronomy and Horticulture: Faculty Publications

Double polyethylene Quonset-style greenhouses offergrowers and farmers a more cost-effective structure than glass- or acrylic-covered structures for growing plants off-season. These greenhouses are especially applicablefor producing off-season high value crops such as fruits and vegetables for local markets. To support this production alternative, this publication contains a list of greenhouse components, the start-up costs associated with these items and an estimate of the number of person hours required to assemble and outfit a 24-foot-by-72-foot double polyethylene, air-inflated greenhouse structure. As there are many options available for building double polyethylene greenhouses, the main purpose of this publication is to identify the …


The ‘Pi 438489b’ By ‘Hamilton’ Snp-Based Genetic Linkage Map Of Soybean [Glycine Max (L.) Merr.] Identified Quantitative Trait Loci That Underlie Seedling Sds Resistance, Kassem My Abdelmajid, Laura Ramos, Leonor Leandro, Gladys Mbofung, D. L. Hyten, Stella K. Kantartzi, Robert L. Grier Iv, Victor N. Njiti, Khalid Meksem Jan 2012

The ‘Pi 438489b’ By ‘Hamilton’ Snp-Based Genetic Linkage Map Of Soybean [Glycine Max (L.) Merr.] Identified Quantitative Trait Loci That Underlie Seedling Sds Resistance, Kassem My Abdelmajid, Laura Ramos, Leonor Leandro, Gladys Mbofung, D. L. Hyten, Stella K. Kantartzi, Robert L. Grier Iv, Victor N. Njiti, Khalid Meksem

Department of Agronomy and Horticulture: Faculty Publications

Soybeans [Glycine max (L.) Merr.] are susceptible to many diseases including fungal diseases such as soybean sudden death syndrome (SDS). Several studies reported SDS resistance quantitative trait loci (QTL) on the soybean genome using different recombinant inbred line (RIL) populations and low density genetic linkage maps. High density exclusively single nucleotide polymorphisms-based (SNP-based) maps were not yet reported in soybean. The objectives of this study were (1) to construct a high density SNP-based genetic linkage map of soybean using the ‘PI438489B’ by ‘Hamilton’ (PIxH, n=50) recombinant inbred line population, and (2) to map QTL for SDS resistance using this …


Structural Variants In The Soybean Genome Localize To Clusters Of Biotic Stress-Response Genes, Leah K. Mchale, William J. Haun, Wayne W. Xu, Pudota B. Bhaskar, Justin E. Anderson, D. L. Hyten, Daniel J. Gerhardt, Jeffrey A. Jeddeloh, Robert M. Stupar Jan 2012

Structural Variants In The Soybean Genome Localize To Clusters Of Biotic Stress-Response Genes, Leah K. Mchale, William J. Haun, Wayne W. Xu, Pudota B. Bhaskar, Justin E. Anderson, D. L. Hyten, Daniel J. Gerhardt, Jeffrey A. Jeddeloh, Robert M. Stupar

Department of Agronomy and Horticulture: Faculty Publications

Genome-wide structural and gene content variations are hypothesized to drive important phenotypic variation within a species. Structural and gene content variations were assessed among four soybean (Glycine max) genotypes using array hybridization and targeted resequencing. Many chromosomes exhibited relatively low rates of structural variation (SV) among genotypes. However, several regions exhibited both copy number and presence-absence variation, the most prominent found on chromosomes 3, 6, 7, 16, and 18. Interestingly, the regions most enriched for SV were specifically localized to gene-rich regions that harbor clustered multigene families. The most abundant classes of gene families associated with these regions …


Identification Of Positive Yield Qtl Alleles From Exotic Soybean Germplasm In Two Backcross Populations, K.-S. Kim, B. W. Diers, D. L. Hyten, M. A. Rouf Mian, J. G. Shannon, R. L. Nelson Jan 2012

Identification Of Positive Yield Qtl Alleles From Exotic Soybean Germplasm In Two Backcross Populations, K.-S. Kim, B. W. Diers, D. L. Hyten, M. A. Rouf Mian, J. G. Shannon, R. L. Nelson

Department of Agronomy and Horticulture: Faculty Publications

Increasing seed yield is an important breeding goal of soybean [Glycine max (L.) Merr.] improvement efforts. Due to the small number of ancestors and subsequent breeding and selection, the genetic base of current soybean cultivars in North America is narrow. The objective of this study was to map quantitative trait loci (QTL) in two backcross populations developed using soybean plant introductions as donor parents. The first population included 116 BC2F3-derived lines developed using ‘‘Elgin’’ as the recurrent parent and PI 436684 as the donor parent (E population). The second population included 93 BC3F …


Molecular Mapping Of Soybean Rust Resistance In Soybean Accession Pi 561356 And Snp Haplotype Analysis Of The Rpp1 Region In Diverse Germplasm, Ki-Seung Kim, Jair R. Unfried, D. L. Hyten, Reid D. Frederick, Glen L. Hartman, Randall L. Nelson, Qijian Song, Brian W. Diers Jan 2012

Molecular Mapping Of Soybean Rust Resistance In Soybean Accession Pi 561356 And Snp Haplotype Analysis Of The Rpp1 Region In Diverse Germplasm, Ki-Seung Kim, Jair R. Unfried, D. L. Hyten, Reid D. Frederick, Glen L. Hartman, Randall L. Nelson, Qijian Song, Brian W. Diers

Department of Agronomy and Horticulture: Faculty Publications

Soybean rust (SBR), caused by Phakopsora pachyrhizi Sydow, is one of the most economically important and destructive diseases of soybean [Glycine max (L.) Merr.] and the discovery of novel SBR resistance genes is needed because of virulence diversity in the pathogen. The objectives of this research were to map SBR resistance in plant introduction (PI) 561356 and to identify single nucleotide polymorphism (SNP) haplotypes within the region on soybean chromosome 18 where the SBR resistance gene Rpp1 maps. One-hundred F2:3 lines derived from a cross between PI 561356 and the susceptible experimental line LD02-4485 were genotyped with genetic …


Advances In Genome Sequencing And Genotyping Technology For Soybean Diversity Analysis, David L. Hyten Jan 2012

Advances In Genome Sequencing And Genotyping Technology For Soybean Diversity Analysis, David L. Hyten

Department of Agronomy and Horticulture: Faculty Publications

The completion of a soybean draft whole genome sequence along with advances in sequencing and genotyping technologies are creating a revolution in soybean genomics. The draft whole genome sequence of soybean is allowing researchers to fully take advantage of this new technology and is rapidly changing how soybean germ plasm is mined. Genetic markers such as SNPs can be quickly identified by using next generation sequencing and assayed on a large number of materials using advanced technologies that can genotype tens of thousands of markers on thousands of individuals very rapidly. This ability to qUickly identify and genotype genetic diversity …


High-Resolution Mapping Of Open Chromatin In The Rice Genome, Wenli Zhang, Yufeng Wu, James C. Schnable, Zixian Zeng, Michael Freeling, Gregory E. Crawford, Jiming Jiang Jan 2012

High-Resolution Mapping Of Open Chromatin In The Rice Genome, Wenli Zhang, Yufeng Wu, James C. Schnable, Zixian Zeng, Michael Freeling, Gregory E. Crawford, Jiming Jiang

Department of Agronomy and Horticulture: Faculty Publications

Gene expression is controlled by the complex interaction of transcription factors binding to promoters and other regulatory DNA elements. One common characteristic of the genomic regions associated with regulatory proteins is a pronounced sensitivity to DNase I digestion. We generated genome-wide high-resolution maps of DNase I hypersensitive (DH) sites from both seedling and callus tissues of rice (Oryza sativa). Approximately 25% of the DH sites from both tissues were found in putative promoters, indicating that the vast majority of the gene regulatory elements in rice are not located in promoter regions. We found 58% more DH sites in …


Template-Based Structure Prediction And Classification Of Transcription Factors In Arabidopsis Thaliana, Tao Lu, Yuedong Yang, Bo Yao, Song Liu, Yaoqi Zhou, Chi Zhang Jan 2012

Template-Based Structure Prediction And Classification Of Transcription Factors In Arabidopsis Thaliana, Tao Lu, Yuedong Yang, Bo Yao, Song Liu, Yaoqi Zhou, Chi Zhang

School of Biological Sciences: Faculty Publications

Transcription factors (TFs) play important roles in plants. However, there is no systematic study of their structures and functions of most TFs in plants. Here, we performed template-based structure prediction for all TFs in Arabidopsis thaliana, with their full-length sequences as well as C-terminal and N-terminal regions. A total of 2,918 model structures were obtained with a high confidence score. We find that TF families employ only a smaller number of templates for DNA-binding domains (DBD) but a diverse number of templates for transcription regulatory domains (TRD). Although TF families are classified according to DBD, their sizes have a significant …


Divergent Functions Of The Myotubularin (Mtm) Homologs Atmtm1 And Atmtm2 In Arabidopsis Thaliana: Evolution Of The Plant Mtm Family, Yong Ding, Ivan Ndamukong, Yang Zhao, Yuannan Xia, Jean-Jack Riethoven, David R. Jones, Nullin Divecha, Zoya Avramova Jan 2012

Divergent Functions Of The Myotubularin (Mtm) Homologs Atmtm1 And Atmtm2 In Arabidopsis Thaliana: Evolution Of The Plant Mtm Family, Yong Ding, Ivan Ndamukong, Yang Zhao, Yuannan Xia, Jean-Jack Riethoven, David R. Jones, Nullin Divecha, Zoya Avramova

School of Biological Sciences: Faculty Publications

Myotubularin and myotubularin-related proteins are evolutionarily conserved in eukaryotes. Defects in their function result in muscular dystrophy, neuronal diseases, and leukemia in humans. In contrast to the animal lineage, where genes encoding both active and inactive myotubularins (phosphoinositide 3-phosphatases) have appeared and proliferated in the basal metazoan group, myotubularin genes are not found in the unicellular relatives of green plants. However, they are present in land plants encoding proteins highly similar to the active metazoan enzymes. Despite their remarkable structural conservation, plant and animal myotubularins have significantly diverged in their functions. While loss of myotubularin function causes severe disease phenotypes …