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Publications from USDA-ARS / UNL Faculty

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Full-Text Articles in Life Sciences

Suppression Of Aflatoxin Production In Aspergillus Species By Selected Peanut (Arachis Hypogaea) Stilbenoids, Victor S. Sobolev, R. S. Arias, Kerestin Goodman, Travis Walk, Valerie Orner, Paola C. Faustinelli, Alicia Massa Jan 2018

Suppression Of Aflatoxin Production In Aspergillus Species By Selected Peanut (Arachis Hypogaea) Stilbenoids, Victor S. Sobolev, R. S. Arias, Kerestin Goodman, Travis Walk, Valerie Orner, Paola C. Faustinelli, Alicia Massa

Publications from USDA-ARS / UNL Faculty

Aspergillus flavus is a soil fungus that commonly invades peanut seeds and often produces carcinogenic aflatoxins. Under favorable conditions, the fungus-challenged peanut plant produces and accumulates resveratrol and its prenylated derivatives in response to such an invasion. These prenylated stilbenoids are considered peanut antifungal phytoalexins. However, the mechanism of peanut−fungus interaction has not been sufficiently studied. We used pure peanut stilbenoids arachidin-1, arachidin-3, and chiricanine A to study their effects on the viability of and metabolite production by several important toxigenic Aspergillus species. Significant reduction or virtually complete suppression of aflatoxin production was revealed in feeding experiments in A ...


Organ-Specific Transcriptome Profiling Of Metabolic And Pigment Biosynthesis Pathways In The Floral Ornamental Progenitor Species Anthurium Amnicola Dressler, Jon Suzuki, Teresita D. Amore, Bernarda Calla, Nathan A. Palmer, Erin D. Scully, Scott E. Sattler, Gautam Sarath, Joanne S. Lichty, Roxanna Y. Myers, Lisa M. Keith, Tracie K. Matsumoto, Scott M. Geib May 2017

Organ-Specific Transcriptome Profiling Of Metabolic And Pigment Biosynthesis Pathways In The Floral Ornamental Progenitor Species Anthurium Amnicola Dressler, Jon Suzuki, Teresita D. Amore, Bernarda Calla, Nathan A. Palmer, Erin D. Scully, Scott E. Sattler, Gautam Sarath, Joanne S. Lichty, Roxanna Y. Myers, Lisa M. Keith, Tracie K. Matsumoto, Scott M. Geib

Publications from USDA-ARS / UNL Faculty

Anthurium amnicola Dressler possesses a number of desirable and novel ornamental traits such as a purple-colored upright spathe, profuse flowering, and floral scent, some of which have been introgressed into modern Anthurium cultivars. As a first step in identifying genes associated with these traits, the transcriptome from root, leaf, spathe, and spadix from an accession of A. amnicola was assembled, resulting in 28,019 putative transcripts representing 19,458 unigenes. Genes involved in pigmentation, including those for the metabolism of chlorophyll and the biosynthesis of carotenoids, phenylpropanoids, and flavonoids were identified. The expression levels of one MYB transcription factor ...


The Lx Report Of The Bean Improvement Cooperative No. 60, March 2017. Mar 2017

The Lx Report Of The Bean Improvement Cooperative No. 60, March 2017.

Publications from USDA-ARS / UNL Faculty

CONTENTS

LX Annual Report of the Bean Improvement Cooperative xi

BIC Coordinating Committee Membership - 1957 to 2017 . xii

BIC Meritorious Service and Distinguished Achievement Award Recipients - 1957 to 2015 xiii

BIC Awards Nomination Request for 2017 xvi

BIC/NAPIA Meeting in 2017 . xix

In Memory of Guillermo E. Galvez-Enriquez xx

RESEARCH PAPERS FOR 2017

OPTIMIZING SPORULATION OF Pseudocercospora griseola IN VITRO • Paula F. de Pádua1, Rafael Pereira1, Luanna B. W. Gomes1 and Elaine A. de Souza1* 1

FINE MAPPING THE BROAD SPECTRUM ANTHRACNOSE RESISTANCE GENE IN AMENDOIM CAVALO 3 • Gilio, T.A.S.1, Oscar P. Hurtado-Gonzales2, Giseli Valentini1, Sandra ...


Characterization Of Small Rna Populations In Non-Transgenic Andaflatoxin-Reducing-Transformed Peanut, Imana L. Power, Phat M. Dang, Victor S. Sobolev, Valerie Orner, Joseph L. Powell, Marshall C. Lamb, Renée S. Arias Jan 2017

Characterization Of Small Rna Populations In Non-Transgenic Andaflatoxin-Reducing-Transformed Peanut, Imana L. Power, Phat M. Dang, Victor S. Sobolev, Valerie Orner, Joseph L. Powell, Marshall C. Lamb, Renée S. Arias

Publications from USDA-ARS / UNL Faculty

Aflatoxin contamination is a major constraint in food production worldwide. In peanut (Arachis hypogaea L.), these toxic and carcinogenic aflatoxins are mainly produced by Aspergillus flavus Link and A. parasiticus Speare. The use of RNA interference (RNAi) is a promising method to reduce or prevent the accumula-tion of aflatoxin in peanut seed. In this study, we performed high-throughput sequencing of small RNApopulations in a control line and in two transformed peanut lines that expressed an inverted repeattargeting five genes involved in the aflatoxin-biosynthesis pathway and that showed up to 100% less aflatoxin B1 than the controls. The objective was to ...


Chemical Interruption Of Late Season Flowering To Improve Harvested Peanut Maturity, Marshall C. Lamb, Ronald B. Sorensen, Christopher L. Butts, Phat M. Dang, C. Y. Chen, Renée S. Arias Jan 2017

Chemical Interruption Of Late Season Flowering To Improve Harvested Peanut Maturity, Marshall C. Lamb, Ronald B. Sorensen, Christopher L. Butts, Phat M. Dang, C. Y. Chen, Renée S. Arias

Publications from USDA-ARS / UNL Faculty

Peanut (Arachis hypogaea) is a botanically indeterminate plant where flowering, fruit initiation, and pod maturity occurs over an extended time period during the growing season. As a result, the maturity and size of individual peanut pods vary considerably at harvest. Immature kernels that meet commercial edible size specifications negatively affect quality during processing due to their increased propensity for off flavors, higher moisture and water activity, and variable roasting properties. As peanuts progress toward maturation, late season flowers set within 40 days till harvest will not have sufficient time to develop into mature, marketable pods prior to harvest. Research was ...


Study Of The Genetic Diversity Of The Aflatoxin Biosynthesis Cluster In Aspergillus Section Flavi Using Insertion/Deletion Markers In Peanut Seeds From Georgia, Usa, Paola C. Faustinelli, Edwin R. Palencia, Victor S. Sobolev, Bruce W. Horn, Hank T. Sheppard, Marshall C. Lamb, Xinye M. Wang, Brian E. Scheffler, Jaime Martinez Castillo, Renee S. Arias Jan 2017

Study Of The Genetic Diversity Of The Aflatoxin Biosynthesis Cluster In Aspergillus Section Flavi Using Insertion/Deletion Markers In Peanut Seeds From Georgia, Usa, Paola C. Faustinelli, Edwin R. Palencia, Victor S. Sobolev, Bruce W. Horn, Hank T. Sheppard, Marshall C. Lamb, Xinye M. Wang, Brian E. Scheffler, Jaime Martinez Castillo, Renee S. Arias

Publications from USDA-ARS / UNL Faculty

Aflatoxins are among themost powerful carcinogens in nature. The major aflatoxin-producing fungi are Aspergillus flavus and A. parasiticus. Numerous crops, including peanut, are susceptible to aflatoxin contamination by these fungi. There has been an increased use of RNA interference (RNAi) technology to control phytopathogenic fungi in recent years. In order to develop molecular tools targeting specific genes of these fungi for the control of aflatoxins, it is necessary to obtain their genome sequences. Although high-throughput sequencing is readily available, it is still impractical to sequence the genome of every isolate. Thus, in this work, the authors proposed a workflow that ...


Aspergillus And Aflatoxin In Groundnut (Arachis Hypogaea L.) And Groundnut Cake In Eastern Ethiopia, Abdi Mohammed, Alemayehu Chala, Mashilla Dejene, Chemeda Fininsa, David A. Hoisington, Victor S. Sobolev, R. S. Arias Jan 2016

Aspergillus And Aflatoxin In Groundnut (Arachis Hypogaea L.) And Groundnut Cake In Eastern Ethiopia, Abdi Mohammed, Alemayehu Chala, Mashilla Dejene, Chemeda Fininsa, David A. Hoisington, Victor S. Sobolev, R. S. Arias

Publications from USDA-ARS / UNL Faculty

This study was conducted to assess major Aspergillus species and aflatoxins associated with groundnut seeds and cake in Eastern Ethiopia and evaluate growers’ management practices. A total of 160 groundnut seed samples from farmers’ stores and 50 groundnut cake samples from cafe and restaurants were collected. Fungal isolation was done from groundnut seed samples. Aspergillus flavus was the dominant species followed by Aspergillus parasiticus. Aflatoxin analyses of groundnut seed samples were performed using ultra performance liquid chromatography; 22.5% and 41.3% of samples were positive, with total aflatoxin concentrations of 786 and 3135 ng g−1 from 2013/2014 ...


Rnai-Mediated Control Of Aflatoxins In Peanut: Method To Analyze Mycotoxin Production And Transgene Expression In The Peanut/Aspergillus Pathosystem, Renee S. Arias, Phat M. Dang, Victor S. Sobolev Dec 2015

Rnai-Mediated Control Of Aflatoxins In Peanut: Method To Analyze Mycotoxin Production And Transgene Expression In The Peanut/Aspergillus Pathosystem, Renee S. Arias, Phat M. Dang, Victor S. Sobolev

Publications from USDA-ARS / UNL Faculty

The Food and Agriculture Organization of the United Nations estimates that 25% of the food crops in the world are contaminated with aflatoxins. That represents 100 million tons of food being destroyed or diverted to non-human consumption each year. Aflatoxins are powerful carcinogens normally accumulated by the fungi Aspergillus flavus and A. parasiticus in cereals, nuts, root crops and other agricultural products. Silencing of five aflatoxin-synthesis genes by RNA interference (RNAi) in peanut plants was used to control aflatoxin accumulation following inoculation with A. flavus. Previously, no method existed to analyze the effectiveness of RNAi in individual peanut transgenic events ...


Ecology, Behavior And Bionomics First Genotyping Of Spodoptera Frugiperda (J. E. Smith) (Lepidoptera: Noctuidae) Progeny From Crosses Between Bt-Resistant And Bt-Susceptible Populations, And 65-Locus Discrimination Of Isofamilies, Renee S. Arias, Maribel Portilla, J. D. Ray, Carlos A. Blanco, S. A. Simpson, Brian E. Scheffler Jul 2015

Ecology, Behavior And Bionomics First Genotyping Of Spodoptera Frugiperda (J. E. Smith) (Lepidoptera: Noctuidae) Progeny From Crosses Between Bt-Resistant And Bt-Susceptible Populations, And 65-Locus Discrimination Of Isofamilies, Renee S. Arias, Maribel Portilla, J. D. Ray, Carlos A. Blanco, S. A. Simpson, Brian E. Scheffler

Publications from USDA-ARS / UNL Faculty

Concerns exist that Bt-resistant populations of Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae) found in Puerto Rico, could spread to continental United States, and about the lack of molecular tools to monitor potential crosses or distinguish populations. In this work, the feasibility of genotyping S. frugiperda crosses between Bacillus thuringiensis (Berliner) (Bacillales: Bacillaceae) (Bt) resistant and susceptible populations using simple sequence repeats (SSRs, or microsatellites) was assessed. Parents and their corresponding progeny (five resistant, five susceptible phenotype) were genotyped using 192 SSRs on three reciprocate crosses alternating male and female from Bt-susceptible and Bt-resistant populations. Oviposition, mortality and fecundity were ...


Development Of A Large Set Of Microsatellite Markers In Zapote Mamey (Pouteria Sapota (Jacq.) H.E. Moore & Stearn) And Their Potential Use In The Study Of The Species, Renee S. Arias, Jaime Martínez-Castillo, V. S. Sobolev, Nasib H. Blancarte-Jaso, S. A. Simpson, Linda L. Ballard, Mary V. Duke, Xiaofen F. Liu, Brian M. Irish, Brian E. Scheffler May 2015

Development Of A Large Set Of Microsatellite Markers In Zapote Mamey (Pouteria Sapota (Jacq.) H.E. Moore & Stearn) And Their Potential Use In The Study Of The Species, Renee S. Arias, Jaime Martínez-Castillo, V. S. Sobolev, Nasib H. Blancarte-Jaso, S. A. Simpson, Linda L. Ballard, Mary V. Duke, Xiaofen F. Liu, Brian M. Irish, Brian E. Scheffler

Publications from USDA-ARS / UNL Faculty

Pouteria sapota is known for its edible fruits that contain unique carotenoids, as well as for its fungitoxic, anti-inflammatory and anti-oxidant activity. However, its genetics is mostly unknown, including aspects about its genetic diversity and domestication process. We did high-throughput sequencing of microsatellite-enriched libraries of P. sapota, generated 5223 contig DNA sequences, 1.8 Mbp, developed 368 microsatellites markers and tested them on 29 individuals from 10 populations (seven wild, three cultivated) from Mexico, its putative domestication center. Gene ontology BLAST analysis of the DNA sequences containing microsatellites showed potential association to physiological functions. Genetic diversity was slightly higher in ...


Effect Of Lysozyme Or Antibiotics On Faecal Zoonotic Pathogens In Nursery Pigs, J E. Wells, E. D. Berry, N Kalchayanand, L A. Rampel, M Kim, W. T. Oliver Jan 2015

Effect Of Lysozyme Or Antibiotics On Faecal Zoonotic Pathogens In Nursery Pigs, J E. Wells, E. D. Berry, N Kalchayanand, L A. Rampel, M Kim, W. T. Oliver

Publications from USDA-ARS / UNL Faculty

Aims: The objective of this study was to determine the effect of lysozyme and antibiotics on zoonotic pathogen shedding in faeces from nursery pigs housed without and with an indirect disease challenge. Methods and Results: Two replicates of approximately 650 pigs each were weaned and randomly assigned to one of 24 pens in either a nursery room that had been fully disinfected or a nursery room left unclean. Pigs were randomly assigned to control diet (Control), control diet + antibiotics (Antibiotic; chlortetracycline and tiamulin), or control diet + lysozyme (Lysozyme; 100 mg kg ^-1 diet). Rectal swab samples were collected on day ...


Seasonal Variation In Vitamin D Status Of Beef Cattle Reared In The Central United States, E Casas, J D. Lippolis, L A. Kuehn, T A. Reinhardt Jan 2015

Seasonal Variation In Vitamin D Status Of Beef Cattle Reared In The Central United States, E Casas, J D. Lippolis, L A. Kuehn, T A. Reinhardt

Publications from USDA-ARS / UNL Faculty

The objective was to retrospectively measure seasonal sunlight-associated variation in serum concentrations of 25-hydroxyvitamin D (25OHD) in beef cattle. The concentration of 25OHD was measured in crossbred animals born from March to May in 2011 and 2012. Vitamin D status 2 to 3 mo after birth (period 1) was only available for 2012 calves and was measured in June 2012. Period 1 animals had serum 25OHD concentrations of 26.3 +- 1.5 ng/mL. The 25OHD concentrations for late summer (period 2) were 46.6 +- 1.4 and 51.0 +- 1.5 ng/mL for 2011 and 2012, respectively. Serum ...


Draft Genome Sequence Of Cercospora Arachidicola, Causal Agent Of Early Leaf Spot In Peanuts, Valerie A. Orner, Emily G. Cantowine, Xinye Monica Wang, Amr Abouelleil, James Bochicchio, Chad Nusbaum, Albert C. Culbreath, Zaid Abdo, Renee S. Arias Jan 2015

Draft Genome Sequence Of Cercospora Arachidicola, Causal Agent Of Early Leaf Spot In Peanuts, Valerie A. Orner, Emily G. Cantowine, Xinye Monica Wang, Amr Abouelleil, James Bochicchio, Chad Nusbaum, Albert C. Culbreath, Zaid Abdo, Renee S. Arias

Publications from USDA-ARS / UNL Faculty

Cercospora arachidicola, causal agent of early leaf spot, is an economically important peanut pathogen. Lack of genetic information about this fungus prevents understanding the role that potentially diverse genotypes may have in peanut breeding programs. Here, we report for the first time a draft genome sequence of C. arachidicola.


Effects Of Refuges On The Evolution Of Resistance To Transgenic Corn By The Western Corn Rootworm, Diabrotica Virgifera Virgifera Leconte, Jennifer Deitloff, Mike W. Dunbar, David A. Ingber, Bruce E. Hibbard, Aaron J. Gassmann Jan 2015

Effects Of Refuges On The Evolution Of Resistance To Transgenic Corn By The Western Corn Rootworm, Diabrotica Virgifera Virgifera Leconte, Jennifer Deitloff, Mike W. Dunbar, David A. Ingber, Bruce E. Hibbard, Aaron J. Gassmann

Publications from USDA-ARS / UNL Faculty

BACKGROUND: Diabrotica virgifera virgifera LeConte is a major pest of corn and causes over a billion dollars of economic loss annually through yield reductions and management costs. Corn producing toxins derived from Bacillus thuringiensis (Bt) has been developed to help manageD. v. virgifera.However, previous studies have demonstrated the ability of this species to evolve resistance to Bt toxins in both laboratory and field settings.

RESULTS: We used an experimental evolution approach to test the refuge strategies for delaying resistance of D. v. virgifera to corn producing Bt toxin Cry34/35Ab1. In the absence of refuges, D. v. virgifera developed ...


De Novo Transcriptome Of The Hemimetabolous German Cockroach (Blattella Germanica), Xiaojie Zhou, Kun Qian, Ying Tong, Junwei Jerry Zhu, Xinghui Qiu, Xiaopeng Zeng Sep 2014

De Novo Transcriptome Of The Hemimetabolous German Cockroach (Blattella Germanica), Xiaojie Zhou, Kun Qian, Ying Tong, Junwei Jerry Zhu, Xinghui Qiu, Xiaopeng Zeng

Publications from USDA-ARS / UNL Faculty

Background: The German cockroach, Blattella germanica, is an important insect pest that transmits various pathogens mechanically and causes severe allergic diseases. This insect has long served as a model system for studies of insect biology, physiology and ecology. However, the lack of genome or transcriptome information heavily hinder our further understanding about the German cockroach in every aspect at a molecular level and on a genome-wide scale. To explore the transcriptome and identify unique sequences of interest, we subjected the B. germanica transcriptome to massively parallel pyrosequencing and generated the first reference transcriptome for B. germanica.

Methodology/Principal Findings: A ...


Competition Between The Filth Fly Parasitoids Muscidifurax Raptor And M. Raptorellus (Hymenoptera: Pteromalidae), C J. Geden, D M. Johnson, P E. Kaufman, C K. Boohene Jan 2014

Competition Between The Filth Fly Parasitoids Muscidifurax Raptor And M. Raptorellus (Hymenoptera: Pteromalidae), C J. Geden, D M. Johnson, P E. Kaufman, C K. Boohene

Publications from USDA-ARS / UNL Faculty

Competition bioassays were conducted with the filth fly pupal parasitoids Muscidurax raptor (Girault & Sanders) and M. raptorellus (Kogan & Legner) (Hymenoptera: Pteromalidae) using house fly Musca domestica L. (Diptera: Muscidae) hosts at different host densities. Muscidifurax raptor had a significant impact on M. raptorellus when hosts were limiting in sequential parasitism tests. Fewer than six M. raptorellus adult progeny emerged from groups of 50 fly pupae that were parasitized by M. raptor at the same time or when M. raptor parasitism preceded M. raptorellus by 48 h, respectively, compared with 42-55 M. raptorellus progeny produced when this species was tested alone ...


Microsporidia Biological Control Agents And Pathogens Of Beneficial Insects, Susan Bjornson, David Oi Jan 2014

Microsporidia Biological Control Agents And Pathogens Of Beneficial Insects, Susan Bjornson, David Oi

Publications from USDA-ARS / UNL Faculty

No abstract provided.


Artificial Diets Used In Mass Production Of The New World Screwworm, Cochliomyia Hominivorax, H Chen, M F. Chaudhury, A Sagel, P L. Philips, S R. Skoda Jan 2014

Artificial Diets Used In Mass Production Of The New World Screwworm, Cochliomyia Hominivorax, H Chen, M F. Chaudhury, A Sagel, P L. Philips, S R. Skoda

Publications from USDA-ARS / UNL Faculty

The New World screwworm, Cochliomyia hominivorax (Coquerel) (Diptera: Calliphoridae), has been eradicated from North and Central America using the sterile insect technique. This success has been based on mass production of high-quality screwworms using artificial diets since 1958. Many diet formulations for both larvae and adults have been developed, mainly driven by cost efficiency and material supply. However, only four larval and two adult diet formulations have been applied in the six sterile fly mass production plants in the USA, Mexico and Panama. Herein, we briefly review the history of screwworm diet research and development, introduce the diet formulations used ...


Predicting Phosphorus Dynamics In Complex Terrains Using A Variable Source Area Hydrology Model, Amy S. Collick, Daniel R. Fuka, Peter J.A. Kleinman, Anthony R. Buda, Jennifer L. Weld, Mike J. White, Tamie L. Veith, Ray B. Bryant, Carl H. Bolster, Zachary M. Easton Jan 2014

Predicting Phosphorus Dynamics In Complex Terrains Using A Variable Source Area Hydrology Model, Amy S. Collick, Daniel R. Fuka, Peter J.A. Kleinman, Anthony R. Buda, Jennifer L. Weld, Mike J. White, Tamie L. Veith, Ray B. Bryant, Carl H. Bolster, Zachary M. Easton

Publications from USDA-ARS / UNL Faculty

Phosphorus (P) loss from agricultural watersheds has long been a critical water quality problem, the control of which has been the focus of considerable research and investment. Preventing P loss depends on accurately representing the hydrological and chemical processes governing P mobilization and transport. The Soil and Water Assessment Tool (SWAT) is a watershed model commonly used to predict run-off and non-point source pollution transport. SWAT simulates run-off employing either the curve number (CN) or the Green and Ampt methods, both assume infiltration-excess run-off, although shallow soils underlain by a restricting layer commonly generate saturation-excess run-off from variable source areas ...


Soils Of Temperate Rainforests Of The North American Pacific Coast, Dunbar N. Carpenter, James G. Bockheim, Paul F. Reich Jan 2014

Soils Of Temperate Rainforests Of The North American Pacific Coast, Dunbar N. Carpenter, James G. Bockheim, Paul F. Reich

Publications from USDA-ARS / UNL Faculty

Temperate rainforests have high conservation and natural resource value, but the soils of this bioregion have not previously been studied as a unit. Here we examine the soils of North America's Pacific coastal temperate rainforests, utilizing databases from the United States Natural Resources Conservation Service and the Canadian Centre for Land and Biological Resources Research to (i) identify the soil taxa, (ii) evaluate the soil properties, and (iii) compare soils in temperate and tropical rainforests. There are strong climate gradientswithin these temperate rainforests,with the mean temperature declining from 11.7 °C to 6.1 °C and the mean ...


Ecotypes Of An Ecologically Dominant Prairie Grass (Andropogon Gerardii) Exhibit Genetic Divergence Across The U.S. Midwest Grasslands’ Environmental Gradient, Miranda M. Grey, Paul St. Amand, Nora M. Bello, Matthew B. Galliart, Mary Knapp, Karen A. Garrett, Theodore J. Morgan, Sarah G. Baer, Brian R. Maricle, Eduard D. Akhunov, Loretta C. Johnson Jan 2014

Ecotypes Of An Ecologically Dominant Prairie Grass (Andropogon Gerardii) Exhibit Genetic Divergence Across The U.S. Midwest Grasslands’ Environmental Gradient, Miranda M. Grey, Paul St. Amand, Nora M. Bello, Matthew B. Galliart, Mary Knapp, Karen A. Garrett, Theodore J. Morgan, Sarah G. Baer, Brian R. Maricle, Eduard D. Akhunov, Loretta C. Johnson

Publications from USDA-ARS / UNL Faculty

Big bluestem (Andropogon gerardii) is an ecologically dominant grass with wide distribution across the environmental gradient of U.S. Midwest grasslands. This system offers an ideal natural laboratory to study population divergence and adaptation in spatially varying climates.

Objectives were to: (i) characterize neutral genetic diversity and structure within and among three regional ecotypes derived from 11 prairies across the U.S. Midwest environmental gradient, (ii) distinguish between the relative roles of isolation by distance (IBD) vs. isolation by environment (IBE) on ecotype divergence, (iii) identify outlier loci under selection and (iv) assess the association between outlier loci and climate ...


Nucleotide Polymorphism And Copy Number Variant Detection Using Exome Capture And Next-Generation Sequencing In The Polyploid Grass Panicum Virgatum, Joseph Evans, Jeongwoon Kim, Kevin L. Childs, Briaenne Vaillancourt, Emily Crisovan, Aruna Nandety, Daniel J. Gerhardt, Todd A. Richmond, Jeffery A. Jeddeloh, Shawn M. Kaeppler, Michael D. Casler, C Robin Buell Jan 2014

Nucleotide Polymorphism And Copy Number Variant Detection Using Exome Capture And Next-Generation Sequencing In The Polyploid Grass Panicum Virgatum, Joseph Evans, Jeongwoon Kim, Kevin L. Childs, Briaenne Vaillancourt, Emily Crisovan, Aruna Nandety, Daniel J. Gerhardt, Todd A. Richmond, Jeffery A. Jeddeloh, Shawn M. Kaeppler, Michael D. Casler, C Robin Buell

Publications from USDA-ARS / UNL Faculty

Switchgrass (Panicum virgatum) is a polyploid, outcrossing grass species native to North America and has recently been recognized as a potential biofuel feedstock crop. Significant phenotypic variation including ploidy is present across the two primary ecotypes of switchgrass, referred to as upland and lowland switchgrass. The tetraploid switchgrass genome is approximately 1400 Mbp, split between two subgenomes, with significant repetitive sequence content limiting the efficiency of re-sequencing approaches for determining genome diversity. To characterize genetic diversity in upland and lowland switchgrass as a first step in linking genotype to phenotype, we designed an exome capture probe set based on transcript ...


Combined Effects Of Phosphorus Nutrition And Elevated Carbon Dioxide Concentration On Chlorophyll Fluorescence, Photosynthesis, And Nutrient Efficiency Of Cotton, Shardendu K. Singh, Vangimalla R. Reddy Jan 2014

Combined Effects Of Phosphorus Nutrition And Elevated Carbon Dioxide Concentration On Chlorophyll Fluorescence, Photosynthesis, And Nutrient Efficiency Of Cotton, Shardendu K. Singh, Vangimalla R. Reddy

Publications from USDA-ARS / UNL Faculty

To examine the combined effects of phosphorus (P) nutrition and CO2 on photosynthesis, chlorophyll fluorescence (CF), and nutrient utilization and uptake, two controlled-environment experiments were conducted using 0.01, 0.05 and 0.20 mM external phosphate each at ambient and elevated CO2 (aCO2: 400 and eCO2: 800 mmol mol–1, respectively). The CF parameters were affected more by P nutrition than by CO2 treatment. Photoinhibition of photosystem II (PSII) was due to increased minimal CF (Fo') and decreased maximal CF (Fm'), and efficiency of energy harvesting (Fv'/Fm'). In addition, reduced electron transport rate (ETR), the quantum yield of ...


Use Of Robust Multivariate Linear Mixed Models For Estimation Of Genetic Parameters For Carcass Traits In Beef Cattle, S. O. Peters, K. Kizilkaya, D. J. Garrick, R. L. Fernando, E. J. Pollak, R. Mark Enns, M. De Donato, O. O. Ajayi, I. G. Imumorin Jan 2014

Use Of Robust Multivariate Linear Mixed Models For Estimation Of Genetic Parameters For Carcass Traits In Beef Cattle, S. O. Peters, K. Kizilkaya, D. J. Garrick, R. L. Fernando, E. J. Pollak, R. Mark Enns, M. De Donato, O. O. Ajayi, I. G. Imumorin

Publications from USDA-ARS / UNL Faculty

Assumptions of normality of residuals for carcass evaluation may make inferences vulnerable to the presence of outliers, but heavy-tail densities are viable alternatives to normal distributions and provide robustness against unusual or outlying observations when used to model the densities of residual effects. We compare estimates of genetic parameters by fitting multivariate Normal (MN) or heavy-tail distributions (multivariate Student’s t and multivariate Slash, MSt and MS) for residuals in data of hot carcass weight (HCW), longissimus muscle area (REA) and 12th to 13th rib fat (FAT) traits in beef cattle using 2475 records from 2007 to 2008 from a ...


Diversification And Ecosystem Services For Conservation Agriculture: Outcomes From Pastures And Integrated Crop–Livestock Systems, Matt A. Sanderson, David Archer, John Hendrickson, Scott Kronberg, Mark Liebig, Kris Nichols, Marty Schmer, Don Tanaka, Jonathan Aguilar Mar 2013

Diversification And Ecosystem Services For Conservation Agriculture: Outcomes From Pastures And Integrated Crop–Livestock Systems, Matt A. Sanderson, David Archer, John Hendrickson, Scott Kronberg, Mark Liebig, Kris Nichols, Marty Schmer, Don Tanaka, Jonathan Aguilar

Publications from USDA-ARS / UNL Faculty

Conservation agricultural systems rely on three principles to enhance ecosystem services: (1) minimizing soil disturbance, (2) maximizing soil surface cover and (3) stimulating biological activity. In this paper, we explore the concept of diversity and its role in maximizing ecosystem services from managed grasslands and integrated agricultural systems (i.e., integrated crop–livestock–forage systems) at the field and farm level.We also examine trade-offs that may be involved in realizing greater ecosystem services. Previous research on livestock production systems, particularly in pastureland, has shown improvements in herbage productivity and reduced weed invasion with increased forage diversity but little response ...


Efficacy And Costs Of Controlling Eastern Redcedar, John Ortmann, James L. Stubbendieck, Robert A. Masters, George H. Pfeiffer, Thomas B. Bragg Oct 2012

Efficacy And Costs Of Controlling Eastern Redcedar, John Ortmann, James L. Stubbendieck, Robert A. Masters, George H. Pfeiffer, Thomas B. Bragg

Publications from USDA-ARS / UNL Faculty

(Juniperus virginiana L.) is reducing grassland productivity across much of the Great Plains. Control methods include broadcast prescribed fire, herbicides, cutting, and individual tree ignition. All methods have disadvantages when used alone. Fire can be ineffective against larger trees. Intensive methods can be too expensive for low-productivity grasslands. The objectives of this research were to determine the effects of broadcast prescribed fie alone as measured at 3 weeks after fire; to compare the effects of picloram herbicide application with or without fire, sawing with or without fire, and individual tree ignition with fire; and to compare all treatment costs. Treatments ...


Productivity Of Well-Watered Panicum Virgatum Does Not Increase With Co2 Enrichment, Philip A. Fay, H. Wayne Polley, Virginia L. Jin, Michael J. Aspinwall Oct 2012

Productivity Of Well-Watered Panicum Virgatum Does Not Increase With Co2 Enrichment, Philip A. Fay, H. Wayne Polley, Virginia L. Jin, Michael J. Aspinwall

Publications from USDA-ARS / UNL Faculty

Aims Rising atmospheric CO2 has been shown to increase aboveground net primary productivity (ANPP) in water-limited perennial grasslands, in part by reducing stomatal conductance and transpiration, thereby reducing depletion of soil moisture. However, the benefits of CO2 enrichment for ANPP will vary with soil type and may be reduced if water limitation is low. Little is known about CO2 effects on ANPP of Panicum virgatum, a perennial C4 tallgrass and potential bioenergy crop. We hypothesized that if water limitation is minimized, (i) CO2 enrichmentwould not increase P. virgatum ANPP because photosynthetic rates of this C ...


Potential Causes And Consequences Of Decreased Body Size In Field Populations Of Coccinella Novemnotata, John Losey, Jordan Perlman, James Kopco, Samuel Ramsey, Louis Hesler, Edward Evans, Leslie Allee, Rebecca Smyth Jan 2012

Potential Causes And Consequences Of Decreased Body Size In Field Populations Of Coccinella Novemnotata, John Losey, Jordan Perlman, James Kopco, Samuel Ramsey, Louis Hesler, Edward Evans, Leslie Allee, Rebecca Smyth

Publications from USDA-ARS / UNL Faculty

Coccinella novemnotata, the nine-spotted lady beetle, was historically one of the most common lady beetles across the US and southern Canada. In the 1980s it became extremely rare and has remained rare. In 2008 adult C. novemnotata were collected from field populations in Oregon and South Dakota and initial observations suggested that these individuals seemed smaller than the mean size of the species historically. These observations led to a series of experiments to determine if there had been significant decrease in size and if any decrease found was due to a genetic change or to environmental factors. In the first ...


Post-Biological Control Invasion Trajectory For Melaleuca Quinquenervia In A Seasonally Inundated Wetland, Philip W. Tipping, Melissa R. Martin, Ryan Pierce, Ted D. Center, Paul R. Pratt, Min B. Rayamajhi Jan 2012

Post-Biological Control Invasion Trajectory For Melaleuca Quinquenervia In A Seasonally Inundated Wetland, Philip W. Tipping, Melissa R. Martin, Ryan Pierce, Ted D. Center, Paul R. Pratt, Min B. Rayamajhi

Publications from USDA-ARS / UNL Faculty

The recruitment and mortality of Melaleuca quinquenervia seedlings were evaluated over a 3-year period in a seasonally inundated wetland in the western Everglades region. The mean (±SE) density of seedlings/ saplingsm-1 declined from 64.8 (±4.5) to 0.5 (±0.2) over the 3 years, a population reduction of 99.2%. Four distinct water regimes characterized this site: dry, dry to wet transition, flooded, and wet to dry transition. Seedling recruitment was highest in the dry to wet transition and lowest in the flooded water regime, while mortality was highest under flooded and dry water regimes. The mean ...


Genomics Of Tropical Fruit Tree Crops, R. S. Arias, James W. Borrone, Cecile L. Tondo, David N. Kuhn, Brian M. Irish, Raymond J. Schnell Jan 2012

Genomics Of Tropical Fruit Tree Crops, R. S. Arias, James W. Borrone, Cecile L. Tondo, David N. Kuhn, Brian M. Irish, Raymond J. Schnell

Publications from USDA-ARS / UNL Faculty

The genetic improvement of tropical fruit trees is limited when compared to progress achieved in temperate fruit trees and annual crops. Tropical fruit tree breeding programs require significant resources to develop new cultivars that are adapted to modern shipping and storage requirements. The use of molecular markers in tropical fruit tree breeding is greatly assisting in solving a number of difficult challenges for breeders such as the development of complex family structures for recombination mapping and for recurrent selection. A review of the literature on molecular markers development and new techniques for increasing single-nucleotide polymorphic markers is discussed. The development ...