Other Plant Sciences Commons^™

Herbicides Applied At Or Shortly After Seeding Are Effective For Weed Control In Seedling Buffalograss, Luqi Li, Matthew D. Sousek, Zachary Reicher

Department of Agronomy and Horticulture: Faculty Publications

Herbicides applied shortly after seeding of buffalograss [Buchloe dactyloides (Nutt.) Engelm.] can help reduce weed pressure and maximize establishment of buffalograss. This study evaluated 12 relatively recently developed herbicides for turf safety and weed control when applied at seeding or 0 or 2 weeks after emergence (WAE) of ‘Bowie’ or ‘Sundancer’ buffalograss. Primary weed species on the site were common purslane (Portulaca oleracea L.), redroot pigweed (Amaranthus retroflexus L.), and/or yellow foxtail [Setaria lutescens (Weigel ex Stuntz) F.T. Hubb.]. Regardless of cultivar, untreated checks had53% weed cover by 6 WAE, whereas most of the herbicide treatments resulted …

Synfind: Compiling Syntenic Regions Across Any Set Of Genomes On Demand, Haibao Tang, Matthew D. Bomhoff, Evan Briones, Liangsheng Zhang, James C. Schnable, Eric Lyons

Department of Agronomy and Horticulture: Faculty Publications

The identification of conserved syntenic regions enables discovery of predicted locations for orthologous and homeologous genes, evenwhennosuchgeneispresent.Thiscapabilitymeansthatsynteny-basedmethodsarefarmoreeffectivethansequencesimilaritybased methods in identifying true-negatives, a necessity forstudying gene loss and gene transposition. However, the identification of syntenicregionsrequirescomplexanalyseswhichmustberepeatedforpairwisecomparisonsbetweenanytwospecies.Therefore,as the number of published genomes increases, there is a growing demand for scalable, simple-to-use applications to perform comparative genomic analyses that cater to both gene family studies and genome-scale studies. We implemented SynFind, a web-based tool that addresses this need. Given one query genome, SynFind is capable of identifying conserved syntenic regions in any set of targetgenomes.SynFindiscapableofreportingper-geneinformation,usefulforresearchersstudyingspecificgenefamilies,aswellas genome-wide data sets of syntenic gene and predicted gene …

A Population Structure And Genome-Wide Association Analysis On The Usda Soybean Germplasm Collection, Nonoy Bandillo, Diego Jarquin, Qijian Song, Randall L. Nelson, Perry Cregan, James Specht, Aaron Lorenz

Department of Agronomy and Horticulture: Faculty Publications

Population structure analyses and genome-wide association studies (GWAS) conducted on crop germplasm collections provide valuable information on the frequency and distribution of alleles governing economically important traits. The value of these analyses is substantially enhanced when the accession numbers can be increased from ~1,000 to ~10,000 or more. In this research, we conducted the first comprehensive analysis of population structure on the collection of 14,000 soybean accessions [Glycine max (L.) Merr. and G. soja Siebold & Zucc.] using a 50KSNP chip. Accessions originating from Japan were relatively homogenous and distinct from the Korean accessions. As a whole, both Japanese and …

Chromatin Immunoprecipitation (Chip) Assay For Detecting Direct And Indirect Protein -Dna Interactions In Magnaporthe Oryzae, Gang Li, Margarita Marroquin-Guzman, Richard A. Wilson

Department of Plant Pathology: Faculty Publications

Chromatin immunoprecipitation (ChIP) is a powerful technology for analyzing protein-DNA interactions in cells. Robust ChIP procedures have been established for investigating direct interactions between protein and DNA. However, detecting indirect protein-DNA interactions in vivo is challenging. Recently, we used ChIP to analyze an indirect protein-DNA interaction between a putative histone demethylase, MoJmjC, and the promoter of the superoxide dismutase 1-encoding gene MoSOD1 in the rice blast fungus Magnaporthe oryzae (M. oryzae) (Fernandez et al., 2014). We tagged MoJmjC with the 3x FLAG epitope (Fernandez et al., 2014), instead of the larger and more commonly used GFP epitope, to mitigate …

Nebline, November/December 2015

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Feature: Chill Out Over the Holidays by Freezing Foods Ahead

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Transgenic Soybean Plants Expressing Asoybean Homolog Of Glycine-Rich Protein 7 (Grp7) And Exhibiting Improved Innate Immunity, James R. Alfano, Anna Joe, Thomas E. Clemente, Zhengqing Fu, Ming Guo, Byeong-Ryool Jeong, Thomas Elthon

Department of Plant Pathology: Faculty Publications

This disclosure provides for transgenic Soybean plants expressing a soybean homolog of glycine-rich protein 7 (GRP7) and exhibiting improved innate immunity and meth ods of making Such plants.

Community Seed Banks: Origins, Evolution, And Prospects, Charles A. Francis

Department of Agronomy and Horticulture: Faculty Publications

As a survey of contemporary community-level seed banks, this is an excellent compilation and instructive guide. The first section provides an overview of how seed banks originated, their varied goals and activities, several contrasting forms of management, and how they organize and perform to meet these goals. An intriguing claim in the book is that the concept of “seed banks is only some three decades old,” while in fact the practice of saving, preserving, and exchanging seed within a community is probably as old as human communities themselves.

Organized seed banks often serve specific functions: preserving seeds, providing seed access …

Adding Genetically Distant Individuals To Training Populations Reduces Genomic Prediction Accuracy In Barley, Aaron Lorenz, Kevin P. Smith

Department of Agronomy and Horticulture: Faculty Publications

One of the most important factors affecting genomic prediction accuracy appears to be training population (TP) composition. The objective of this study was to evaluate the effect of genomic relationship on genomic prediction accuracy and determine if adding increasingly unrelated individuals to a TP can reduce prediction accuracy. To accomplish this, a population of barley (Hordeum vulgare L.) lines from the University of Minnesota (lines denoted as MN) and North Dakota State University (lines denoted as ND) breeding programs were used for model training. Predictions were validated using two independent sets of progenies derived from MN  MN crosses …

Switchgrass Germplasm Resources, Michael D. Casler, Kenneth P. Vogel, Melanie Harrison

Department of Agronomy and Horticulture: Faculty Publications

Switchgrass (Panicum virgatum L.) is an important native grass and dominant member of the tallgrass prairie ecosystem. It is used for conservation, restoration, livestock feed production, and bioenergy feedstock production. The purpose of this review is to describe the biological and geographical basis for switchgrass germplasm diversity and to provide a resource for scientists and outreach personnel to find switchgrass germplasm to meet their needs. Upland and lowland ecotypes represent the most important polymorphism in switchgrass, with distinct but overlapping geographic distributions. Variation in ploidy exists within both ecotypes, with 2n = 4x = 36 the dominant ploidy …

The Khmer Software Package: Enabling Efficient Nucleotide Sequence Analysis, Michael R. Crusoe, Hussien F. Alameldin, Sherine Awad, Elmar Boucher, Adam Caldwell, Reed Cartwright, Amanda Charbonneau, Bede Constantinides, Greg Edvenson, Scott Fay, Jacob Fenton, Thomas Fenzl, Jordan Fish, Leonor Garcia-Gutierrez, Phillip Garland, Jonathan Gluck, Iván González, Sarah Guermond, Jiarong Guo, Aditi Gupta, Joshua R. Herr, Adina Howe, Alex Hyer, Andreas Härpfer, Luiz Irber, Rhys Kidd, David Lin, Justin Lippi, Tamer Mansour, Pamela Mca'nulty, Eric Mcdonald, Jessica Mizzi, Kevin D. Murray, Joshua R. Nahum, Kaben Nanlohy, Alexander Johan Nederbragt, Humberto Ortiz-Zuazaga, Jeramia Ory, Jason Pell, Charles Pepe-Ranney, Zachary N. Russ, Camille Scott, Josiah Seaman, Scott Sievert 38, Jared Simpson, Connor T. Skennerton, James Spencer, Ramakrishnan Srinivasan, Daniel Standage, James A. Stapleton, Susan R. Steinman, Joe Stein, Benjamin Taylor, Will Trimble, Heather L. Wiencko, Michael Wright, Brian Wyss, Qingpeng Zhang, En Zyme, C. Titus Brown, Erich Schwarz

Department of Plant Pathology: Faculty Publications

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer.

Nebline, October 2015

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Feature: We All Benefit From Pollinator Habitats

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Screening Of Olive Cultivars For Tolerance To Fusicladium Oleagineum In South Africa, Zakhele Cyril Msimango

Professional Agricultural Workers Journal

Abstract

This study evaluated commercial olive cultivars for resistance to olive leaf spot (OLS). A growth chamber trial was undertaken with one temperature treatment (16°C) applied during inoculation while a relative humidity (RH) of above 80% was maintained. Plants were kept for 48 hours at 99% RH after inoculation and then moved to shade netted area for disease development at a temperature of 25±5°C. The results were used for categorizing the eight olive cultivars evaluated in this study according to their OLS susceptibility. ‘Frantoio’ was categorized as most tolerant; ‘Nandi’ and ‘Leccino’ were found to be moderately tolerant, and ‘Nocellara …

Community Involvement To Address A Long-Standing Invasive Species Problem: Aspects Of Civic Ecology In Practice, Rebecca W. Dolan, Kelly Harris, Mark Adler

Scholarship and Professional Work - LAS

Invasive non-native species (INS) are found in every city around the globe, but their impacts in urban settings as biological agents of visual pollution that block views of natural landscapes and disconnect citizens from nature are not as often addressed as comprehensively as their impacts in natural areas or agricultural settings. The multiple impacts of INS in cities make them ideal candidates for aspects of Civic Ecology Practice, where local environmental stewardship action is taken to enhance green infrastructure and community well-being in urban and other human-dominated systems. We present details of a community driven program focused on removal of …

A Unique 5' Translation Element Discovered In Triticum Mosaic Virus, Robyn Roberts, Jincan Zhang, Laura K. Mayberry, Satyanarayana Tatineni, Karen S. Browning, Aurelie M. Rakotondrafara

Department of Plant Pathology: Faculty Publications

Several plant viruses encode elements at the 5' end of their RNAs, which, unlike most cellular mRNAs, can initiate translation in the absence of a 5' m7GpppG cap. Here, we describe an exceptionally long (739-nucleotide [nt]) leader sequence in triticum mosaic virus (TriMV), a recently emerged wheat pathogen that belongs to the Potyviridae family of positive-strand RNA viruses. We demonstrate that the TriMV 5' leader drives strong cap-independent translation in both wheat germ extract and oat protoplasts through a novel, noncanonical translation mechanism. Translation preferentially initiates at the 13th start codon within the leader sequence independently of eIF4E but involves …

Nebline, September 2015

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Feature: 4-H Youth “Let the Good Times Grow” at Super Fair

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Prescribed Fire Monitoring Report, Tallgrass Prairie National Preserve 2014 (Iqcs Fire Number 285382, 285383, 266782, 285677), Sherry A. Leis, Sarah E. Hinman

United States National Park Service: Publications

Introduction

In 2014, the preserve’s federal and NGO partners conducted prescribed fires during March, April, and October that encompassed 8129.8 acres of Tallgrass Prairie National Preserve (TAPR). This was a unique burn year in that prescribed burns occurred in the spring, the traditional burn season, and the fall. Fall burns were conducted to support needed archaeological surveys as part of the environmental compliance for a symphony event scheduled for June 2015 at the preserve. Burns at TAPR were coordinated with local US Fish and Wildlife Service (USFWS), The Nature Conservancy (TNC), and various units of the National Park Service.

Burns …

Nebline, August 2015

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Feature: Nutrition Education Program Reaches 15-Year-Milestone Teaching Nutrition in Lincoln Schools

Food & Health

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Special pullout section: Lancaster County Super Fair 2015 Schedule & Map

Occurrence Of An Herbicide-Resistant Plant Trait In Agricultural Field Margins, Karla L. Gag, David J. Gibson, Bryan G. Young, Julie M. Young, Joseph L. Matthews, Stephen C. Weller, Robert G. Wilson

Department of Agronomy and Horticulture: Faculty Publications

Agricultural environments allow study of evolutionary change in plants. An example of evolution within agroecological systems is the selection for resistance to the herbicide glyphosate within the weed, Conyza canadensis. Changes in survivorship and reproduction associated with the development of glyphosate resistance (GR) may impact fitness and influence the frequency of occurrence of the GR trait. We hypothesized that site characteristics and history would affect the occurrence of GR C. canadensis in field margins. We surveyed GR occurrence in field margins and asked whether there were correlations between GR occurrence and location, crop rotation, GR crop trait rotation, crop type, …

Nebline, July 2015

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Feature: Reduce Bullying and Cyberbullying Through Social and Emotional Learning

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Nebline, June 2015

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Feature: After-Harvest Care Of Asparagus

Food & Health

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Extension Calendar

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