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Genome-Wide Association Studies Of Doubled Haploid Exotic Introgression Lines For Root System Architecture Traits In Maize (Zea Mays L.), Darlene L. Sanchez, Sisi Liu, Rania Ibrahim, Michael Blanco, Thomas Lubberstedt 2018 Iowa State University

Genome-Wide Association Studies Of Doubled Haploid Exotic Introgression Lines For Root System Architecture Traits In Maize (Zea Mays L.), Darlene L. Sanchez, Sisi Liu, Rania Ibrahim, Michael Blanco, Thomas Lubberstedt

Agronomy Publications

Root system architecture (RSA) is becoming recognized as important for water and nutrient acquisition in plants. This study focuses on finding single nucleotide polymorphisms (SNPs) associated with seedling RSA traits from 300 doubled haploid (DH) lines derived from crosses between Germplasm Enhancement of Maize (GEM) accessions and inbred lines PHB47 and PHZ51. These DH lines were genotyped using 62,077 SNP markers, while root and shoot phenotype data were collected from 14-day old seedlings. Genome-wide association studies (GWAS) were conducted using three models to offset false positives/negatives. Multiple SNPs associated with seedling root traits were detected, some of which ...


Arthropod Fauna Associated With Wild And Cultivated Cranberries In Wisconsin, Shawn A. Steffan, Merritt E. Singleton, Michael L. Draney, Elissa M. Chasen, Kyle E. Johnson, Juan E. Zalapa 2018 USDA, Agricultural Research Service

Arthropod Fauna Associated With Wild And Cultivated Cranberries In Wisconsin, Shawn A. Steffan, Merritt E. Singleton, Michael L. Draney, Elissa M. Chasen, Kyle E. Johnson, Juan E. Zalapa

The Great Lakes Entomologist

The cranberry (Vaccinium macrocarpon Aiton) is an evergreen, trailing shrub native to North American peatlands. It is cultivated commercially in the US and Canada, with major production centers in Wisconsin, Massachusetts, New Jersey, Washington, Québec, and British Columbia. Despite the agricultural importance of cranberry in Wisconsin, relatively little is known of its arthropod associates, particularly the arachnid fauna. Here we report preliminary data on the insect and spider communities associated with wild and cultivated cranberries in Wisconsin. We then compare the insect and spider communities of wild cranberry systems to those of cultivated cranberries, indexed by region. Approximately 7,400 ...


Salmonella And Fecal Indicator Bacteria Survival In Soils Amended With Poultry Manure, Claire E. Hruby, Michelle L. Soupir, Thomas B. Moorman, Carl H. Pederson, Rameshwar S. Kanwar 2018 Iowa State University

Salmonella And Fecal Indicator Bacteria Survival In Soils Amended With Poultry Manure, Claire E. Hruby, Michelle L. Soupir, Thomas B. Moorman, Carl H. Pederson, Rameshwar S. Kanwar

Agricultural and Biosystems Engineering Publications

Minimizing the risks associated with manure-borne pathogenic microorganisms requires an understanding of microbial survival under realistic field conditions. The objective of this 3-year study was to assess the fate of Salmonella (SALM) and fecal indicator bacteria (FIB), E. coli (EC) and enterococci (ENT), in glacial till-derived soils, after application of poultry manure (PM) to cornfields under chisel-plowed (CP) or no-till (NT) management. From 2010 to 2012, soil samples were obtained each spring at 0–15- and 15–30-cm depths, to determine whether over-wintering of target bacteria had occurred. Sampling was followed by application of PM at low (PM1) and high ...


Qtl Mapping In Three Connected Populations Reveals A Set Of Consensus Genomic Regions For Low Temperature Germination Ability In Zea Mays L., Xuhui Li, Guihua Wang, Junjie Fu, Li Li, Guangyao Jia, Lisha Ren, Thomas Lubberstedt, Guoying Wang, Jianhua Wang, Riliang Gu 2018 China Agricultural University

Qtl Mapping In Three Connected Populations Reveals A Set Of Consensus Genomic Regions For Low Temperature Germination Ability In Zea Mays L., Xuhui Li, Guihua Wang, Junjie Fu, Li Li, Guangyao Jia, Lisha Ren, Thomas Lubberstedt, Guoying Wang, Jianhua Wang, Riliang Gu

Agronomy Publications

Improving seed vigor in response to cold stress is an important breeding objective in maize that allows early sowing. Using two cold tolerant inbred lines 220 and P9-10 and two susceptible lines Y1518 and PH4CV, three connected F2:3 populations were generated for detecting quantitative trait locus (QTL) related to seed low-temperature germination ability. At 10°C, two germination traits (emergence rate and germination index) were collected from a sand bed and three seedling traits (seedling root length, shoot length, and total length) were extracted from paper rolls. Significant correlations were found among all traits in all populations. Via single-population ...


Overlapping Residual Herbicides For Control Of Photosystem (Ps) Ii- And 4-Hydroxyphenylpyruvate Dioxygenase (Hppd)-Inhibitor-Resistant Palmer Amaranth (Amaranthus Palmeri S. Watson) In Glyphosate-Resistant Maize, Parminder S. Chahal, Zahoor Ahmad Ganie, Amit J. Jhala 2018 University of Nebraska-Lincoln

Overlapping Residual Herbicides For Control Of Photosystem (Ps) Ii- And 4-Hydroxyphenylpyruvate Dioxygenase (Hppd)-Inhibitor-Resistant Palmer Amaranth (Amaranthus Palmeri S. Watson) In Glyphosate-Resistant Maize, Parminder S. Chahal, Zahoor Ahmad Ganie, Amit J. Jhala

Agronomy & Horticulture -- Faculty Publications

A Palmer amaranth (Amaranthus palmeri S. Watson) biotype has evolved resistance to photosystem (PS) II- (atrazine) and 4-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibiting herbicides (mesotrione, tembotrione, and topramezone) in maize seed production field in Nebraska, USA. The objectives of this study were to determine the effect of soil residual pre-emergence (PRE) herbicides followed by (fb) tank-mixture of residual and foliar active post-emergence (POST) herbicides on PS-II- and HPPD-inhibitor-resistant Palmer amaranth control, maize yield, and net economic returns. Field experiments were conducted in a grower’s field infested with PS II- and HPPD-inhibitor-resistant Palmer amaranth near Shickley in Fillmore County, Nebraska, USA in ...


Aac Penhold Canada Prairie Spring Red Wheat, R. D. Cuthbert, R. M. DePauw, R. E. Knox, Asheesh K. Singh, T. N. McCaig, B. McCallum, T. Fetch, B. L. Beres 2018 Agriculture and Agri-Food Canada

Aac Penhold Canada Prairie Spring Red Wheat, R. D. Cuthbert, R. M. Depauw, R. E. Knox, Asheesh K. Singh, T. N. Mccaig, B. Mccallum, T. Fetch, B. L. Beres

Asheesh Singh

AAC Penhold, an awned hard red spring wheat (Triticum aestivum L.) cultivar, yielded significantly more grain than 5700PR while maturing 2 days earlier, and 7.5 cm shorter stature. The seed size was significantly larger than 5700PR and 5701PR, with a test weight significantly heavier than both checks. AAC Penhold expressed resistance to prevalent races of leaf rust and common bunt, and moderate resistance to fusarium head blight and stem rust. AAC Penhold had higher grain and flour protein than the checks and improved Hagberg Falling Number, amylograph viscosity, and water absorption. AAC Penhold is eligible for grades of the ...


Identifying New Sources Of Resistance To Brown Stem Rot In Soybean, Chantal E. McCabe, Asheesh K. Singh, Leonor F. Leandro, Silvia R. Cianzio, Michelle A. Graham 2018 Iowa State University

Identifying New Sources Of Resistance To Brown Stem Rot In Soybean, Chantal E. Mccabe, Asheesh K. Singh, Leonor F. Leandro, Silvia R. Cianzio, Michelle A. Graham

Asheesh Singh

Brown stem rot (BSR), caused by the fungus Phialophora gregata f. sp. sojae (Allington & D.W. Chamberlain) W. Gams (syn. Cadophora gregata), causes yield losses up to 38%. Three dominant BSR-resistant genes have been identified: Rbs1, Rbs2, and Rbs3. Additional BSR resistance loci will complement breeding efforts by expanding the soybean [Glycine max (L.) Merr.] genetic base. The objective of this research was to determine if PI 594637, PI 594638B, PI 594650A, and PI 594858B contained novel BSR resistance genes. The accessions were crossed to three genotypes with known BSR resistance genes and populations were developed for allelism studies. A ...


Leveraging Genomic Prediction To Scan Germplasm Collection For Crop Improvement, Leonardo de Azevedo Peixoto, Tara C. Moellers, Jiaoping Zhang, Aaron J. Lorenz, Leonardo L. Bhering, William D. Beavis, Asheesh K. Singh 2018 Federal University of Vicosa

Leveraging Genomic Prediction To Scan Germplasm Collection For Crop Improvement, Leonardo De Azevedo Peixoto, Tara C. Moellers, Jiaoping Zhang, Aaron J. Lorenz, Leonardo L. Bhering, William D. Beavis, Asheesh K. Singh

Asheesh Singh

The objective of this study was to explore the potential of genomic prediction (GP) for soybean resistance against Sclerotinia sclerotiorum (Lib.) de Bary, the causal agent of white mold (WM). A diverse panel of 465 soybean plant introduction accessions was phenotyped for WM resistance in replicated field and greenhouse tests. All plant accessions were previously genotyped using the SoySNP50K BeadChip. The predictive ability of six GP models were compared, and the impact of marker density and training population size on the predictive ability was investigated. Cross-prediction among environments was tested to determine the effectiveness of the prediction models. GP models ...


Advancing Our Understanding Of Charcoal Rot In Soybeans, Martha P. Romero Luna, Daren Mueller, Alemu Mengistu, Asheesh K. Singh, Glen L. Hartman, Kiersten A. Wise 2018 Purdue University

Advancing Our Understanding Of Charcoal Rot In Soybeans, Martha P. Romero Luna, Daren Mueller, Alemu Mengistu, Asheesh K. Singh, Glen L. Hartman, Kiersten A. Wise

Asheesh Singh

Charcoal rot [Macrophomina phaseolina (Tassi) Goid] of soybean [Glycine max (L.) Merr.] is an important but commonly misidentified disease, and very few summary articles exist on this pathosystem. Research conducted over the past 10 yr has improved our understanding of the environment conducive to disease development, host resistance, and improved disease diagnosis and management. This article summarizes the currently available research with an emphasis on disease management.


Delayed Senescence In Soybean: Terminology, Research Update, And Survey Results From Growers, C. J. Harbach, T. W. Allen, C. R. Bowen, J. A. Davis, C. B. Hill, M. Leitman, B. R. Leonard, D. S. Mueller, G. B. Padgett, X. A. Phillips, R. W. Schneider, E. J. Sikora, A. K. Singh, G. L. Hartman 2018 University of Illinois at Urbana-Champaign

Delayed Senescence In Soybean: Terminology, Research Update, And Survey Results From Growers, C. J. Harbach, T. W. Allen, C. R. Bowen, J. A. Davis, C. B. Hill, M. Leitman, B. R. Leonard, D. S. Mueller, G. B. Padgett, X. A. Phillips, R. W. Schneider, E. J. Sikora, A. K. Singh, G. L. Hartman

Asheesh Singh

The terms used to describe symptoms of delayed senescence in soybean often are used inconsistently or interchangeably and do not adequately distinguish the observed symptoms in the field. Various causes have been proposed to explain the development of delayed senescence symptoms. In this article, we review published reports on delayed senescence symptoms in soybean, summarize current research findings, provide examples of terms related to specific symptoms, and present an overview of the results of a multi-state survey directed to soybean growers to understand their concerns about delayed soybean senescence. Some of these terms, such as green bean syndrome and green ...


Main And Epistatic Loci Studies In Soybean For Sclerotinia Sclerotiorum Resistance Reveal Multiple Modes Of Resistance In Multi-Environments, Tara C. Moellers, Arti Singh, Jiaoping Zhang, Jae Brungardt, Mehdi Kabbage, Daren S. Mueller, Craig R. Grau, Ashish Ranjan, Damon L. Smith, R. V. Chowdy-Reddy, Asheesh K. Singh 2018 Iowa State University

Main And Epistatic Loci Studies In Soybean For Sclerotinia Sclerotiorum Resistance Reveal Multiple Modes Of Resistance In Multi-Environments, Tara C. Moellers, Arti Singh, Jiaoping Zhang, Jae Brungardt, Mehdi Kabbage, Daren S. Mueller, Craig R. Grau, Ashish Ranjan, Damon L. Smith, R. V. Chowdy-Reddy, Asheesh K. Singh

Asheesh Singh

Genome-wide association (GWAS) and epistatic (GWES) studies along with expression studies in soybean [Glycine max (L.) Merr.] were leveraged to dissect the genetics of Sclerotinia stem rot (SSR) [caused by Sclerotinia sclerotiorum (Lib.) de Bary], a significant fungal disease causing yield and quality losses. A large association panel of 466 diverse plant introduction accessions were phenotyped in multiple field and controlled environments to: (1) discover sources of resistance, (2) identify SNPs associated with resistance, and (3) determine putative candidate genes to elucidate the mode of resistance. We report 58 significant main effect loci and 24 significant epistatic interactions associated with ...


Genetic Architecture Of Charcoal Rot (Macrophomina Phaseolina) Resistance In Soybean Revealed Using A Diverse Panel, Sara M. Coser, R. V. Chowda Reddy, Jiaoping Zhang, Daren S. Mueller, Alemu Mengistu, Kiersten A. Wise, Tom W. Allen, Arti Singh, Asheesh K. Singh 2018 Iowa State University

Genetic Architecture Of Charcoal Rot (Macrophomina Phaseolina) Resistance In Soybean Revealed Using A Diverse Panel, Sara M. Coser, R. V. Chowda Reddy, Jiaoping Zhang, Daren S. Mueller, Alemu Mengistu, Kiersten A. Wise, Tom W. Allen, Arti Singh, Asheesh K. Singh

Asheesh Singh

Charcoal rot (CR) disease caused by Macrophomina phaseolina is responsible for significant yield losses in soybean production. Among the methods available for controlling this disease, breeding for resistance is the most promising. Progress in breeding efforts has been slow due to the insufficient information available on the genetic mechanisms related to resistance. Genome-wide association studies (GWAS) enable unraveling the genetic architecture of resistance and identification of causal genes. The aims of this study were to identify new sources of resistance to CR in a collection of 459 diverse plant introductions from the USDA Soybean Germplasm Core Collection using field and ...


A Survey To Better Understand The Use Of The Terms “Colluvium” And “Alluvium”, Bradley A. Miller, Jérôme Juilleret 2018 Iowa State University

A Survey To Better Understand The Use Of The Terms “Colluvium” And “Alluvium”, Bradley A. Miller, Jérôme Juilleret

Bradley A. Miller

We need your help to fully understand how scientists from different backgrounds define the terms “colluvium” and “alluvium.” We ask that you contribute your perspective by taking the survey at http://goo.gl/forms/fV8RBWKjis. The closing deadline is October 31, 2016. The feedback so far has been positive, and many participants have described the experience as fun. Many commented on how the survey challenged their thinking about these sediments, causing them to more carefully consider potential gaps in their definitions for the terms and their strategies for identifying the materials. Others have expressed great interest in the results because ...


A Foxtail Mosaic Virus Vector For Virus-Induced Gene Silencing In Maize, Yu Mei, Chunquan Zhang, Bliss M. Kernodle, John H. Hill, Steven A. Whitham 2018 Iowa State University

A Foxtail Mosaic Virus Vector For Virus-Induced Gene Silencing In Maize, Yu Mei, Chunquan Zhang, Bliss M. Kernodle, John H. Hill, Steven A. Whitham

Steven Whitham

Plant viruses have been widely used as vectors for foreign gene expression and virus-induced gene silencing (VIGS). A limited number of viruses have been developed into viral vectors for the purposes of gene expression or VIGS in monocotyledonous plants, and among these, the tripartite viruses Brome mosaic virus and Cucumber mosaic virus have been shown to induce VIGS in maize (Zea mays). We describe here a new DNA-based VIGS system derived from Foxtail mosaic virus (FoMV), a monopartite virus that is able to establish systemic infection and silencing of endogenous maize genes homologous to gene fragments inserted into the FoMV ...


Virus-Induced Gene Silencing And Transient Gene Expression In Soybean (Glycine Max) Using Bean Pod Mottle Virus Infectious Clones, Steven A. Whitham, Lori M. Lincoln, R. V. Chowda-Reddy, Jaime D. Dittman, Jamie A. O'Rourke, Michelle A. Graham 2018 Iowa State University

Virus-Induced Gene Silencing And Transient Gene Expression In Soybean (Glycine Max) Using Bean Pod Mottle Virus Infectious Clones, Steven A. Whitham, Lori M. Lincoln, R. V. Chowda-Reddy, Jaime D. Dittman, Jamie A. O'Rourke, Michelle A. Graham

Steven Whitham

Virus-induced gene silencing (VIGS) is a powerful and rapid approach for determining the functions of plant genes. The basis of VIGS is that a viral genome is engineered so that it can carry fragments of plant genes, typically in the 200 to 300 base pair size range. The recombinant viruses are used to infect experimental plants, and wherever the virus invades, the target gene or genes will be silenced. VIGS is thus transient, and in the span of a few weeks, it is possible to design VIGS constructs and then generate loss-of-function phenotypes through RNA silencing of the target genes ...


Soybean Functional Genomics: Bridging The Genotype-To-Phenotype Gap, Jamie A. O'Rourke, Michelle A. Graham, Steven A. Whitham 2018 United States Department of Agriculture

Soybean Functional Genomics: Bridging The Genotype-To-Phenotype Gap, Jamie A. O'Rourke, Michelle A. Graham, Steven A. Whitham

Steven Whitham

Technological advances coupled with the economic importance of soybean have led to increased efforts to understand gene function and associate genes with phenotypes of agronomic and fundamental interest. Functional genomics approaches aim to develop sufficient understanding needed to bridge the genotype-to-phenotype gap. In general terms, functional genomics approaches begin by using highly parallelized methods to analyze genomes, transcriptomes, proteomes, and metabolomes to generate hypotheses about genes that control phenotypes. Candidate genes are then tested for their contributions to phenotypes through various methods such as RNA silencing, genetic mutation, or overexpression. In this chapter, we review the current approaches, tools, and ...


Dynamic Transcriptome Profiling Of Bean Common Mosaic Virus (Bcmv) Infection In Common Bean (Phaseolus Vulgaris L.), Kathleen Martin, Jugpreet Singh, John H. Hill, Steven A. Whitham, Steven B. Cannon 2018 Kansas State University

Dynamic Transcriptome Profiling Of Bean Common Mosaic Virus (Bcmv) Infection In Common Bean (Phaseolus Vulgaris L.), Kathleen Martin, Jugpreet Singh, John H. Hill, Steven A. Whitham, Steven B. Cannon

Steven Whitham

Background

Bean common mosaic virus (BCMV) is widespread, with Phaseolus species as the primary host plants. Numerous BCMV strains have been identified on the basis of a panel of bean varieties that distinguish the pathogenicity types with respect to the viral strains. The molecular responses in Phaseolus to BCMV infection have not yet been well characterized.

Results

We report the transcriptional responses of a widely susceptible variety of common bean (Phaseolus vulgaris L., cultivar ‘Stringless green refugee’) to two BCMV strains, in a time-course experiment. We also report the genome sequence of a previously unreported BCMV strain. The interaction with ...


A Viral Protease Relocalizes In The Presence Of The Vector To Promote Vector Performance, Aurélie Bak, Andrea L. Cheung, Chunling Yang, Steven A. Whitham, Clare L. Casteel 2018 University of California, Davis

A Viral Protease Relocalizes In The Presence Of The Vector To Promote Vector Performance, Aurélie Bak, Andrea L. Cheung, Chunling Yang, Steven A. Whitham, Clare L. Casteel

Steven Whitham

Vector-borne pathogens influence host characteristics relevant to host–vector contact, increasing pathogen transmission and survival. Previously, we demonstrated that infection with Turnip mosaic virus, a member of one of the largest families of plant-infecting viruses, increases vector attraction and reproduction on infected hosts. These changes were due to a single viral protein, NIa-Pro. Here we show that NIa-Pro responds to the presence of the aphid vector during infection by relocalizing to the vacuole. Remarkably, vacuolar localization is required for NIa-Pro’s ability to enhance aphid reproduction on host plants, vacuole localization disappears when aphids are removed, and this phenomenon occurs ...


Description And Codification Of Miscanthus × Giganteus Growth Stages For Phenological Assessment, Mauricio D. Tejera, Emily A. Heaton 2018 Iowa State University

Description And Codification Of Miscanthus × Giganteus Growth Stages For Phenological Assessment, Mauricio D. Tejera, Emily A. Heaton

Emily Heaton

Triploid Miscanthus × giganteus (Greef et Deu. ex Hodkinson et Renvoize) is a sterile, perennial grass used for biomass production in temperate environments. While M. × giganteus has been intensively researched, a scale standardizing description of M. × giganteus morphological stages has not been developed. Here we provide such a scale by adapting the widely-used Biologische Bundesanstalt, Bundessortenamt, CHemische Industrie (BBCH) scale and its corresponding numerical code to describe stages of morphological development in M. × giganteus using observations of the “Freedom” and “Illinois” clone in Iowa, USA. Descriptive keys with images are also presented. Because M. × giganteus plants overlap in the field, the ...


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 2018 USDA-ARS National Peanut Research Laboratory

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 ...


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