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Soydb: A Knowledge Database Of Soybean Transcription Factors, Zheng Wang, Marc Libault, Trupti Joshi, Babu Valliyodan, Henry T. Nguyen, Dong Xu, Gary Stacey, Jianlin Cheng 2010 University of Missouri

Soydb: A Knowledge Database Of Soybean Transcription Factors, Zheng Wang, Marc Libault, Trupti Joshi, Babu Valliyodan, Henry T. Nguyen, Dong Xu, Gary Stacey, Jianlin Cheng

Agronomy & Horticulture -- Faculty Publications

Background: Transcription factors play the crucial rule of regulating gene expression and influence almost all biological processes. Systematically identifying and annotating transcription factors can greatly aid further understanding their functions and mechanisms. In this article, we present SoyDB, a user friendly database containing comprehensive knowledge of soybean transcription factors.

Description: The soybean genome was recently sequenced by the Department of Energy-Joint Genome Institute (DOE-JGI) and is publicly available. Mining of this sequence identified 5,671 soybean genes as putative transcription factors. These genes were comprehensively annotated as an aid to the soybean research community. We developed SoyDB - a knowledge database ...


Rna-Seq Atlas Of Glycine Max: A Guide To The Soybean Transcriptome, Andrew J. Severin, Jenna L. Woody, Yung-Tsi Bolon, Bindu Joseph, Brian W. Diers, Andrew D. Farmer, Gary J. Muehlbauer, Rex T. Nelson, David Grant, James E. Specht, Michelle A. Graham, Steven B. Cannon, Gregory D. May, Carroll P. Vance, Randy C. Shoemaker 2010 Iowa State University

Rna-Seq Atlas Of Glycine Max: A Guide To The Soybean Transcriptome, Andrew J. Severin, Jenna L. Woody, Yung-Tsi Bolon, Bindu Joseph, Brian W. Diers, Andrew D. Farmer, Gary J. Muehlbauer, Rex T. Nelson, David Grant, James E. Specht, Michelle A. Graham, Steven B. Cannon, Gregory D. May, Carroll P. Vance, Randy C. Shoemaker

Agronomy & Horticulture -- Faculty Publications

Background: Next generation sequencing is transforming our understanding of transcriptomes. It can determine the expression level of transcripts with a dynamic range of over six orders of magnitude from multiple tissues, developmental stages or conditions. Patterns of gene expression provide insight into functions of genes with unknown annotation.

Results: The RNA Seq-Atlas presented here provides a record of high-resolution gene expression in a set of fourteen diverse tissues. Hierarchical clustering of transcriptional profiles for these tissues suggests three clades with similar profiles: aerial, underground and seed tissues. We also investigate the relationship between gene structure and gene expression and find ...


Emissions Savings In The Corn-Ethanol Life Cycle From Feeding Coproducts To Livestock, Virgil R. Bremer, Adam Liska, Terry J. Klopfenstein, Galen E. Erickson, Haishun Yang, Daniel T. Walters, Kenneth G. Cassman 2010 University of Nebraska - Lincoln

Emissions Savings In The Corn-Ethanol Life Cycle From Feeding Coproducts To Livestock, Virgil R. Bremer, Adam Liska, Terry J. Klopfenstein, Galen E. Erickson, Haishun Yang, Daniel T. Walters, Kenneth G. Cassman

Agronomy & Horticulture -- Faculty Publications

Environmental regulations on greenhouse gas (GHG) emissions from corn (Zea mays L.)-ethanol production require accurate assessment methods to determine emissions savings from coproducts that are fed to livestock. We investigated current use of coproducts in livestock diets and estimated the magnitude and variability in the GHG emissions credit for coproducts in the corn-ethanol life cycle. The coproduct GHG emissions credit varied by more than twofold, from 11.5 to 28.3 g CO2e per MJ of ethanol produced, depending on the fraction of coproducts used without drying, the proportion of coproduct used to feed beef cattle (Bos ...


Morphological Features Of Wheat Grain And Genotype Affecting Flour Yield, Mark Andrew Edwards 2010 Southern Cross University

Morphological Features Of Wheat Grain And Genotype Affecting Flour Yield, Mark Andrew Edwards

Theses

Although the wheat grain comprises 82 - 86% starchy endosperm, only approximately 76 - 78% is able to be separated using current milling technology. Suitability for primary processing depends on three main characteristics that are in turn influenced to varying degrees by the genetic origin of wheat and agro-climatic conditions during plant development: the endosperm to bran ratio, kernel hardness and ease of separation of bran and endosperm. Among these, hardness appears to be an essential factor in wheat milling behavior also important to the food processing industries. Accumulated evidence supports the prominent influence of the puroindoline (pin) proteins on grain hardness ...


Copy Number Variation Shapes Genome Diversity In Arabidopsis Over Immediate Family Generational Scales, Seth Debolt 2010 University of Kentucky

Copy Number Variation Shapes Genome Diversity In Arabidopsis Over Immediate Family Generational Scales, Seth Debolt

Horticulture Faculty Publications

Arabidopsis thaliana is the model plant and is grown worldwide by plant biologists seeking to dissect the molecular underpinning of plant growth and development. Gene copy number variation (CNV) is a common form of genome natural diversity that is currently poorly studied in plants and may have broad implications for model organism research, evolutionary biology, and crop science. Herein, comparative genomic hybridization (CGH) was used to identify and interrogate regions of gene CNV across the A. thaliana genome. A common temperature condition used for growth of A. thaliana in our laboratory and many around the globe is 22 degrees C ...


High-Throughput Snp Discovery Through Deep Resequencing Of A Reduced Representation Library To Anchor And Orient Scaffolds In The Soybean Whole Genome Sequence, David L. Hyten, Steven B Cannon, Qijian Song, Nathan Weeks, Edward W Fickus, Randy C Shoemaker, James E. Specht, Andrew D Farmer, Gregory D May, Perry B Cregan 2010 USDA-ARS

High-Throughput Snp Discovery Through Deep Resequencing Of A Reduced Representation Library To Anchor And Orient Scaffolds In The Soybean Whole Genome Sequence, David L. Hyten, Steven B Cannon, Qijian Song, Nathan Weeks, Edward W Fickus, Randy C Shoemaker, James E. Specht, Andrew D Farmer, Gregory D May, Perry B Cregan

Agronomy & Horticulture -- Faculty Publications

Background: The Soybean Consensus Map 4.0 facilitated the anchoring of 95.6% of the soybean whole genome sequence developed by the Joint Genome Institute, Department of Energy, but its marker density was only sufficient to properly orient 66% of the sequence scaffolds. The discovery and genetic mapping of more single nucleotide polymorphism (SNP) markers were needed to anchor and orient the remaining genome sequence. To that end, next generation sequencing and high-throughput genotyping were combined to obtain a much higher resolution genetic map that could be used to anchor and orient most of the remaining sequence and to help ...


Spring Grazing Impacts On The Vegetation Of Reed Canarygrass–Invaded Wetlands, Heidi Hilhouse, Susan J. Tunnell, James L. Stubbendieck 2010 University of Nebraska–Lincoln

Spring Grazing Impacts On The Vegetation Of Reed Canarygrass–Invaded Wetlands, Heidi Hilhouse, Susan J. Tunnell, James L. Stubbendieck

Agronomy & Horticulture -- Faculty Publications

The Rainwater Basin region in Nebraska is critically important stopover habitat for spring waterfowl migrations, but the ability of these sites to produce sufficient food for migrating waterfowl is endangered by the invasion of reed canarygrass (Phalaris arundinacea L.). This species produces thick litter layers and abundant aboveground biomass, reducing germination and seedling survival of the annual plant species responsible for much of the seed production in the area. Cattle grazing often is used as a management tool in the Rainwater Basin to slow or reverse reed canarygrass invasion and to improve growing conditions for more desirable plant species. However ...


‘Food For Life’: Looking Beyond The Horizon, Charles Francis, John W. Doran 2010 University of Nebraska - Lincoln

‘Food For Life’: Looking Beyond The Horizon, Charles Francis, John W. Doran

Agronomy & Horticulture -- Faculty Publications

Our real challenge appears to be anticipating what the major challenges and constraints will be to food production and distribution a decade or more into the future. This could be called ‘Beyond the Horizon’ thinking. Today there is little disagreement over the massive depletion on a global scale of two essential inputs to agriculture: fossil fuels and fresh water. We also recognize that phosphorus is found in concentrated form in only a few deposits in nature, and that agriculture is rapidly using this limited resource and dispersing it through harvested products and soil loss from fields in forms that make ...


Evaluation Of The Intercom Model For Predicting Growth Of Forest Herbs, Zorica S. Popović, J. L. Lindquist 2010 Siniša Stanković Institute for Biological Research

Evaluation Of The Intercom Model For Predicting Growth Of Forest Herbs, Zorica S. Popović, J. L. Lindquist

Agronomy & Horticulture -- Faculty Publications

The ecophysiological model INTERCOM was evaluated for its suitability in predicting the growth of perennial forest herbs. A field experiment was conducted to obtain data on photosynthesis and growth parameters of two spring flowering understorey geophytes. Results were used to parameterize the model and its performance was evaluated using the average normalized difference (AE) between predicted and observed biomass and the leaf area index. The model was assumed to provide accurate simulations if the AE was smaller than 0.4. Adjusting the photosynthetic intensity parameters in the model to reflect observed changes in photosynthesis throughout the growing period resulted in ...


Growth And Fitness Components Of Wild × Cultivated Sorghum Bicolor (Poaceae) Hybrids In Nebraska, Lilyrani Sahoo, Jared J. Schmidt, Jeffrey F. Pedersen, Donald Lee, John L. Lindquist 2010 University of Nebraska — Lincoln

Growth And Fitness Components Of Wild × Cultivated Sorghum Bicolor (Poaceae) Hybrids In Nebraska, Lilyrani Sahoo, Jared J. Schmidt, Jeffrey F. Pedersen, Donald Lee, John L. Lindquist

Agronomy & Horticulture -- Faculty Publications

Premise of the study: Gene flow from crops to wild relatives has received considerable attention since the advent of genetically modified crops. Numerous researchers have found wild – crop hybrids to be nearly as fit as their wild parents, which suggests that crop genes may persist in wild populations. Components of the ecological fitness of cultivated sorghum, its wild relative, shattercane, and their hybrids have not been studied.

Methods: To assess the potential for gene introgression into shattercane, we crossed cultivated sorghum to a single inbred shattercane line to produce F1 hybrids and measured growth and several components of ecological ...


Increased Weed Diversity, Density And Above-Ground Biomass In Long-Term Organic Crop Rotations, Samuel E. Wortman, John L. Lindquist, Milton J. Haar, Charles Francis 2010 University of Nebraska-Lincoln

Increased Weed Diversity, Density And Above-Ground Biomass In Long-Term Organic Crop Rotations, Samuel E. Wortman, John L. Lindquist, Milton J. Haar, Charles Francis

Agronomy & Horticulture -- Faculty Publications

While weed management is consistently a top priority among farmers, there is also growing concern for the conservation of biodiversity. Maintaining diverse weed communities below bioeconomic thresholds may provide ecosystem services for the crop and the surrounding ecosystem. This study was conducted to determine if weed diversity, density and biomass differ within and among organic and conventional crop rotations. In 2007 and 2008, we sampled weed communities in four long-term crop rotations near Mead, Nebraska using seedbank analyses (elutriation and greenhouse emergence) and above-ground biomass sampling. Two conventional crop rotations consisted of a corn (Zea mays) or sorghum (Sorghum bicolor ...


Isolation Of The Phycodnavirus Pbcv-1 By Biological Laser Printing, Lisa A. Fitzgerald, Peter K. Wu, James R. Gurnon, Justin C. Biffinger, Bradley R. Ringeisen, James L. Van Etten 2010 U.S. Naval Research Laboratory

Isolation Of The Phycodnavirus Pbcv-1 By Biological Laser Printing, Lisa A. Fitzgerald, Peter K. Wu, James R. Gurnon, Justin C. Biffinger, Bradley R. Ringeisen, James L. Van Etten

Papers in Plant Pathology

The Phycodnaviridae family of viruses is diverse genetically but similar morphologically. These viruses infect eukaryotic algal hosts from both fresh and marine waters, and are an important component of aqueous environments. They play important roles in the dynamics of algal blooms, nutrient cycling, algal community structure, and possibly gene transfer between organisms. As such, it is important to identify new viruses within the Phycodnaviridae family. Biological laser printing (BioLP) was used to isolate single virus particles from solution. BioLP prints droplets containing a single virus particle directly onto a host medium, thereby enabling viruses to be isolated from unmodified samples ...


Isolation Of The Phycodnavirus Pbcv-1 By Biological Laser Printing, Lisa A. Fitzgerald, Peter K. Wu, James Gurnon, Justin C. Biffinger, Bradley R. Ringeisen, James L. Van Etten 2010 U.S. Naval Research Laboratory, Washington, DC

Isolation Of The Phycodnavirus Pbcv-1 By Biological Laser Printing, Lisa A. Fitzgerald, Peter K. Wu, James Gurnon, Justin C. Biffinger, Bradley R. Ringeisen, James L. Van Etten

Papers in Plant Pathology

The Phycodnaviridae family of viruses is diverse genetically but similar morphologically. These viruses infect eukaryotic algal hosts from both fresh and marine waters, and are an important component of aqueous environments. They play important roles in the dynamics of algal blooms, nutrient cycling, algal community structure, and possibly gene transfer between organisms. As such, it is important to identify new viruses within the Phycodnaviridae family. Biological laser printing (BioLP) was used to isolate single virus particles from solution. BioLP prints droplets containing a single virus particle directly onto a host medium, thereby enabling viruses to be isolated from unmodified samples ...


Relations Of Cercospora Beticola With Host Plants And Fungal Antagonists, Robert T. Lartey, Soumitra Ghoshroy, TheCan Caesar-TonThat, Andrew W. Lenssen, Robert G. Evans 2010 United States Department of Agriculture

Relations Of Cercospora Beticola With Host Plants And Fungal Antagonists, Robert T. Lartey, Soumitra Ghoshroy, Thecan Caesar-Tonthat, Andrew W. Lenssen, Robert G. Evans

Agronomy Publications

Cerco pora leaf pot (CLS) cau ed by Cercospora beticola Sacc., is sti ll considered to be the mo t important foliar di ease of ugar beel. The di ea e ha been reported wherever ugar beet i grO\\ n (Bieiholder and Weltzien 1972). Since the di ease wa fir t identified. management of CLS of ugar beet has been an ongoing mi ion of plant pathologists. Toda}. everal trategie are available and applied either s ingly or in combination to manage the di ea e. The e management trategie , which were ummarized by Windels et al. (1998), include cultural ...


Soil As A History Book, Bradley Allen Miller 2010 Iowa State University

Soil As A History Book, Bradley Allen Miller

Agronomy Publications

Soil is one of the most influential components of our enviroronment. It is a complex mixture of physical, chemical, and biological processes providing innumerable ecosystem services. The properties of our soil today support our way of life. It filters our water, contains our wastes, and is the substrate for the production of our food. Combined with a good climate, the convergence of the right soil properties here in Iowa has given its citizens the opportunity to be net exporters of food and feed. That opportunity gives Iowans the ability to feed themselves and prosper economically through the sale of excess ...


Structural And Functional Divergence Of A 1-Mb Duplicated Region In The Soybean (Glycine Max) Genome And Comparison To An Orthologous Region From Phaseolus Vulgaris, Jer-Young Lin, Robert M. Stupar, Christian Hans, D. L. Hyten, Scott A. Jackson 2010 Purdue University

Structural And Functional Divergence Of A 1-Mb Duplicated Region In The Soybean (Glycine Max) Genome And Comparison To An Orthologous Region From Phaseolus Vulgaris, Jer-Young Lin, Robert M. Stupar, Christian Hans, D. L. Hyten, Scott A. Jackson

Agronomy & Horticulture -- Faculty Publications

Soybean (Glycine max) has undergone at least two rounds of polyploidization, resulting in a paleopolyploid genome that is a mosaic of homoeologous regions. To determine the structural and functional impact of these duplications, we sequenced two ~1-Mb homoeologous regions of soybean, Gm8 and Gm15, derived from the most recent ~13 million year duplication event and the orthologous region from common bean (Phaseolus vulgaris), Pv5. We observed inversions leading to major structural variation and a bias between the two chromosome segments as Gm15 experienced more gene movement (gene retention rate of 81% in Gm15 versus 91% in Gm8) and a nearly ...


Fine Mapping The Soybean Aphid Resistance Gene Rag1 In Soybean, Ki-Seung Kim, Stephanie Bellendir, Karen A. Hudson, Curtis B. Hill, Glen L. Hartman, D. L. Hyten, Matthew E. Hudson, Brian W. Diers 2010 University of Illinois

Fine Mapping The Soybean Aphid Resistance Gene Rag1 In Soybean, Ki-Seung Kim, Stephanie Bellendir, Karen A. Hudson, Curtis B. Hill, Glen L. Hartman, D. L. Hyten, Matthew E. Hudson, Brian W. Diers

Agronomy & Horticulture -- Faculty Publications

The soybean aphid (Aphis glycines Matsumura) is an important soybean [Glycine max (L.) Merr.] pest in North America. The dominant aphid resistance gene Rag1 was previously mapped from the cultivar ‘Dowling’ to a 12 cM marker interval on soybean chromosome 7 (formerly linkage group M). The development of additional genetic markers mapping closer to Rag1 was needed to accurately position the gene to improve the effectiveness of markerassisted selection (MAS) and to eventually clone it. The objectives of this study were to identify single nucleotide polymorphisms (SNPs) near Rag1 and to position these SNPs relative to Rag1. To generate a ...


A High Density Integrated Genetic Linkage Map Of Soybean And The Development Of A 1536 Universal Soy Linkage Panel For Quantitative Trait Locus Mapping, D. L. Hyten, Ik-Young Choi, Qijian Song, James E. Specht, Thomas E. Carter Jr., Randy C. Shoemaker, Eun-Young Hwang, Lakshmi K. Matukumalli, P. B. Cregan 2010 USDA-ARS, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland

A High Density Integrated Genetic Linkage Map Of Soybean And The Development Of A 1536 Universal Soy Linkage Panel For Quantitative Trait Locus Mapping, D. L. Hyten, Ik-Young Choi, Qijian Song, James E. Specht, Thomas E. Carter Jr., Randy C. Shoemaker, Eun-Young Hwang, Lakshmi K. Matukumalli, P. B. Cregan

Agronomy & Horticulture -- Faculty Publications

Single nucleotide polymorphisms (SNPs) are the marker of choice for many researchers due to their abundance and the high-throughput methods available for their multiplex analysis. Only recently have SNP markers been available to researchers in soybean [Glycine max (L.) Merr.] with the release of the third version of the consensus genetic linkage map that added 1141 SNP markers to the map. Our objectives were to add 2500 additional SNP markers to the soybean integrated map and select a set of 1536 SNPs to create a universal linkage panel for high-throughput soybean quantitative trait locus (QTL) mapping. The GoldenGate assay is ...


An Integrative Approach To Genomic Introgression Mapping, Andrew J. Severin, Gregory A. Peiffer, Wayne W. Xu, D. L. Hyten, Bruna Bucciarelli, Jamie A. O'Rourke, Yung-Tsi Bolon, David Grant, Andrew D. Farmer, Gregory D. May, Carroll P. Vance, Randy C. Shoemaker, Robert M. Stupar 2010 Iowa State University

An Integrative Approach To Genomic Introgression Mapping, Andrew J. Severin, Gregory A. Peiffer, Wayne W. Xu, D. L. Hyten, Bruna Bucciarelli, Jamie A. O'Rourke, Yung-Tsi Bolon, David Grant, Andrew D. Farmer, Gregory D. May, Carroll P. Vance, Randy C. Shoemaker, Robert M. Stupar

Agronomy & Horticulture -- Faculty Publications

Near-isogenic lines (NILs) are valuable genetic resources for many crop species, including soybean (Glycine max). The development of new molecular platforms promises to accelerate the mapping of genetic introgressions in these materials. Here, we compare some existing and emerging methodologies for genetic introgression mapping: single-feature polymorphism analysis, Illumina GoldenGate single nucleotide polymorphism (SNP) genotyping, and de novo SNP discovery via RNA-Seq analysis of next-generation sequence data. We used these methods to map the introgressed regions in an iron-inefficient soybean NIL and found that the three mapping approaches are complementary when utilized in combination. The comparative RNA-Seq approach offers several additional ...


Abundance Of Ssr Motifs And Development Of Candidate Polymorphic Ssr Markers (Barcsoyssr_1.0) In Soybean, Qijian Song, Gaofeng Jia, Youlin Zhu, David Grant, Rex T. Nelson, Eun-Young Hwang, D. L. Hyten, P. B. Cregan 2010 USDA-ARS, Soybean Genomics and Improvement Lab., Beltsville, MD

Abundance Of Ssr Motifs And Development Of Candidate Polymorphic Ssr Markers (Barcsoyssr_1.0) In Soybean, Qijian Song, Gaofeng Jia, Youlin Zhu, David Grant, Rex T. Nelson, Eun-Young Hwang, D. L. Hyten, P. B. Cregan

Agronomy & Horticulture -- Faculty Publications

Simple sequence repeat (SSR) genetic markers, also referred to as microsatellites, function in map-based cloning and for marker-assisted selection in plant breeding. The objectives of this study were to determine the abundance of SSRs in the soybean genome and to develop and test soybean SSR markers to create a database of locus-specific markers with a high likelihood of polymorphism. A total of 210,990 SSRs with di-, tri-, and tetranucleotide repeats of five or more were identified in the soybean whole genome sequence (WGS) which included 61,458 SSRs consisting of repeat units of di- (≥10), tri- (≥8), and tetranucleotide ...


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