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Economic Contribution Of The Agricultural Sector To The Arkansas Economy In 2017, Leah English, Jennie Popp, Wayne Miller 2019 University of Arkansas, Fayetteville

Economic Contribution Of The Agricultural Sector To The Arkansas Economy In 2017, Leah English, Jennie Popp, Wayne Miller

Research Reports and Research Bulletins

Agriculture and associated agricultural activities are major contributors to the Arkansas economy. Agriculture is defined as the sum of agricultural production and processing activities, unless otherwise specified, and includes crop and animal production and processing, agricultural support industries, forestry and forest products, and textile goods. Agriculture contributes to the economy through direct agricultural production and value-added processing, and also leads to economic activity in other parts of the economy. This report is the eleventh in a series of reports examining agriculture’s economic contribution to the Arkansas economy. The total economic contribution of agriculture (direct, indirect, and induced effects) on ...


The Maize Brown Midrib2 (Bm2) Gene Encodes A Methylenetetrahydrofolate Reductase That Contributes To Lignin Accumulation, Ho Man Tang, Sanzhen Liu, Sarah Hill-Skinner, Wei Wu, Danielle Reed, Cheng-Ting Yeh, Dan Nettleton, Patrick S. Schnable 2019 Iowa State University

The Maize Brown Midrib2 (Bm2) Gene Encodes A Methylenetetrahydrofolate Reductase That Contributes To Lignin Accumulation, Ho Man Tang, Sanzhen Liu, Sarah Hill-Skinner, Wei Wu, Danielle Reed, Cheng-Ting Yeh, Dan Nettleton, Patrick S. Schnable

Dan Nettleton

The midribs of maize brown midrib (bm) mutants exhibit a reddish‐brown color associated with reductions in lignin concentration and alterations in lignin composition. Here, we report the mapping, cloning, and functional and biochemical analyses of the bm2 gene. The bm2 gene was mapped to a small region of chromosome 1 that contains a putative methylenetetrahydrofolate reductase (MTHFR) gene, which is down‐regulated in bm2 mutant plants. Analyses of multiple Mu‐induced bm2‐Mu mutant alleles confirmed that this constitutively expressed gene is bm2. Yeast complementation experiments and a previously published biochemical characterization show that the bm2 gene encodes a ...


Extreme‐Phenotype Genome‐Wide Association Study (Xp‐Gwas): A Method For Identifying Trait‐Associated Variants By Sequencing Pools Of Individuals Selected From A Diversity Panel, Jinliang Yang, Haiying Jiang, Cheng-Ting Yeh, Jianming Yu, Jeffrey A. Jeddeloh, Dan Nettleton, Patrick S. Schnable 2019 Iowa State University

Extreme‐Phenotype Genome‐Wide Association Study (Xp‐Gwas): A Method For Identifying Trait‐Associated Variants By Sequencing Pools Of Individuals Selected From A Diversity Panel, Jinliang Yang, Haiying Jiang, Cheng-Ting Yeh, Jianming Yu, Jeffrey A. Jeddeloh, Dan Nettleton, Patrick S. Schnable

Dan Nettleton

Although approaches for performing genome‐wide association studies (GWAS) are well developed, conventional GWAS requires high‐density genotyping of large numbers of individuals from a diversity panel. Here we report a method for performing GWAS that does not require genotyping of large numbers of individuals. Instead XP‐GWAS (extreme‐phenotype GWAS) relies on genotyping pools of individuals from a diversity panel that have extreme phenotypes. This analysis measures allele frequencies in the extreme pools, enabling discovery of associations between genetic variants and traits of interest. This method was evaluated in maize (Zea mays) using the well‐characterized kernel row number ...


Complexity And Specificity Of The Maize (Zea Mays L.) Root Hair Transcriptome, Stefan Hey, Jutta Baldauf, Nina Opitz, Andrew Lithio, Asher Pasha, NIcholas Provart, Dan Nettleton, Frank Hochholdinger 2019 University of Bonn

Complexity And Specificity Of The Maize (Zea Mays L.) Root Hair Transcriptome, Stefan Hey, Jutta Baldauf, Nina Opitz, Andrew Lithio, Asher Pasha, Nicholas Provart, Dan Nettleton, Frank Hochholdinger

Dan Nettleton

Root hairs are tubular extensions of epidermis cells. Transcriptome profiling demonstrated that the single cell-type root hair transcriptome was less complex than the transcriptome of multiple cell-type primary roots without root hairs. In total, 831 genes were exclusively and 5585 genes were preferentially expressed in root hairs [false discovery rate (FDR) ≤1%]. Among those, the most significantly enriched Gene Ontology (GO) functional terms were related to energy metabolism, highlighting the high energy demand for the development and function of root hairs. Subsequently, the maize homologs for 138 Arabidopsis genes known to be involved in root hair development were identified and ...


Substantial Contribution Of Genetic Variation In The Expression Of Transcription Factors To Phenotypic Variation Revealed By Erd-Gwas, Hung-ying Lin, Qiang Liu, Xiao Li, Jinliang Yang, Sanzhen Liu, Yinlian Huang, Michael J. Scanlon, Dan Nettleton, Patrick S. Schnable 2019 Iowa State University

Substantial Contribution Of Genetic Variation In The Expression Of Transcription Factors To Phenotypic Variation Revealed By Erd-Gwas, Hung-Ying Lin, Qiang Liu, Xiao Li, Jinliang Yang, Sanzhen Liu, Yinlian Huang, Michael J. Scanlon, Dan Nettleton, Patrick S. Schnable

Dan Nettleton

Background: There are significant limitations in existing methods for the genome-wide identification of genes whose expression patterns affect traits.

Results: The transcriptomes of five tissues from 27 genetically diverse maize inbred lines were deeply sequenced to identify genes exhibiting high and low levels of expression variation across tissues or genotypes. Transcription factors are enriched among genes with the most variation in expression across tissues, as well as among genes with higher-than-median levels of variation in expression across genotypes. In contrast, transcription factors are depleted among genes whose expression is either highly stable or highly variable across genotypes. We developed a ...


Spotted Cotton Oligonucleotide Microarrays For Gene Expression Analysis, Joshua A. Udall, Lex E. Flagel, Foo Cheung, Andrew W. Woodard, Ran Hovav, Ryan Adam Rapp, Jordan M. Swanson, Jinsuk J. Lee, Alan R. Gingle, Dan Nettleton, Christopher D. Town, Z. Jeffrey Chen, Jonathan F. Wendel 2019 Brigham Young University - Provo

Spotted Cotton Oligonucleotide Microarrays For Gene Expression Analysis, Joshua A. Udall, Lex E. Flagel, Foo Cheung, Andrew W. Woodard, Ran Hovav, Ryan Adam Rapp, Jordan M. Swanson, Jinsuk J. Lee, Alan R. Gingle, Dan Nettleton, Christopher D. Town, Z. Jeffrey Chen, Jonathan F. Wendel

Dan Nettleton

Microarrays offer a powerful tool for diverse applications plant biology and crop improvement. Recently, two comprehensive assemblies of cotton ESTs were constructed based on three Gossypium species. Using these assemblies as templates, we describe the design and creation and of a publicly available oligonucleotide array for cotton, useful for all four of the cultivated species. Synthetic oligonucleotide probes were generated from exemplar sequences of a global assembly of 211,397 cotton ESTs derived from >50 different cDNA libraries representing many different tissue types and tissue treatments. A total of 22,787 oligonucleotide probes are included on the arrays, optimized to ...


Mu Transposon Insertion Sites And Meiotic Recombination Events Co-Localize With Epigenetic Marks For Open Chromatin Across The Maize Genome, Sanzhen Liu, Cheng-Ting Yeh, Tieming Ji, Kai Ying, Haiyan Wu, Ho Man Tang, Yan Fu, Daniel S. Nettleton, Patrick S. Schnable 2019 Iowa State University

Mu Transposon Insertion Sites And Meiotic Recombination Events Co-Localize With Epigenetic Marks For Open Chromatin Across The Maize Genome, Sanzhen Liu, Cheng-Ting Yeh, Tieming Ji, Kai Ying, Haiyan Wu, Ho Man Tang, Yan Fu, Daniel S. Nettleton, Patrick S. Schnable

Dan Nettleton

The Mu transposon system of maize is highly active, with each of the ∼50–100 copies transposing on average once each generation. The approximately one dozen distinct Mutransposons contain highly similar ∼215 bp terminal inverted repeats (TIRs) and generate 9-bp target site duplications (TSDs) upon insertion. Using a novel genome walking strategy that uses these conserved TIRs as primer binding sites, Mu insertion sites were amplified from Mu stocks and sequenced via 454 technology. 94% of ∼965,000 reads carried Mu TIRs, demonstrating the specificity of this strategy. Among these TIRs, 21 novel Mu TIRs were discovered, revealing additional ...


Maize Inbreds Exhibit High Levels Of Copy Number Variation (Cnv) And Presence/Absence Variation (Pav) In Genome Content, Nathan M. Springer, Kai Ying, Yan Fu, Tieming Ji, Cheng-Ting Yeh, Yi Jia, Wei Wu, Todd Richmond, Jacob Kitzman, Heidi Rosenbaum, A. Leonardo Iniguez, W. Brad Barbazuk, Jeffrey A. Jeddeloh, Daniel S. Nettleton, Patrick S. Schnable 2019 University of Minnesota

Maize Inbreds Exhibit High Levels Of Copy Number Variation (Cnv) And Presence/Absence Variation (Pav) In Genome Content, Nathan M. Springer, Kai Ying, Yan Fu, Tieming Ji, Cheng-Ting Yeh, Yi Jia, Wei Wu, Todd Richmond, Jacob Kitzman, Heidi Rosenbaum, A. Leonardo Iniguez, W. Brad Barbazuk, Jeffrey A. Jeddeloh, Daniel S. Nettleton, Patrick S. Schnable

Dan Nettleton

Following the domestication of maize over the past ∼10,000 years, breeders have exploited the extensive genetic diversity of this species to mold its phenotype to meet human needs. The extent of structural variation, including copy number variation (CNV) and presence/absence variation (PAV), which are thought to contribute to the extraordinary phenotypic diversity and plasticity of this important crop, have not been elucidated. Whole-genome, array-based, comparative genomic hybridization (CGH) revealed a level of structural diversity between the inbred lines B73 and Mo17 that is unprecedented among higher eukaryotes. A detailed analysis of altered segments of DNA conservatively estimates that ...


Duplicate Gene Expression In Allopolyploid Gossypium Reveals Two Temporally Distinct Phases Of Expression Evolution, Lex E. Flagel, Joshua A. Udall, Dan Nettleton, Jonathan F. Wendel 2019 Iowa State University

Duplicate Gene Expression In Allopolyploid Gossypium Reveals Two Temporally Distinct Phases Of Expression Evolution, Lex E. Flagel, Joshua A. Udall, Dan Nettleton, Jonathan F. Wendel

Dan Nettleton

Polyploidy has played a prominent role in shaping the genomic architecture of the angiosperms. Through allopolyploidization, several modern Gossypium (cotton) species contain two divergent, although largely redundant genomes. Owing to this redundancy, these genomes can play host to an array of evolutionary processes that act on duplicate genes. We compared homoeolog (genes duplicated by polyploidy) contributions to the transcriptome of a natural allopolyploid and a synthetic interspecific F1 hybrid, both derived from a merger between diploid species from the Gossypium A-genome and D-genome groups. Relative levels of A- and D-genome contributions to the petal transcriptome were determined for 1,383 ...


Comparison Of Transcript Profiles In Wild-Type And O2 Maize Endosperm In Different Genetic Backgrounds, Hongwu Jia, Dan Nettleton, Joan M. Peterson, Gricelda Vasquez-Carrillo, Jean-Luc Jannink, M. Paul Scott 2019 Monsanto

Comparison Of Transcript Profiles In Wild-Type And O2 Maize Endosperm In Different Genetic Backgrounds, Hongwu Jia, Dan Nettleton, Joan M. Peterson, Gricelda Vasquez-Carrillo, Jean-Luc Jannink, M. Paul Scott

Dan Nettleton

Mutations in the Opaque2 (O2) gene of maize (Zea mays L.) improve the nutritional value of maize by reducing the level of zeins in the kernel. The phenotype of o2 grain is controlled by many modifier genes and is therefore strongly dependent on genetic background. We propose two hypotheses to explain differences in phenotypic severity in different genetic backgrounds: (i) Specific genes are differentially (o2 vs. wild-type) expressed only in certain genotypes, and (ii) A set of genes are differentially expressed in all backgrounds, but the degree of differential expression differs in different backgrounds. To determine the extent to which ...


A Diallel Analysis Of A Maize Donor Population Response To In Vivo Maternal Haploid Induction I: Inducibility, Gerald N. De La Fuente, Ursula K. Frei, Benjamin Trampe, Daniel Nettleton, Wei Zhang, Thomas Lubberstedt 2019 Iowa State University

A Diallel Analysis Of A Maize Donor Population Response To In Vivo Maternal Haploid Induction I: Inducibility, Gerald N. De La Fuente, Ursula K. Frei, Benjamin Trampe, Daniel Nettleton, Wei Zhang, Thomas Lubberstedt

Dan Nettleton

The maize in vivo maternal doubled haploid (DH) system is an important tool used by maize breeders and geneticists around the world. The ability to rapidly produce DH lines of maize for breeding allows breeders to quickly respond to new selection criteria based on the ever changing biotic and abiotic stresses that maize is subjected to across its growing area. There are two important steps in the generation of DH lines using the in vivo maternal DH system: 1) the production and identification of haploid progeny, and 2) the doubling of genomes to create fertile, diploid inbred lines that can ...


A Clade-Specific Arabidopsis Gene Connects Primary Metabolism And Senescence, Dallas C. Jones, Wenguang Zheng, Sheng Huang, Chuanlong Du, Xuefeng Zhao, Ragothaman M. Yennamalli, Taner Z. Sen, Dan Nettleton, Eve S. Wurtele, Ling Li 2019 Iowa State University

A Clade-Specific Arabidopsis Gene Connects Primary Metabolism And Senescence, Dallas C. Jones, Wenguang Zheng, Sheng Huang, Chuanlong Du, Xuefeng Zhao, Ragothaman M. Yennamalli, Taner Z. Sen, Dan Nettleton, Eve S. Wurtele, Ling Li

Dan Nettleton

Nearly immobile, plants have evolved new components to be able to respond to changing environments. One example is Qua Quine Starch (QQS, AT3G30720), an Arabidopsis thaliana-specific orphan gene that integrates primary metabolism with adaptation to environment changes. SAQR (Senescence-Associated and QQS-Related, AT1G64360), is unique to a clade within the family Brassicaceae; as such, the gene may have arisen about 20 million years ago. SAQR is up-regulated in QQS RNAi mutant and in the apx1 mutant under light-induced oxidative stress. SAQR plays a role in carbon allocation: overexpression lines of SAQR have significantly decreased starch content; conversely, in a saqr ...


Native Grass And Legume Biology And Establishment, Arvid A. Boe, P. J. Johnson 2019 South Dakota State University

Native Grass And Legume Biology And Establishment, Arvid A. Boe, P. J. Johnson

Arvid Boe

No abstract provided.


Transcriptome And Physiological Analyses For Revealing Genes Involved In Wheat Response To Endoplasmic Reticulum Stress., Xing Yu, Tanchun Wang, Meichen Zhu, Liting Zhang, Fengzhi Zhang, Enen Jing, Yongzhe Ren, Zhiqiang Wang, Zeyu Xin, Tongbao Lin 2019 Touro College

Transcriptome And Physiological Analyses For Revealing Genes Involved In Wheat Response To Endoplasmic Reticulum Stress., Xing Yu, Tanchun Wang, Meichen Zhu, Liting Zhang, Fengzhi Zhang, Enen Jing, Yongzhe Ren, Zhiqiang Wang, Zeyu Xin, Tongbao Lin

Touro College of Osteopathic Medicine (Middletown) Publications and Research

BACKGROUND: Wheat production is largely restricted by adverse environmental stresses. Under many undesirable conditions, endoplasmic reticulum (ER) stress can be induced. However, the physiological and molecular responses of wheat to ER stress remain poorly understood. We used dithiothreitol (DTT) and tauroursodeoxycholic acid (TUDCA) to induce or suppress ER stress in wheat cells, respectively, with the aim to reveal the molecular background of ER stress responses using a combined approach of transcriptional profiling and morpho-physiological characterization.

METHODS: To understand the mechanism of wheat response to ER stress, three wheat cultivars were used in our pre-experiments. Among them, the cultivar with a ...


Addressing The Challenges Facing Wheat Production: Nebraska And International Breeding Efforts, Sarah Blecha 2019 University of Nebraska - Lincoln

Addressing The Challenges Facing Wheat Production: Nebraska And International Breeding Efforts, Sarah Blecha

Doctoral Documents from Doctor of Plant Health Program

Bread wheat, Triticum aestivum L., provides 20 percent of the global daily calorie intake. It is the third most important food crop, after rice and corn. Biotic challenges significantly reduce wheat yield; chemical control can be a solution but can be cost prohibitive for subsistence farmers. For many farmers, genetic resistance to biotic stresses can be the most cost effective solution.

The International Center for Agricultural Research in the Dry Areas (ICARDA) and the Nebraska Small Grains Breeding Program have been addressing these wheat production challenges. ICARDA is part of an international research consortium to increase wheat yield and tolerance ...


Neonicotinoids In U.S. Maize: Insecticide Substitution Effects And Environmental Risk, Edward D. Perry, Giancarlo Moschini 2019 Kansas State University

Neonicotinoids In U.S. Maize: Insecticide Substitution Effects And Environmental Risk, Edward D. Perry, Giancarlo Moschini

CARD Working Papers

This study exploits a novel dataset containing more than 89,000 farm-level surveys over a 17-year period to investigate how neonicotinoid seed treatments in maize, now ubiquitous, have affected the use of other insecticides. Neonicotinoid insecticides are the most used class of insecticides in the world, but they are controversial because of their high toxicity to honeybees. In the United States, maize production accounts for the majority of neonicotinoid use, mostly as seed treatments. We find that neonicotinoids substituted for other major insecticides: plots planted with neonicotinoid- treated seeds were 52% and 47% less likely to be treated with a ...


Development And Application Of A Quantitative Bioassay To Evaluate Maize Silk Resistance To Corn Earworm Herbivory Among Progenies Derived From Peruvian Landrace Piura, Miriam D. Lopez, Tesia S. Dennison, Tina M. Paque, Marna D. Yandeau-Nelson, Craig A. Abel, Nick Lauter 2019 Iowa State University

Development And Application Of A Quantitative Bioassay To Evaluate Maize Silk Resistance To Corn Earworm Herbivory Among Progenies Derived From Peruvian Landrace Piura, Miriam D. Lopez, Tesia S. Dennison, Tina M. Paque, Marna D. Yandeau-Nelson, Craig A. Abel, Nick Lauter

Genetics, Development and Cell Biology Publications

Corn earworm (CEW), Helicoverpa zea (Boddie), (Lepidoptera: Noctuidae), is a major insect pest of corn (Zea mays spp. mays L.). CEW larvae feed on silks, kernels and cobs, causing substantial yield and quality losses both through herbivory and by vectoring pathogens. The long-term goal of this work is to elucidate the genetic and biochemical basis of a potentially novel CEW resistance source discovered in silk tissue of Piura 208, a Peruvian landrace of maize (PI 503849). We developed a quantitative CEW bioassay and tested it on four populations that contrast alleles from Piura 208 with those from GT119, a CEW-susceptible ...


Utilization Of Reduced Haploid Vigor For Phenomic Discrimination Of Haploid And Diploid Maize Seedlings, Kimberly Vanous, Talukder Jubery, Ursula K. Frei, Baskar Ganapathysubramanian, Thomas Lubberstedt 2019 Iowa State University

Utilization Of Reduced Haploid Vigor For Phenomic Discrimination Of Haploid And Diploid Maize Seedlings, Kimberly Vanous, Talukder Jubery, Ursula K. Frei, Baskar Ganapathysubramanian, Thomas Lubberstedt

Mechanical Engineering Publications

Potential benefits of incorporating embryo culture (EC) into a doubled haploid (DH) program, including shortening the breeding cycle and increasing chromosome doubling rates, make the laborious and tedious task of excising embryos worth the effort. Difficulties arise during embryo selection considering the marker gene R1-nj, which is typically used in DH programs, is not expressed in early stages after pollination. Although transgenic approaches have been implemented to bypass this issue, there is so far no known non-transgenic method of selecting haploid embryos. The findings of this study reveal methods of selecting haploid embryos that allow the possibility of incorporating EC ...


Development Of An Innovative And Sustainable One-Step Method For Rapid Plant Dna Isolation For Targeted Pcr Using Magnetic Ionic Liquids, Arianna Marengo, Cecilia Cagliero, Barbara Sgorbini, Jared L. Anderson, Miranda N. Emaus, Carlo Bicchi, Cinzia M. Bertea, Patrizia Rubiolo 2019 Università di Torino

Development Of An Innovative And Sustainable One-Step Method For Rapid Plant Dna Isolation For Targeted Pcr Using Magnetic Ionic Liquids, Arianna Marengo, Cecilia Cagliero, Barbara Sgorbini, Jared L. Anderson, Miranda N. Emaus, Carlo Bicchi, Cinzia M. Bertea, Patrizia Rubiolo

Chemistry Publications

Background

Nowadays, there is an increasing demand for fast and reliable plant biomolecular analyses. Conventional methods for the isolation of nucleic acids are time-consuming and require multiple and often non-automatable steps to remove cellular interferences, with consequence that sample preparation is the major bottleneck in the bioanalytical workflow. New opportunities have been created by the use of magnetic ionic liquids (MILs) thanks to their affinity for nucleic acids.

Results

In the present study, a MIL-based magnet-assisted dispersive liquid–liquid microextraction (maDLLME) method was optimized for the extraction of genomic DNA from Arabidopsis thaliana (L.) Heynh leaves. MILs containing different metal ...


Arkansas Cotton Variety Test 2018, Fred Bourland, A. Beach, C. Kennedy, L. Martin, B. Robertson 2019 University of Arkansas, Fayetteville

Arkansas Cotton Variety Test 2018, Fred Bourland, A. Beach, C. Kennedy, L. Martin, B. Robertson

Research Series

The primary goal of the Arkansas Cotton Variety Test is to provide unbiased data regarding the agronomic performance of cotton varieties and advanced breeding lines in the major cotton-growing areas of Arkansas. This information helps seed companies establish marketing strategies and assists producers in choosing varieties to plant. These annual evaluations will then facilitate the inclusion of new, improved genetic material in Arkansas cotton production. Adaptation of varieties is determined by evaluating the lines at five University of Arkansas System Division of Agriculture research sites (Manila, Keiser, Judd Hill, Marianna, and Rohwer). Entries in the 2018 Arkansas Cotton Variety Test ...


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