Agriculture Commons^™

Gene Mapping Via Bulked Segregant Rna-Seq (Bsr-Seq), Sanzhen Liu, Cheng-Ting Yeh, Ho Man Tang, Dan Nettleton, Patrick S. Schnable

Dan Nettleton

Bulked segregant analysis (BSA) is an efficient method to rapidly and efficiently map genes responsible for mutant phenotypes. BSA requires access to quantitative genetic markers that are polymorphic in the mapping population. We have developed a modification of BSA (BSR-Seq) that makes use of RNA-Seq reads to efficiently map genes even in populations for which no polymorphic markers have been previously identified. Because of the digital nature of next-generation sequencing (NGS) data, it is possible to conduct de novo SNP discovery and quantitatively genotype BSA samples by analyzing the same RNA-Seq data using an empirical Bayesian approach. In addition, analysis …

Divergence Of Usda Trade Payments For Corn, Soybean, And Wheat Producers And ‘Nowcasts’ Of Tariff Impacts, Matthew Elliott, Lisa Elliott

Matthew Elliott

No abstract provided.

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

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 trait, which was …

Estimation And Testing Of Gene Expression Heterosis, Tieming Ji, Peng Liu, Dan Nettleton

Dan Nettleton

Heterosis, also known as the hybrid vigor, occurs when the mean phenotype of hybrid offspring is superior to that of its two inbred parents. The heterosis phenomenon is extensively utilized in agriculture though the molecular basis is still unknown. In an effort to understand phenotypic heterosis at the molecular level, researchers have begun to compare expression levels of thousands of genes between parental inbred lines and their hybrid offspring to search for evidence of gene expression heterosis. Standard statistical approaches for separately analyzing expression data for each gene can produce biased and highly variable estimates and unreliable tests of heterosis. …

Extensive Tissue-Specific Transcriptomic Plasticity In Maize Primary Roots Upon Water Deficit, Nina Opitz, Caroline Marcon, Anja Paschold, Waqas Ahmed Malik, Andrew Lithio, Ronny Brandt, Hans-Peter Piepho, Dan Nettleton, Frank Hochholdinger

Dan Nettleton

Water deficit is the most important environmental constraint severely limiting global crop growth and productivity. This study investigated early transcriptome changes in maize (Zea mays L.) primary root tissues in response to moderate water deficit conditions by RNA-Sequencing. Differential gene expression analyses revealed a high degree of plasticity of the water deficit response. The activity status of genes (active/inactive) was determined by a Bayesian hierarchical model. In total, 70% of expressed genes were constitutively active in all tissues. In contrast, <3% (50 genes) of water deficit-responsive genes (1915) were consistently regulated in all tissues, while >75% (1501 genes) were specifically regulated in a single root tissue. Water deficit-responsive genes were most numerous in the …

Reduced-Dimension Clustering For Vegetation Segmentation, Brian L. Steward, Lei F. Tian, Dan Nettleton, Lie Tang

Dan Nettleton

Segmentation of vegetation is a critical step in using machine vision for field automation tasks. A new method called reduced-dimension clustering (RDC) was developed based on theoretical considerations about the color distribution of field images. RDC performed unsupervised classification of pixels in field images into vegetation and background classes. Bayes classifiers were then trained and used for vegetation segmentation. The performance of the classifiers trained using the RDC method was compared with that of other segmentation methods. The RDC method produced segmentation performance that was consistently high, with average segmentation success rates of 89.6% and 91.9% across both cloudy and …

Parallel Genome-Wide Expression Profiling Of Host And Pathogen During Soybean Cyst Nematode Infection Of Soybean, Nagabhushana Ithal, Justin Recknor, Dan Nettleton, Leonard Hearne, Tom Maier, Thomas J. Baum, Melissa G. Mitchum

Dan Nettleton

Global analysis of gene expression changes in soybean (Glycine max) and Heterodera glycines (soybean cyst nematode [SCN]) during the course of infection in a compatible interaction was performed using the Affymetrix GeneChip soybean genome array. Among 35,611 soybean transcripts monitored, we identified 429 genes that showed statistically significant differential expression between uninfected and nematode-infected root tissues. These included genes encoding enzymes involved in primary metabolism; biosynthesis of phenolic compounds, lignin, and flavonoids; genes related to stress and defense responses; cell wall modification; cellular signaling; and transcriptional regulation. Among 7,431 SCN transcripts monitored, 1,850 genes showed statistically significant differential …

Sequence Mining And Transcript Profiling To Explore Cyst Nematode Parasitism, Axel A. Elling, Makedonka Mitreva, Xiaowu Gai, John Martin, Justin Recknor, Eric L. Davis, Richard S. Hussey, Dan Nettleton, James P. Mccarter, Thomas J. Baum

Dan Nettleton

Background: Cyst nematodes are devastating plant parasites that become sedentary within plant roots and induce the transformation of normal plant cells into elaborate feeding cells with the help of secreted effectors, the parasitism proteins. These proteins are the translation products of parasitism genes and are secreted molecular tools that allow cyst nematodes to infect plants.

Results: We present here the expression patterns of all previously described parasitism genes of the soybean cyst nematode, Heterodera glycines, in all major life stages except the adult male. These insights were gained by analyzing our gene expression dataset from experiments using the Affymetrix Soybean …

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 complexity of …

Flor Revisited (Again): Eqtl And Mutational Analysis Of Nb-Lrr Mediated Immunity To Powdery Mildew In Barley, Roger P. Wise, Priyanka Surana, Gregory S. Fuerst, Ruo Xu, Divya Mistry, Julie A. Dickerson, Dan Nettleton Dr.

Dan Nettleton

Genes encoding early signaling events in pathogen defense often are identified only by their phenotype. Such genes involved in barley-powdery mildew interactions include Mla, specifying race-specific resistance; Rar1 (Required for Mla12-specified resistance1), and Rom1 (Restoration of Mla-specified resistance1). The HSP90-SGT1-RAR1 complex appears to function as chaperone in MLA-specified resistance, however, much remains to be discovered regarding the precise signaling underlying plant immunity. Genetic analyses of fast-neutron mutants derived from CI 16151 (Mla6) uncovered a novel locus, designated Rar3 (Required for Mla6-specified resistance3). Rar3 segregates independent of Mla6 and Rar1, and rar3 mutants are susceptible to Blumeria graminis f. sp. hordei …

Identification Of Differentially Expressed Gene Categories In Microarray Studies Using Nonparametric Multivariate Analysis, Dan Nettleton, Justin Recknor, James M. Reecy

Dan Nettleton

The field of microarray data analysis is shifting emphasis from methods for identifying differentially expressed genes to methods for identifying differentially expressed gene categories. The latter approaches utilize a priori information about genes to group genes into categories and enhance the interpretation of experiments aimed at identifying expression differences across treatments. While almost all of the existing approaches for identifying differentially expressed gene categories are practically useful, they suffer from a variety of drawbacks. Perhaps most notably, many popular tools are based exclusively on gene-specific statistics that cannot detect many types of multivariate expression change. We have developed a nonparametric …

Biphasic Gene Expression Changes Elicited By Phakopsora Pachyrhizi In Soybean Correlate With Fungal Penetration And Haustoria Formation, Katherine T. Schneider, Martijn Van De Mortel, Timothy J. Bancroft, Edward J. Braun, Dan Nettleton, Rex T. Nelson, Reid D. Frederick, Thomas J. Baum, Michelle Graham, Steven A. Whitham

Dan Nettleton

Inoculation of soybean (Glycine max) plants with Phakopsora pachyrhizi, the causal organism of Asian soybean rust, elicits a biphasic response characterized by a burst of differential gene expression in the first 12 h. A quiescent period occurs from 24 to 48 h after inoculation, in which P. pachyrhizi continues to develop but does not elicit strong host responses, followed by a second phase of intense gene expression. To correlate soybean responses with P. pachyrhizi growth and development, we inoculated the soybean cultivar Ankur (accession PI462312), which carries the Rpp3 resistance gene, with avirulent and virulent isolates …

Distinct Biphasic Mrna Changes In Response To Asian Soybean Rust Infection, Martijn Van De Mortel, Justin C. Recknor, Michelle Graham, Dan Nettleton, Jaime D. Dittman, Rex T. Nelson, Claudia V. Godoy, Ricardo V. Abdelnoor, Alvaro M.R. Almeida, Thomas J. Baum, Steven A. Whitham

Dan Nettleton

Asian soybean rust (ASR), caused by Phakopsora pachyrhizi, is now established in all major soybean-producing countries. Currently, there is little information about the molecular basis of ASR–soybean interactions, which will be needed to assist future efforts to develop effective resistance. Toward this end, abundance changes of soybean mRNAs were measured over a 7-day ASR infection time course in mock-inoculated and infected leaves of a soybean accession (PI230970) carrying the Rpp2 resistance gene and a susceptible genotype (Embrapa-48). The expression profiles of differentially expressed genes (ASR-infected compared with the mock-inoculated control) revealed a biphasic response to ASR in each genotype. …

Developmental Transcript Profiling Of Cyst Nematode Feeding Cells In Soybean Roots, Nagabhushana Ithal, Justin Recknor, Dan Nettleton, Tom Maier, Thomas J. Baum, Melissa G. Mitchum

Dan Nettleton

Cyst nematodes of the genus Heterodera are obligate, sedentary endoparasites that have developed highly evolved relationships with specific host plant species. Successful parasitism involves significant physiological and morphological changes to plant root cells for the formation of specialized feeding cells called syncytia. To better understand the molecular mechanisms that lead to the development of nematode feeding cells, transcript profiling was conducted on developing syncytia induced by the soybean cyst nematode Heterodera glycines in soybean roots by coupling laser capture microdissection with high-density oligonucleotide microarray analysis. This approach has identified pathways that may play intrinsic roles in syncytium induction, formation, and …

Differentially Expressed Genes In Blood From Young Pigs Between Two Swine Lines Divergently Selected For Feed Efficiency: Potential Biomarkers For Improving Feed Efficiency, Haibo Liu, Yet T. Nguyen, Daniel S. Nettleton, Jack C. M. Dekkers, Christopher K. Tuggle

Dan Nettleton

The goal of this study was to find potential gene expression biomarkers in blood of piglets that can be used to predict pigs’ future feed efficiency. Using RNA-seq technology, we found 453 genes were differentially expressed (false discovery rate (FDR) ≤ 0.05) in the blood of two Yorkshire lines of pigs divergently selected for feed efficiency (FE) based on residual feed intake (RFI). Genes involved in several biosynthetic processes were overrepresented among genes more highly expressed in the low RFI line compared to the high RFI line. Weighted gene co-expression network analysis (WGCNA) also revealed genes involved in some of …

The Uneven Influence Of Climate Trends And Agricultural Policies On Maize Production In The Yucatan Peninsula, Mexico, Sofia Mardero, Bridgit Schmook, Jorge Omar Lopez-Martinez, Lizette Cicero, Claudia Radel, Zachary Christman

Zachary Christman

Maize is an important staple crop in Mexico, and the recent intensification of climate variability, in combination with non-climatic forces, has hindered increases in production, especially for smallholder farmers. This article demonstrates the influence of these drivers on maize production trends in the three states of the Yucatan Peninsula using a mixed methods approach of climatic analysis and semi-structured interviews. Climate trend analysis and generalized additive models (GAMs) demonstrate relationships between production and climatic variability, using 1980–2010 precipitation and temperature data. Data from forty interviews with government officials and representatives of farmers' associations (gathered in 2015 and 2016) highlight the …

Descriptions Of Life-Stages Of Blastobasis Repartella (Lepidoptera: Gelechioidea: Coleophoridae: Blastobasinae) And Observations On Its Biology In Switchgrass, D. Adamski, P. J. Johnson, A. A. Boe, Jeffrey Bradshaw, Alan Pultyniewicz

Arvid Boe

Blastobasis repartella (Dietz) is a borer in the proaxis and basal nodes and internodes of above ground stems of Panicum virgatum L. (Poaceae). The adult and immature stages are described herein, including diagnoses of the adult and larva, as this insect may be easily confused with a closely related grass-feeding congener, Blastobasis graminea Adamski, which is also known to occur in the United States. The biology of B. repartella is described. Figures of the adult, illustrations of the male and female genitalia, wing venation, the chaetotaxy of the larva (supplemented with scanning electron micrographs), and pupa are provided. Bassus difficilis …

Symptoms, Distribution And Abundance Of The Stem-Boring Caterpillar, Blastobasis Repartella (Dietz), In Switchgrass, Jarrad R. Prasifka, Jeffrey Bradshaw, Arvid A. Boe, Dokyoung Lee, David Adamski, Michael E. Gray

Arvid Boe

A potential pest of switchgrass, Panicum virgatum L., was first detected in South Dakota in 2004, where death of partially emerged leaves was noted in a small proportion of tillers. Similar “dead heart” symptoms were observed in switchgrass in Illinois during 2008 and adults of a stem-boring caterpillar were collected and identified as Blastobasis repartella (Dietz). In 2009, a survey of the central United States was used to estimate the distribution and abundance of this insect. In eight northern states, B. repartella was consistently found in both cultivated plots and natural stands of switchgrass. In four southern states, B. repartella …

Jual Obat-Kuat-Pria Black Ant King Pills-Di Jakarta "082227555114", Noval Muhlisin

Noval Muhlisin

Sustainable Agriculture Lesson For Middle School Classrooms, Sara Colombe, Madhav P. Nepal, Jennifer Mclaughlin, Matthew L. Miller, Larry B. Browning, P. Troy White

Madhav Nepal

In this lesson, students will learn about sustainability, where farmers/agriculturists can meet the needs of food, fiber, and fuel for the growing population. Students learn about growing population, its growth rate, major food source, sustainability barrel, potential ripple effects of positive impacts as well as the food waste and its effects.

Using Drones For Precision Agriculture, Jiyul Chang, Madhav P. Nepal

Madhav Nepal

In this teaching module, students will learn what Precision Agriculture is and how to apply drone into Precision Agriculture practices. To use data (images) taken by drone, students will learn the basic theory of Remote Sensing. Using images, students learn how to make NDVI (Normalized Difference Vegetation Index) maps and how to apply drone (remote sensing technique) in agriculture.

A Sophomore Level Introduction To Engineering Design Course, Norman Muzzy, Michelle L. Soupir, Steven J. Hoff

Norman Muzzy

Iowa State University has a sophomore level course that is known as ABE 218. The objectives of this course include learning a structured approach to engineering design, preparing the students for internships, learning the basics of project management, and connecting the theoretical engineering paper designs to physical reality. This informal paper discusses how the course is structured, identifies the lab projects that are part of the course, and discusses some of the results and challenges associated with ABE 218.

Applying What You Have Learned, Gretchen Mosher, Norman Muzzy, Dana Woolley

Norman Muzzy

Last April, a group of over 110 students presented their Capstone projects in the Department of Agricultural and Biosystems Engineering at Iowa State University. The Capstone program serves students in engineering and technology and is a required component of all ABE undergraduates. Capstone programs in engineering and technology are divided into two phases: a first-semester focus on defining the scope of the problem, and an emphasis on solution development and evaluation in the second semester. At the end of the first semester, the teams present their accomplishments at a poster session, where they receive feedback from ABE faculty and industry …

Formeas200_Spring2019 (1) (2).Xlsx, Curtis Vanderschaaf

Curtis VanderSchaaf

Combining Survey And Non-Survey Data For Improved Sub-Area Prediction Using A Multi-Level Model, Jae Kwang Kim, Zhonglei Wang, Zhengyuan Zhu, Nathan B. Cruze

Zhengyuan Zhu

Combining information from different sources is an important practical problem in survey sampling. Using a hierarchical area-level model, we establish a framework to integrate auxiliary information to improve state-level area estimates. The best predictors are obtained by the conditional expectations of latent variables given observations, and an estimate of the mean squared prediction error is discussed. Sponsored by the National Agricultural Statistics Service of the US Department of Agriculture, the proposed model is applied to the planted crop acreage estimation problem by combining information from three sources, including the June Area Survey obtained by a probability-based sampling of lands, administrative …

Nitrogen Fertilizer Suppresses Mineralization Of Soil Organic Matter In Maize Agroecosystems, Navreet K. Mahal, William R. Osterholz, Fernando E. Miguez, Hanna J. Poffenbarger, John E. Sawyer, Daniel C. Olk, Sotirios V. Archontoulis, Michael J. Castellano

John E. Sawyer

The possibility that N fertilizer increases soil organic matter (SOM) mineralization and, as a result, reduces SOM stocks has led to a great debate about the long-term sustainability of maize-based agroecosystems as well as the best method to estimate fertilizer N use efficiency (FNUE). Much of this debate is because synthetic N fertilizer can positively or negatively affect SOM mineralization via several direct and indirect pathways. Here, we test a series of hypotheses to determine the direction, magnitude, and mechanism of N fertilizer effect on SOM mineralization and discuss the implications for methods to estimate FNUE.Wemeasured the effect of synthetic …

Apa Gejala Kelamin Keluar Nanah Dan Darah Adakan Obatnya Yang Ampuh, Ayudia Denature

ayudia denature

Fiscal Reform Scenarios And Accessibility 2018.08.20.Docx, Guillermo Fernandez

Guillermo Fernandez

Highest And Best Use Determinations In Agricultural Land Assessments, Matthew Elliott, Lisa Elliott, Tong Wang

Matthew Elliott