Digital Commons Network^™

Enhancing Digestibility And Ethanol Yield Of Populus Wood Via Expression Of An Engineered Monolignol 4-O-Methyltransferase, Yuanheng Cai, Kewei Zhang, Hoon Kim, Guichuan Hou, Xuebin Zhang, Huijun Yang, Huan Feng, Lisa Miller, John Ralph, Chang-Jun Liu

Huan Feng

Producing cellulosic biofuels and bio-based chemicals from woody biomass is impeded by the presence of lignin polymer in the plant cell wall. Manipulating the monolignol biosynthetic pathway offers a promising approach to improved processability, but often impairs plant growth and development. Here, we show that expressing an engineered 4-O-methyltransferase that chemically modifies the phenolic moiety of lignin monomeric precursors, thus preventing their incorporation into the lignin polymer, substantially alters hybrid aspens’ lignin content and structure. Woody biomass derived from the transgenic aspens shows a 62% increase in the release of simple sugars and up to a 49% increase in the …

Drought Responsive Gene Expression Regulatory Divergence Between Upland And Lowland Ecotypes Of A Perennial C4 Grass, John T. Lovell, Scott Schwartz, David B. Lowry, Eugene V. Shakirov, Jason E. Bonnette, Xiaoyu Weng, Mei Wang, Jenifer Johnson, Avinash Sreedasyam, Christopher Plott, Jerry Jenkins, Jeremy Schmutz, Thomas E. Juenger

Yevgeniy (Eugene) Shakirov

Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; however, surprisingly few studies have examined how genome-wide patterns of gene expression G×E are manifested in response to environmental stress and other selective agents that cause climatic adaptation. Here, we characterize drought-responsive expression divergence between upland (drought-adapted) and lowland (mesic) ecotypes of the perennial C₄ grass, Panicum hallii, in natural field conditions. Overall, we find that cis-regulatory elements contributed to gene expression divergence across 47% of genes, 7.2% of which exhibit drought-responsive G×E. …

Tal Effector-Nucleotide Targeter (Tale-Nt) 2.0: Tools For Tal Effector Design And Target Prediction, Erin L. Doyle, Nicholas J. Booher, Daniel S. Standage, Daniel F. Voytas, Volker P. Brendel, John K. Vandyk, Adam J. Bogdanove

Nicholas J. Booher

Transcription activator-like (TAL) effectors are repeat-containing proteins used by plant pathogenic bacteria to manipulate host gene expression. Repeats are polymorphic and individually specify single nucleotides in the DNA target, with some degeneracy. A TAL effector-nucleotide binding code that links repeat type to specified nucleotide enables prediction of genomic binding sites for TAL effectors and customization of TAL effectors for use in DNA targeting, in particular as custom transcription factors for engineered gene regulation and as site-specific nucleases for genome editing. We have developed a suite of web-based tools called TAL Effector-Nucleotide Targeter 2.0 (TALE-NT 2.0;https://boglab.plp.iastate.edu/) that enables design …

United States Midwest Soil And Weather Conditions Influence Anaerobic Potentially Mineralizable Nitrogen, Jason D. Clark, Kristen S. Veum, Fabian G. Fernandez, James J. Camberato, Paul R. Carter, Richard B. Ferguson, David W. Franzen, Daniel E. Kaiser, Newell R. Kitchen, Carrie A.M. Laboski, Emerson D. Nafziger, John E. Sawyer, John F. Shanahan

Jason Clark

Nitrogen provided to crops through mineralization is an important factor in N management guidelines. Understanding of the interactive effects of soil and weather conditions on N mineralization needs to be improved. Relationships between anaerobic potentially mineralizable N (PMN_an) and soil and weather conditions were evaluated under the contrasting climates of eight US Midwestern states. Soil was sampled (0–30 cm) for PMN_an analysis before pre-plant N application (PP_0N) and at the V5 development stage from the pre-plant 0 (V5_0N) and 180 kg N ha⁻¹ (V5_180N) rates and incubated for 7, 14, …

Predicting Economic Optimal Nitrogen Rate With The Anaerobic Potentially Mineralizable Nitrogen Test, Jason D. Clark, Fabian G. Fernandez, Kristen S. Veum, James J. Camberato, Paul R. Carter, Richard B. Ferguson, David W. Franzen, Daniel E. Kaiser, Newell R. Kitchen, Carrie A.M. Laboski, Emerson D. Nafziger, Carl J. Rosen, John E. Sawyer, John F. Shanahan

Jason Clark

Estimates of mineralizable N with the anaerobic potentially mineralizable N (PMN_an) test could improve predictions of corn (Zea mays L.) economic optimal N rate (EONR). A study across eight US midwestern states was conducted to quantify the predictability of EONR for single and split N applications by PMN_an. Treatment factors included different soil sample timings (pre-plant and V5 development stage), planting N rates (0 and 180 kg N ha⁻¹), and incubation lengths (7, 14, and 28 d) with and without initial soil NH₄–N included with PMN_an. Soil was sampled …

A Public–Industry Partnership For Enhancing Corn Nitrogen Research And Datasets: Project Description, Methodology, And Outcomes, Newell R. Kitchen, John F. Shanahan, Curtis J. Ransom, Christopher J. Bandura, Gregory M. Bean, James J. Camberato, Paul R. Carter, Jason D. Clark, Richard B. Ferguson, Fabian G. Fernandez, David W. Franzen, Carrie A.M. Laboski, Emerson D. Nafziger, Zhisheng Qing, John E. Sawyer, Matt Shafer

Jason Clark

Due to economic and environmental consequences of N lost from fertilizer applications in corn (Zea mays L.), considerable public and industry attention has been devoted to the development of N decision tools. Needed are research and databases and associated metadata, at numerous locations and years to represent a wide geographic range of soil and weather scenarios, for evaluating tool performance. The goals of this research were to conduct standardized corn N rate response field studies to evaluate the performance of multiple public-domain N decision tools across diverse soils and environmental conditions, develop and publish new agronomic science for improved …

Phomopsis Stem Canker Of Sunflower In North America: Correlation With Climate And Solutions Through Breeding And Management, Brent S. Hulke, Samuel G. Markell, Nolan C. Kane, Febina M. Mathew

Febina Mathew

Climate change is occurring in the central US and is interacting with agroecological factors to increase biotic stress in sunflower. Certain species of Diaporthe cause Phomopsis stem canker in sunflower and other dicotyledonous weeds and crops. The increase in precipitation already observed in the states of North Dakota, South Dakota, and Minnesota have increased the chances of outbreaks of necrotrophic pathogens, like Diaporthe. We discuss how climate trends, combined with technological, management, and economic interactions, are correlated with increasing incidence of Phomopsis stem canker in these and adjacent areas in North America. Further, we discuss management options and the …

Nitrogen Requirements Of Ethiopian Mustard For Biofuel Feedstock In South Dakota, Phillip Alberti, Shannon Osborne, Febina Mathew, Shakaut Ali, Heidi Sieverding, Sandeep Kumar, Thandiwe Nieya

Febina Mathew

Ethiopian mustard (Brassica carinata A. Braun) is a non-food oilseed crop that has received attention for its potential as a low-input biofuel feedstock suitable for production in the semiarid regions of the Northern Great Plains (NGP). Because B. carinata is a new crop to the NGP, the best management practices have yet to be developed. The objective of the study was to evaluate the effects of N fertilizer rate on seed yield, seed oil concentration, and oil yield of B. carinata and to determine the economic optimum N fertilizer rates. Field studies were conducted at two locations in South …

Drainage Water Quality Impacts Of Agricultural Management Practices: Effectof Manure Application Timing And Cover Crops, Brian Dougherty, Carl Pederson, Matt Helmers, Michelle Soupir, Dan Andersen, Antonio Mallarino, John Sawyer

John E. Sawyer

A primary objective of this study is to evaluate the impact of various cropping and nutrient management systems on crop yields and drainage water quality. This progress report only includes the first-year corn grain yield results. Treatment comparisons include the impact of early fall vs. late fall vs. spring application of liquid swine manure, nitrification inhibitor with late fall swine manure application, cereal rye cover crop, and gypsum application. These comparisons will be conducted for multiple years and used to develop appropriate manure and nutrient management practices to minimize water contamination potential and enhance the use of swine manure as …

Harvesting Fertilized Rye Cover Crop: Simulated Revenue, Net Energy, And Drainage Nitrogen Loss, R. W. Malone, J. F. Obrycki, Douglas L. Karlen, T. C. Kaspar, D. B. Jaynes, T. B. Parkin, S. H. Lence, G. W. Feyereisen, Q. X. Fang, T. L. Richard, K. Gillette

Douglas L Karlen

Harvesting fertilized rye (Secale cereale L.) cover crop has been suggested as a method to increase producer revenue and biofuel feedstock production, but drainage N loss impacts are currently unknown. Using the tested Root Zone Water Quality Model (RZWQM) across several N rates, spring application of 120 kg N ha^-1 prior to winter rye harvest reduced drainage N loss by 54% compared with no cover crop and by 18% compared with planted rye that was neither fertilized nor harvested. Estimates of producer revenue and net energy were also positive, with 8.3 Mg ha^-1 of harvested rye biomass. …

Regenerating Agricultural Landscapes With Perennial Groundcover For Intensive Crop Production, Kenneth J. Moore, Robert P. Anex, Amani E. Elobeid, Shuizhang Fei, Cornelia B. Flora, A. Susana Goggi, Keri L. Jacobs, Prashant Jha, Amy L. Kaleita, Douglas L. Karlen, David A. Laird, Andrew W. Lenssen, Thomas Lubberstedt, Marshall D. Mcdaniel, D. Raj Raman, Sharon L. Weyers

Douglas L Karlen

The Midwestern U.S. landscape is one of the most highly altered and intensively managed ecosystems in the country. The predominant crops grown are maize (Zea mays L.) and soybean [Glycine max (L.) Merr]. They are typically grown as monocrops in a simple yearly rotation or with multiple years of maize (2 to 3) followed by a single year of soybean. This system is highly productive because the crops and management systems have been well adapted to the regional growing conditions through substantial public and private investment. Furthermore, markets and supporting infrastructure are highly developed for both crops. As maize and …

Future Prospects For Corn As A Biofuel Crop, Kenneth J. Moore, Douglas L. Karlen, Kendall R. Lamkey

Douglas L Karlen

Ethanol production from corn grain has increased signifi cantly during the past ten years in the US. This increase was driven by government policy guided by the Renewable Fuel Standard (RFS) and embodied in the Volumetric Ethanol Excise Tax Credit and other legislation created to promote a biofuels industry. As corn grain ethanol production approaches the target set out in the RFS, the industry is looking to develop capacity for producing advanced biofuels, primarily from agricultural wastes and dedicated energy crops. The residues remaining following corn harvest have been identifi ed as a voluminous and readily available feedstock for advanced …

Reducing Agriculture's Contribution To Nitrate Contamination Of Surface Waters, Dana L. Dinnes, Cynthia A. Cambardella, Thomas S. Colvin, Daniel B. Jaynes, Douglas L. Karlen

Douglas L Karlen

One of the most prevalent environmental issues throughout the Midwest is nitrate (N03) contamination of surface waters. Non-point source pollution resulting from nitrogen (N) fertilizer use on artificially drained agricultural land has been identified as a major contributor to this problem. High levels of nitratenitrogen (N03-N) in water supplies pose risks to humans and livestock (Tyson et. al., 1992), and has cost some communities millions of dollars for N03 removal. The city of Des Moines, Iowa alone has spent in excess of 5.3 million dollars, not including labor costs, for nitrate treatment of its drinking waters from 1992-1996 (Graham, 1997). …

An Evaluation Of Soil Survey Crop Yield Interpretations For Two Central Iowa Farms, A. L. Steinwand, D. L. Karlen, T. E. Fenton

Douglas L Karlen

This study was conducted on four adjacent 16-ha (40-ac) fields within the Clarion-Nicollet-Webster soil association to (1) determine if crop yield interpretations derived from 1:15840 soil survey maps could be used for developing field-scale management plans: and (2) to determine if soils in adjacent fields were derived using a computer-based Soil Information System (SIS) and compared with measured yields. Soil map units in all four fields were taxonomically variable, but this did not affect expected crop yields. Average expected and measured corn and soybean yields agreed within 9 and 12% for conentional management at the field-scale. We conclude that yield …

An Evaluation Of Soil Survey Crop Yield Interpretations For Two Central Iowa Farms, A. L. Steinwand, D. L. Karlen, T. E. Fenton

Douglas L Karlen

This study was conducted on four adjacent 16-ha (40-ac) fields within the Clarion-Nicollet-Webster soil association to (1) determine if crop yield interpretations derived from 1:15840 soil survey maps could be used for developing field-scale management plans: and (2) to determine if soils in adjacent fields were derived using a computer-based Soil Information System (SIS) and compared with measured yields. Soil map units in all four fields were taxonomically variable, but this did not affect expected crop yields. Average expected and measured corn and soybean yields agreed within 9 and 12% for conentional management at the field-scale. We conclude that yield …

Determining The Functions Of Novel Genes Required For Photosynthesis, Gillian Gomer, Moshe Kafri, Martin Jonikas

Gillian Gomer

Statistical And Machine Learning Methods Evaluated For Incorporating Soil And Weather Into Corn Nitrogen Recommendations, Curtis J. Ransom, Newell R. Kitchen, James J. Camberato, Paul R. Carter, Richard B. Ferguson, Fabián G. Fernández, David W. Franzen, Carrie A. M. Laboski, D. Brenton Myers, Emerson D. Nafziger, John E. Sawyer, John F. Shanahan

John E. Sawyer

Nitrogen (N) fertilizer recommendation tools could be improved for estimating corn (Zea mays L.) N needs by incorporating site-specific soil and weather information. However, an evaluation of analytical methods is needed to determine the success of incorporating this information. The objectives of this research were to evaluate statistical and machine learning (ML) algorithms for utilizing soil and weather information for improving corn N recommendation tools. Eight algorithms [stepwise, ridge regression, least absolute shrinkage and selection operator (Lasso), elastic net regression, principal component regression (PCR), partial least squares regression (PLSR), decision tree, and random forest] were evaluated using a dataset …

Gene Expression Programs During Shoot, Root, And Callus Development In Arabidopsis Tissue Culture, Ping Che, Sonia Lall, Dan Nettleton, Stephen H. Howell

Dan Nettleton

Shoots can be regenerated from Arabidopsis (Arabidopsis thaliana) root explants in tissue culture through a two-step process requiring preincubation on an auxin-rich callus induction medium. Regenerating tissues can be directed along different developmental pathways leading to the formation of shoots, new roots, or callus by transferring to the appropriate organ induction medium. Using gene-profiling methods, we identified groups of genes that serve as molecular signatures of the different developmental processes, i.e. genes that were specifically up- or down-regulated on one developmental pathway, but not on others. One transcription factor gene that was up-regulated during early shoot development was …

Hierarchical Modeling And Differential Expression Analysis For Rna-Seq Experiments With Inbred And Hybrid Genotypes, Andrew Lithio, Dan Nettleton

Dan Nettleton

The performance of inbred and hybrid genotypes is of interest in plant breeding and genetics. High-throughput sequencing of RNA (RNA-seq) has proven to be a useful tool in the study of the molecular genetic responses of inbreds and hybrids to environmental stresses. Commonly used experimental designs and sequencing methods lead to complex data structures that require careful attention in data analysis. We demonstrate an analysis of RNA-seq data from a split-plot design involving drought stress applied to two inbred genotypes and two hybrids formed by crosses between the inbreds. Our generalized linear modeling strategy incorporates random effects for whole-plot experimental …

Nested Hierarchical Functional Data Modeling And Inference For The Analysis Of Functional Plant Phenotypes, Yuhang Xu, Yehua Li, Dan Nettleton

Dan Nettleton

In a plant science Root Image Study, the process of seedling roots bending in response to gravity is recorded using digital cameras, and the bending rates are modeled as functional plant phenotype data. The functional phenotypes are collected from seeds representing a large variety of genotypes and have a three-level nested hierarchical structure, with seeds nested in groups nested in genotypes. The seeds are imaged on different days of the lunar cycle, and an important scientific question is whether there are lunar effects on root bending. We allow the mean function of the bending rate to depend on the lunar …

Root Type-Specific Reprogramming Of Maize Pericycle Transcriptomes By Local High Nitrate Results In Disparate Lateral Root Branching Patterns, Peng Yu, Jutta A. Baldauf, Andrew Lithio, Caroline Marcon, Dan Nettleton, Chunjian Li, Frank Hochholdinger

Dan Nettleton

The adaptability of root system architecture to unevenly distributed mineral nutrients in soil is a key determinant of plant performance. The molecular mechanisms underlying nitrate dependent plasticity of lateral root branching across the different root types of maize are only poorly understood. In this study, detailed morphological and anatomical analyses together with cell type-specific transcriptome profiling experiments combining laser capture microdissection with RNA-seq were performed to unravel the molecular signatures of lateral root formation in primary, seminal, crown, and brace roots of maize (Zea mays) upon local high nitrate stimulation. The four maize root types displayed divergent branching …

Stability Of Single-Parent Gene Expression Complementation In Maize Hybrids Upon Water Deficit Stress, Caroline Marcon, Anja Paschold, Waqas Ahmed Malik, Andrew Lithio, Jutta A. Baldauf, Lena Altrogge, Nina Opitz, Christa Lanz, Heiko Schoof, Dan Nettleton, Hans-Peter Piepho, Frank Hochholdinger

Dan Nettleton

Heterosis is the superior performance of F1 hybrids compared with their homozygous, genetically distinct parents. In this study, we monitored the transcriptomic divergence of the maize (Zea mays) inbred lines B73 and Mo17 and their reciprocal F1 hybrid progeny in primary roots under control and water deficit conditions simulated by polyethylene glycol treatment. Single-parent expression (SPE) of genes is an extreme instance of gene expression complementation, in which genes are active in only one of two parents but are expressed in both reciprocal hybrids. In this study, 1,997 genes only expressed in B73 and 2,024 genes …

Understanding Anhydrous Ammonia Application In Soil, John E. Sawyer

John E. Sawyer

What happens when anhydrous ammonia is injected into soil?

Several physical and chemical reactions take place following anhydrous ammonia injection: dissolution in water, reaction with soil organic matter and clay, and attachment of ammonium ions on the soil cation exchange complex. These reactions all tend to limit the movement of ammonia, with water having the greatest initial effect. The highest concentration of ammonia is at/near the point of injection, with a tapering of the concentration toward the outer edge of the retention zone. Usually the greatest ammonia concentration is within the first inch or two of the injection point, with …

Flood Adulterated Grain - Nutrient Supply To Crops When Land Applied, John E. Sawyer, Antonio Mallarino

John E. Sawyer

Flooding has been extensive in several areas of Iowa this spring. In some cases, stored grain has been affected by flood waters. Land application of flood adulterated grain as a nutrient source for a future crop may be an option for some. See the Iowa Dept. of Natural Resources (IDNR) and Iowa Dept. of Agriculture and Land Stewardship (IDALS) publication for Proper Management of Flooded Grain and Hay. That publication states “Farms disposing of spoiled grain and feed on their own property can land apply damaged grain at the following application rates: 146 bu corn/acre and 50 bu soybean/acre”. …

Anhydrous Ammonia Application -- Spring 2019, John E. Sawyer

John E. Sawyer

It was a late harvest in fall 2018. Soils were wet and frozen when it was time to apply anhydrous ammonia. Those situations resulted in much less than normal anhydrous ammonia application last fall. Therefore, considerable anhydrous ammonia needs to be applied this spring. There is only so much capacity to switch from one nitrogen (N) fertilizer product to another. In Iowa, historically the two largest N fertilizers are anhydrous ammonia (largest) and urea-ammonium nitrate (UAN) solution, with granulated urea a distant third.

Springtime Precipitation – A Tool For Estimating Nitrogen Application Need For Corn, John E. Sawyer

John E. Sawyer

Wet springtime conditions typically raise questions about the status of applied nitrogen (N). Or the question, do I need to apply additional N to my cornfields? At this time we do not know what the weather/precipitation will be for the entire springtime, but the extended period of wet conditions this spring is of concern. A summary of long-term N rate trials with continuous corn and corn rotated with soybean conducted at seven ISU research and demonstration farms in Iowa from 1999 to 2016 has been an on-going basis for indicating the potential for needing an N rate greater than the …

Nitrogen Fertilization Options With Delayed Or Rescue Applications, John E. Sawyer

John E. Sawyer

It’s been a wait-go-stop (repeat) corn planting season this spring. Whether you planted early or are just now getting corn planted, it seems planting windows were short and rushed. In some cases this meant planting (corn/soybean) and worrying later about getting nitrogen (N) applied. And in some areas of Iowa, wetter than normal conditions are raising questions about supplemental N application. What are the options for sidedress N?

Effects Of Unharvested, Shattered, Or Hailed-Out Soybean Fields On Nutrient Supply For Corn, John E. Sawyer

John E. Sawyer

Flooded fields and wet soil conditions in the fall 2018 meant some soybean fields were not, or are not going to be harvested. Also, some fields occasionally experienced significant shattering or a hailstorm in the fall where soybean seed is knocked from the plants and thus not harvested. When the grain is not harvested, nitrogen (N), phosphorus (P), and potassium (K) nutrients returned to the soil in the soybean grain can be accounted for when planning nutrient applications for the next crop. Other nutrients will also be returned, but most are not a fertilization need in Iowa soils. An estimate …

Laser Microdissection Of Narrow Sheath Mutant Maize Uncovers Novel Gene Expression In The Shoot Apical Meristem, Xiaolan Zhang, Shahinez Madi, Lisa Borsuk, Dan Nettleton, Robert J. Elshire, Brent Buckner, Diane Janick-Buckner, Jon Beck, Marja Timmermans, Patrick S. Schnable, Michael J. Scanlon

Dan Nettleton

Microarrays enable comparative analyses of gene expression on a genomic scale, however these experiments frequently identify an abundance of differentially expressed genes such that it may be difficult to identify discrete functional networks that are hidden within large microarray datasets. Microarray analyses in which mutant organisms are compared to nonmutant siblings can be especially problematic when the gene of interest is expressed in relatively few cells. Here, we describe the use of laser microdissection microarray to perform transcriptional profiling of the maize shoot apical meristem (SAM), a ~100-μm pillar of organogenic cells that is required for leaf initiation. Microarray analyses …

Scanning Microarrays At Multiple Intensities Enhances Discovery Of Differentially Expressed Genes, David S. Skibbe, Xiujuan Wang, Xuefeng Zhao, Lisa A. Borsuk, Dan Nettleton, Patrick S. Schnable

Dan Nettleton

Motivation: Scanning parameters are often overlooked when optimizing microarray experiments. A scanning approach that extends the dynamic data range by acquiring multiple scans of different intensities has been developed.

Results: Data from each of three scan intensities (low, medium, high) were analyzed separately using multiple scan and linear regression approaches to identify and compare the sets of genes that exhibit statistically significant differential expression. In the multiple scan approach only one-third of the differentially expressed genes were shared among the three intensities, and each scan intensity identified unique sets of differentially expressed genes. The set of differentially expressed genes from …