Physical Sciences and Mathematics Commons^™

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, …

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. …

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). …

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 …

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 …

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 …

Comparative Gene Expression Profiles Between Heterotic And Non-Heterotic Hybrids Of Tetraploid Medicago Sativa, Xuehui Li, Yanling Wei, Dan Nettleton, E. Charles Brummer

Dan Nettleton

Background: Heterosis, the superior performance of hybrids relative to parents, has clear agricultural value, but its genetic control is unknown. Our objective was to test the hypotheses that hybrids expressing heterosis for biomass yield would show more gene expression levels that were different from midparental values and outside the range of parental values than hybrids that do not exhibit heterosis.

Results: We tested these hypotheses in three Medicago sativa (alfalfa) genotypes and their three hybrids, two of which expressed heterosis for biomass yield and a third that did not, using Affymetrix M. truncatula GeneChip arrays. Alfalfa hybridized to approximately 47% …

Use Of Legume Green Manures As Nitrogen Sources For Corn Production, Matt Liebman, Rhonda L. Graef, Daniel Nettleton, Cynthia A. Cambardella

Dan Nettleton

Recent volatility in supplies and prices of natural gas and synthetic nitrogen (N) fertilizer suggests a need to develop and refine alternative strategies for supplying N to corn. In this study, conducted in north-eastern Iowa, we examined the use of red clover and alfalfa green manures as means of supplying N to a succeeding corn crop. Red clover intercropped with oat produced significantly more biomass and contained more N than alfalfa intercropped with oat. Tilling green manures in the fall or delaying tillage until the following spring did not have a consistent effect on green manure N content. Without N …

Complementation Contributes To Transcriptome Complexity In Maize (Zea Mays L.) Hybrids Relative To Their Inbred Parents, Anja Paschold, Yi Jia, Caroline Marcon, Steve Lund, Nick B. Larson, Cheng-Ting Yeh, Stephan Ossowski, Christa Lanz, Dan Nettleton, Patrick S. Schnable, Frank Hochholdinger

Dan Nettleton

Typically, F₁-hybrids are more vigorous than their homozygous, genetically distinct parents, a phenomenon known as heterosis. In the present study, the transcriptomes of the reciprocal maize (Zea mays L.) hybrids B73×Mo17 and Mo17×B73 and their parental inbred lines B73 and Mo17 were surveyed in primary roots, early in the developmental manifestation of heterotic root traits. The application of statistical methods and a suitable experimental design established that 34,233 (i.e., 86%) of all high-confidence maize genes were expressed in at least one genotype. Nearly 70% of all expressed genes were differentially expressed between the two parents and 42%–55% …

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 …

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 …

Non-Syntenic Genes Drive Rtcs-Dependent Regulation Of The Embryo Transcriptome During Formation Of Seminal Root Primordia In Maize (Zea Mays L.), Huanhuan Tai, Nina Opitz, Andrew Lithio, Xin Lu, Dan Nettleton, Frank Hochholdinger

Dan Nettleton

Seminal roots of maize are pivotal for early seedling establishment. The maize mutant rootless concerning crown and seminal roots (rtcs) is defective in seminal root initiation during embryogenesis. In this study, the transcriptomes of wild-type and rtcs embryos were analyzed by RNA-Seq based on histological results at three stages of seminal root primordia formation. Hierarchical clustering highlighted that samples of each genotype grouped together along development. Determination of their gene activity status revealed hundreds of genes specifically transcribed in wild-type or rtcs embryos, while K-mean clustering revealed changes in gene expression dynamics between wild-type and rtcs during embryo …

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 …

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 …

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 …

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

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; …

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 …

Nitrogen Fertilizer Rate Effects On Soil Organic Carbon In Iowa Continuous Corn And Corn-Soybean Systems, Hanna J. Poffenbarger, Daniel W. Barker, Matthew J. Helmers, Fernando E. Miguez, John E. Sawyer, Johan Six, Michael J. Castellano

John E. Sawyer

Nitrogen fertilizer rate is a key factor affecting soil organic C (SOC) in corn-based cropping systems. The objective of this study was to determine the change in SOC in response to long-term N rates for continuous corn and corn-soybean cropping systems at two sites in Iowa. Soil samples were collected to a depth of 15 cm in 1999 and again in 2014 after 15 years of corn N rate treatments ranging from 0 to 269 kg ha^-1. The soil samples were analyzed for total C and N concentrations. For continuous corn at both sites, the average annual change …

A Smartphone-Based Device For Measuring Soil Organic Matter, Meng Lu

Meng Lu

The project evaluated the potential of utilizing a smartphone-based system for the in-field analysis of Soil Organic Matter. Although it demonstrated that the performance of the smartphone-based spectrometer can be comparable to commercial spectrometers, the results suggest that it is challenging to identify the spectral “signatures” of the SOM due to the morphology and moisture variation of soil samples.

Winter Grazing Management, Stephen K. Barnhart, James R. Russell, Douglas L. Karlen, Michael J. Tidman

Douglas L Karlen

Why winter grazing? Beef cow herd and sheep flock records show that winter feeding costs are livestock producers' single largest production expense. Managing through winter weather while keeping feeding costs low is an essential part of maintaining a profitable operation. Iowa's climate generally allows forage growth only during a 7-to-8 month period. Extending the grazing of this forage--even an extra 3 or 4 weeks in late autumn and winter--is an economical way to maintain or increase livestock profitability. Some producers extend the grazing season by using stockpiled forage, whereas others use crop residue, and many combine the use of stockpiled …

Winter Rye Cover Crop Biomass Production, Degradation, And N Recycling, J. L. Pantoja, J. E. Sawyer, D. W. Barker

John E. Sawyer

Winter rye (Secale cereale L.) as a cover crop can take up residual inorganic N between annual row crops and therefore be used to help reduce NO3 -–N loss from fields and movement to water systems. However, does the rye N uptake affect N recycling to soil and add to plant available N? The rye carbon:nitrogen (C:N) ratio could also influence N recycling. The objectives of this study were to evaluate rye biomass degradation and N recycling after spring rye termination in a no-till corn (Zea mays L.) - soybean [Glycine max. (L.) Merr.] rotation. A two year experiment (2010-2011) …

Corn And Soybean Response To Sulfur Application On Iowa Soils, J. E. Sawyer, D. W. Barker

John E. Sawyer

Historically sulfur (S) application has not been recommended on Iowa soils for com and soybean production. Prior research has not determined a consistent need for S fertilization in Iowa, with field research indicating no com or soybean yield response to applied S at virtually every site studied (Thorup and Leitch 1975; Webb, 1978; Alesii 1982; Killorn, 1984; Sexton et al., 1998; Mallarino et al., 2000). The soil supply, in combination with sources such as manure and atmospheric deposition has apparently met com and soybean S needs. Sulfur deficiencies have been reported over the years in various areas of the Midwestern …

Wait Until Soil Temps Drop Before Applying Anhydrous Ammonia, John E. Sawyer, Barbara Stewart, William Ehm

John E. Sawyer

With the early harvest, Iowa’s conservation leaders are encouraging farmers to wait until soil temperatures lower before applying anhydrous ammonia (NH3) this fall. Anhydrous ammonia applied before daily soil temperatures remain below 50 degrees Fahrenheit and continue trending lower can result in the nitrogen loss that can impact crop development and have negative environmental impacts, such as enhanced leaching into groundwater and streams once converted to nitrate.

Wet Conditions And Change In Soil Profile Nitrate, John E. Sawyer

John E. Sawyer

I wrote an ICM News article February 21, 2013, that provided a summary of fall soil profile nitrate sampling results following the 2012 corn harvest. As I cautioned in that and other articles, the amount of nitrate-N that might remain for a 2013 corn crop depends on springtime rainfall. Unfortunately, much of Iowa has received considerable precipitation since soils thawed, especially the eastern two-thirds of Iowa. The two maps of the Midwest region show the total precipitation and deviation from normal since March 7, 2013. Tile lines are flowing again, and nitrate in the profile will move with percolating water. …

Sulfur Emerges As A Nutritional Issue In Iowa Alfalfa Production, John E. Sawyer, Brian J. Lang, Daniel W. Barker

John E. Sawyer

Sulfur is often classified as a “secondary” essential element, mainly due to a smaller plant requirement, but also because it is less frequently applied as a fertilizer compared to N, P, and K. This has certainly been the case in Iowa, where research had not documented S deficiency or fertilization need for optimal crop production. However, if deficient, S can have a dramatic effect on plant growth and crop productivity – more than the classification “secondary” would imply.

Assessing The Potential To Decrease The Gulf Of Mexico Hypoxic Zone With Midwest Us Perennial Cellulosic Feedstock Production, Andy Vanloocke, Tracy E. Twine, Christopher J. Kucharik, Carl J. Bernacchi

Andy VanLoocke

The goal of this research was to determine the changes in streamflow, dissolved inorganic nitrogen (DIN) leaching and export to the Gulf of Mexico associated with a range of large-scale dedicated perennial cellulosic bioenergy production scenarios within in the Mississippi–Atchafalaya River Basin (MARB). To achieve this goal, we used Agro-IBIS, a vegetation model capable of simulating the biogeochemistry of row crops, miscanthus and switchgrass, coupled with THMB, a hydrology model capable of simulating streamflow and DIN export. Simulations were conducted at varying fertilizer application rates (0–200 kg N ha -1) and fractional replacement (5–25%) of current row crops with miscanthus …