Horticulture Commons^™

Changes In Soil Microbial Communities After 10 Years Of Winter Wheat Cultivation Versus Fallow In An Organic-Poor Soil In The Loess Plateau Of China, Hui Tian, Hui Wang, Xiaoli Hui, Zhaohui Wang, Rhae A. Drijber, Jinshan Liu

Department of Agronomy and Horticulture: Faculty Publications

Agricultural management methods, such as cultivation or fallowing, have led to significant changes in soil fertility and hence, crop yield. Such changes may have stemmed from changes in soil microbial communities and associated biogeochemical processes. This phenomenon is particularly true in organic-poor soil in the Loess Plateau of China. In this study, we examined three existing soil management regimes as part of a 10-year field experiment and evaluated their effects on fungal and bacterial community structures by performing high-throughput 454 pyrosequencing. These management regimes were (i) fertilized winter wheat (Triticum aestivum L.) (FW), (ii) continuous …

Regeneration And Invasion Of Cottonwood Riparian Forest Following Wildfire, Carissa L. Wonkka, Dirac L. Twidwell Jr., Christine H. Bielski, Craig R. Allen, Michael C. Stambaugh

Department of Agronomy and Horticulture: Faculty Publications

Populus deltoides is considered to be a weak resprouter and highly susceptible to wildfire, but few post-wildfire studies have tracked P. deltoides response and resprouting within the Great Plains of North America. Following a wildfire in southwestern Kansas, U.S.A., we surveyed burned and unburned areas of a cottonwood riparian forest along the Cimarron River that included a major understory invader, tamarisk (Tamarix ramosissima Ledeb.). We tested the following hypotheses, which are consistent with the current understanding of P. deltoides response to wildfire in the Great Plains: (1) regeneration of P. deltoides will be low in areas burned by the …

Genome-Guided Phylo-Transcriptomic Methods And The Nuclear Phylogentic Tree Of The Paniceae Grasses, Jacob D. Washburn, James C. Schnable, Gavin C. Conant, Thomas P. Brutnell, Ying Shao, Yang Zhang, Martha Ludwig, Gerrit Davidse, J. Chris Pires

Department of Agronomy and Horticulture: Faculty Publications

The past few years have witnessed a paradigm shift in molecular systematics from phylogenetic methods (using one or a few genes) to those that can be described as phylogenomics (phylogenetic inference with entire genomes). One approach that has recently emerged is phylo-transcriptomics (transcriptome-based phylogenetic inference). As in any phylogenetics experiment, accurate orthology inference is critical to phylo-transcriptomics. To date, most analyses have inferred orthology based either on pure sequence similarity or using gene-tree approaches. The use of conserved genome synteny in orthology detection has been relatively under-employed in phylogenetics, mainly due to the cost of sequencing genomes. While current trends …

Genetic Basis Of The Very Short Life Cycle Of ‘Apogee’ Wheat, Genqiao Li, Rungravee Boontung, Carol Powers, Vikas Belamkar, Tianrong Huang, Fang Miao, P. Stephen Baenziger, Liuling Yan

Department of Agronomy and Horticulture: Faculty Publications

Background: ‘Apogee’ has a very short life cycle among wheat cultivars (flowering 25 days after planting under a long day and without vernalization), and it is a unique genetic material that can be used to accelerate cycling breeding lines. However, little is known about the genetic basis of the super-short life of Apogee wheat.

Results: In this study, Apogee was crossed with a strong winter wheat cultivar ‘Overland’, and 858 F₂ plants were generated and tested in a greenhouse under constant warm temperature and long days. Apogee wheat was found to have the early alleles for four flowering time …

Genome-Wide Characterization Of Non-Reference Transposable Element Insertion Polymorphisms Reveals Genetic Diversity In Tropical And Temperate Maize, Xianjun Lai, James C. Schnable, Zhengqiao Liao, Jie Xu, Gengyun Zhang, Chuan Li, Erliang Hu, Tingzhao Rong, Yunbi Xu, Yanli Li

Department of Agronomy and Horticulture: Faculty Publications

Background: Maize was originally domesticated in a tropical environment but is now widely cultivated at temperate latitudes. Temperate and tropical maize populations have diverged both genotypically and phenotypically. Tropical maize lines grown in temperate environments usually exhibit delayed flowering, pollination, and seed set, which reduces their grain yield relative to temperate adapted maize lines. One potential mechanism by which temperate maize may have adapted to a new environment is novel transposable element insertions, which can influence gene regulation. Recent advances in sequencing technology have made it possible to study variation in transposon content and insertion location in large sets of …

Long-Term Tillage Impact On Soil Hydraulic Properties, Humberto Blanco-Canqui, Brian J. Weinhold, Virginia L. Jin, Marty R. Schmer, Leonard C. Kibet

Department of Agronomy and Horticulture: Faculty Publications

An improved understanding of the impact of tillage systems on soil hydraulic properties is necessary to conserve and manage soil water under a changing climate. The objective of this study was to specifically measure soil hydraulic properties (total porosity, water infiltration, saturated hydraulic conductivity, and water retention characteristics) in no-till, chisel plow, disk, and moldboard plow systems under rainfed continuous corn (Zea mays L.) after 35 yr on silty clay loam soils in eastern Nebraska. We measured ponded water infiltration (positive soil water pressure) and tension (-1 kPa matric potential) infiltration to exclude macropore (>125 mm diameter) flow. …

Reversing Resistance To Tembotrione In An Amaranthus Tuberculatus (Var. Rudis) Population From Nebraska, Usa With Cytochrome P450 Inhibitors, Maxwel C. Oliveira, Todd A. Gaines, Franck E. Dayan, Eric L. Patterson, Amit J. Jhala, Stevan Z. Knezevic

Department of Agronomy and Horticulture: Faculty Publications

Background: A population of Amaranthus tuberculatus (var. rudis) was confirmed resistant to 4-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibitor herbicides (mesotrione, tembotrione, and topramezone) in a seed corn/soybean rotation in Nebraska. Further investigation confirmed a non-target-site resistance mechanism in this population. The main objective of this study was to explore the role of cytochrome P450 inhibitors in restoring the efficacy of HPPD-inhibitor herbicides on the HPPD-inhibitor resistant A. tuberculatus population from Nebraska, USA (HPPD-R).

Background: A population of Amaranthus tuberculatus (var. rudis) was confirmed resistant to 4-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibitor herbicides (mesotrione, tembotrione, and topramezone) in a seed corn/soybean rotation in Nebraska. Further investigation confirmed …

Can Cover Crop Use Allow Increased Levels Of Corn Residue Removal For Biofuel In Irrigated And Rainfed Systems?, S. J. Ruis, Humberto Blanco-Canqui, Paul J. Jasa, R. B. Ferguson, G. Slater

Department of Agronomy and Horticulture: Faculty Publications

Corn (Zea mays L.) residue removal at high rates can result in negative impacts to soil ecosystem services. The use of cover crops could be a potential strategy to ameliorate any adverse effects of residue removal while allowing greater removal levels. Hence, the objective of this study was to determine changes in water erosion potential, soil organic C (SOC) and total N concentration, and crop yields under early- and late-terminated cover crop (CC) combined with five levels of corn residue removal after 3 years on rainfed and irrigated no-till continuous corn in Nebraska. Treatments were no CC, early- and …

Using An Unmanned Aerial Vehicle To Evaluate Nitrogen Variability And Height Effect With An Active Crop Canopy Sensor, Brian Krienke, Richard B. Ferguson, Michael Schlemmer, Kyle Holland, David B. Marx, Kent M. Eskridge

Department of Agronomy and Horticulture: Faculty Publications

Ground-based active sensors have been used in the past with success in detecting nitrogen (N) variability within maize production systems. The use of unmanned aerial vehicles (UAVs) presents an opportunity to evaluate N variability with unique advantages compared to ground-based systems. The objectives of this study were to: determine if a UAV was a suitable platform for use with an active crop canopy sensor to monitor in-season N status of maize, if UAV’s were a suitable platform, is the UAV and active sensor platform a suitable substitute for current handheld methods, and is there a height effect that may be …

Dissecting The Genetic Basis Of Local Adaptation In Soybean, Nonoy B. Bandillo, Justin E. Anderson, Michael B. Kantar, Robert M. Stupar, James E. Specht, George L. Graef, Aaron J. Lorenz

Department of Agronomy and Horticulture: Faculty Publications

Soybean (Glycine max) is the most widely grown oilseed in the world and is an important source of protein for both humans and livestock. Soybean is widely adapted to both temperate and tropical regions, but a changing climate demands a better understanding of adaptation to specific environmental conditions. Here, we explore genetic variation in a collection of 3,012 georeferenced, locally adapted landraces from a broad geographical range to help elucidate the genetic basis of local adaptation. We used geographic origin, environmental data and dense genome-wide SNP data to perform an environmental association analysis and discover loci displaying steep …

Comparison Of Organic And Integrated Nutrient Management Strategies For Reducing Soil N2O Emissions, Rebecca F. Graham, Samuel E. Wortman, Cameron M. Pittelkow

Department of Agronomy and Horticulture: Faculty Publications

To prevent nutrient limitations to crop growth, nitrogen is often applied in agricultural systems in the form of organic inputs (e.g., crop residues, manure, compost, etc.) or inorganic fertilizer. Inorganic nitrogen fertilizer has large environmental and economic costs, particularly for low-input smallholder farming systems. The concept of combining organic, inorganic, and biological nutrient sources through Integrated Nutrient Management (INM) is increasingly promoted as a means of improving nutrient use efficiency by matching soil nutrient availability with crop demand. While the majority of previous research on INM has focused on soil quality and yield, potential climate change impacts have rarely been …

Rooting For Food Security In Sub-Saharan Africa, Nicolas Guilpart, Patricio Grassini, Justin Van Wart, Haishun Yang, Martin K. Van Ittersum, Lenny G.J. Van Bussel, Joost Wolf, Lieven Claessens, Johan G.B. Leenaars, Kenneth G. Cassman

Department of Agronomy and Horticulture: Faculty Publications

There is a persistent narrative about the potential of Sub-Saharan Africa (SSA) to be a ‘grain breadbasket’ because of large gaps between current low yields and yield potential with good management, and vast land resources with adequate rainfall. However, rigorous evaluation of the extent to which soils can support high, stable yields has been limited by lack of data on rootable soil depth of sufficient quality and spatial resolution. Here we use location-specific climate data, a robust spatial upscaling approach, and crop simulation to assess sensitivity of rainfed maize yields to root-zone water holding capacity. We find that SSA could …

Can Yield Gap Analysis Be Used To Inform R & D Prioritisation?, P. A. J. Van Oort, K. Saito, I. Dieng, P. Grassini, K. G. Cassman, M. K. Van Ittersum

Department of Agronomy and Horticulture: Faculty Publications

The phrase “biggest bang for a buck” is associated with the policy making question that governments and development agencies face: “Where and which crops should receive highest priority for improving local and global food supply?”. A first step of prioritisation is to identify region x crop combinations for which high impact can be anticipated. We developed a new method for this prioritisation exercise and applied it to data from the Global Yield Gap and Water Productivity Atlas (GYGA). Our prioritisation distinguishes between two policy objectives (humanitarian and economic) and builds upon the relative yield gap and climate risk. Results of …

Supplemental Material For: Multi-Site Evaluation Of Apex For Water Quality: Ii. Regional Parameterization, Nathan O. Nelson, Claire Baffaut, John A. Lory, G.M.M.M. Anomaa Senaviratne, Ammar B. Bhandari, Ranjith P. Udawatta, Daniel W. Sweeney, Matt J. Helmers, Mike W. Van Liew, Antonio P. Mallarino, Charles S. Wortmann

Department of Agronomy and Horticulture: Faculty Publications

Model performance was assessed using Nash-Sutcliffe model efficiency (NSE), coefficient of determination (r²), and percent bias (PBIAS) as defined by Moriasi et al. (2007 and 2015). Threshold values indicating acceptable model performance based on these statistics are dependent on the spatial and temporal scales of the data, water quality constituents of interest, and the modeling objectives (Moriasi et al., 2015). Although some standard values have been suggested (Moriasi et al., 2007 and 2015), considerable variability exist in the published literature. For instance Ramanarayan et al. (1997) considered r² >0.5 and NSE >0.40 as satisfactory for simulation of …

Multisite Evaluation Of Apex For Water Quality: I. Best Professional Judgment Parameterization, Claire Baffaut, Nathan O. Nelson, John A. Lory, G.M.M.M. Anomaa Senaviratne, Ammar B. Bhandari, Ranjith P. Udawatta, Daniel W. Sweeney, Matt J. Helmers, M. W. Van Liew, Antonio P. Mallarino, Charles S. Wortmann

Department of Agronomy and Horticulture: Faculty Publications

The Agricultural Policy Environmental eXtender (APEX) model is capable of estimating edge-of-field water, nutrient, and sediment transport and is used to assess the environmental impacts of management practices. The current practice is to fully calibrate the model for each site simulation, a task that requires resources and data not always available. The objective of this study was to compare model performance for flow, sediment, and phosphorus transport under two parameterization schemes: a best professional judgment (BPJ) parameterization based on readily available data and a fully calibrated parameterization based on site-specific soil, weather, event flow, and water quality data. The analysis …

Genotype, Environment, Seeding Rate, And Top-Dressed Nitrogen Effects On End-Use Quality Of Modern Nebraska Winter Wheat, Madhav Bhatta, Teshome Regassa, Devin J. Rose, P. Stephen Baenziger, Kent M. Eskridge, Dipak K. Santra, Rachana Poudel

Department of Agronomy and Horticulture: Faculty Publications

Background: Fine-tuning production inputs such as seeding rate, nitrogen (N), and genotype may improve end-use quality of hard red winter wheat (Triticum aestivium L.) when growing conditions are unpredictable. Studies were conducted at the Agronomy Research Farm (ARF; Lincoln, NE, USA) and the High Plains Agricultural Laboratory (HPAL; Sidney, NE, USA) in 2014 and 2015 in Nebraska, USA, to determine the effects of genotype (6), environment (4), seeding rate (3), and flag leaf top-dressed N (0 and 34 kg N ha⁻¹) on the end-use quality of winter wheat.

Results: End-use quality traits were influenced by environment, genotype, …

Author Correction: Genome-Guided Phylo-Transcriptomic Methods And The Nuclear Phylogenetic Tree Of The Paniceae Grasses, Jacob D. Washburn, James C. Schnable, Gavin C. Conant, Thomas P. Brutnell, Ying Shao, Yang Zhang, Martha Ludwig, Gerrit Davidse, J. Chris Pires

Department of Agronomy and Horticulture: Faculty Publications

The original version of this Article contained an error in the title of the paper, where the word “Phylogenetic” was incorrectly given as “Phylogentic”. This has now been corrected in the PDF and HTML versions of the Article, and in the accompanying Supplementary Information file.

Lettuce Learn: Student Reflections On Building And Sustaining A Community Donation Garden, Hannah Dankbar, Emily K. Zimmerman, Carrie Chennault, Andrea D. Basche, Jacqueline Ann Nester, Maritza Pierre, Gabrielle Roesch-Mcnally

Department of Agronomy and Horticulture: Faculty Publications

This article emerged from conversations that we and fellow graduate students have had in building a community donation garden. We created the garden with a vision of enacting food justice in our community, but over the past four years we have experienced complexities with our vision. In this article, we share the complexities with which we have wrestled, how we have encouraged thoughtful dialogue among fellow scholars about these shortcomings and the intricate workings of the agrifood system, and the lessons we have learned through these experiences as early-career scholar-activists. This article represents our collective and individual voices as graduate …

The Impact Of Continuous Living Cover On Soil Hydrologic Properties: A Meta-Analysis, Andrea D. Basche, Marcia Delonge

Department of Agronomy and Horticulture: Faculty Publications

Increased rainfall variability due to climate change threatens the efficacy of critical soil ecosystem services. One strategy to negate effects of too much or not enough rainfall is to improve soil water properties. Practices that offer “continuous living cover” can enhance soil water storage and other soil hydrologic properties relative to annual crop systems, but to what extent such benefits can accrue, under different conditions, remains under-quantified. To address these uncertainties, we conducted a meta-analysis that included 27 studies representing 93 paired observations measuring two soil hydrologic properties: porosity and the water retained at field capacity. All experiments compared the …

Research Topics To Scale Up Cover Crop Use: Reflections From Innovative Iowa Farmers, Andrea D. Basche, Gabrielle E. Roesch-Mcnally

Department of Agronomy and Horticulture: Faculty Publications

Cover crops as a conservation practice continue to receive attention from farmers, researchers, media, and policy makers, given their ability to effectively reduce water pollution and improve soil quality. Recent estimates of cover crop use across the midwestern Corn Belt, as well as the United States, demonstrate large acreage increases over the last number of years. The annual Sustainable Agriculture Research and Education–Conservation Technology Information Center (SARE– CTIC) survey found that nationally cover crop acreage doubled from 2011 to 2016, based on farmers self-reporting cover crop planting (CTIC 2016). However, the total cover crop acreage based on 2012 Census of …