Agronomy and Crop Sciences Commons^™

Genomic Selection For Yield And Seed Composition Stability In An Applied Soybean Breeding Program, Benjamin Mark Harms

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Stability traits are of primary importance in plant breeding to ensure consistency in phenotype across a range of environments. However, selection efficiency and accuracy for stability traits can be hindered due to the requirement of obtaining phenotype data across multiple years and environments for proper stability analysis. Genomic selection is a method that allows prediction of a phenotype prior to observation in the field using genome-wide marker data and phenotype data from a training population. To assess prediction of stability traits, two elite-yielding soybean populations developed three years apart in the same breeding program were used. The individuals in each …

Plasticity Of Sorghum Biomass And Inflorescence Traits In Response To Nitrogen Application, Kyle M. Linders

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Nitrogen is an essential nutrient required for growth and development in plants. Insufficient nitrogen availability can reduce vegetative growth and grain yield. However, nitrogen is a costly input for farmers, is energy intensive to manufacture, and runoff of excess nitrogen fertilizer impacts water quality. Compared to its close relative, maize, sorghum has much greater resilience to nitrogen and water deficit, and heat stress, allowing sorghum to be grown with fewer inputs and on marginal land. Variation in total biomass accumulation and grain yield between sorghum accessions, as well as between nitrogen conditions, can be largely explained by differences in vegetative …

Irrigation-As-A-Service For Smallholder Farmers, Ishani Lal

Department of Agricultural Economics: Dissertations, Theses, and Student Research

Irrigation is a crucial management practice that can help increase food security among smallholders globally while mitigating climate change impacts. High-efficiency irrigation technologies such as drip kits and sprinkler systems are relatively expensive and smallholder farmers cannot afford them to buffer crop yields against low precipitation. In many developing countries, farmers participate in robust informal markets for renting and sharing of irrigation equipment. Such services may be operated by farmers or via a third party such as irrigation start-ups, water user associations, non-governmental organizations, or even government agencies. These services are referred to collectively as Irrigation-as-a-Service (IaaS).

The objective of …

Investigating Effect Of Seed Source And Developing Germination Protocols To Improve Success In Restoration Of Arkansas Tallgrass Prairies, Rhiannon Spencerosa

Graduate Theses and Dissertations

American tallgrass prairie has faced losses estimated at 87-98% of original land area since European settlement. Native seeds are often used to supplement struggling or extinct plant populations in tallgrass prairie restoration and establishment sites. Two main considerations in restoration and establishment are from where to source seed and how to obtain high germination rates. In order to determine the effect of seed source, a common garden experiment was performed in Fayetteville, Arkansas in 2022 with five prairie species: Andropogon gerardii (big bluestem), Bouteloua curtipendula (sideoats grama), Panicum virgatum (switchgrass), Schizachyrium scoparium (little bluestem), and Sorghastrum nutans (Indiangrass). Seed was …

Winter Hardy Small Cereals For Grazing Or Silage In Eastern Nebraska, Abigail M. Sartin

Department of Animal Science: Dissertations, Theses, and Student Research

Two, 3-year studies were conducted to evaluate the value of cereal rye, winter wheat, and winter triticale as forage sources for either for silage or early spring grazing. For silage, the objective was to evaluate species and maturity effects on dry matter yield, nutritive value, and fermentation of small cereal silage. There are no major differences between wheat, rye, or triticale in terms of the relative timing of each species reached each maturity stage. There are no differences among species in dry matter (DM) yield, except for wheat which tends to decline at soft dough due to senescence of the …

Influence Of Cover Crops On Soybean Yield And Partial Returns As An Alternative To Double-Crop Soybean In Arkansas, Drew Kirkpatrick, Trenton L. Roberts, Kris Brye, Jeremy Ross

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

The number of hectares dedicated to winter wheat (Triticum aestivum L.) in the southern United States has been trending downward for almost a decade, presenting an opportunity for producers to utilize alternatives in their soybean [Glycine max (L.) Merr.] rotations, such as winter cover crops. A study was established to compare the cover crops to traditional cropping systems by determining the effect each had on a successive soybean crop and to examine partial economic returns. Cropping systems implemented were winter fallow, winter wheat, and seven cover crop treatments, including cereal rye (Secale cereale L.), black-seeded oat ( …

A Deep Learning Framework For Processing And Classification Of Hyperspectral Rice Seed Images Grown Under High Day And Night Temperatures, Víctor Díaz-Martínez, Jairo Orozco-Sandoval, Vidya Manian, Balpreet K. Dhatt, Harkamal Walia

Department of Agronomy and Horticulture: Faculty Publications

A framework combining two powerful tools of hyperspectral imaging and deep learning for the processing and classification of hyperspectral images (HSI) of rice seeds is presented. A seed-based approach that trains a three-dimensional convolutional neural network (3D-CNN) using the full seed spectral hypercube for classifying the seed images from high day and high night temperatures, both including a control group, is developed. A pixel-based seed classification approach is implemented using a deep neural network (DNN). The seed and pixel-based deep learning architectures are validated and tested using hyperspectral images from five different rice seed treatments with six different high temperature …

Corn Grain Marketing Strategy Unbiasing For 2023, Matthew Stockton, Shannon Sand

Cornhusker Economics

Discusses cognitive biasing errors that may be employed--in the context of corn market strategizing--such as the Dunning-Krueger effect, availability or distancing bias, gambler's fallacy, and anchoring bias.

Entropy And Energy Profiles Of Chemical Reactions, Johannes C. B. Dietschreit, Dennis J. Diestler, Rafael Gómez-Bombarelli

Department of Agronomy and Horticulture: Faculty Publications

The description of chemical processes at the molecular level is often facilitated by use of reaction coordinates, or collective variables (CVs). The CV measures the progress of the reaction and allows the construction of profiles that track the evolution of a specific property as the reaction progresses. Whereas CVs are routinely used, especially alongside enhanced sampling techniques, links between profiles and thermodynamic state functions and reaction rate constants are not rigorously exploited. Here, we report a unified treatment of such reaction profiles. Tractable expressions are derived for the free-energy, internal-energy, and entropy profiles as functions of only the CV. We …

Divergent Metabolic Changes In Rhizomes Of Lowland And Upland Switchgrass (Panicum Virgatum) From Early Season Through Dormancy Onset, Nathan A. Palmer, Gautam Sarath, Michael J. Bowman, Aaron J. Saathoff, Serge J. Edmé, Robert B. Mitchell, Christian M. Tobias, Soundararajan Madhavan, Erin D. Scully, Scott E. Sattler

Department of Agronomy and Horticulture: Faculty Publications

High-biomass-yielding southerly adapted switchgrasses (Panicum virgatum L.) frequently suffer from unpredictable winter hardiness at more northerly sites arising from damage to rhizomes that prevent effective spring regrowth. Previously, changes occurring over the growing season in rhizomes sampled from a cold-adapted tetraploid upland cultivar, Summer, demonstrated a role for abscisic acid (ABA), starch accumulation, and transcriptional reprogramming as drivers of dormancy onset and potential keys to rhizome health during winter dormancy. Here, rhizome metabolism of a high-yielding southerly adapted tetraploid switchgrass cultivar, Kanlow—which is a significant source of genetics for yield improvement—was studied over a growing season at a northern …

Herbicide Drift Vs. Crop Resilience – The Influence Of Micro-Rates, Milan Brankov, Bruno Canella Vieira, Miloš Rajković, Milena Simić, Vukadinović Jelena, Violeta Mandić, Vesna Dragičević

Department of Agronomy and Horticulture: Faculty Publications

A greenhouse study was conducted to test the effects of low herbicide dose exposure on different crops measuring visible damages, plant height, leaf area, and dry matter. Seven crops were tested: lettuce (Lactuca sativa L.) cv. Novosadska majska maslena, oil pumpkin (Cucurbita maxima Duch) cv. Olivija, oilseed rape (Brassica napus L.) cv. NS Ras, pepper (Capsicum annuum L.) cv. Kurtovska kapija, soybean (Glycine max (L.) Merr) cv. ZP Laura, sunflower (Helianthus annuus L.) cv. NS Kruna, and tomato (Solanum lycopersicum L.) cv. Dunavski Rubin. Herbicide dicamba in the range of 0.14 to 1 …

Deficit Irrigation Management For Irrigated Corn In Nebraska: Economically Viable?, Lia Nogueira, Cory Walters, Emily O'Donnell, E. Wesley F. Peterson, Suat Irmak

Cornhusker Economics

In this study we determine the economic value of deficit irrigation management using both technological and methodological advancements. The use of soil moisture probes represents the technological improvement. We provide improvements in the methodology as follows. Regarding data, we employ a field-size study, instead of plots, where the irrigation decision is determined by the moisture level in the soil measured through a soil moisture probe. Regarding the understanding of the yield response to water, although we examine the commonly used quadratic function, we improve upon this specification by also examining an alternative response function, the linear response stochastic plateau. Our …

Late Postemergence Glufosinate-Based Programs For Glyphosate-Resistant Palmer Amaranth Control In Dicamba/Glufosinate/Glyphosate-Resistant Soybean, Vipan Kumar, Jatinder S. Aulakh, Rui Liu, Amit J. Jhala

Department of Agronomy and Horticulture: Faculty Publications

Glyphosate-resistant (GR) Palmer amaranth (Amaranthus palmeri S. Watson) is widespread in the Central Great Plains. Introduction of newly developed dicamba/glufosinate/glyphosate (DGG)-resistant soybean varieties allows postemergence (POST) applications of dicamba and glufosinate for in-season control of GR Palmer amaranth. Limited information exists on the effectiveness of glufosinate applied late-POST for tall (70–90 cm) GR Palmer amaranth control in DGG-resistant soybean. The objectives of this study were to (1) determine the effectiveness of late-POST glufosinate-based programs for GR Palmer amaranth control, and (2) determine the impact of those programs on soybeans grain yields. Ten glufosinatebased programs were tested in a field …

A Leaf-Level Spectral Library To Support High-Throughput Plant Phenotyping: Predictive Accuracy And Model Transfer, Nuwan K. Wijewardane, Huichun Zhang, Jinliang Yang, James C. Schnable, Daniel P. Schachtman, Yufeng Ge

Department of Agronomy and Horticulture: Faculty Publications

Leaf-level hyperspectral reflectance has become an effective tool for high-throughput phenotyping of plant leaf traits due to its rapid, low-cost, multi-sensing, and non-destructive nature. However, collecting samples for model calibration can still be expensive, and models show poor transferability among different datasets. This study had three specific objectives: first, to assemble a large library of leaf hyperspectral data (n=2460) from maize and sorghum; second, to evaluate two machine-learning approaches to estimate nine leaf properties (chlorophyll, thickness, water content, nitrogen, phosphorus, potassium, calcium, magnesium, and sulfur); and third, to investigate the usefulness of this spectral library for predicting external datasets …

Protecting Wa Crops Issue 29 - April 2023, Department Of Primary Industries And Regional Development, Western Australia

Protecting WA Crops

Protecting WA Crops Issue 29 - April 2023 contents:

• GRDC Perth Research Updates 2023 – Pathology and virology
• How long do sclerotinia sclerotia survive in WA?
• Insecticidal control of green peach aphid and turnip yellows virus: resistance threats, limitations, and future alternatives
• Meet Crop Protection team member – Jean Galloway

Efficacy Of Biocontrol Against Chrysomelid Pests In Lab Vs Field Studies: Potential Biases Of Setting And Phylogenetic Subgroups, Blake Hudson

2023 Midwest Ecology & Evolution Conference

The beetle family Chrysomelidae is a speciose group of voracious herbivores with a wide number of ecological implications. While some Chrysomelid species have been introduced or augmented as biological control agents of invasive plants, many other species have found success as economically important pests of field crops and stored grains, leading to severe yield losses in cucurbits, legumes, and other systems. Controlling such pests, especially in the field, is particularly difficult due to the timing of their complex life cycles, the fossorial nature of many species’ larvae, and ability to produce multiple generations in a single growing season. This study …

Experimentation On Nebraska Farms For Sustaining Soil Health Management, Fernanda Souza Krupek

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Soil health management practices have increasingly been promoted across US agroecosystems to address many interrelated environmental and economic food system challenges. Sustaining conservation behavior – through farmer’s adoption and continued use of practices – is key for achieving many soil health-related intended social-ecological benefits. Using a range of scientific methods, from lab-based experiments to on-farm research to farmer interviews, the overall objective of this dissertation research was to explore soil and human dimension considerations to design farming and knowledge transfer systems for sustaining soil health management in the US Midwest. In a multivariate analysis of ten on-farm research sites, we …

Arkansas Cotton Variety Test 2022, F. Bourland, A. Beach, B. Milano, B. Guest, C. Kennedy, L. Martin, B. Robertson

Arkansas Agricultural Experiment Station Research Series

The primary goal of the Arkansas Cotton Variety Test is to provide unbiased data regarding the agronomic performance of cotton varieties and advanced breeding lines in the major cotton-growing areas of Arkansas. This information helps seed companies establish marketing strategies and assists producers in choosing varieties to plant. These annual evaluations will then facilitate the inclusion of new, improved genetic material in Arkansas cotton production. Adaptation of varieties is determined by evaluating the lines at five University of Arkansas System Division of Agriculture research sites (Manila, Keiser, Judd Hill, Marianna, and Rohwer). The 2022 tests at Rohwer were adversely affected …

Predicting Site‑Specific Economic Optimal Nitrogen Rate Using Machine Learning Methods And On‑Farm Precision Experimentation, Alfonso De Lara, Taro Mieno, Joe D. Luck, Laila A. Puntel

Department of Agronomy and Horticulture: Faculty Publications

Applying at the economic optimal nitrogen rate (EONR) has the potential to increase nitrogen (N) fertilization efficiency and profits while reducing negative environmental impacts. On-farm precision experimentation (OFPE) provides the opportunity to collect large amounts of data to estimate the EONR. Machine learning (ML) methods such as generalized additive models (GAM) and random forest (RF) are promising methods for estimating yields and EONR. Twenty OFPE N trials in wheat and barley were conducted and analyzed with soil, terrain and remote-sensed variables to address the following objectives: (1) to quantify the spatial variability of winter crops yield and the yield response …

A Plea For Scale, And Why It Matters For Invasive Species Management, Biodiversity And Conservation, Nicholas A. Mcmillan, Samuel D. Fuhlendorf, Craig A. Davis, Robert G. Hamilton, Landon. K. Neumann, Samantha M. Cady

Department of Agronomy and Horticulture: Faculty Publications

1. Invasive species are suspected to be major contributors to biodiversity declines worldwide. Counterintuitively, however, invasive species effects are likely scale dependent and are hypothesized to be positively related to biodiversity at large spatial scales. Past studies investigating the effect of invasion on biodiversity have been mostly conducted at small scales (<100 m²) that cannot represent large dynamic landscapes by design. Therefore, replicated experimental evidence supporting a negative effect of invasive plants on biodiversity is lacking across many landscape types, including large grasslands.

2. We collected data across eight large (333–809 ha) grassland landscapes managed with pyric herbivory—that is the recoupling …

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Soil Depth And Geographic Distance Modulate Bacterial Β-Diversity In Deep Soil Profiles Throughout The U.S. Corn Belt, Lucas Dantas Lopes, Stephanie L. Futrell, Emily E. Wright, Gerasimos J. Danalatos, Michael J. Castellano, Tony J. Vyn, Sotirios V. Archontoulis, Daniel P. Schachtman

Department of Agronomy and Horticulture: Faculty Publications

Understanding how microbial communities are shaped across spatial dimensions is of fundamental importance in microbial ecology. However, most studies on soil biogeography have focused on the topsoil microbiome, while the factors driving the subsoil microbiome distribution are largely unknown. Here we used 16S rRNA amplicon sequencing to analyse the factors underlying the bacterial β-diversity along vertical (0–240 cm of soil depth) and horizontal spatial dimensions (~500,000 km²) in the U.S. Corn Belt. With these data we tested whether the horizontal or vertical spatial variation had stronger impacts on the taxonomic (Bray-Curtis) and phylogenetic (weighted Unifrac) β-diversity. Additionally, we …

Graph Convolutional Network Using Adaptive Neighborhood Laplacian Matrix For Hyperspectral Images With Application To Rice Seed Image Classification, Jairo Orozco, Vidya Manian, Estefania Alfaro, Harkamal Walia, Balpreet K. Dhatt

Department of Agronomy and Horticulture: Faculty Publications

Graph convolutional neural network architectures combine feature extraction and convolutional layers for hyperspectral image classification. An adaptive neighborhood aggregation method based on statistical variance integrating the spatial information along with the spectral signature of the pixels is proposed for improving graph convolutional network classification of hyperspectral images. The spatial-spectral information is integrated into the adjacency matrix and processed by a single-layer graph convolutional network. The algorithm employs an adaptive neighborhood selection criteria conditioned by the class it belongs to. Compared to fixed window-based feature extraction, this method proves effective in capturing the spectral and spatial features with variable pixel neighborhood …

Harvest Aids Did Not Advance Maturity Of Non-Shatter Pennycress, Julija A. Cubins, Samantha Wells, Russ W. Gesch, Gregg A. Johnson, Maninder K. Walia, Ratan Chopra, M. David Marks, Rebecca D. Swenson, Katherine Anna Frels

Department of Agronomy and Horticulture: Faculty Publications

Reliance on summer annual crops in the Upper Midwest results in fallow land from late fall through early spring, providing opportunities to integrate winter crops, such as pennycress (Thlapsi arvense L.), onto the landscape. Pennycress agronomics have primarily been studied using unimproved wild-type lines prone to seed shatter, resulting in significant yield loss if not harvested early. However, high plant and seed moisture complicates harvest and seed storage. A new breeding line with a reducedshatter mutation made it possible to use harvest aids to reduce plant moisture without the risk of seed loss. The objectives of this study were …

A Role For Heritable Transcriptomic Variation In Maize Adaptation To Temperate Environments, Guangchao Sun, Huihui Yu, Peng Wang, Martha Lopez‑Guerrero, Ravi V. Mural, Olivier N. Mizero, Marcin Grzybowski, Baoxing Song, Karin V. Van Dijk, Daniel P. Schachtman, Chi Zhang, James C. Schnable

Department of Agronomy and Horticulture: Faculty Publications

Background: Transcription bridges genetic information and phenotypes. Here, we evaluated how changes in transcriptional regulation enable maize (Zea mays), a crop originally domesticated in the tropics, to adapt to temperate environments.

Result: We generated 572 unique RNA-seq datasets from the roots of 340 maize genotypes. Genes involved in core processes such as cell division, chromosome organization and cytoskeleton organization showed lower heritability of gene expression, while genes involved in anti-oxidation activity exhibited higher expression heritability. An expression genome-wide association study (eGWAS) identified 19,602 expression quantitative trait loci (eQTLs) associated with the expression of 11,444 genes. A …

Recombination Hotspots In Soybean [Glycine Max (L.) Merr.], Samantha Mcconaughy, Keenan L. Amundsen, Qijian Song, Vince Pantalone, D. Hyten

Department of Agronomy and Horticulture: Faculty Publications

Recombination allows for the exchange of genetic material between two parents, which plant breeders exploit to make improved cultivars. This recombination is not distributed evenly across the chromosome. Recombination mostly occurs in euchromatic regions of the genome and even then, recombination is focused into clusters of crossovers termed recombination hotspots. Understanding the distribution of these hotspots along with the sequence motifs associated with them may lead to methods that enable breeders to better exploit recombination in breeding. To map recombination hotspots and identify sequence motifs associated with hotspots in soybean [Glycine max (L.) Merr.], two biparental recombinant inbred lines …

Carbon Farming: A Preliminary Economic Analysis Of Carbon Credits For No-Till And Cover Crops, Drew Havens, Richard K. Perrin, Lilyan E. Fulginiti

Cornhusker Economics

Summary Based on experimental data about the amount of carbon sequestered and estimated implementation costs, our preliminary results show that the average cost of sequestering carbon via no-till (about $22 per ton of CO₂e) appears to be much lower than the $51 per ton social value of sequestering that ton. In contrast, our preliminary results show that the average costs of sequestration via adoption of cover crops is much higher, about $60 per ton. Depending on how accurate soil carbon models are in predicting sequestration on individual fields to qualify them for enrollment, reimbursement costs for planting cover …

Large And Stable Genome Edits At The Sorghum Alpha Kafirin Locus Result In Changes In Chromatin Accessibility And Globally Increased Expression Of Genes Encoding Lysine Enrichment, J. Preston Hurst, Abou Yobi, Aixia Li, Shirley Sato, Thomas E. Clemente, Ruthie Angelovici

Department of Agronomy and Horticulture: Faculty Publications

Introduction: Sorghum is a resilient and widely cultivated grain crop used for feed and food. However, it’s grain is deficient in lysine, an essential amino acid. This is due to the primary seed storage proteins, the alpha-kafirins, lacking lysine. It has been observed that reductions in alpha-kafirin protein results in rebalancing of the seed proteome and a corresponding increase in non-kafirin proteins which leads to an increased lysine content. However, the mechanisms underlying proteome rebalancing are unclear. This study characterizes a previously developed gene edited sorghum line, with deletions at the alpha kafirin locus.

Methods: A single consensus …

Large And Stable Genome Edits At The Sorghum Alpha Kafirin Locus Result In Changes In Chromatin Accessibility And Globally Increased Expression Of Genes Encoding Lysine Enrichment, J. Preston Hurst, Abou Yobi, Aixia Li, Shirley Sato, Thomas E. Clemente, Ruthie Angelovici, David R. Holding

Department of Agronomy and Horticulture: Faculty Publications

Introduction: Sorghum is a resilient and widely cultivated grain crop used for feed and food. However, it’s grain is deficient in lysine, an essential amino acid. This is due to the primary seed storage proteins, the alpha-kafirins, lacking lysine. It has been observed that reductions in alpha-kafirin protein results in rebalancing of the seed proteome and a corresponding increase in non-kafirin proteins which leads to an increased lysine content. However, the mechanisms underlying proteome rebalancing are unclear. This study characterizes a previously developed gene edited sorghum line, with deletions at the alpha kafirin locus.

Methods: A single consensus …

An International Wheat Diversity Panel Reveals Novel Sources Of Genetic Resistance To Tan Spot In Australia, Julian Taylor, Dorthe Jorgensen, Caroline S. Moffat, Ken J. Chalmers, Rebecca Fox, Grant J. Hollaway, Melissa J. Cook, Stephen M. Neate, Pao Theen See, Manisha Shankar

Biosecurity Research Articles

Tan spot is a foliar disease in wheat caused by the fungal pathogen Pyrenophora tritici-repentis (Ptr) and has been reported to generate up to 50% yield losses under favourable disease conditions. Although farming management practices are available to reduce disease, the most economically sustainable approach is establishing genetic resistance through plant breeding. To further understand the genetic basis for disease resistance, we conducted a phenotypic and genetic analysis study using an international diversity panel of 192 wheat lines from the Maize and Wheat Improvement Centre (CIMMYT), the International Centre for Agriculture in the Dry Areas (ICARDA) and Australian (AUS) wheat …

Analysis And Installation Of A Demonstration Agroforestry Orchard For Californian Mediterranean Plant Communities, Brandon Hurd

Master of Science in Environmental Sciences and Management Projects

Climate-appropriate agroforestry can provide low-input food security and ecosystem services for local Californian Mediterranean climates, while conserving natural resources (e.g., water, nitrogen, etc.). This project showcases a variety of agroforestry methods for five common plant communities of California and other analogous Mediterranean climates at the CAFES Experimental Farm on the campus of Cal Poly San Luis Obispo. Plant community species and their ethnobotanical uses were analyzed to mimic and incorporate aspects of native flora. Agricultural plants were also characterized to represent each of the five selected plant communities. GIS was used to assess the project site for soil, slope, and …