Agronomy and Crop Sciences Commons^™

Mulch And Groundcover Effects On Soil Temperature And Moisture, Surface Reflectance, Grapevine Water Potential, And Vineyard Weed Management, Christina M. Bavougian, Paul E. Read

Department of Agronomy and Horticulture: Faculty Publications

The objectives of this research were to identify alternatives to glyphosate for intra- row (under-trellis) vineyard floor management and to evaluate the potential for intra- row and inter-row (alleyway) groundcovers to reduce vegetative vigor of `Marquette' grapevines (Vitis spp.) in a southeast Nebraska vineyard. The experiment was a randomized factorial design with five intra-row treatments (crushed glass mulch [CG], distillers' grain mulch [DG], creeping red fescue [CRF], non-sprayed control [NSC], and glyphosate [GLY]) and three inter-row treatments (creeping red fescue [CRF], Kentucky bluegrass [KB], and resident vegetation [RV]). Treatments were established in 2010-2011 and measurements were conducted during 2012 …

Unlocking The Novel Genetic Diversity And Population Structure Of Synthetic Hexaploid Wheat, Madhav Bhatta, Alexey Morgounov, Vikas Belamkar, Jesse Poland, P. Stephen Baenziger

Department of Agronomy and Horticulture: Faculty Publications

Background: Synthetic hexaploid wheat (SHW) is a reconstitution of hexaploid wheat from its progenitors (Triticum turgidum ssp. durum L.; AABB x Aegilops tauschii Coss.; DD) and has novel sources of genetic diversity for broadening the genetic base of elite bread wheat (BW) germplasm (T. aestivum L). Understanding the diversity and population structure of SHWs will facilitate their use in wheat breeding programs. Our objectives were to understand the genetic diversity and population structure of SHWs and compare the genetic diversity of SHWs with elite BW cultivars and demonstrate the potential of SHWs to broaden the genetic base …

Parallel Altitudinal Clines Reveal Trends In Adaptive Evolution Of Genome Size In Zea Mays, Paul Bilinski, Patrice S. Albert, Jeremy J. Berg, James A. Birchler, Mark N. Grote, Anne Lorant, Juvenal Quezada, Kelly Swarts, Jinliang Yang, Jeffrey Ross-Ibarra

Department of Agronomy and Horticulture: Faculty Publications

While the vast majority of genome size variation in plants is due to differences in repetitive sequence, we know little about how selection acts on repeat content in natural populations. Here we investigate parallel changes in intraspecific genome size and repeat content of domesticated maize (Zea mays) landraces and their wild relative teosinte across altitudinal gradients in Mesoamerica and South America. We combine genotyping, low coverage whole-genome sequence data, and flow cytometry to test for evidence of selection on genome size and individual repeat abundance. We find that population structure alone cannot explain the observed variation, implying that …

Can Bangladesh Produce Enough Cereals To Meet Future Demand?, J. Timsina, J. Wolf, N. Guilpart, L.G.J. Van Bussel, P. Grassini, J. Van Wart, A. Hossain, H. Rashid, S. Islam, M.K. Van Ittersum

Department of Agronomy and Horticulture: Faculty Publications

Bangladesh faces huge challenges in achieving food security due to its high population, diet changes, and limited room for expanding cropland and cropping intensity. The objective of this study is to assess the degree to which Bangladesh can be self-sufficient in terms of domestic maize, rice and wheat production by the years 2030 and 2050 by closing the existing gap (Yg) between yield potential (Yp) and actual farm yield (Ya), accounting for possible changes in cropland area. Yield potential and yield gaps were calculated for the three crops using well-validated crop models and site-specific weather,management and soil data, and upscaled …

Tetracycline And Sulfonamide Antibiotic Resistance Genes In Soils From Nebraska Organic Farming Operations, Marylynn Cadena, Lisa M. Durso, Daniel N. Miller, Heidi M. Waldrip, B. L. Castleberry, Rhae A. Drijber, Charles S. Wortmann

Department of Agronomy and Horticulture: Faculty Publications

There is widespread agreement that agricultural antibiotic resistance should be reduced, however, it is unclear from the available literature what an appropriate target for reduction would be. Organic farms provide a unique opportunity to disentangle questions of agricultural antibiotic drug use from questions of antibiotic resistance in the soil. In this study, soil was collected from 12 certified organic farms in Nebraska, evaluated for the presence of tetracycline and sulfonamide resistance genes (n = 15 targets), and correlated to soil physical, chemical, and biological parameters. Tetracycline and sulfonamide antibiotic resistance genes (ARGs) were found in soils from all 12 …

An Efficient And Improved Method For Virus-Induced Gene Silencing In Sorghum, Dharmendra Kumar Singh, Hee-Kyung Lee, Ismail M. Dweikat, Kirankumar S. Mysore

Department of Agronomy and Horticulture: Faculty Publications

Background: Although the draft genome of sorghum is available, the understanding of gene function is limited due to the lack of extensive mutant resources. Virus-induced gene silencing (VIGS) is an alternative to mutant resources to study gene function. This study reports an improved and efficient method for Brome mosaic virus (BMV)-based VIGS in sorghum.

Methods: Sorghum plants were rub-inoculated with sap prepared by grinding 2 g of infected Nicotiana benthamiana leaf in 1 ml 10 mM potassium phosphate buffer (pH 6.8) and 100 mg of carborundum abrasive. The sap was rubbed on two to three top leaves of sorghum. Inoculated …

Water Productivity Of Rainfed Maize And Wheat: A Local To Global Perspective, Juan I. Rattalino Edreira, Nicolas Guilpart, Victor Sadras, Kenneth G. Cassman, Martin K. Van Ittersum, Rene L.M. Schils, Patricio Grassini

Department of Agronomy and Horticulture: Faculty Publications

Water productivity (WP) is a robust benchmark for crop production in relation to available water supply across spatial scales. Quantifying water-limited potential (WPw) and actual on-farm (WPa) WP to estimate WP gaps is an essential first step to identify the most sensitive factors influencing production capacity with limited water supply. This study combines local weather, soil, and agronomic data, and crop modeling in a spatial framework to determine WPw and WPa at local and regional levels for rainfed cropping systems in 17 (maize) and 18 (wheat) major grain-producing countries representing a wide range of cropping systems, from intensive, highyield maize …

Isolation And Analysis Of Microbial Communities In Soil, Rhizosphere, And Roots In Perennial Grass Experiments, Morgan R. Mcpherson, Peng Wang, Robert B. Mitchell, Daniel P. Schachtman

Department of Agronomy and Horticulture: Faculty Publications

Plant and soil microbiome studies are becoming increasingly important for understanding the roles microorganisms play in agricultural productivity. The purpose of this manuscript is to provide detail on how to rapidly sample soil, rhizosphere, and endosphere of replicated field trials and analyze changes that may occur in the microbial communities due to sample type, treatment, and plant genotype. The experiment used to demonstrate these methods consists of replicated field plots containing two, pure, warm-season grasses (Panicum virgatum and Andropogon gerardii) and a low-diversity grass mixture (A. gerardii, Sorghastrum nutans, and Bouteloua curtipendula). Briefly, plants …

Mapping Rootable Depth And Root Zone Plant-Available Water Holding Capacity Of The Soil Of Sub-Saharan Africa, Johan G. B. Leenaars, Lieven Claessens, Gerard B.M. Heuvelink, Tom Hengl, Maria Ruiperez Gonzalez, Lenny G.J. Van Bussel, Nicolas Guilpart, Haishun Yang, Kenneth G. Cassman

Department of Agronomy and Horticulture: Faculty Publications

In rainfed crop production, root zone plant-available water holding capacity (RZ-PAWHC) of the soil has a large influence on crop growth and the yield response to management inputs such as improved seeds and fertilisers. However, data are lacking for this parameter in sub-Saharan Africa (SSA). This study produced the first spatially explicit, coherent and complete maps of the rootable depth and RZ-PAWHC of soil in SSA. We compiled georeferenced data from 28,000 soil profiles from SSA, which were used as input for digital soil mapping (DSM) techniques to produce soil property maps of SSA. Based on these soil properties, we …

Management And Modeling Of Winter-Time Basil Cultivars Grown With A Cap Mat System, George E. Meyer, M. Elizabeth Conley, Ellen T. Paparozzi

Department of Agronomy and Horticulture: Faculty Publications

Basil (Ocimum basilicum) is a high value crop, currently grown in the field and greenhouses in Nebraska. Winter-time, greenhouse studies were conducted during 2015 and 2016, focusing on cultivars of basil grown on a Cap MAT II® system with various levels of fertilizer application. The goal was to select high value cultivars that could be grown in Nebraska greenhouses. The studies used water content, electrical conductivity, photosynthetically active radiation (PAR), and relative humidity, air and soil media temperature sensors. Greenhouse systems can be very complex, even though controlled by mechanical heating and cooling. Uncertain or ambiguous environmental and …

Managing Grazing Lands To Improve Soils And Promote Climate Change Adaptation And Mitigation: A Global Synthesis, Marcia Delonge, Andrea D. Basche

Department of Agronomy and Horticulture: Faculty Publications

The potential to improve soils to help farmers and ranchers adapt to and mitigate climate change has generated significant enthusiasm. Within this discussion, grasslands have surfaced as being particularly important, due to their geographic range, their capacity to store substantial quantities of carbon relative to cultivated croplands and their potential role in mitigating droughts and floods. However, leveraging grasslands for climate change mitigation and adaptation will require a better understanding of how farmers and ranchers who rely on them for their livelihoods can improve management and related outcomes. To investigate opportunities for such improvements, we conducted a meta-analysis of field …

Climate Change Challenges Require Collaborative Research To Drive Agrifood System Transformation, Gabrielle E. Roesch-Mcnally, Andrea D. Basche, Rebecca Schewe

Department of Agronomy and Horticulture: Faculty Publications

The recent Climate Science Special Report released as part of the Fourth National Climate Assessment confirms that we are living through the warmest period in modern civilization and that human activities are the primary driver of this warming (Wuebbles et al., 2017). These climatic changes have and will continue to impact global agricultural production, with food security and production consequences that will be felt unequally across the planet. Agricultural activities contribute to global warming emissions, while also offering opportunities for greenhouse gas mitigation. It is clear that the agrifood system will have to adapt to a changing climate. To better …

Hunger In The Land Of Plenty: Local Responses To Food Insecurity In Iowa, Gabrielle E. Roesch-Mcnally, Jacqueline Ann Nester, Andrea D. Basche, Eric Christianson, Emily Zimmerman

Department of Agronomy and Horticulture: Faculty Publications

Story County (estimated population 92,406 in 2013) lies in the heart of central Iowa, a state renowned for its remarkable agricultural productivity. Iowa leads all states for production of corn, soybean, and hogs. Revenues from agricultural products in Iowa total more than $30 billion annually according the 2012 Agricultural Census (USDA-NASS 2014). This productivity stems from a favorable natural and political environment. The temperate climate, productive soils, and gentle topography are ideal for our production system of commodity agriculture facilitated by federal policies, which include subsidized crop insurance and commodity payments (Horrigan, Lawrence, and Walker 2002). Despite this productivity and …

Strawberry Cultivars Vary In Productivity, Sugars And Phytonutrient Content When Grown In A Greenhouse During The Winter, Ellen T. Paparozzi, George Meyer, Vicki Schlegel, Erin Blankenship, Stacy A. Adams, M. Elizabeth Conley, Benjamin A. Loseke, Paul Read

Department of Agronomy and Horticulture: Faculty Publications

In many areas of the US, fresh locally grown berries are not available during the winter. With this in mind, a research study comprised of three experiments was conducted focused on cultivar selection for berry yield, number, sweetness and phytonutrient content. Using a capillary mat system with under bench heating within a double-layer polyethylene greenhouse, strawberries were grown in the Great Plains Region of the US during the winter. During experiment 1, 12 cultivars were grown; berries were weighed, counted and analyzed for sugars and phytonutrients. “Albion” plants produced a high number/mass of berries, had relatively high sugar content but …

Social–Ecological Landscape Patterns Predict Woody Encroachment From Native Tree Plantings In A Temperate Grassland, Victoria M. Donovan, Jessica L. Burnett, Christine H. Bielski, Hannah E. Birge, Rebecca Bevans, Dirac L. Twidwell Jr, Craig R. Allen

Department of Agronomy and Horticulture: Faculty Publications

Afforestation is often viewed as the purposeful planting of trees in historically non-forested grasslands, but an unintended consequence is woody encroachment, which should be considered part of the afforestation process. In North America’s temperate grassland biome, Eastern redcedar (Juniperus virginiana L.) is a native species used in tree plantings that aggressively invades in the absence of controlling processes. Cedar is a well-studied woody encroacher, but little is known about the degree to which cedar windbreaks, which are advocated for in agroforestry programs, are contributing to woody encroachment, what factors are associated with cedar spread from windbreaks, nor where encroachment …

Optimising The Identification Of Causal Variants Across Varying Genetic Architectures In Crops, Chenyong Miao, Jinliang Yang, James C. Schnable

Department of Agronomy and Horticulture: Faculty Publications

Association studies use statistical links between genetic markers and the phenotype variation across many individuals to identify genes controlling variation in the target phenotype. However, this approach, particularly conducted on a genome-wide scale (GWAS), has limited power to identify the genes responsible for variation in traits controlled by complex genetic architectures. In this study, we employ real-world genotype datasets from four crop species with distinct minor allele frequency distributions, population structures and linkage disequilibrium patterns. We demonstrate that different GWAS statistical approaches provide favourable trade-offs between power and accuracy for traits controlled by different types of genetic architectures. FarmCPU provides …

A Novel Lidar-Based Instrument For High-Throughput, 3d Measurement Of Morphological Traits In Maize And Sorghum, Suresh Thapa, Feiyu Zhu, Harkamal Walia, Hongfeng Yu, Yufeng Ge

Department of Agronomy and Horticulture: Faculty Publications

Recently, imaged-based approaches have developed rapidly for high-throughput plant phenotyping (HTPP). Imaging reduces a 3D plant into 2D images, which makes the retrieval of plant morphological traits challenging. We developed a novel LiDAR-based phenotyping instrument to generate 3D point clouds of single plants. The instrument combined a LiDAR scanner with a precision rotation stage on which an individual plant was placed. A LabVIEW program was developed to control the scanning and rotation motion, synchronize the measurements from both devices, and capture a 360^◦ view point cloud. A data processing pipeline was developed for noise removal, voxelization, triangulation, and plant …

Empirical Comparisons Of Different Statistical Models To Identify And Validate Kernel Row Number-Associated Variants From Structured Multi-Parent Mapping Populations Of Maize, Jinliang Yang, Cheng-Ting Yeh, Raghuprakash Kastoori Ramamurthy, Xinshuai Qi, Rohan L. Fernando, Jack C. M. Dekkers, Dorian J. Garrick, Dan Nettleton, Patrick Schnable

Department of Agronomy and Horticulture: Faculty Publications

Advances in next generation sequencing technologies and statistical approaches enable genomewide dissection of phenotypic traits via genome-wide association studies (GWAS). Although multiple statistical approaches for conducting GWAS are available, the power and cross-validation rates of many approaches have been mostly tested using simulated data. Empirical comparisons of single variant (SV) and multi-variant (MV) GWAS approaches have not been conducted to test if a single approach or a combination of SV and MV is effective, through identification and cross-validation of trait-associated loci. In this study, kernel row number (KRN) data were collected from a set of 6,230 entries derived from the …

Linked Read Technology For Assembling Large Complex And Polyploid Genomes, Alina Ott, James C. Schnable, Cheng-Ting Yeh, Linjiang Wu, Chao Liu, Heng-Cheng Hu, Clifton L. Dalgard, Soumik Sarkar, Patrick Schnable

Department of Agronomy and Horticulture: Faculty Publications

Background: Short read DNA sequencing technologies have revolutionized genome assembly by providing high accuracy and throughput data at low cost. But it remains challenging to assemble short read data, particularly for large, complex and polyploid genomes. The linked read strategy has the potential to enhance the value of short reads for genome assembly because all reads originating from a single long molecule of DNA share a common barcode. However, the majority of studies to date that have employed linked reads were focused on human haplotype phasing and genome assembly.

Results: Here we describe a de novo maize B73 genome assembly …

Maize Genomes To Fields: 2014 And 2015 Field Season Genotype, Phenotype, Environment, And Inbred Ear Image Datasets, Naser Alkhalifah, Darwin A. Campbell, Celeste M. Falcon, Jack M. Gardiner, Nathan D. Miller, Maria Cinta Romay, Ramona Walls, Renee Walton, Cheng-Ting Yeh, Martin Bohn, Jessica Bubert, Edward S. Buckler, Ignacio Ciampitti, Sherry Flint-Garcia, Michael A. Gore, Christopher Graham, Candice Hirsch, James B. Holland, David Hooker, Shawn Kaeppler, Joseph Knoll, Nick Lauter, Elizabeth C. Lee, Aaron Lorenz, Jonathan P. Lynch, Stephen P. Moose, Seth C. Murray, Rebecca Nelson, Torbert Rocheford, Oscar Rodriguez, James C. Schnable, Brian Scully, Margaret Smith, Nathan Springer, Peter Thomison, Mitchell Tuinstra, Randall J. Wisser, Wenwei Xu, David Ertl, Patrick S. Schnable, Natalia De Leon, Edgar P. Spalding, Jode Edwards, Carolyn J. Lawrence-Dill

Department of Agronomy and Horticulture: Faculty Publications

Objectives: Crop improvement relies on analysis of phenotypic, genotypic, and environmental data. Given large, well-integrated, multi-year datasets, diverse queries can be made: Which lines perform best in hot, dry environments? Which alleles of specific genes are required for optimal performance in each environment? Such datasets also can be leveraged to predict cultivar performance, even in uncharacterized environments. The maize Genomes to Fields (G2F) Initiative is a multi-institutional organization of scientists working to generate and analyze such datasets from existing, publicly available inbred lines and hybrids. G2F’s genotype by environment project has released 2014 and 2015 datasets to the public, with …