Botany Commons^™

Doublethink And Scale Mismatch Polarize Policies For An Invasive Tree, Caleb P. Roberts, Daniel R. Uden, Craig R. Allen, Dirac L. Twidwell Jr.

Department of Agronomy and Horticulture: Faculty Publications

Mismatches between invasive species management policies and ecological knowledge can lead to profound societal consequences. For this reason, natural resource agencies have adopted the scientifically-based density-impact invasive species curve to guide invasive species management. We use the density-impact model to evaluate how well management policies for a native invader (Juniperus virginiana) match scientific guidelines. Juniperus virginiana invasion is causing a sub-continental regime shift from grasslands to woodlands in central North America, and its impacts span collapses in endemic diversity, heightened wildfire risk, and crashes in grazing land profitability. We (1) use land cover data to identify the stage …

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 …

Phenotypic Data From Inbred Parents Can Improve Genomic Prediction In Pearl Millet Hybrids, Zhikai Liang, Shashi K. Gupta, Cheng-Ting Yeh, Yang Zhang, Daniel W. Ngu, Ramesh Kumar, Hemant T. Patil, Kanulal D. Mungra, Dev Vart Yadav, Abhishek Rathore, Rakesh K. Srivastava, Rajeev Gupta, Jinliang Yang, Rajeev K. Varshney, Patrick S. Schnable, James C. Schnable

Department of Agronomy and Horticulture: Faculty Publications

Pearl millet is a non-model grain and fodder crop adapted to extremely hot and dry environments globally. In India, a great deal of public and private sectors’ investment has focused on developing pearl millet single cross hybrids based on the cytoplasmic-genetic male sterility (CMS) system, while in Africa most pearl millet production relies on open pollinated varieties. Pearl millet lines were phenotyped for both the inbred parents and hybrids stage. Many breeding efforts focus on phenotypic selection of inbred parents to generate improved parental lines and hybrids. This study evaluated two genotyping techniques and four genomic selection schemes in pearl …

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 …

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 …

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 …

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 …

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 …

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 …

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 …

Quantifying Variance Across Spatial Scales As Part Of Fire Regime Classifications, Rheinhardt Scholtz, Samuel D. Fuhlendorf, Sherry A. Leis, Joshua J. Picotte, Dirac L. Twidwell Jr

Department of Agronomy and Horticulture: Faculty Publications

The emergence of large-scale fire classifications and products informed by remote sensing data has enabled opportunities to include variability or heterogeneity as part of modern fire regime classifications. Currently, basic fire metrics such as mean fire return intervals are calculated without considering spatial variance in a management context. Fire return intervals are also only applicable at a particular grain size (defined as the spatial unit of interest) even though they are typically applied homogeneously. In this study, we utilized a 29-yr fire occurrence database to show how spatial variance changes with respect to grain as postulated by Wiens (1989) when …

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 …

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 …

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 …

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 …

Phosphate Deficiency Negatively Affects Early Steps Of The Symbiosis Between Common Bean And Rhizobia, Mariel C. Isidra-Arellano, Maria Del Rocio Reyero-Saavedra, Maria Del Socorro Sanchez-Correa, Lise Pingault, Sidharth Sen, Trupti Joshi, Lourdes Girard, Norma A. Castro-Guerrero, David G. Mendoza-Cozatl, Marc Libault, Oswaldo Valdes-Lopez

Department of Agronomy and Horticulture: Faculty Publications

Phosphate (Pi) deficiency reduces nodule formation and development in different legume species including common bean. Despite significant progress in the understanding of the genetic responses underlying the adaptation of nodules to Pi deficiency, it is still unclear whether this nutritional deficiency interferes with the molecular dialogue between legumes and rhizobia. If so, what part of the molecular dialogue is impaired? In this study, we provide evidence demonstrating that Pi deficiency negatively affects critical early molecular and physiological responses that are required for a successful symbiosis between common bean and rhizobia. We demonstrated that the infection thread formation and the expression …

Increasing Predictive Ability By Modeling Interactions Between Environments, Genotype And Canopy Coverage Image Data For Soybeans, Diego Jarquin, Reka Howard, Alencar Xavier, Sruti Das Choudhury

Department of Agronomy and Horticulture: Faculty Publications

Phenomics is a new area that offers numerous opportunities for its applicability in plant breeding. One possibility is to exploit this type of information obtained from early stages of the growing season by combining it with genomic data. This opens an avenue that can be capitalized by improving the predictive ability of the common prediction models used for genomic prediction. Imagery (canopy coverage) data recorded between days 14–71 using two collection methods (ground information in 2013 and 2014; aerial information in 2014 and 2015) on a soybean nested association mapping population (SoyNAM) was used to calibrate the prediction models together …

Long-Term Winter Wheat (Triticum Aestivum L.) Seasonal Irrigation Amount, Evapotranspiration, Yield, And Water Productivity Under Semiarid Climate, Koffi Djaman, Michael O'Neill, Curtis K. Owen, Daniel Smeal, Margaret West, Dallen Begay, Samuel Allen, Komlan Koudahe, Suat Irmak, Kevin Lombard

Department of Agronomy and Horticulture: Faculty Publications

A long-term field experiment was conducted from 2002 to 2014 for the evaluation of yield and water productivity of three winter wheat varieties—Kharkof, Scout 66, and TAM107—under sprinkler irrigation at New Mexico State University Agricultural Science Center at Farmington, NM. Winter wheat daily evapotranspiration was estimated following the United Nations Food and Agriculture Organization FAO crop coefficient approach (ETc = Kc ETo), and crop water use efficiency (CWUE), evapotranspiration water use efficiency (ETWUE), and irrigation water use efficiency (IWUE) were estimated for each growing season. There was inter-annual variation in seasonal precipitation and irrigation amounts. Seasonal irrigation amounts varied from …