Agronomy and Crop Sciences Commons^™

Improving Fertilizer Recommendations For Nepalese Farmers With The Help Of Soil-Testing Mobile Van, Sunil Pandey, Netra Prasad Bhatta, Prakash Paudel, Rajan Pariyar, Kiran Hari Maskey, Janardan Khadka, Tuk Bahadur Thapa, Balaram Rijal, Dinesh Panday

Department of Agronomy and Horticulture: Faculty Publications

Smallholder farmers dominate agriculture in Nepal. These farmers have poor knowledge about agriculture and lack of support for soil management and integrated plant-nutrient systems. Focusing on the importance and need for soil-fertility management, a soil-testing mobile van program has recently been introduced in Nepal by Soil Management Directorate, Hariharbhawan. With the introduction of the mobile lab, famers can get their soil tested for nutrient deficiencies and fertilizer requirements at their doorsteps. Using mobile lab, spatial distributions of chemical properties, including pH, organic matter (OM), total nitrogen (N), available phosphorus (as P₂O₅), and available potassium (as K …

Is Conservation Agriculture A Potential Option For Cereal-Based Sustainable Farming System In The Eastern Indo-Gangetic Plains Of Nepal?, Dipendra Pokharel, Raj Kant Jha, Thakur Prasad Tiwari, Mahesh Kumar Gathala, Hari Krishna Shrestha, Dinesh Panday

Department of Agronomy and Horticulture: Faculty Publications

A decline in land and water productivity, increase in the cost of cultivation, and labor-intensive practices are affecting the cereal-based farming system in Nepal, particularly in the Indo-Gangetic Plains (IGP). Conservation agriculture (CA) practices have been found to be the climate-, energy-, and labor-smart and sustainable agricultural production technologies. Sustainable and Resilient Farming System Intensification (SRFSI) has been working since 2014 in response to the sustainability of the cereal-based (rice–wheat and rice–maize) farming in Sunsari and Dhanusha districts of Nepal. This study was conducted to assess the adoption and scaling up of CA in addition to input usage, production, net …

Improving An Active-Optical Reflectance Sensor Algorithm Using Soil And Weather Information, G. M. Bean, N. R. Kitchen, J. J. Camberato, R. B. Ferguson, F. G. Fernandez, D. W. Franzen, C. A. M. Laboski, E. D. Nafziger, J. E. Sawyer, P. C. Scharf, J. Schepers, J. S. Shanahan

Department of Agronomy and Horticulture: Faculty Publications

Active-optical reflectance sensors (AORS) use light reflectance characteristics from a crop canopy as an indicator of the plant’s N health. However, studies have shown AORS algorithms used in conjunction with measured reflectance characteristics for corn (Zea mays L.) N fertilizer rate recommendations are not consistently accurate. Our objective was to determine if soil and weather information could be utilized with an AORS algorithm developed at the University of Missouri (ALG_MU) to improve in-season (~V9 corn development stage) N fertilizer recommendations. Nitrogen response trials were conducted across eight states over three growing seasons, totaling 49 sites with soils …

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 …

Epigenomic Plasticity Of Arabidopsis Msh1 Mutants Under Prolonged Cold Stress, Sunil Kumar Kenchanmane Raju, Mon-Ray Shao, Yashitola Wamboldt, Sally A. Mackenzie

Department of Agronomy and Horticulture: Faculty Publications

Dynamic transcriptional and epigenetic changes enable rapid adaptive benefit to environmental fluctuations. However, the underlying mechanisms and the extent to which this occurs are not well known. MutS Homolog 1 (MSH1) mutants cause heritable developmental phenotypes accompanied by modulation of defense, phytohormone, stress‐response, and circadian rhythm genes, as well as heritable changes in DNA methylation patterns. Consistent with gene expression changes, msh1 mutants display enhanced tolerance for abiotic stress including drought and salt stress, while showing increased susceptibility to freezing temperatures. Despite changes in defense and biotic stress‐response genes, msh1 mutants showed increasing susceptibility to the bacterial pathogen Pseudomonas syringae. …

Lignocellulosic-Based Bioenergy And Water Quality Parameters: A Review, Bharat Sharma Acharya, Humberto Blanco-Canqui

Department of Agronomy and Horticulture: Faculty Publications

High rates of crop residue removal as biofuel feedstocks could increase losses of nonpoint source pollutants, negatively affecting water quality. An alternative to residue removal can be growing dedicated bioenergy crops such as warm season grasses (WSGs) and short-rotation woody crops (SRWCs). Yet, our understanding of the implications of growing dedicated bioenergy crops on water quality is limited. Thus, we (i) synthesized and compared the impacts of crop residue removal, WSGs, and SRWCs on water quality parameters (i.e., sediment and nutrient runoff, and nutrient leaching) and (ii) identified research gaps for growing dedicated energy crops. Literature indicates that residue removal …

Hops On A Quarter-Acre, Stacy A. Adams

Department of Agronomy and Horticulture: Faculty Publications

This publication presents information on how to develop a quarter-acre hop yard, suitably sized to explore the unique production methods associated with this specialty crop. Emerging growers with an interest in growing hop should gain knowledge about its unique plant growth and development, culture, common pests and diseases, and harvest handling. Using information in this publication, growers should be able to experiment with hop production and harvesting so that they can develop a measured vision for future production of this crop.

Biomass Production Of Herbaceous Energy Crops In The United States: Field Trial Results And Yield Potential Maps From The Multiyear Regional Feedstock Partnership, Dokyoung Lee, Ezra Aberle, Eric K. Anderson, William Anderson, Brian S. Baldwin, David D. Baltensperger, Michael Barrett, Jurg Blumenthal, Stacy Bonos, Joe Bouton, David I. Bransby, Charlie Brummer, Pane S. Burks, Chengci Chen, Christopher Daly, Jose Egenolf, Rodney L. Farris, John H. Fike, Roch E. Gaussoin, John R. Gill, Kenneth Gravois, Michael D. Halbleib, Anna Hale, Wayne Hanna, Keith Harmoney, Emily A. Heaton, Ron W. Heiniger, Lindsey Hoffman, Chang O. Hong, Gopal Kakani, Robert Kallenbach, Bisoondat Macoon, James C. Medley, Ali Missaoui, Robert B. Mitchell, Ken J. Moore, Jesse I. Morrison, Gary N. Odvody, Jonathan D. Richwine, Richard Ogoshi, Jimmy Ray Parrish, Lauren Quinn, Ed Richard, William L. Rooney, J. Brett Rushing, Ronnie Schnell, Matt Sousek, Scott A. Staggenborg, Thomas Tew, Goro Uehara, Donald R. Viands, Thomas Voigt, David Williams, Linda Williams, Lloyd Ted Wilson, Andrew Wycislo, Yubin Yang, Vance Owens

Department of Agronomy and Horticulture: Faculty Publications

Current knowledge of yield potential and best agronomic management practices for perennial bioenergy grasses is primarily derived from small-scale and short-term studies, yet these studies inform policy at the national scale. In an effort to learn more about how bioenergy grasses perform across multiple locations and years, the U.S. Department of Energy (US DOE)/Sun Grant Initiative Regional Feedstock Partnership was initiated in 2008. The objectives of the Feedstock Partnership were to (1) provide a wide range of information for feedstock selection (species choice) and management practice options for a variety of regions and (2) develop national maps of potential feedstock …

A Transcriptome‑Snp‑Derived Linkage Map Of Apios Americana (Potato Bean) Provides Insights About Genome Re‑Organization And Synteny Conservation In The Phaseoloid Legumes, Jugpreet Singh, Scott R. Kalberer, Vikas Belamkar, Teshale Assefa, Matthew N. Nelson, Andrew D. Farmer, William J. Blackmon, Steven B. Cannon

Department of Agronomy and Horticulture: Faculty Publications

Apios (Apios americana; “apios”), a tuberous perennial legume in the Phaseoleae tribe, was widely used as a food by Native Americans. Work in the last 40 years has led to several improved breeding lines. Aspects of the pollination biology (complex floral structure and tripping mechanism) have made controlled crosses difficult, and the previous reports indicated that the plant is likely primarily an outcrosser. We used a pseudo-testcross strategy to construct a genetic map specific to the maternal parent. The map was built using single-nucleotide polymorphism markers identified by comparing the expressed sequences of individuals in the mapping population …

Enhancing Resolution Of Natural Methylome Reprogramming Behavior In Plants, Robersy Sanchez, Xiaodong Yang, Hardik Kundariya, Jose R. Barreras, Yashitola Wamboldt, Sally A. Mackenzie

Department of Agronomy and Horticulture: Faculty Publications

We have developed a novel methylome analysis procedure, Methyl-IT, based on information thermodynamics and signal detection. Methylation analysis involves a signal detection problem, and the method was designed to discriminate methylation regulatory signal from background noise induced by thermal fluctuations. Comparison with three commonly used programs and various available datasets to furnish a comparative measure of resolution by each method is included. To confirm results, methylation analysis was integrated with RNAseq and network enrichment analyses. Methyl-IT enhances resolution of genome methylation behavior to reveal network-associated responses, offering resolution of gene pathway influences not attainable with previous methods.

Assessing Explanatory Factors For Variation In On-Farm Irrigation In Us Maize-Soybean Systems, Katherine E.B. Gibson, Haishun S. Yang, Trenton E. Franz, Dean E. Eisenhauer, John B. Gates, Paolo Nasta, Bhupinder S. Farmaha, Patricio Grassini

Department of Agronomy and Horticulture: Faculty Publications

Irrigation exhibits large variation across producer fields, even within same region and year. A knowledge gap exists relative to factors that explain this variation, in part due to lack of availability of high-quality irrigation data from multiple field-years. This study assessed sources of variation in irrigation using a large database collected during 9 years (2005–2013) from ca. 1400 maize and soybean producer fields in Nebraska, central USA (total of 12,750 field-year observations). The study area is representative of ca. 4.5 million ha of irrigated land sown with maize and soybean. Influence of biophysical (weather, soil, and crop type) and behavioral …

Prospects For Increasing Sugarcane And Bioethanol Production On Existing Crop Area In Brazil, Fábio R. Marin, Geraldo B. Martha Jr., Kenneth Cassman, Patricio Grassini

Department of Agronomy and Horticulture: Faculty Publications

This article assesses sugarcane yield gaps (YG) in Brazil to determine the degree to which production can be increased without land expansion. In our scenario assessments, we evaluated how much of the projected sugarcane demand to 2024 (for both sugar and bioethanol) can be satisfied through YG closure. The current national average yield is 62% of yield potential estimated for rainfed conditions (i.e., a YG of 38%). Continuing the historical rate of yield gain is not sufficient to meet the projected demand without an area expansion by 5% and 45% for lowand high-demand scenarios, respectively. Closing the exploitable YG to …

Biomass Yield Of Warm-Season Grasses Affected By Nitrogen And Harvest Management, Chamara S. Weerasekara, Newell R. Kitchen, Shibu Jose, Peter P. Motavalli, Sougata Bardhan, Robert B. Mitchell

Department of Agronomy and Horticulture: Faculty Publications

Native perennial warm-season grasses (NPWSG) have drawn interest as bioenergy feedstocks due to their high productivity with minimal amounts of inputs under a wide range of environments. Nitrogen fertility and harvest timing are critical management practices when optimizing biomass yield of NPWSG. Our objective was to quantify the impact of N fertilizer rate and timing in combination with harvest timing and frequency on NPWSG yield. Research was conducted in 2014 and 2015 on four field-plot locations in Missouri. The experiment was a split-plot design with three replications where N rate and harvest timing were the main and sub-plot treatments, respectively. …

Mapping Rootable Depth And Root Zone Plant-Available Water Holding Capacity Of The Soil Of Sub-Saharan Africa, John 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 …

Lowland Rice Nutrient Responses For The Guinea And Sudan Savannas Of Nigeria, Christogonus K. Daudu, Enemona M. Ugbaje, Eunice Y. Oyinlola, Bitrus D. Tarfa, Adamu A. Yakubu, Ishaku Y. Amapu, Charles S. Wortmann

Department of Agronomy and Horticulture: Faculty Publications

Yield response of irrigated lowland rice (Oryza sativa L.) to nutrient application was determined to improve the information base for fertilizer use in the Sudan and Southern Guinea Savannas of Nigeria. Economically optimal rates (EOR) and agronomic efficiency (AE) were determined. Five N levels and four levels each P, K, and Zn were evaluated with two varieties at two locations. Nitrogen effects varied by variety and location but mean paddy yield with 0 kg ha^–1 N was 3.4 Mg ha^–1 and was increased by 1.3 Mg ha^–1 with 40 kg ha^–1 N. The mean EOR …

Lowland Rice Nutrient Responses For The Guinea And Sudan Savannas Of Nigeria, Christogonus K. Daudu, Enemona M. Ugbaje, Eunice Y. Oyinlola, Bitrus D. Tarfa, Adamu A. Yakubu, Ishaku Y. Amapu, Charles S. Wortmann

Department of Agronomy and Horticulture: Faculty Publications

Copyright © 2018 by the American Society of Agronomy

This is an open access article

doi:10.2134/agronj2017.08.0469

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 …

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 …

Genotype-Corrector: Improved Genotype Calls For Genetic Mapping In F2 And Ril Populations, Chenyong Miao, Jingping Fang, Delin Li, Pingping Liang, Xingtan Zhang, Jinliang Yang, James C. Schnable, Haibao Tang

Department of Agronomy and Horticulture: Faculty Publications

F₂ and recombinant inbred lines (RILs) populations are very commonly used in plant genetic mapping studies. Although genome-wide genetic markers like single nucleotide polymorphisms (SNPs) can be readily identified by a wide array of methods, accurate genotype calling remains challenging, especially for heterozygous loci and missing data due to low sequencing coverage per individual. Therefore, we developed Genotype-Corrector, a program that corrects genotype calls and imputes missing data to improve the accuracy of genetic mapping. Genotype-Corrector can be applied in a wide variety of genetic mapping studies that are based on low coverage whole genome sequencing (WGS) or Genotyping-by-Sequencing …

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 …

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 …

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 …

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 …

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 …

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 …

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 …

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 …