Other Plant Sciences Commons^™

A Chickpea Genetic Variation Map Based On The Sequencing Of 3,366 Genomes, Rajeev K. Varshney, Manish Roorkiwal, Shuai Sun, Prasad Bajaj, Annapurna Chitikineni, Mahendar Thudi, Narendra P. Singh, Xiao Du, Hari D. Upadhyaya, Diego Jarquin

Department of Agronomy and Horticulture: Faculty Publications

Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources1 . So far, few chickpea (Cicerarietinum) germplasm accessions have been characterized at the genome sequence level2 . Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. A divergence tree using genes present in around 80% of individuals in one species allowed us to estimate the divergence of …

Global Distribution And Richness Of Armillaria And Related Species Inferred From Public Databases And Amplicon Sequencing Datasets, Rachel A. Koch, Joshua Herr

Department of Plant Pathology: Faculty Publications

Armillaria is a globally distributed fungal genus most notably composed of economically important plant pathogens that are found predominantly in forest and agronomic systems. The genus sensulato has more recently received attention for its role in woody plant decomposition and in mycorrhizal symbiosis with specific plants. Previous phylogenetic analyses suggest that around 50 species are recognized globally. Despite this previous work, no studies have analyzed the global species richness and distribution of the genus using data derived from fungal community sequencing datasets or barcoding initiatives. To assess the global diversity and species richness of Armillaria, we mined publicly available sequencing …

Using Uav Technology Paired With Multispectral Cameras To Assess Crown Rust Epidemics In Oats, Turner A. Graham

LSU Master's Theses

Crown rust, caused by Puccinia cornonata f. sp. avenae, is a common disease of oats (Avena sativa) found virtually everywhere oats are cultivated. This disease has caused yield losses of 10 to 40% worldwide. Early detection is important for effective management. A more recently utilized technology in agriculture is unmanned aerial vehicles (UAVs). UAVs, or drones, equipped with cameras are now being used as a resource to take images of fields to identify pests and other issues that may be occurring. Normalized differentiated vegetative index (NDVI) is a numerical indicator used to determine the vegetative health of …

Nebline, Nov./Dec.2021

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Holiday Food Tips

Recipes of the Month

Traditions Rituals and Routines During a COVID-19 Holiday Season

Wise Use of Private Water and Wastewater Systems Can Make the Holidays More Peaceful

Dormant Lawn Seeding

Garden Guide: Things to Do This Month

4-H Thanks 2021 Sponsors

Farmland Trends and Lease Considerations for 2022 Workshop

Upcoming Early Childhood Trainings

Ag Society Annual Election & Meeting

Heart of 4-H Volunteer Award, Jamie Wood

Heart of 4-H Volunteer Award, Julia Plugge

Slime, Jelly Worms & Goo: Food Science 4-H Workshop, Dec. 4

Finger Knit 4-H Workshop, Dec. 11

2021 4-H Horse Awards Night

4-H Announcements …

University Research On Winter Growing Of Container-Grown Strawberries Translates To Grower's Farm Trial, Stacy A. Adams, Ellen T. Paparozzi, Ryan Pekarek, Dave P. Lambe, George Meyer, M. Elizabeth Conley, Paul Read

Department of Agronomy and Horticulture: Faculty Publications

Strawberries are only seasonally available in Nebraska (NE). If an affordable heated structure can be designed, then opportunity exists to increase on-farm income by producing strawberries off-season during high-value market periods. A series of university greenhouse trials were conducted from 2010 to 2012. The varieties Evie-2 and Seascape were identified as being most productive under a low technology growing scheme. A new research project, which ran from fall to late spring (2013–2014), was designed to determine if this production scheme would translate to a commercial grower. Varieties Seascape and Evie-2 (each at two grades indicated by +) and San Andreas …

Growing Faba Beans On The South Coast Of Western Australia, Sarah Belli, Carla Milazzo, Emma Pearse, King Yin Lui, Grace Williams, Jeremy Lemon

Grain and other field crops published reports

Editors: Megan Abrahams, Andrew Blake and Vanessa Stewart (DPIRD)

Foreword

Thirty-three years ago I started work in Esperance on broadleaf crops. One of the best things my boss set up for me was arranging visits with several lupin farmers so I could follow their crops from seeding, through the growing season, to harvest. It was a great way to quickly get an idea of the choices farmers make and the reasons why.

With today’s busy lives, most farmers would be hard pressed to have the luxury of visiting many other farmers multiple times to learn how to grow a crop. …

Control Of Acetolactate Synthase Inhibitor/Glyphosate-Resistant Palmer Amaranth (Amaranthus Palmeri) In Isoxaflutole/Glufosinate/Glyphosate-Resistant Soybean, Jasmine Mausbach, Suat Irmak, Debalin Sarangi, John L. Lindquist, Amit J. Jhala

Department of Agronomy and Horticulture: Faculty Publications

Palmer amaranth is the most problematic and troublesome weed in agronomic cropping systems in the United States. Acetolactate synthase (ALS) inhibitor and glyphosate-resistant (GR) Palmer amaranth has been confirmed in Nebraska and it is widespread in several counties. Soybean resistant to isoxaflutole/glufosinate/glyphosate has been developed that provides additional herbicide site of action for control of herbicide-resistant weeds. The objectives of this study were to evaluate herbicide programs for control of ALS inhibitor/GR Palmer amaranth and their effect on Palmer amaranth density and biomass, as well as soybean injury and yield in isoxaflutole/glufosinate/glyphosate-resistant soybean. Field experiments were conducted in a grower's …

Transcriptomics Reveals The Putative Mycoparasitic Strategy Of The Mushroom Entoloma Abortivum On Species Of The Mushroom Genus Armillaria, Rachel A. Koch, Joshua Herr

Department of Plant Pathology: Faculty Publications

During mycoparasitism, a fungus—the host—is parasitized by another fungus—the mycoparasite. The genetic underpinnings of these relationships have been best characterized in ascomycete fungi. However, within basidiomycete fungi, there are rare instances of mushroom-forming species parasitizing the reproductive structures, or sporocarps, of other mushroom-forming species, which have been rarely investigated on a genetic level. One of the most enigmatic of these occurs between Entoloma abortivum and species of Armillaria, where hyphae of E. abortivum are hypothesized to disrupt the development of Armillaria sporocarps, resulting in the formation of carpophoroids. However, it remains unknown whether carpophoroids are the direct result of a …

Identification And Validation Of High Ld Hotspot Genomic Regions Harboring Stem Rust Resistant Genes On 1b, 2a (Sr38), And 7b Chromosomes In Wheat, Shamseldeen Eltaher, Amira M.I. Mourad, P Stephen Baenziger, Stephen Wegulo, Vikas Belamkar, Ahmed Sallam

Department of Agronomy and Horticulture: Faculty Publications

Stem rust caused by Puccinia graminis f. sp. tritici Eriks. is an important disease of common wheat globally. The production and cultivation of genetically resistant cultivars are one of the most successful and environmentally friendly ways to protect wheat against fungal pathogens. Seedling screening and genome-wide association study (GWAS) were used to determine the genetic diversity of wheat genotypes obtained on stem rust resistance loci. At the seedling stage, the reaction of the common stem rust race QFCSC in Nebraska was measured in a set of 212 genotypes from F3:6 lines. The results indicated that 184 genotypes (86.8%) had different …

Spatial Frameworks For Robust Estimation Of Yield Gaps, Juan I. Rattalino Edreira, José F. Andrade, Kenneth G. Cassman, Martin K. Ittersum, Marloes P. Van Loon, Patricio Grassini

Department of Agronomy and Horticulture: Faculty Publications

Food security interventions and policies need reliable estimates of crop production and the scope to enhance production on existing cropland. Here we assess the performance of two widely used ‘top-down’ gridded frameworks (Global Agro-ecological Zones and Agricultural Model Intercomparison and Improvement Project) versus an alternative ‘bottom-up’ approach (Global Yield Gap Atlas). The Global Yield Gap Atlas estimates extra production potential locally for a number of sites representing major breadbaskets and then upscales the results to larger spatial scales. We find that estimates from top-down frameworks are alarmingly unlikely, with estimated potential production being lower than current farm production at some …

Development Of A Genomic Prediction Pipeline For Maintaining Comparable Sample Sizes In Training And Testing Sets Across Prediction Schemes Accounting For The Genotype-By-Environment Interaction, Reyna Persa, Martin Grondona, Diego Jarquin

Department of Agronomy and Horticulture: Faculty Publications

The global growing population is experiencing challenges to satisfy the food chain supply in a world that faces rapid changes in environmental conditions complicating the development of stable cultivars. Emergent methodologies aided by molecular marker information such as marker assisted selection (MAS) and genomic selection (GS) have been widely adopted to assist the development of improved genotypes. In general, the implementation of GS is not straightforward, and it usually requires cross-validation studies to find the optimum set of factors (training set sizes, number of markers, quality control, etc.) to use in real breeding applications. In most cases, these different scenarios …

A Machine Learning Interpretation Of The Contribution Of Foliar Fungicides To Soybean Yield In The North‐Central United States, Denis A. Shah, Thomas R. Butts, Spyridon Mourtzinis, Juan I. Rattalino Edreira, Patricio Grassini, Shawn P. Conley, Paul D. Esker

Department of Agronomy and Horticulture: Faculty Publications

Foliar fungicide usage in soybeans in the north-central United States increased steadily over the past two decades. An agronomically-interpretable machine learning framework was used to understand the importance of foliar fungicides relative to other factors associated with realized soybean yields, as reported by growers surveyed from 2014 to 2016. A database of 2738 spatially referenced fields (of which 30% had been sprayed with foliar fungicides) was fit to a random forest model explaining soybean yield. Latitude (a proxy for unmeasured agronomic factors) and sowing date were the two most important factors associated with yield. Foliar fungicides ranked 7th out of …

A Phytobacterial Tir Domain Effector Manipulates Nad+ To Promote Virulence, Samuel Eastman, Thomas Smith, Mark A. Zaydman, Panya Kim, Samuel Martinez, Neha Damaraju, Aaron Diantonio, Jeffrey Milbrandt, Thomas E. Clemente, James R. Alfano, Ming Guo

Department of Plant Pathology: Faculty Publications

• The Pseudomonas syringae DC3000 type III effector HopAM1 suppresses plant immunity and contains a Toll/interleukin-1 receptor (TIR) domain homologous to immunity-related TIR domains of plant nucleotide-binding leucine-rich repeat receptors that hydrolyze nicotinamide adenine dinucleotide (NAD⁺) and activate immunity. In vitro and in vivo assays were conducted to determine if HopAM1 hydrolyzes NAD⁺ and if the activity is essential for HopAM1’s suppression of plant immunity and contribution to virulence.
• HPLC and LC-MS were utilized to analyze metabolites produced from NAD⁺ by HopAM1 in vitro and in both yeast and plants. Agrobacterium-mediated transient expression and in planta …

Implications Of Cover Crop Planting And Termination Timing On Rainfed Maize Production In Semi-Arid Cropping Systems, Alexandre T. Rosa, Cody Creech, Roger W. Elmore, Daran Rudnick, John L. Lindquist, Miguel Fudolig, Liberty E. Butts, Rodrigo Werle

Department of Agronomy and Horticulture: Faculty Publications

Despite the potential to increase soil organic matter, cycle soil nutrients, and suppress weeds, there is a concern that cover crops (CCs) soil water use negatively impacts subsequent crops in water-limited environments. Cover crop management practices such as planting and termination timing may mitigate the detrimental impacts of CCs in semi-arid cropping systems. To determine the effects of CCs under water-limited environments, we evaluated the total CC biomass produced in the fall and spring, soil water content during the subsequent maize growing season, weed density and biomass, crop residue, and soil nutrients at the maize V6 development stage, and maize …

Contributions Of Individual Cover Crop Species To Rainfed Maize Production In Semi-Arid Cropping Systems, Alexandre T. Rosa, Cody Creech, Roger W. Elmore, Daran Rudnick, John L. Lindquist, Liberty Butts, Italo K. Pinho De Faria, Rodrigo Werle

Department of Agronomy and Horticulture: Faculty Publications

Cover crop (CC) species selection can contribute to reducing soil penetration resistance (brassica species), improved soil nitrogen (N) cycling (legume species), and suppression of weeds (grass species). However, one of the main concerns about including CCs in water-limited environments is soil water use and the consequences to subsequent crops. To determine the effects of individual CC species under water-limited environments, we evaluated fall and spring CC biomass produced, and soil water and N content, penetration resistance, weed density and biomass during the maize growing season, and maize grain yield. The experiment was conducted under a winter wheat-maize-fallow rotation at two …

Advancing Agricultural Research Using Machine Learning Algorithms, Spyridon Mourtzinis, Paul D. Esker, James E. Specht, Shawn P. Conley

Department of Agronomy and Horticulture: Faculty Publications

Rising global population and climate change realities dictate that agricultural productivity must be accelerated. Results from current traditional research approaches are difficult to extrapolate to all possible fields because they are dependent on specific soil types, weather conditions, and background management combinations that are not applicable nor translatable to all farms. A method that accurately evaluates the effectiveness of infinite cropping system interactions (involving multiple management practices) to increase maize and soybean yield across the US does not exist. Here, we utilize extensive databases and artificial intelligence algorithms and show that complex interactions, which cannot be evaluated in replicated trials, …

Final Selection Of Quality Protein Popcorn Hybrids, Leandra Parsons, Ying Ren, Abou Yobi, Ruthie Angelovici, Oscar Rodriguez, David R. Holding

Department of Agronomy and Horticulture: Faculty Publications

Quality Protein Popcorn (QPP) BC₂F₅ inbred lines were produced through an interpopulation breeding system between Quality Protein Maize dent (QPM) and elite popcorn germplasm. In 2019, five QPP F₁ hybrids were selected for further evaluation due to superior agronomics, endosperm protein quality, and popping quality traits. Though these BC₂F₅ QPP hybrids were phenotypically similar to their popcorn parents, the QPP cultivars conveyed slightly inferior popping characteristics when compared to the original popcorn germplasm. The objective of this study was twofold. First, BC₂F₅ inbred lines were crossed to their popcorn parents …

Influence Of Planting Date, Maturity Group, Harvest Aids And Fungicide Application On Soybean (Glycine Max (L.) Seed Quality, Ana Priscila Campos

LSU Master's Theses

Field studies evaluated the influence of planting date, maturity group, and harvest timing on soybean yield and seed quality at the LSU AgCenter Northeast (NERS), Macon Ridge, and Dean Lee Research Stations in 2018-2020. In addition, the influence of harvest aid and fungicide application on seed quality impact from delayed harvest and environment was investigated at NERS in 2019 and 2020 in both field and environmentally controlled growth chambers. Soybean yield was maximized when maturity group IV and V soybean varieties were planted between Mid-April and Mid-May. Earlier and later planting dates did not result in maximized yield. Planting date …

Nebline, September/October 2021

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

4-H Youth Help Celebrate 150 Years of Lancaster County Fair

Farm to School Connections in Lancaster County

Recipe of the Month

Uses of Compost

Garden Guide: Things to Do This Month

GroBigRed Virtual Learning Series

Medically Important Spiders in Nebraska: The Black Widow and Brown Recluse

Herd Health Vaccinations

4-H Announcements for enrolled 4-H'ers or 4-H volunteers

4-H State Public Speaking Top Results

Eight Lancaster 4-H Clubs Receive Governor’s Ag Excellence Awards

Sam’s Club Donates $1,000 to 4-H Council

Heart of 4-H Volunteer Award: Tim & Jenny Higgins

Heart of 4-H Volunteer Award: JJ & Amy Frink

Youth Science Day …

Three Lc-Ms Plant Metabolomics Studies Of Hop (Humulus) Species: Wild H. Neomexicanus, Drought Stress, And Agricultural Terroir, Taylan Morcol

Dissertations, Theses, and Capstone Projects

The hop plant (Humulus L., Cannabaceae) is a dioecious, perennial, twining vine with a long history of human use. Nowadays, hop plants are generally grown for their inflorescences (“cones”), which are used in brewing for their phytochemical metabolites. Many of these metabolites are involved in plant stress response and communication. Genetics and environment are two major factors that affect plant metabolism. In three separate metabolomics studies, this project examined the effects of both genetic and environmental factors on hop phytochemistry.

In the first study, 23 hop genotypes were grown in two different locations in the Pacific Northwest region of …