Botany 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 …

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 …

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 …

Rebecca Fillyaw Ms Thesis Data For Publication In The Journal Sustainability, Rebecca Fillyaw, Melinda Donnelly, Linda Walters

CEELAB Research Data

By combatting erosion and increasing habitat, mangrove living shorelines are an effective alternative to hard-armoring in tropical and subtropical areas. An experimental red mangrove living shoreline was deployed within Mosquito Lagoon, Florida, using a factorial design to test the impact of mangrove age, breakwater presence, and mangrove placement on mangrove survival within the first year of deployment. Mixed mangrove age treatments were included to identify if seedling (11-month-old) survival could be enhanced by the presence of transitional (23-month-old) and adult (35 to 47-month-old) mangroves. Environmental factors were monitored to detect possible causes of mangrove mortalities. Approximately half (50.6%) of mangroves …

Algal Biodiversity Survey Of The Middle Chattahoochee River Using Dna Metabarcoding, Amanda Howell

Theses and Dissertations

Aquatic plants play vital roles in water systems by providing ecological services, and one group that is understudied is algae. Algae play a crucial role in water systems as bioindicators and primary producers. They can be challenging to identify with the naked eye, so researchers have been using DNA metabarcoding, where DNA belonging to specific taxa can be isolated and identified from water samples. The objective of this study was to conduct an algal biodiversity survey on the middle Chattahoochee River system in Georgia. Water samples (1L) were filtered and sent to RTL Genomics for sequencing and processing; the data …

Effects Of Redwood Bark And Leaf Leachate On Different Lichen Populations Found Within The Redwood Forest Of Arcata, Ca, Courtney Michelle Harris, Phoebe Hughes

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

No abstract provided.

2021 Summer/Fall Newsletter, Plaster Creek Stewards

Newsletters

Highlights:

Summer Supercrew

Plaster Creek Hike + Discovery

Green Team

Diversity Training

Visit with Chariman Ron Yob

Fall Event: Environmental Justice in Our Watershed

Planting Partners

Curb Cut Rain Garden Highlight

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 …

Wildflower Pollen Quality In Roadside Habitats, With Particular Emphasis On Hedera Helix, Aoife Mcmullin, Paul Hamilton

SURE Journal: Science Undergraduate Research Experience Journal

The quality of air is of more significance today than ever before. Human population growth and pollutants emitted through fossil fuel consumption put pressures on air quality. It is widely acknowledged that atmospheric pollutants negatively impact human health; the same is also true for the health of wildlife and plants exposed to these pollutants (Brunekreef & Holgate, 2002; EEA, 2019; Schiavoni, et al., 2017). Pollen and seed formation of flowering plants have been affected when grown in areas of poor air quality (Azzazy, 2016; Sénéchal, et al., 2015). The purpose of this research was to assess pollen of …

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 …

Global Population Divergence Of A Cosmopolian Desert Plant, Victor Ryan Alfaro

Biology ETDs

Genetic and phenotypic variation can have different patterns within a species if it has populations with contrasting histories. Populations can have discrete differences that are shaped by different evolutionary scenarios, but within each population, range, or region, traits and association with fitness can also be affected by both edaphic and landscape variation. For my dissertation, I surveyed and experimentally analyzed variation and adaptive potential in Sahara mustard (Brassica tournefortii), a desert annual that has endemic, invasive, and agricultural populations in Africa, Asia, and the Americas. Although my multi-trait analysis generated complex results, my findings can be applied to …

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 …

Effects Of Micro-Rates Of 2,4-D And Dicamba On Lettuce And Pumpkin In Nebraska, Xinzheng Chen

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

Off-target herbicide injury from dicamba and 2,4-D is an increasingly common problem for specialty crop growers in the Midwestern United States. Both lettuce (Lactuca sativa L.) and pumpkin (Cucurbita spp.) are common specialty crops grown in Nebraska, and their proximity to corn and soybean production makes these crops susceptible to herbicide drift injury and yield loss. The objectives of this thesis research was to quantify crop injury and yield loss in greenhouse- and field-grown lettuce and field-grown pumpkins at different growth stages after exposure to sub-lethal doses of dicamba or 2,4-D. Dose response curves were generated to determine …

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 …

Predicting Non-Native Insect Impact: Focusing On The Trees To See The Forest, Ashley N. Schulz, Angela M. Mech, Matthew P. Ayres, Jamal J.K. Gandhi, Nathan P. Havill, Daniel A. Herms, Angela M. Hoover, Ruth A. Hufbauer, Andrew M. Liebhold, Travis D. Marsico, Kenneth F. Raffa, Patrick C. Tobin, Daniel R. Uden, Kathryn A. Thomas

Department of Agronomy and Horticulture: Faculty Publications

Non-native organisms have invaded novel ecosystems for centuries, yet we have only a limited understanding of why their impacts vary widely from minor to severe. Predicting the impact of non-established or newly detected species could help focus biosecurity measures on species with the highest potential to cause widespread damage. However, predictive models require an understanding of potential drivers of impact and the appropriate level at which these drivers should be evaluated. Here, we used non-native, specialist herbivorous insects of forest ecosystems to test which factors drive impact and if there were differences based on whether they used woody angiosperms or …