Agronomy and Crop Sciences Commons^™

Poisson Hurdle Model-Based Method For Clustering Microbiome Features, Zhili Qiao, Elle Barnes, Susannah Tringe, Daniel P. Schachtman, Peng Liu

Department of Agronomy and Horticulture: Faculty Publications

Motivation: High-throughput sequencing technologies have greatly facilitated microbiome research and have generated a large volume of microbiome data with the potential to answer key questions regarding microbiome assembly, structure and function. Cluster analysis aims to group features that behave similarly across treatments, and such grouping helps to highlight the functional relationships among features and may provide biological insights into microbiome networks. However, clustering microbiome data are challenging due to the sparsity and high dimensionality.

Results: We propose a model-based clustering method based on Poisson hurdle models for sparse microbiome count data. We describe an expectation–maximization algorithm and a …

Addressing Challenges Of Dryland Production Of Sunflowers And Corn In The Semi-Arid High Plains Of Nebraska, Zhan Orazov

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

Corn and sunflower are value crops for America. Cultivation of corn and sunflower often vary depending on growing environment. Selecting appropriate planting dates, hybrids and plant density frequently concerns farmers. This concern is understandable because the decision made directly impacts final income. The objectives were to evaluate interaction of corn and sunflower planting dates and hybrid maturity and evaluate interaction of corn flex hybrids and plant density under conditions of western Nebraska. Nine corn hybrids with relative maturity ranging from 86 to 105 days were sown between early May and late June in first and between late April and early …

Evaluation Of Triticale Lines Compared To Wheat Cultivars In Terms Of Agronomic Traits Using Supervised Learning Methods And Multivariate Statistics, Sara Farokhzadeh, Hossein Shahsavand Hassani

The Philippine Agricultural Scientist

The first man-made cereal grain triticale merges the yield and quality potential of wheat with tolerance of rye against environmental stresses. To find the traits with the greatest impact on the superiority of triticale over wheat, four promising triticale lines and six bread wheat varieties were evaluated in a randomized complete block design (RCBD) with three replications in the field of the Agricultural Research Station of Shiraz University, Iran. Attribute weighting algorithms revealed main leaf width (MLW), grain number per spike (GN/S), spikelet number per spike (SN/S), 1000-grain weight (TGW), plant height (PHT), main leaf length (MLL), and grain yield …

Insights On The Behavior Of Nano-Copper In The Agroecosystem: Mycorrhizal Associations With Spearmint (Mentha Spicata), Suzanne Annette Apodaca

Open Access Theses & Dissertations

Nanotechnology offers significant potential benefits to our society, including the agriculture sector. With the advancement of nano-enabled agrochemicals towards sustainable and efficient agricultural practices, it is essential to address environmental issues associated with the use of nanoscale materials. The same properties that give promise to applications of nanotechnology in modern agriculture could have unintended consequences on ecosystem dynamics. A point of concern for risk management is the impact of engineered nanomaterials (ENMs) to beneficial microbial communities, which support a variety of ecosystem services.

Use of copper (Cu) products in agriculture are based on their abundance, role as a micronutrient, and …

Arkansas Soybean Research Studies 2021, Jeremy Ross

Arkansas Agricultural Experiment Station Research Series

Arkansas is the leading soybean-producing state in the mid-southern United States. Arkansas ranked 11th in soybean production in 2021 compared to the other soybean-producing states in the U.S. The state represented 3.49% of the total U.S. soybean production and 3.49% of the total acres planted in soybean in 2021. The 2021 state soybean average yield was 52.0 bushels per acre, setting a new state record and surpassing the previous yield record of 51.5 bushels per acre set in 2020. The top five soybean-producing counties in 2021 were Mississippi, Phillips, Crittenden, Poinsett, and Arkansas (Table 1). These five counties accounted for …

Nitrification Inhibitor, Nitrogen Source, And Herbicide Effects On Soil Nitrogen Transformations And Corn Yield, William Neels

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

Nitrogen fertilizer management continue to be challenging due to potential nitrogen losses under variable weather conditions. The objective of this was to evaluate the performance of nitrification inhibitors, nitrogen sources and herbicides on in-season nitrogen availability and agronomy indicators. A two site-year field experiment was conducted in silty clay loam soil in corn phase of the corn-soybean rotation at Central Nebraska. The treatments included three herbicide (no pre-emergence, Acuron, Resicore) and five nitrogen treatments: 1) control, 2) anhydrous ammonia, 3) anhydrous ammonia without nitrification inhibitor, 4) urea with nitrification inhibitors, and 5) urea without nitrification inhibitors. Results indicated that nitrogen …

Deciphering The Genetic Architecture Of Key Female Floral Traits For Hybrid Wheat Seed Production, Juan David Jimenez

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

Wheat (Triticum aestivum L.) is a staple cereal that provides 20% of the calories and proteins in human intake (Ray et al., 2013). Global population is projected to increase to 9.7 billion by 2050. Food production must increase by 70% to feed this future population. Wheat production is in crisis due to political and environmental challenges and is projected to decline by 0.8% in 2022 (FAO, 2022). To ensure food security yield genetic gain must increase by around 1.4% annually. Taking advantage of heterosis, hybrid wheat has the potential to boost grain yield. However, hybrid wheat seed production systems …

A Glass Bead Semi-Hydroponic System For Intact Maize Root Exudate Analysis And Phenotyping, Martha G. Lopez-Guerrero, Peng Wang, Felicia Phares, Daniel P. Schachtman, Sophie Alvarez, Karin V. Van Dijk

Department of Agronomy and Horticulture: Faculty Publications

Background: Although there have been numerous studies describing plant growth systems for root exudate collection, a common limitation is that these systems require disruption of the plant root system to facilitate exudate collection. Here, we present a newly designed semi-hydroponic system that uses glass beads as solid support to simulate soil impedance, which combined with drip irrigation, facilitates growth of healthy maize plants, collection and analysis of root exudates, and phenotyping of the roots with minimal growth disturbance or root damage. Results: This system was used to collect root exudates from seven maize genotypes using water or 1 mM CaCl2, …

Comparative Genome Analysis Of Plant Ascomycete Fungal Pathogens With Different Lifestyles Reveals Distinctive Virulence Strategies, Yansu Wang, Jie Wu, Jiacheng Yan, Ming Guo, Lei Xu, Liping Hou, Quan Zou

Department of Agronomy and Horticulture: Faculty Publications

Background: Pathogens have evolved diverse lifestyles and adopted pivotal new roles in both natural ecosystems and human environments. However, the molecular mechanisms underlying their adaptation to new lifestyles are obscure. Comparative genomics was adopted to determine distinct strategies of plant ascomycete fungal pathogens with different lifestyles and to elucidate their distinctive virulence strategies. Results: We found that plant ascomycete biotrophs exhibited lower gene gain and loss events and loss of CAZyme-encoding genes involved in plant cell wall degradation and biosynthesis gene clusters for the production of secondary metabolites in the genome. Comparison with the candidate effectome detected distinctive variations between …

Biobased Sprayable Mulch Films Suppressed Annual Weeds In Vegetable Crops, Eliott Gloeb, Sibel Irmak, Loren Isom, John L. Lindquist, Samuel E. Wortman

Department of Agronomy and Horticulture: Faculty Publications

Biobased sprayable mulch (BSM) films are a potential alternative to herbicides, polyethylene plastic mulch film, and hand weeding for specialty crops. We developed a series of BSM films using locally available biomaterials [including corn (Zea mays) starch, glycerol, keratin hydrolysate, corn gluten meal, corn zein, eggshells, and isolated soy (Glycine max) protein] and tested their effects on weeds and crop yield during a total of seven greenhouse or field trials between 2017 and 2019 in Nebraska, USA. Application rates of BSM films applied in pots (greenhouse), planting holes in plastic film (field), or bed tops (field) …

Comparative Genomics Of Five Valsa Species Gives Insights On Their Pathogenicity Evolution, Guangchao Sun, Shichang Xie, Lin Tang, Chao Zhao, Mian Zhang, Lili Huang

Department of Agronomy and Horticulture: Faculty Publications

Valsa is a genus of ascomycetes within the Valsaceae family. This family includes many wood destructive pathogens such as the well known Valsa mali and Valsa pyri which cause canker diseases in fruit trees and threaten the global fruit production. Lack of genomic information of this family is impeding our understandings about their evolution and genetic basis of their pathogenicity divergence. Here, we report genome assemblies of Valsa malicola, Valsa persoonii, and Valsa sordida which represent close relatives of Valsa mali and Valsa pyri with different host preferences. Comparative genomics analysis revealed that segmental rearrangements, inversions, and translocations …

Successful Creation Of Seedless (Sterile) Leucaena Germplasm Developed From Interspecific Hybridisation For Use As Forage, Daniel Real, Clinton K. Revell Dr, Yong Han, Chengdao Li, Marieclaire Castello, C. D. Bailey

Grain and Other Field Crops Research Articles

Context: The legume shrub/tree leucaena (Leucaena leucocephala (Lam.) de Wit.) is highly regarded as a cattle fodder, although it is considered an environmental weed in many parts of Australia.

Aims: We investigated the feasibility of developing a forage variety of triploid leucaena through interspecific hybridisation that is sterile (without seeds) as a strategy to mitigate its weed risk.

Methods: A conventional breeding strategy was used to create triploid hybrids from hand-crosses between tetraploid and diploid species of leucaena. Molecular markers were developed to confirm successful crosses and flow cytometry was used to confirm the ploidy level. The plants are being …

A Non-Destructive Approach For Measuring Rice Panicle-Level Photosynthetic Responses Using 3d-Image Reconstruction, Jaspinder Singh Dharni, Balpreet Kaur Dhatt, Puneet Paul, Tian Gao, Tala Awada, Harel Bacher4, Zvi Peleg, Paul E. Staswick, Jason Hupp, Hongfeng Yu, Harkamal Walia

Department of Agronomy and Horticulture: Faculty Publications

Background: Our understanding of the physiological responses of rice inflorescence (panicle) to environmental stresses is limited by the challenge of accurately determining panicle photosynthetic parameters and their impact on grain yield. This is primarily due to the lack of a suitable gas exchange methodology for panicles and non-destructive methods to accurately determine panicle surface area.

Results: To address these challenges, we have developed a custom panicle gas exchange cylinder compatible with the LiCor 6800 Infra-red Gas Analyzer. Accurate surface area measurements were determined using 3D panicle imaging to normalize the panicle-level photosynthetic measurements. We observed differential responses in …

Bison Movements Change With Weather: Implications For Their Continued Conservation In The Anthropocene, Nicholas A. Mcmillan, Samuel D. Fuhlendorf, Barney Luttbeg, Laura E. Goodman, Craig A. Davis, Brady W. Allred, Robert G. Hamilton

Department of Agronomy and Horticulture: Faculty Publications

Animal movement patterns are affected by complex interactions between biotic and abiotic landscape conditions, and these patterns are being altered by weather variability associated with a changing climate. Some animals, like the American plains bison (Bison bison L.; hereafter, plains bison), are considered keystone species, thus their response to weather variability may alter ecosystem structure and biodiversity patterns. Many movement studies of plains bison and other ungulates have focused on point-pattern analyses (e.g., resource-selection) that have provided information about where these animals move, but information about when or why these animals move is limited. For example, information surrounding the …

The Genome Of Orychophragmus Violaceus Provides Genomic Insights Into The Evolution Of Brassicaceaepolyploidizationandits Distinct Traits, Kang Zhang, Yinqing Yang, Xin Zhang, Lingkui Zhang, Yu Fu, Zhongwei Guo, Shumin Chen, Jian Wu, James C. Schnable, Keke Yi, Xiaowu Wang, Feng Cheng

Department of Agronomy and Horticulture: Faculty Publications

Orychophragmus violaceus, referred to as ‘‘eryuelan’’ (February orchid) in China, is an early-flowering ornamental plant. The high oil content and abundance of unsaturated fatty acids in O. violaceus seeds make it a potential high-quality oilseed crop. Here, we generated a whole-genome assembly for O. violaceus using Nanopore and Hi-C sequencing technologies. The assembled genome of O. violaceus was ~1.3 Gb in size, with 12 pairs of chromosomes. Through investigation of ancestral genome evolution, we determined that the genome of O. violaceus experienced a tetraploidization event from a diploid progenitor with the translocated proto-Calepineae karyotype. Comparisons between the reconstructed subgenomes …

Novel Single-Nucleotide Variants For Morpho-Physiological Traits Involved In Enhancing Drought Stress Tolerance In Barley, Ibrahim S. Elbasyoni, Shamseldeen Eltaher, Sabah Morsy, Alsayed M. Mashaheet, Ahmed M. Abdallah, Heba G. Ali, Samah A. Mariey, P. Stephen Baenziger, Katherine Anna Frels

Department of Agronomy and Horticulture: Faculty Publications

Barley (Hordeum vulgare L.) thrives in the arid and semi-arid regions of the world; never-theless, it suffers large grain yield losses due to drought stress. A panel of 426 lines of barley was evaluated in Egypt under deficit (DI) and full irrigation (FI) during the 2019 and 2020 growing seasons. Observations were recorded on the number of days to flowering (NDF), total chlorophyll content (CH), canopy temperature (CAN), grain filling duration (GFD), plant height (PH), and grain yield (Yield) under DI and FI. The lines were genotyped using the 9K Infinium iSelect single nucleotide polymorphisms (SNP) genotyping platform, which …

Foliar Application Of Acetic Acid And Effectiveness Against Drought At Different Time Points In Soybean Development, Miranda Rudolph

Scholars Week

Abstract

Drought is arguably the most serious environmental factor affecting crop production today. A plants response to drought stress is extremely complex, affecting numerous metabolic pathways that are all interconnected in their responses. Due to this complex nature, scientists do not fully understand the implications of different treatments and how they affect these processes. Acetic acid has been shown to improve plant growth and resistance to drought stress, but exactly how it accomplishes this is also unknown. Soybeans (Glycine max) are one of the most important crops worldwide and can suffer significant yield loss due to drought stress. As climate …

Genome‑Wide Association Analyses Of Leaf Rust Resistance In Cultivated Emmer Wheat, Dhondup Lhamo, Qun Sun, Qijun Zhang, Xuehui Li, Jason D. Fiedler, Guangmin Xia, Justin D. Faris, Yong‑Qiang Gu, Upinder Gill, Xiwen Cai, Maricelis Acevedo, Steven S. Xu

Department of Agronomy and Horticulture: Faculty Publications

Leaf rust, caused by Puccinia triticina (Pt), constantly threatens durum (Triticum turgidum ssp. durum) and bread wheat (Triticum aestivum) production worldwide. A Pt race BBBQD detected in California in 2009 poses a potential threat to durum production in North America because resistance source to this race is rare in durum germplasm. To find new resistance sources, we assessed a panel of 180 cultivated emmer wheat (Triticum turgidum ssp. dicoccum) accessions for seedling resistance to BBBQD and for adult resistance to a mixture of durum-specific races BBBQJ, CCMSS, and MCDSS in the field, and genotyped …

Pestfacts Wa Issue 21 - November 2022, Cindy L. Webster, Ciara Beard, Geoff J. Thomas

PestFacts WA

PestFacts WA Issue 21 - November 2022 contents:

• Final PestFacts WA newsletter for 2022!
• Green bridge management over summer
• PestFacts WA continues successful collaboration with Agworld and Back Paddock

Pestfacts Wa Issue 20 - November 2022, Ciara Beard, Geoff J. Thomas, Dustin Severtson

PestFacts WA

PestFacts WA Issue 20 - November 2022 contents:

• Phomopsis can be a risk when grazing lupin stubble
• Meet PestFacts WA team member – Dusty Severtson

Historical Corn Price Evolution Implications For Pre-Harvest Hedging, Cory Walters, Richard K. Preston

Cornhusker Economics

Commodity markets evolve through information provided by participating buyers and sellers and throughout this process the conditions in which commodity markets work are revealed. Producer pre-harvest commodity marketing can be further developed by incorporating information on how commodity markets work, leading to better farm financial performance.

We investigate how commodity markets have historically evolved from spring to fall. While changes in future prices appear random in any given year, observing average daily prices over 32 years could uncover a seasonal tendency. In the past 32 years, the average daily price tends to be higher in the spring than the fall, …

Salt Tolerance Qtls Of An Endemic Rice Landrace, Horkuch At Seedling And Reproductive Stages, Taslima Haque, Sabrina M. Elias, Samsad Razzaque, Sudip Biswas, Sumaiya Farah Khan, G. M. Nurnabi Azad Jewel, Md. Sazzadur Rahman, Thomas E. Juenger, Zeba I. Seraj

Department of Agronomy and Horticulture: Faculty Publications

Salinity has a significant negative impact on production of rice. To cope with the increased soil salinity due to climate change, we need to develop salt tolerant rice varieties that can maintain their high yield. Rice landraces indigenous to coastal Bangladesh can be a great resource to study the genetic basis of salt adaptation. In this study, we implemented a QTL analysis framework with a reciprocal mapping population developed from a salt tolerant landrace Horkuch and a high yielding rice variety IR29. Our aim was to detect genetic loci that contributes to the salt adaptive responses of the two …

Rice Chalky Grain 5 Regulates Natural Variation For Grain Quality Under Heat Stress, Anil Kumar Nalini Chandran, Jaspreet Sandhu, Larissa Irvin, Puneet Paul, Balpreet K. Dhatt, Waseem Hussain, Tian Gao, Paul E. Staswick, Hongfeng Yu, Gota Morota, Harkamal Walia

Department of Agronomy and Horticulture: Faculty Publications

Heat stress occurring during rice (Oryza sativa) grain development reduces grain quality, which often manifests as increased grain chalkiness. Although the impact of heat stress on grain yield is well-studied, the genetic basis of rice grain quality under heat stress is less explored as quantifying grain quality is less tractable than grain yield. To address this, we used an image-based colorimetric assay (Red, R; and Green, G) for genome-wide association analysis to identify genetic loci underlying the phenotypic variation in rice grains exposed to heat stress. We found the R to G pixel ratio (RG) derived from mature …

Effect Of Water Stress On Weed Germination, Growth Characteristics, And Seed Production: A Global Meta-Analysis, Mandeep Singh, Resham Thapa, Meetpal Singh Kukal, Suat Irmak, Steven Mirsky, Amit J. Jhala

Department of Agronomy and Horticulture: Faculty Publications

Weeds compete with crops for soil moisture, along with other resources, which can impact the germination, growth, and seed production of weeds; however, this impact has not been systematically recorded and synthesized across diverse studies. To address this knowledge gap, a global meta-analysis was conducted using 1,196 paired observations from 86 published articles assessing the effect of water stress on weed germination, growth characteristics, and seed production. These studies were conducted and published during 1970 through 2020 across four continents (Asia, Australia, Europe, and North America). Imposed water stress was expressed as solution osmotic potential (ψsolution), soil water potential (ψsoil), …

Alfalfa Water Productivity And Yield Gaps In The U.S. Central Great Plains, Kaylin P. Fink, Patricio Grassini, Alexandre Rocateli, Leonardo M. Bastos, Jude Kastens, Luke P. Ryan, Xiaomao Lin, Andres Patrignani, Romulo P. Lollato

Department of Agronomy and Horticulture: Faculty Publications

Context: Yield gap (Yg) analyses using farmer-reported yield and management data have been performed for a number of annual grain crops, but it lacks for perennial forages. The U.S. accounts for 21 % of the global alfalfa production with a large rainfed area located in the central Great Plains, serving as an interesting case-study for Yg in perennial forages. Most existing alfalfa Yg analyses quantified the magnitude of the Yg but failed to identify associated management practices to reduce it. Challenging this analysis, a systematic benchmark for alfalfa water productivity [WP, kg dry matter per mm evapotranspiration (ETc)] that …

Agronomic And Quality Impact Of A Shortened Translocation For Wheat Streak Mosaic Virus Resistance, Mary J. Guttieri, Robert L. Bowden, Guorong Zhang, Scott Haley, Katherine Anna Frels, Gary L. Hein, Katherine W. Jordan

Department of Agronomy and Horticulture: Faculty Publications

Wheat streak mosaic virus (WSMV) is a mite-vectored virus with substantial economic impact on wheat production. One of the effective sources of resistance to WSMV, Wsm1, is carried on a translocation from Thinopyrum intermedium. The original whole arm form of this translocation (T4DL·4JsS) was highly effective against WSMV but carried a substantial yield penalty in the absence of the virus. Shorter recombinants of the Th. intermedium translocation are now available. This study characterized the agronomic performance of near-isogenic sib-pair families in 10 yield trials using one of these shortened T4DL·4DS-4J^sS translocations, named “rec213,” in the absence …

The Genomic And Bulked Segregant Analysis Of Curcuma Alismatifolia Revealed Its Diverse Bract Pigmentation, Xuezhu Liao, Yuanjun Ye, Xiaoni Zhang, Dan Peng, Mengmeng Hou, Gaofei Fu, Jianjun Tan, Jianli Zhao, Rihong Jiang, Yechun Xu, Jinmei Liu, Jinliang Yang, Wusheng Liu, Luke R. Tembrock, Genfa Zhu, Zhiqiang Wu

Department of Agronomy and Horticulture: Faculty Publications

Compared with most flowers where the showy part comprises specialized leaves (petals) directly subtending the reproductive structures, most Zingiberaceae species produce showy ‘‘flowers’’ through modifications of leaves (bracts) subtending the true flowers throughout an inflorescence. Curcuma alismatifolia, belonging to the Zingiberaceae family, a plant species originating from Southeast Asia, has become increasingly popular in the flower market worldwide because of its varied and esthetically pleasing bracts produced in different cultivars. Here, we present the chromosome-scale genome assembly of C. alismatifolia ‘‘Chiang Mai Pink’’ and explore the underlying mechanisms of bract pigmentation. Comparative genomic analysis revealed C. alismatifolia contains a …

Pestfacts Wa Issue 18 - October 2022, Cindy L. Webster, Svetlana Micic, Alan Lord, Ciara Beard, Andrea Hills, Daniel Huberli

PestFacts WA

PestFacts WA Issue 18 - October 2022 contents:

• Avoid snail contamination in wheat
• Be mindful of chemical withholding periods if spraying for native budworm
• Glume blotch and false (pseudo) black chaff in wheat
• Powdery mildew found in canola and lupin
• Rhizoctonia bare patches are common this year

Cyclic Adp Ribose Isomers: Production, Chemical Structures, And Immune Signaling, Mohammad K. Manik, Yun Shi, Sulin Li, Mark A. Zaydman, Neha Damaraju, Samuel Eastman, Thomas G. Smith, Weixi Gu, Veronika Masic, Tamim Mosaiab, James S. Weagley, Steven J. Hancock, Eduardo Vasquez, Lauren Hartley-Tassell, Nestoras Kargios, Natsumi Maruta, Bryan Y.J. Lim, Hayden Burdett, Michael J. Landsberg, Mark A. Schembri, Ivan Prokes, Lijiang Song, Murray Grant, Aaron Diantonio, Jeffrey D. Nanson, Ming Guo, Jeffrey Milbrandt, Thomas Ve, Bostjan Kobe

Department of Agronomy and Horticulture: Faculty Publications

Cyclic adenosine diphosphate (ADP)–ribose (cADPR) isomers are signaling molecules produced by bacterial and plant Toll/interleukin-1 receptor (TIR) domains via nicotinamide adenine dinucleotide (oxidized form) (NAD+) hydrolysis. We show that v-cADPR (2′cADPR) and v2-cADPR (3′cADPR) isomers are cyclized by O-glycosidic bond formation between the ribose moieties in ADPR. Structures of 2′cADPR-producing TIR domains reveal conformational changes that lead to an active assembly that resembles those of Toll-like receptor adaptor TIR domains. Mutagenesis reveals a conserved tryptophan that is essential for cyclization. We show that 3′cADPR is an activator of ThsA effector proteins from the bacterial antiphage defense system termed Thoeris and …

The Storm In World Fertilizer Markets Continues, John C. Beghin

Cornhusker Economics

This article updates the recent article on world fertilizer markets by Beghin and Nogueira (2021), which noted the perfect storm affecting global fertilizer markets through high demand, droughts affecting fertilizer supply, high fossil energy prices, COVID 19-related supply-chain disruptions, and trade policies, all conspiring to elevate fertilizer nominal prices to levels not seen since 2008. In the last 10 months, the Ukraine-Russia war and associated trade sanctions have exacerbated the disruptions in fossil energy, grain, vegetable oil, and fertilizer markets already present in 2021. On the more hopeful side, some United States trade policy developments will help reduce US fertilizer …