Agricultural Science Commons^™

Comprehensive Comparative Genomic And Transcriptomic Analyses Of The Legume Genes Controlling The Nodulation Process, Zhenzhen Qiao, Lise Pingault, Mehrnoush Nourbakhsh-Rey, Marc Libault

Department of Agronomy and Horticulture: Faculty Publications

Nitrogen is one of the most essential plant nutrients and one of the major factors limiting crop productivity. Having the goal to perform a more sustainable agriculture, there is a need to maximize biological nitrogen fixation, a feature of legumes. To enhance our understanding of the molecular mechanisms controlling the interaction between legumes and rhizobia, the symbiotic partner fixing and assimilating the atmospheric nitrogen for the plant, researchers took advantage of genetic and genomic resources developed across different legume models (e.g., Medicago truncatula, Lotus japonicus, Glycine max, and Phaseolus vulgaris) to identify key regulatory protein coding genes of the nodulation …

Comparison Of An Ultra-Low Volume (Ulv) Sprayer Against A Conventional Sprayer, For Foliar Fertiliser And Fungicide Applications In Turfgrass, Jason Connor Ferguson, Roch E. Gaussoin, John A. Eastin, Matthew D. Sousek, Greg R. Kruger

Department of Agronomy and Horticulture: Faculty Publications

Two field studies (I and II) at the University of Nebraska-Lincoln: John Seaton Anderson Turfgrass Research Facility near Mead, NE, USA, were conducted to determine if a new ultra-low volume (ULV) sprayer can apply foliar nutrient, growth regulator, and fungicide treatments, in a manner similar to that of a conventional sprayer. Treatments were applied over creeping bentgrass ‘L-93’ (Agrostis stolonifera L.) managed as a fairway at 561 l · ha⁻¹ and 47 l · ha⁻¹ with the conventional and ULV sprayer, respectfully. Data were collected for chlorophyll content with a chlorophyll meter, and for the normalised difference …

Estimated Costs Of Producing Hops In Nebraska, David P. Lambe, Stacy A. Adams

Department of Agronomy and Horticulture: Faculty Publications

Hop production opportunities exist in Nebraska given heightened interest by craft brewers for unique and locally produced hop. Farmers are additionally exploring opportunities to diversify for improved on-farm income. Strategic planning, market considerations, and having a clear plan of implementation are critical, as well as, predicting infrastructural and production costs one would expect towards planning for profitability in this specialty crop. This publication provides information on how to determine productivity, infrastructural investment, and operational costs associated with the initial development of the hop production operation.

Midwest Vegetable Trial Report For 2015, Elizabeth Maynard

Purdue Fruit and Vegetable Research Reports

This is a compilation of 19 research trial reports from six land-grant universities in the midwestern United States. Crops include bok choy, cantaloupe, cucumber, pepper, pumpkin, sweet corn, squash, tomato, and watermelon. Several crops were evaluated in high tunnels or hoophouses. Most trials evaluated different cultivars or varieties, including one investigating cantaloupe variety influence on cucumber beetle presence and incidence of bacterial wilt. Four reports addressed specific growing practices: the use of poly-coated urea to supply nitrogen to sweet corn, biochar use in a high tunnel bag culture system, use of cereal rye cover crop in butternut squash, and pollinizer …

Mini- And Heirloom Sweet Pepper Variety Performance In High Tunnels, 2015, Elizabeth Maynard, Israel S. Calsoyas

Purdue Fruit and Vegetable Research Reports

Trials on mini sweet peppers and other specialty sweet peppers in the Midwest have not recently been reported. We undertook this project to compare yield and fruit characteristics of hybrid and heirloom peppers grown in high tunnels using organic and conventional production methods.

Midwest Vegetable Trial Report For 2015, Elizabeth Maynard

Midwest Vegetable Trial Reports

This is a compilation of 19 research trial reports from six land-grant universities in the midwestern United States. Crops include bok choy, cantaloupe, cucumber, pepper, pumpkin, sweet corn, squash, tomato, and watermelon. Several crops were evaluated in high tunnels or hoophouses. Most trials evaluated different cultivars or varieties, including one investigating cantaloupe variety influence on cucumber beetle presence and incidence of bacterial wilt. Four reports addressed specific growing practices: the use of poly-coated urea to supply nitrogen to sweet corn, biochar use in a high tunnel bag culture system, use of cereal rye cover crop in butternut squash, and pollinizer …

Supersweet Sweet Corn Cultivar Evaluation For Northern Indiana, 2015, Elizabeth Maynard, Israel S. Calsoyas

Midwest Vegetable Trial Reports

This paper reports on thirteen bicolor, two yellow, and three white supersweet sweet corn entries that were evaluated at the Pinney-Purdue Agricultural Center in Wanatah, Indiana.

Mini- And Heirloom Sweet Pepper Variety Performance In High Tunnels, 2015, Elizabeth Maynard, Israel S. Calsoyas

Midwest Vegetable Trial Reports

Trials on mini sweet peppers and other specialty sweet peppers in the Midwest have not recently been reported. We undertook this project to compare yield and fruit characteristics of hybrid and heirloom peppers grown in high tunnels using organic and conventional production methods.

Supersweet Sweet Corn Cultivar Evaluation For Northern Indiana, 2015, Elizabeth Maynard, Israel S. Calsoyas

Purdue Fruit and Vegetable Research Reports

This paper reports on thirteen bicolor, two yellow, and three white supersweet sweet corn entries that were evaluated at the Pinney-Purdue Agricultural Center in Wanatah, Indiana.

Proteomic Profiling Of Maize Opaque Endosperm Mutants Reveals Selective Accumulation Of Lysine-Enriched Proteins, Kyla J. Morton, Shangang Jia, Chi Zhang, David R. Holding

Department of Agronomy and Horticulture: Faculty Publications

Reduced prolamin (zein) accumulation and defective endoplasmic reticulum (ER) body formation occurs in maize opaque endosperm mutants opaque2 (o2), floury2 (fl2), defective endosperm*B30 (DeB30), and Mucronate (Mc), whereas other opaque mutants such as opaque1 (o1) and floury1 (fl1) are normal in these regards. This suggests that other factors contribute to kernel texture. A liquid chromatography approach coupled with tandem mass spectrometry (LC-MS/MS) proteomics was used to compare non-zein proteins of nearly isogenic opaque endosperm mutants. In total, 2762 proteins were identified that were enriched for biological processes such …

Shrubland Resilience Varies Across Soil Types: Implications For Operationalizing Resilience In Ecological Restoration, Carissa L. Wonkka, Dirac L. Twidwell, Jacob B. West, William E. Rogers

Department of Agronomy and Horticulture: Faculty Publications

In ecosystems with alternative stable states, restoration success can be thought of as overcoming the resilience of an undesirable state to promote an alternative state that yields greater ecosystem services. Since greater resilience of undesirable states translates into reduced restoration potential, quantifying differences in resilience can enhance restoration planning. In the context of shrub- encroached rangeland restoration, shrubland resilience is the capacity of a woody vegetated state to absorb management interventions designed to produce a more desirable grass- dominated state, and remain within its current regime. Therefore, differences in the resilience of a state can be quantifi ed in a …

Growing Sensitivity Of Maize To Water Scarcity Under Climate Change, Qingfeng Meng, Xinping Chen, David B. Lobell, Zhenling Cui, Yi Zhang, Haishun Yang, Fusuo Zhang

Department of Agronomy and Horticulture: Faculty Publications

Climate change can reduce crop yields and thereby threaten food security. The current measures used to adapt to climate change involve avoiding crops yield decrease, however, the limitations of such measures due to water and other resources scarcity have not been well understood. Here, we quantify how the sensitivity of maize to water availability has increased because of the shift toward longer-maturing varieties during last three decades in the Chinese Maize Belt (CMB). We report that modern, longer-maturing varieties have extended the growing period by an average of 8 days and have significantly offset the negative impacts of climate change …

Information Thermodynamics Of Cytosine Dna Methylation, Robersy Sanchez Rodriguez, Sally Ann Mackenzie

Department of Agronomy and Horticulture: Faculty Publications

Cytosine DNA methylation (CDM) is a stable epigenetic modification to the genome and a widespread regulatory process in living organisms that involves multicomponent molecular machines. Genome-wide cytosine methylation patterning participates in the epigenetic reprogramming of a cell, suggesting that the biological information contained within methylation positions may be amenable to decoding. Adaptation to a new cellular or organismal environment also implies the potential for genome-wide redistribution of CDM changes that will ensure the stability of DNA molecules. This raises the question of whether or not we would be able to sort out the regulatory methylation signals from the CDM background …

Horizontal Gene Acquisitions, Mobile Element Proliferation, And Genome Decay In The Host-Restricted Plant Pathogen Erwinia Tracheiphila, Lori R. Shapiro, Erin D. Scully, Timonthy J. Straub, Jihye Park, Andrew G. Stephenson, Gwyn A. Beattie, Mark L. Gleason, Roberto Kolter, Miguel C. Coelho, Consuelo M. De Moraes, Mark C. Mescher, Olga Zhaxybayeva

Department of Agronomy and Horticulture: Faculty Publications

Modern industrial agriculture depends on high-density cultivation of genetically similar crop plants, creating favorable conditions for the emergence of novel pathogens with increased fitness in managed compared with ecologically intact settings. Here, we present the genome sequence of six strains of the cucurbit bacterial wilt pathogen Erwinia tracheiphila (Enterobacteriaceae) isolated from infected squash plants in New York, Pennsylvania, Kentucky, and Michigan. These genomes exhibit a high proportion of recent horizontal gene acquisitions, invasion and remarkable amplification of mobile genetic elements, and pseudogenization of approximately 20% of the coding sequences. These genome attributes indicate that E. tracheiphila recently emerged as a …

Herbicide Options For Effective Weed Management In Dry Directseeded Rice Under Scented Rice-Wheat Rotation Of Western Indo- Gangetic Plains, Vijay Singh, Mangi L. Jat, Zahoor A. Ganie, Bhagirath S. Chauhan, Raj K. Gupta

Department of Agronomy and Horticulture: Faculty Publications

Farmers' participatory field trials were conducted at Madhuban, and Taraori, the two participatory experimental sites/locations of the Cereal Systems Initiative for South Asia (CSISA), a collaborative project of IRRI and CIMMYT in Karnal district of Haryana, India, during Kharif (wet season) 2010 and 2011. This research aimed to evaluate preemergence (PRE) and postemergence (POST) herbicides for providing feasible and economically viable weed management options to farmers for predominant scented rice varieties. Treatments with pendimethalin PRE fb bispyribac-sodium þ azimsulfuron POST had lower weed biomass at 45 days after sowing (DAS). At Madhuban, highest grain yield of scented basmati rice (3.43 …

Prospects For Increasing Sugarcane And Bioethanol Production On Existing Crop Area In Brazil, Fabio R. Martin, Geraldo B. Martha,Jr, Kenneth G. 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 …

Glyphosate-Resistant Weed Control And Soybean Injury In Response To Different Ppo-Inhibiting Herbicides, Jatinder S. Aulakh, P. S. Chahal, Amit J. Jhala

Department of Agronomy and Horticulture: Faculty Publications

In Nebraska, 5-enolpyruvyl shikimate-3-phosphate synthase (EPSPS) as well as acetolactate synthase (ALS)-inhibitor-resistant weeds occur in many soybean fields where herbicides from these modes-of-action have been frequently used in the past. Currently, the protoporphyrinogen oxidase (PPO)-inhibitors are the only effective herbicides for POST control of both glyphosate- and ALS-inhibitor-resistant weeds in soybean. Greenhouse experiments were conducted in 2014 to evaluate the efficacy of PPO-inhibitors applied POST for the control of three glyphosate-resistant (GR) weeds and potential for soybean injury, when applied at two growth stages. All herbicide treatments controlled 10- and 20-cm tall GR common waterhemp ≥ 95% at 21 DAT. …

Estimation Of The Degree Of Diversity For Some Iraqi Wheat Varieties Through Issr, Srap And Rapd Markers, Dhafir H. Al-Kaab, Majid Sh. Hamdalla, Ismail M. Dweikat, Noora J. Al-Saedi

Department of Agronomy and Horticulture: Faculty Publications

DNA-based molecular markers such as Inter Simple Sequence Repeat (ISSR), Sequence-Related Amplified polymorphism (SRAP) and Random Amplified Polymorphic DNA (RAPD) were used in this study to examine the genetic differences among sixteen Iraqi wheat varieties. Seventy three primers out of 177 were reproducible and showed clear amplified bands. The degree of genetic diversity, Polymorphism information content (PIC) and resolving power (RP) were estimated. All the studied molecular markers were informative and showed good ability to classify and distinguish 16 wheat varieties. Total number of polymorphic bands is 134, 221 and 55 for ISSR, SRAP and RAPD respectively. PIC and RP …

Nutrients In The Nexus, Eric A. Davidson, Rachel L. Nifong, Richard B. Ferguson, Cheryl Palm, Deanna L. Osmond, Jill S. Baron

Department of Agronomy and Horticulture: Faculty Publications

Synthetic nitrogen (N) fertilizer has enabled modern agriculture to greatly improve human nutrition during the twentieth century, but it has also created unintended human health and environmental pollution challenges for the twentyfirst century. Averaged globally, about half of the fertilizer-N applied to farms is removed with the crops, while the other half remains in the soil or is lost from farmers’ fields, resulting in water and air pollution. As human population continues to grow and food security improves in the developing world, the dual development goals of producing more nutritious food with low pollution will require both technological and socioeconomic …

The C-Terminal Motif Of Siago1b Is Required For The Regulation Of Growth, Development And Stress Responses In Foxtail Millet (Setaria Italica (L.) P. Beauv), Xiaotong Liu, Sha Tang, Guanqing Jia, James C. Schnable, Haixia Su, Chanjuan Tang, Hui Zhi, Xianmin Diao

Department of Agronomy and Horticulture: Faculty Publications

Foxtail millet (Setaria italica (L.) P. Beauv), which belongs to the Panicoideae tribe of the Poaceae, is an important grain crop widely grown in Northern China and India. It is currently developing into a novel model species for functional genomics of the Panicoideae as a result of its fully available reference genome sequence, small diploid genome (2n=18, ~510 Mb), short life cycle, small stature and prolific seed production. Argonaute 1 (AGO1), belonging to the argonaute (AGO) protein family, recruits small RNAs and regulates plant growth and development. Here, we characterized an AGO1 mutant (siago1b) in foxtail millet, which …

Genomic Prediction Models For Grain Yield Of Spring Bread Wheat In Diverse Agro-Ecological Zones, C. Saint Pierre, Juan Burgueño, Jose Crossa, G. Fuentes Dávila, P. Figueroa López, E. Solís Moya, J. Ireta Moreno, V. M. Hernández Muela, V. M. Zamora Villa, P. Vikram, K. Mathews, C. Sansaloni, D. Sehgal, Diego Jarquin, P. Wenzl, Sukhwinder Singh

Department of Agronomy and Horticulture: Faculty Publications

Genomic and pedigree predictions for grain yield and agronomic traits were carried out using high density molecular data on a set of 803 spring wheat lines that were evaluated in 5 sites characterized by several environmental co-variables. Seven statistical models were tested using two random cross-validations schemes. Two other prediction problems were studied, namely predicting the lines’ performance at one site with another (pairwise-site) and at untested sites (leave-one-site-out). Grain yield ranged from 3.7 to 9.0 t ha⁻¹ across sites. The best predictability was observed when genotypic and pedigree data were included in the models and their interaction with …

Genomic Prediction Of Gene Bank Wheat Landraces, José Crossa, Diego Jarquin, Jorge Franco, Paulino Pérez-Rodríguez, Juan Burgueño, Carolina Saint-Pierre, Prashant Vikram, Carolina Sansaloni, Cesar Petroli, Denis Akdemir, Clay Sneller, Matthew Reynolds, Maria Tattaris, Thomas Payne, Carlos Guzman, Roberto J. Peña, Peter Wenzl, Sukhwinder Singh

Department of Agronomy and Horticulture: Faculty Publications

This study examines genomic prediction within 8416 Mexican landrace accessions and 2403 Iranian landrace accessions stored in gene banks. The Mexican and Iranian collections were evaluated in separate field trials, including an optimum environment for several traits, and in two separate environments (drought, D and heat, H) for the highly heritable traits, days to heading (DTH), and days to maturity (DTM). Analyses accounting and not accounting for population structure were performed. Genomic prediction models include genotype × environment interaction (G × E). Two alternative prediction strategies were studied: (1) random cross-validation of the data in 20% training (TRN) and 80% …

Registration Of ‘Ne05548’ (Husker Genetics Brand Panhandle) Hard Red Winter Wheat, P. Stephen Baenziger, R. A. Graybosch, T. Regassa, R. N. Klein, Greg R. Kruger, D. K. Santra, L. Xu, D. J. Rose, S. N. Wegulo, Y. Jin, J. Kolmer, G. L. Hein, M.-S. Chen, G. Bai, R. L. Bowden, J. Poland

Department of Agronomy and Horticulture: Faculty Publications

Western Nebraska wheat producers and those in adjacent areas want taller wheat (Triticum aestivum L.) cultivars that retain their height under drought for better harvestability. ‘NE05548’ (Reg. No. CV-1117, PI 670462) hard red winter wheat was developed cooperatively by the Nebraska Agricultural Experiment Station and the USDA-ARS and released in January 2014 by the developing institutions. NE05548 was released primarily for its superior performance under rainfed conditions in western Nebraska and adjacent areas of the Great Plains and its tall plant stature. NE05548 was selected from the cross NE97426/NE98574 made in 1999 where the pedigree of NE97426 is ‘Brigantina’/2*‘Arapahoe’ …

Multi-Population Selective Genotyping To Identify Soybean [Glycine Max (L.) Merr.] Seed Protein And Oil Qtls, Piyaporn Phansak, Watcharin Soonsuwon, David L. Hyten, Qijian Song, Perry B. Cregan, George L. Graef, James E. Specht

Department of Agronomy and Horticulture: Faculty Publications

Plant breeders continually generate ever-higher yielding cultivars, but also want to improve

seed constituent value, which is mainly protein and oil, in soybean [Glycine max (L.) Merr.]. Identification of genetic loci governing those two traits would facilitate that effort. Though genome-wide association offers one such approach, selective genotyping of multiple biparental populations offers a complementary alternative, and was evaluated here, using 48 F2:3 populations (n = ~224 plants) created by mating 48 high protein germplasm accessions to cultivars of similar maturity, but with normal seed protein content. All F2:3 progeny were phenotyped for seed protein and oil, but only …

Accuracy Of Genomic Prediction In Switchgrass (Panicum Virgatum L.) Improved By Accounting For Linkage Disequilibrium, Guillaume P. Ramstein, Joseph Evans, Shawn M. Kaeppler, Robert B. Mitchell, Kenneth P. Vogel, C. Robin Buell, Michael D. Casler

Department of Agronomy and Horticulture: Faculty Publications

Switchgrass is a relatively high-yielding and environmentally sustainable biomass crop, but further genetic gains in biomass yield must be achieved to make it an economically viable bioenergy feedstock. Genomic selection (GS) is an attractive technology to generate rapid genetic gains in switchgrass, and meet the goals of a substantial displacement of petroleum use with biofuels in the near future. In this study, we empirically assessed prediction procedures for genomic selection in two different populations, consisting of 137 and 110 half-sib families of switchgrass, tested in two locations in the United States for three agronomic traits: dry matter yield, plant height, …

Root Biomass And Soil Carbon Response To Growing Perennial Grasses For Bioenergy, Leonard C. Kibet, Humberto Blanco-Canqui, Robert B. Mitchell, Walter H. Schacht

Department of Agronomy and Horticulture: Faculty Publications

Background: Dedicated bioenergy crops such as switchgrass (Panicum virgatum L.), miscanthus [Miscanthus x giganteus (Mxg)], indiangrass [Sorghastrum nutans (L.) Nash], and big bluestem (Andropogon gerardii Vitman) can provide cellulosic feedstock for biofuel production while maintaining or improving soil and environmental quality. To better understand bioenergy crop effects on soils, we studied changes in soil properties of a Tomek silt loam under inorganic fertilization of switchgrass after 4 years and warm-season grass monocultures and mixtures after 6 years in eastern Nebraska.

Methods: The first experiment had two study factors: two switchgrass harvest dates (August and …

Alkaline Stress And Iron Deficiency Regulate Iron Uptake And Riboflavin Synthesis Gene Expression Differently In Root And Leaf Tissue: Implications For Iron Deficiency Chlorosis, En-Jung Hsieh, Brian M. Waters

Department of Agronomy and Horticulture: Faculty Publications

Iron (Fe) is an essential mineral that has low solubility in alkaline soils, where its deficiency results in chlorosis. Whether low Fe supply and alkaline pH stress are equivalent is unclear, as they have not been treated as separate variables in molecular physiological studies. Additionally, molecular responses to these stresses have not been studied in leaf and root tissues simultaneously. We tested how plants with the Strategy I Fe uptake system respond to Fe deficiency at mildly acidic and alkaline pH by measuring root ferric chelate reductase (FCR) activity and expression of selected Fe uptake genes and riboflavin synthesis genes. …

Multi-Phase Us Spread And Habitat Switching Of A Post-Columbian Invasive, Sorghum Halepense, U. Uzay Sezen, Jacob N. Barney, Daniel Z. Atwater, Gary A. Pederson, Jeffrey F. Pedersen, J. Mike Chandler, T. Stan Cox, Sheila Cox, Peter Dotray, David Kopec, Steven E. Smith, Jill Schroeder, Steven D. Wright, Yuannian Jiao, Wenqian Kong, Valorie Goff, Susan Auckland, Lisa K. Rainville, Gary J. Pierce, Cornelia Lemke, Rosana Compton, Christine Phillips, Alexandra Kerr, Matthew Mettler, Andrew H. Paterson

Department of Agronomy and Horticulture: Faculty Publications

Johnsongrass (Sorghum halepense) is a striking example of a post-Columbian founder event. This natural experiment within ecological time-scales provides a unique opportunity for understanding patterns of continent-wide genetic diversity following range expansion. Microsatellite markers were used for population genetic analyses including leaf-optimized Neighbor-Joining tree, pairwise FST, mismatch analysis, principle coordinate analysis, Tajima's D, Fu's F and Bayesian clusterings of population structure. Evidence indicates two geographically distant introductions of divergent genotypes, which spread across much of the US ingeophylogeny, gene flow patterns can be inferred to have involved five phases. Centers of genetic diversity have shifted from two introduction …

Genomic Prediction Of Single Crosses In The Early Stages Of A Maize Hybrid Breeding Pipeline, Dnyaneshwar C. Kadam, Sarah M. Potts, Martin O. Bohn, Alexander E. Lipka, Aaron J. Lorenz

Department of Agronomy and Horticulture: Faculty Publications

Prediction of single-cross performance has been a major goal of plant breeders since the beginning of hybrid breeding. Recently, genomic prediction has shown to be a promising approach, but only limited studies have examined the accuracy of predicting single-cross performance. Moreover, no studies have examined the potential of predicting single crosses among random inbreds derived from a series of biparental families, which resembles the structure of germplasm comprising the initial stages of a hybrid maize breeding pipeline. The main objectives of this study were to evaluate the potential of genomic prediction for identifying superior single crosses early in the hybrid …

The Draft Genome Of The C3 Panicoid Grass Species Dichanthelium Oligosanthes, Anthony J. Studer, James C. Schnable, Sarit Weissmann, Allison R. Kolbe, Michael R. Mckain, Ying Shao, Asaph B. Cousins, Elizabeth A. Kellogg, Thomas P. Brutnell

Department of Agronomy and Horticulture: Faculty Publications

Background: Comparisons between C₃ and C₄ grasses often utilize C₃ species from the subfamilies Ehrhartoideae or Pooideae and C₄ species from the subfamily Panicoideae, two clades that diverged over 50 million years ago. The divergence of the C₃ panicoid grass Dichanthelium oligosanthes from the independent C₄ lineages represented by Setaria viridis and Sorghum bicolor occurred approximately 15 million years ago, which is significantly more recent than members of the Bambusoideae, Ehrhartoideae, and Pooideae subfamilies. D. oligosanthes is ideally placed within the panicoid clade for comparative studies of C₃ and C₄ grasses.

Results: …