Agricultural Science Commons^™

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 …

Proceedings Of The 43rd Annual Meeting, Southern Soybean Disease Workers (March 9-10, 2016, Pensacola Beach, Florida), Trey Price, Tom Allen, Travis Faske, Eduardo Chagas Da Silva

Southern Soybean Disease Workers: Conference Proceedings

Contents

Schedule

Southern United States Soybean Disease Loss Estimates for 2015. TW Allen, CA Bradley, JP Damicone, NS Dufault, TR Faske, CA Hollier, T Isakeit, RC Kemerait, NM Kleczewski, SR Koenning, HL Mehl, JD Mueller, C Overstreet, PP Price, EJ Sikora, TN Spurlock, and H Young

Soilborne Disease Symposium (Tom Allen, moderator)

Integrated management of sudden death syndrome. D Mueller, L Leandro, Y Kandel, C Bradley, M Chilvers, A Tenuta, and K Wise

Field screening for stem canker: an outdated exercise or a necessary service for soybean growers? K Rowe and T Kirkpatrick

Nematode associated diseases in soybean. C Overstreet, …

Arsenic Analysis: Comparative Arsenic Groundwater Concentration In Relation To Soil And Vegetation, Rominna E. Valentine Vecorena

Electronic Theses, Projects, and Dissertations

Arsenic (As) is a toxic semi-metallic element found in groundwater, soils, and plants. Natural and anthropogenic sources contribute to the distribution of arsenic in the environment. Arsenic’s toxic and mobile behavior is associated with its speciation ability. There are two types of arsenic available to the environment, inorganic and organic arsenic. Of the two, inorganic arsenic is more toxic to humans and more mobile in the environment. Two inorganic compounds responsible for arsenic contamination are trivalent arsenite, As (III), and pentavalent arsenate, As (V). Trivalent arsenate is considered to be more soluble, toxic, and mobile than pentavalent arsenate. Arsenic’s absorptive …

Ws-2 Introgression In A Proportion Of Arabidopsis Thaliana Col-0 Stock Seed Produces Specific Phenotypes And Highlights The Importance Of Routine Genetic Verification, Mon-Ray Shao, Vikas Shedge, Hardik Kundariya, Fredric R. Lehle, Sally Ann Mackenzie

Department of Agronomy and Horticulture: Faculty Publications

Arabidopsis thaliana is an important model organism with a robust network of resources that has been of enormous value to the plant science research community. The use of isogenic material as a reference point or control is critical for many types of experiments in plant molecular biology and genetics. Recently, we noticed that some seed from a common source of the widely used Columbia-0 (Col-0) strain gave rise to plants showing features atypical for this strain. Whole-genome DNA-sequencing and allelespecific PCR assays confirmed that the abnormal individuals contain multiple introgressions from the ecotype Wassilewskija-2 (Ws-2), as described below. This …

Student-Conducted Farmer Video Interviews, Jenn K. Simons, Justin Van Wart, Charles Francis, Kristyn Harms

Department of Agronomy and Horticulture: Faculty Publications

High school agricultural education teachers have expressed concern about the lack of easily accessible educational materials dealing with contemporary topics in sustainable agriculture. There are numerous textbooks and monographs available for farmers and students at the college level, including the highly practical resources available from the Sustainable Agriculture Research and Education (SARE) book series on soil fertility (Magdoff and van Es, 2010), cover crops (Bowman et al., 2007) and building a farm business (DiGiacomo et al., 2003), among others. Although these are full of color photos and easily accessible graphs and tables, they are still in the print media category. …

Impact Assessment Of Integrated Pest Management (Ipm) Strategy For Suppression Of Mango-Infesting Fruit Flies In Kenya, Beatrice W. Muriithi, Hippolyte D. Affognon, Gracious M. Diiro, Sarah W. Kingori, Chrysantus M. Tanga, Peterson W. Nderitu, Samira A. Mohamed, Sunday Ekesi

All Peer-Reviewed Publications

We utilized two waves of data collected from a sample of mango farmers in Meru County in Kenya to evaluate the impact of Integrated Pest Management (IPM) strategy for controlling fruit flies in mango-production. We specifically explored the effect of five IPM practices including parasitoids (p) and Metarhizium anisopliae-based biopesticides (biop), orchard sanitation (os), spot spray of food bait (fb) and male annihilation technique (mat) on three outcome indicators: farmer pesticide expenditure, farm-level mango fruit yield losses and profit. We fitted difference-in-difference and household fixed effects regression models that account for unobserved heterogeneity across households. Our estimates differentiated the impact …

Comparative Evaluation Of The Effect Of Methyl Bromide Fumigation And Phytosanitary Irradiation On The Quality Of Fresh Strawberries, Tamar Serapian, Anuradha Prakash

Food Science Faculty Articles and Research

Fresh strawberries are highly perishable and have a short shelf-life especially when the cold chain is not maintained. Strawberries exported to Asia are currently fumigated with methyl bromide for phytosanitary purposes, which exposes strawberries to warm temperatures for several hours and air freight without temperature control, resulting in a shelf life of just a few days in the destination country. Irradiation offers an efficacious alternative to fumigation and can be performed on cold fruit. This study was conducted to compare the quality of strawberries subject to methyl bromide fumigation or irradiation followed by simulated commercial air freight shipment of strawberries …

Review Of Land Capability Assessment For The Swan Valley, Peter Tille, Angela Stuart-Street

Resource management technical reports

Land capability review for the Swan Valley.

The land capability review of the Swan Valley examined and updated previous soil and capability studies done in the area, which are still considered highly relevant for the planning requirements of the Swan Valley. As a result we have updated information on the potential for irrigated agriculture in the Swan Valley which will guide decision-making in the future.

This review uses a modified version of a new approach to presenting information for land use planning, developed by DAFWA in the Mid West region.

The main findings of the review include:

• The alluvial terraces …

Arkansas Cotton Variety Test 2015, Fred Bourland, A. Beach, C. Kennedy, L. Martin, A. Rouse, B. Robertson

Arkansas Agricultural Experiment Station Research Series

The primary goal of the Arkansas Cotton Variety Test is to provide unbiased data regarding the agronomic performance of cotton varieties and advanced breeding lines in the major cotton-growing areas of Arkansas. This information helps seed companies establish marketing strategies and assists producers in choosing varieties to plant. These annual evaluations will then facilitate the inclusion of new, improved genetic material in Arkansas cotton production.

Influence Of Temperature On Intra- And Interspecific Resource Utilization Within A Community Of Lepidopteran Maize Stemborers, Eric Siaw Ntiri, Paul Andre Calatayud, Johnnie Van Den Berg, Fritz Schulthess, Bruno Pierre Le Ru

All Peer-Reviewed Publications

Competition or facilitation characterises intra- And interspecific interactions within communities of species that utilize the same resources. Temperature is an important factor influencing those interactions and eventual outcomes. The noctuid stemborers, Busseola fusca and Sesamia calamistis and the crambid Chilo partellus attack maize in sub-Saharan Africa. They often occur as a community of interacting species in the same field and plant at all elevations. The influence of temperature on the intra- And interspecific interactions among larvae of these species, was studied using potted maize plants exposed to varying temperatures in a greenhouse and artificial stems kept at different constant temperatures …

Developing And Deploying Insect Resistant Maize Varieties To Reduce Pre-And Post-Harvest Food Losses In Africa, Tadele Tefera, Stephen Mugo, Yoseph Beyene

All Peer-Reviewed Publications

Maize grain yield in Africa is low, 1.5 t ha−1 compared to the global average of 4.9 t ha−1. Maize production in Africa is constrained by various abiotic (drought, soil fertility) and biotic factors (insect pests, weeds and diseases). Stem borers and postharvest insect pests play considerable roles in reducing maize yield through damaging the leaves, stems, ears, and kernels. Stem borers can cause 10–15 % yield losses while the postharvest insect pests, particularly, the larger grain borer and maize weevil, can cause 14–36 % grain losses. The use of chemical insecticides has been recommended; however, in addition to health …

Winter Cover Crops Impact On The Distribution Of Soil Inorganic Nitrogen And Subsequent Crop Uptake And Yield Following Fall Applied Anhydrous Ammonium, William Travis Deppe

Theses and Dissertations

The pairing of cover crops with spring application of nitrogen has shown improved nitrogen efficiency in corn production systems. However, studies have shown that only 50% of central Illinois farmers practice spring application of nitrogen. Furthermore, the literature demonstrates that in years with above average rainfall, fall applied N management systems are more susceptible to N loading relative to spring systems. Therefore, the objective of this research was to determine the efficacy of winter cover crops to impact the distribution of soil inorganic N following fall applied anhydrous ammonium. The experimental site is located at the Illinois State University Research …

Corn Era Hybrid Response To Nitrogen Fertilization, Krishna P. Woli, Matthew J. Boyer, Roger Wesley Elmore, John E. Sawyer, Lori J. Abendroth, Daniel W. Barker

Department of Agronomy and Horticulture: Faculty Publications

Corn (Zea mays L.) N use is of continued interest due to agronomic performance and environmental issues. This 2-yr study evaluated era hybrid response to fertilizer nitrogen (FN) rate in a factorial arrangement of one popular hybrid per five decades (1960–2000 eras) and five N rates (0–224 kg N ha^–1). An additional hybrid per era was grown at 168 kg N ha^–1. Hybrid productivity and nitrogen use efficiency (NUE) increased across the eras, but not between the 1980 and 1990 eras. Grain yield (GY) increased 65% and total plant biomass 43%, however, total plant nitrogen …

Growing Potato Profitably For Organic Dry Matter Production In Western Nebraska, Alexander Pavlista, Jessica J. Groskopf

Panhandle Research and Extension Center

Growing potato conventionally for dehydration is not economically feasible. The key cost would be seed under organic farming. The objective is to identify seed-piece sizes and spacings producing a profitable return for potato dehydration in western Nebraska. Atlantic potatoes were grown under dryland conditions using organic practices. Rain was 205, 270, and 360 mm in 2013, 2014, and 2015. Seed-pieces were hand-cut into five weights from 42.5 to 85.0 g and planted in five spacings from 15.2 to 45.7 cm. Seeding rates were 1.02 to 6.1 Mg/ha. Yield was highest at the spacing of 15.2 cm (16.1 Mg/ha) and decreased …

Post Weaning Supplementation Of April-Born Polypay And White Dorper Lambs Grazing Alfalfa/Orchardgrass Pasture, Lauren N. Wood

Theses and Dissertations--Animal and Food Sciences

The effect of post-weaning supplementation of April-born Polypay and White Dorper lambs grazing alfalfa/orchardgrass pasture during two grazing seasons from June to September was studied. One hundred seventy Polypay and 133 White Dorper lambs were randomly allotted to supplemented (2% BW daily) and unsupplemented groups. It was discovered that Polypay lambs weighed more than White Dorpers at wearning, when the grazing season began, and at the end of the 80 (Year 1) and 85 (Year 2) grazing season (P < 0.01). Polypay lambs gained faster (P < 0.01) than White Dorpers. Supplemented lambs gained faster (P < 0.01) than unsupplemented and Polypays had a greater response to supplementation (P < 0.01) than White Dorpers. Polypays had higher (P < 0.01) fecal egg counts, an indicator of Haemonchus contortus infestation. Supplementation did not have any consistent effect on reducing Haemonchus contortus infestation. Differences in forage characteristics of Polypay and White Dorper lambs did appear. Differences in alfalfa and orchardgrass dry matter, neutral detergent fiber, acid detergent fiber, and crude protein availability were measured by subtracting enter from exit availabilities. The largest decrease of alfalfa components from exit to enter was found with unsupplemented Polypays. No consistent effect was found for orchardgrass components.

Mapping Qtls And Association Of Differentially Expressed Gene Transcripts For Multiple Agronomic Traits Under Different Nitrogen Levels In Sorghum, Malleswari Gelli, Sharon E. Mitchell, Kan Liu, Thomas E. Clemente, Donald P. Weeks, Chi Zhang, David R. Holding, Ismail M. Dweikat

Department of Agronomy and Horticulture: Faculty Publications

Background: Sorghum is an important C₄ crop which relies on applied Nitrogen fertilizers (N) for optimal yields, of which substantial amounts are lost into the atmosphere. Understanding the genetic variation of sorghum in response to limited nitrogen supply is important for elucidating the underlying genetic mechanisms of nitrogen utilization.

Results: A bi-parental mapping population consisting of 131 recombinant inbred lines (RILs) was used to map quantitative trait loci (QTLs) influencing different agronomic traits evaluated under normal N (100 kg.ha⁻¹ fertilizer) and low N (0 kg.ha⁻¹ fertilizer) conditions. A linkage map spanning 1614 cM was developed …

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 …

Simulating Long-Term Impacts Of Cover Crops And Climate Change On Crop Production And Environmental Outcomes In The Midwestern United States, Andrea D. Basche, Sotririos V. Archontoulis, Thomas C. Kaspar, Dan B. Jaynes, Timothy B. Parkin, Fernando E. Miguez

Department of Agronomy and Horticulture: Faculty Publications

It is critical to evaluate conservation practices that protect soil and water resources from climate change in the Midwestern United States, a region that produces one-quarter of the world’s soybeans and one-third of the world’s maize. An over-winter cover crop in a maize–soybean rotation offers multiple potential benefits that can reduce the impacts of higher temperatures and more variable rainfall; some of the anticipated changes for the Midwest. In this experiment we used the Agricultural Production Systems sIMulator (APSIM) to understand how winter rye cover crops impact crop production and environmental outcomes, given future climate change. We first tested APSIM …

Decipher The Molecular Response Of Plant Single Cell Types To Environmental Stresses, Mehrnoush Nourbakhsh-Rey, Marc Libault

Department of Agronomy and Horticulture: Faculty Publications

The analysis of the molecular response of entire plants or organs to environmental stresses suffers from the cellular complexity of the samples used. Specifically, this cellular complexity masks cell-specific responses to environmental stresses and logically leads to the dilution of the molecular changes occurring in each cell type composing the tissue/organ/plant in response to the stress.Therefore, to generate a more accurate picture of these responses, scientists are focusing on plant single cell type approaches. Several cell types are now considered as models such as the pollen, the trichomes, the cotton fiber, various root cell types including the root hair cell, …

Organic Struggle: The Movement For Sustainable Agriculture In The United States [Book Review], Charles A. Francis

Department of Agronomy and Horticulture: Faculty Publications

Organic Struggle chronicles the challenges encountered by innovators in a growing segment of the U.S. food production and marketing system. Practiced for millennia by farmers before the introduction of chemical fertilizers and pesticides, and first developed more formally in Europe, organic farming practices began to gain prominence in the United States only in the 1950s. Far more than a system for producing food, this strategy has become a focus for those supporting healthy and pesticide-free products, for some who embrace the organic system as a food movement, and by many who disagree with the current domination of the country’s food …

Draft Genome Sequence Of Erwinia Tracheiphila, An Economically Important Bacterial Pathogen Of Cucurbits, Lori R. Shapiro, Erin D. Scully, Dana Roberts, Timothy J. Straub, Scott M. Geib, Jihye Park, Andrew G. Stephenson, Erika Salaau Rojas, Quin Liu, Gwyn Beattie, Mark Gleason, Consuelo M. De Moraes, Mark C. Mescher, Shelby G. Fleischer, Roberto Kolter, Naomi Pierce, Olga Zhaxybayeva

Department of Agronomy and Horticulture: Faculty Publications

Erwinia tracheiphila is one of the most economically important pathogens of cucumbers, melons, squashes, pumpkins, and gourds in the northeastern and midwestern United States, yet its molecular pathology remains uninvestigated. Here, we report the first draft genome sequence of an E. tracheiphila strain isolated from an infected wild gourd (Cucurbita pepo subsp. texana) plant. The genome assembly consists of 7 contigs and includes a putative plasmid and at least 20 phage and prophage elements.

Muts Homolog1 Silencing Mediates Orf220 Substoichiometric Shifting And Causes Male Sterility In Brassica Juncea, Na Zhao, Xinyue Xu, Yashitola Wamboldt, Sally Ann Mackenzie, Xiaodong Yang, Zhongyuan Hu, Jinghua Yang, Mingfang Zhang

Department of Agronomy and Horticulture: Faculty Publications

Cytoplasmic male sterility (CMS) has consistently been associated with the expression of mitochondrial open reading frames (ORFs) that arise from genomic rearrangements. Spontaneous fertility reversion in CMS has been observed in several cases, but a clear understanding of fertility reversion controlled by nuclear genetic influences has been lacking. Here, we identified spontaneous fertile revertant lines for Brassica juncea CMS cytoplasm in which the mitochondrial genome has undergone substoichiometric shifting (SSS) to suppress ORF220 copy number. We placed ORF220, with or without a mitochondrial targeting presequence, under the control of the CaMV35S and AP3 promoters in Arabidopsis to confirm that ORF220 …

Long-Term Impacts Of Fuel Treatments On Tree Growth And Aboveground Biomass Accumulation In Ponderosa Pine Forests Of The Northern Rocky Mountains, Kate A. Clyatt

Graduate Student Theses, Dissertations, & Professional Papers

In western North America, many low-elevation, dry forest types historically experienced frequent, low-severity fires. However, European settlement and fire suppression policies have contributed to over a century of fire exclusion, substantially altering forest structure and composition. There is considerable interest in restoring fire resilient characteristics to these forests through fuel reduction treatments. One limitation of current research on the impacts of fuel treatments is treatment longevity, as few studies have been able to quantify long-term responses to commonly applied treatments. This research evaluated tree growth and aboveground biomass responses 23 years after treatment in two silvicultural installations with different underburning …

Prospects Of Genomic Prediction In The Usda Soybean Germplasm Collection: Historical Data Creates Robust Models For Enhancing Selection Of Accessions, Diego Jarquin, James Specht, Aaron Lorenz

Department of Agronomy and Horticulture: Faculty Publications

The identification and mobilization of useful genetic variation from germplasm banks for use in breeding programs is critical for future genetic gain and protection against crop pests. Plummeting costs of next-generation sequencing and genotyping is revolutionizing the way in which researchers and breeders interface with plant germplasm collections. An example of this is the high density genotyping of the entire USDA Soybean Germplasm Collection. We assessed the usefulness of 50K SNP data collected on 18,480 domesticated soybean (G. max) accessions and vast historical phenotypic data for developing genomic prediction models for protein, oil, and yield. Resulting genomic prediction models explained …

Corn (Zea Mays L.) Seeding Rate Optimization In Iowa, Usa, Mark A. Licht, Andrew W. Lenssen, Roger W. Elmore

Department of Agronomy and Horticulture: Faculty Publications

Collecting soil, topography, and yield information has become more feasible and reliable with advancements in precision technologies. Combined with the accessibility of precision technologies and services to farmers, there has been increased interest and ability to make site-specific crop management decisions. The objective of this research was to develop procedures to optimize corn seeding rates and maximize yield using soil and topographic parameters. Experimental treatments included five seeding rates (61 750; 74 100; 86 450; 98 800; and 111 150 seeds ha^-1) in a randomized complete block design in three central Iowa fields from 2012 to 2014 (nine …

Effects Of Corn (Zea Mays L.) Stover Removal And Leaching On Soil Test And Whole Plant K Levels In Corn And K Fertilization/High-Input Treatments On Soybean Using Site-Specific Management To Increase Soybean (Glycine Max) Production In South Dakota, Nick J. Schiltz

Electronic Theses and Dissertations

Potassium is important for crop production. Corn stover removal has the potential to reduce exchangeable and soluble soil potassium (K+) needed for optimal plant growth in addition to grain yield. An experiment was conducted in Aurora, SD, USA, to observe the effects of corn stover removal on water soluble and exchangeable soil test K+ (STK) levels and corn grain yields across a five-year period. Abundant K+ reserves were recorded between the initial and final sampling periods. While corn grain yields were affected by removing corn biomass, exchangeable and solution K+ levels were relatively unaffected by stover removal. Potassium fertilizer has …

Senescence Of Native Perennial Warm Season Grasses Senescence Associated Switchgrass Transcriptome, Michaellong Tran

Electronic Theses and Dissertations

Senescence of perennial crops enable continuous harvests after one sowing event. Perennials senesce at adapted rates of their native environments; however, early senescencing crops do not maximize the growing season as nutrient reallocation takes precedence. Chlorophyll degradation and nitrogen reallocation was observed to occur rapidly between mid to late September. Transcriptome analysis on early and late senescencing switchgrass cultivars reveals upregulation of starch metabolism, light reactions, Calvin-Benson Cycle, and anthocyanin synthesis in late senescencing switchgrass. Morphological variations between the two germplasms prolong the growing season of late senescencing switchgrass, maximizing yield. Expression of mRNA as senescence progresses and between the …

Restoration Of Eroded Lands With Biochar As Soil Amendment In South Dakota, Saroop S. Sandhu

Electronic Theses and Dissertations

Biochar is produced from incomplete pyrolysis of plant biomass. Due to the unique properties of biochar such as a higher number of micropores, surface area and carbon content, and recalcitrant nature of carbon, biochar is hypothesized to improve physical and hydrological properties of soil. This study assesses the impact of biochar on soil organic carbon, physical and hydrological properties of two landscape positions under a corn (Zea mays L.)-soybean (Glycine max L.) rotation. Three types of biochar including corn stover, ponderosa pine (Pinus ponderosa Lawson and C. Lawson) wood residue, and switchgrass (Panicum virgatum L.) were applied in the field …

Construction Of High Resolution Genetic Linkage Maps To Improve The Soybean Genome Sequence Assembly Glyma1.01, Qijian Song, Jerry Jenkins, Gaofeng Jia, David L. Hyten, Vince Pantalone, Scott A. Jackson, Jeremy Schmutz, Perry B. Cregan

Department of Agronomy and Horticulture: Faculty Publications

Background: A landmark in soybean research, Glyma1.01, the first whole genome sequence of variety Williams 82 (Glycine max L. Merr.) was completed in 2010 and is widely used. However, because the assembly was primarily built based on the linkage maps constructed with a limited number of markers and recombinant inbred lines (RILs), the assembled sequence, especially in some genomic regions with sparse numbers of anchoring markers, needs to be improved. Molecular markers are being used by researchers in the soybean community, however, with the updating of the Glyma1.01 build based on the high-resolution linkage maps resulting from this research, …

Genome-Wide Discriminatory Information Patterns Of Cytosine Dna Methylation, Robersy Sanchez, Sally A. Mackenzie

Department of Agronomy and Horticulture: Faculty Publications

Cytosine DNA methylation (CDM) is a highly abundant, heritable but reversible chemical modification to the genome. Herein, a machine learning approach was applied to analyze the accumulation of epigenetic marks in methylomes of 152 ecotypes and 85 silencing mutants of Arabidopsis thaliana. In an information-thermodynamics framework, two measurements were used: (1) the amount of information gained/lost with the CDM changes I_R and (2) the uncertainty of not observing a SNP LC_R. We hypothesize that epigenetic marks are chromosomal footprints accounting for different ontogenetic and phylogenetic histories of individual populations. A machine learning approach is proposed to …