Burgeoning demand for sweetpotato [Ipomoea batatas (L.) Lam] is being driven by strong consumer consumption of fries and robust fresh market sales. Acreage has rebounded to meet needs, but increased supply has weighed negatively on fresh market prices, and processing sweetpotato is generally at a low price point. Growers are challenged with increasing production costs and labor is the most expensive input; reducing labor costs through mechanized harvest is critical. Many popular varieties of sweetpotato are highly susceptible to skinning damage and the problems that are associated with exposed root flesh such as rotting, weight loss, and sunken areas. The present study compared methods to assess skinning damage and determine if it is possible to breed for a more skinning resistant variety to aid in further mechanization. A torque wrench was found best at quantifying the amount of force required to cause skinning damage. A two year study of a parent and offspring population using the torque wrench found a heritability estimate of 0.10 on an individual plant basis and a 0.63 heritability on a family basis. It is assumed that an estimate above 0.50 is sufficient to improve a trait and data showed utility using families in breeding scheme, albeit this brings complications. The research also examined genes differentially expressed at skinning injury sites in 2 different environments. Over expression of genes involved in healing may decrease damage that does occur after skinning damage and complement a more durable skin. Consequences of skinning are lessened by curing roots (32° C; 85% relative humidity for 5 days); wound sites are rapidly healed with nominal desiccation. Cyt P450 and Ext, genes associated with periderm formation and wound healing, were found up-regulated in a curing environment compared to skinned sites at ambient outside conditions (conditions varied from approximately 26-30°C, with 50-70% RH ) over multiple time points (2 h, 4 h, and 24 h after skinning). Multiple genes associated with stress were found up-regulated in the ambient conditions. It is hypothesized that selection of genotypes with a more durable skin and enhanced repair mechanisms may further the quest towards mechanized harvest.

Cotton is sold by weight, but a bales lint price per pound is determined by its fiber quality profile. Cotton quality is defined by a set of standardized properties (length, strength, elongation, uniformity, color, trash, and micronaire) collected on every United States bale. Each cotton fiber is the remnant of a single cell which upon harvest exists as a dry, hollow tube of crystalline cellulose. The length, perimeter, and thickness are a fibers physical dimensions. These dimensions influence both the mechanics involved in yarn spinning and the quality of the yarn produced. Genetic and environmental factors affect the development and consequently, the final properties of cotton crops. However, information is lacking about the degree of influence they impart, especially on fiber perimeter (fineness) and cell wall thickness (maturity), both components of micronaire. The goals of this dissertation were to: 1) Summarize and review the techniques available to industry to measure fiber perimeter and maturity in order to discuss their advantages and limitations, 2) Validate the use Cottonscope to measure fiber quality variation, 3) Determine the significance of within-plant yield variation, and 4) Determine the significance of within-plant quality variation. Small differences in micronaire are often indistinguishable, making breeding efforts difficult. With new instruments, selecting for the components of micronaire may increase selection efficiency and genetic gain compared to breeding for micronaire directly. In addition, these results show that yield and quality within genotypes are highly variable, and a significant amount of the variation is attributable to a bolls fruiting site. Substantial bias can be introduced if boll sampling does not consider fruiting position. The results show that plot sampling techniques can greatly influence fiber quality testing results and as a result the effectiveness of genetic selection. The Cottonscope is a very accurate and precise tool for measuring fiber fineness and maturity ratio and improving the interpretation of micronaire. Micronaire had strong correlation with fiber fineness data. Breeding for lower micronaire would be a useful strategy to improve fiber fineness in environments where low fiber maturity is not a problem.

<p> Soil studies have traditionally been limited to the upper 2-m, while deep regolith &ndash; semi-consolidated materials from soil to bedrock &ndash; remains relatively unexplored, leaving many questions about the weathering processes of the near earth surface. Regolith (soil plus weathered bedrock) was studied across an elevation transect (405 m to 2700 m) of the west slope of southern Sierra Nevada mountains as a bioclimosequence. </p><p> In chapter one, effects of subtle differences in lithology and temperature were evaluated to measure degree of pedogenesis in regolith at rain- and snow- dominated sites. Biotite content in fine sand fractions was positively correlated with regolith thickness at rain-dominated and snow-dominated sites. Mineral grain size was negatively correlated with regolith thickness at the rain-dominated site. Meanwhile, the degree of regolith transformation, evaluated based on clay and secondary Fe oxide concentrations, was related to annual heat energy load from 0.5 to 10-m hard bedrock, where the proxy of energy input was mediated by temperature with depth. </p><p> In chapter two, a significant reservoir of carbon (C) within weathered bedrock was discovered. Small measurable amounts of C detected in deep regolith summed to large pools at locations where the regolith was thick. Although temperature and precipitation not effected on C density in deep regolith, the influence of climate had an indirect effect on C stock because it governed weathered bedrock thickness. Weathered bedrock had been reported to store deep C by 9% to 30% of the total regolith C inventory due to thickness of 0.7 to 7.6 m. Furthermore, a hypothetical scenario of global C stocks in weathered bedrock of 4-m thickness is 201 Pg, which help to explain a &ldquo;hidden&rdquo; C sink in the global C budget. In the third chapter, physical, chemical and mineralogical properties were measured at three elevations to understand climatic controls on weathering in soil and weathered bedrock. Evidence of chemical weathering was most pronounced in soil at the mid-elevation, while evidence of physical weathering was greatest in weathered bedrock at the high elevation where deep water percolation was highest. The concentration of nutrients was lower in weathered bedrock than that of soil, but due its thickness weathered bedrock was reservoir of plant essential nutrients. Moreover, available water content was large when summed over weathered bedrock thickness.</p><p> New spatial trends in ecosystem services were revealed by expanding our concept of soil to include deep regolith. This work was first to document factors that influence spatial trends of regolith (soil to weathered bedrock) characteristics in the Sierra Nevada. Characterization of deep regolith under different weathering environments improves our understanding of regulating factors for ecosystems health. The differentiation between weathering trends of soil and weathered bedrock could be used in the future to predict conditions in weathered bedrock at large scales.</p><p>

A glasshouse study was conducted on the Louisiana State University campus in Baton Rouge to evaluate herbicide activity on Nealley's sprangletop. Herbicides were applied to Nealleys sprangletop plants in the one-two tiller stage with height of 20-30 cm. Nealley's sprangletop control, leaf number, height, tiller number, and fresh weight biomass were evaluated. Nealley's sprangletop treated with glyphosate, quizalofop, fenoxaprop, and clethodim was controlled 89 to 99%. A field study was conducted at the LSU AgCenter Rice Research Station (RRS) and a grower location (GL) to evaluate herbicide rates and timings for control of Nealley's sprangletop in drill-seeded rice. Herbicide treatments were cyhalofop at 271, 314, and 417 g ai ha-1 and fenoxaprop at 66, 86, and 122 g ai ha-1 applied pre- or post-flood, propanil at 3360 g ai ha-1 applied pre-flood, and propanil plus thiobencarb at 5040 g ai ha-1 applied pre-flood. Cyhalofop increased control of Nealley's sprangletop compared with control observed with propanil plus thiobencarb. Nealley's sprangletop treated with fenoxaprop at 86 or 122 g ha-1 pre-flood resulted in increased control of Nealley's sprangletop over propanil or propanil plus thiobencarb. Field studies were conducted at the RRS and a GL on drill-seeded rice to evaluate removal timings of Nealley's sprangletop and the impact on rice yield. Fenoxaprop was applied at 122 g ha-1 at 7, 14, 21, 28, 35, and 42 days after emergence (DAE). Rice from the 7 DAE removal yielded 1910 kg ha-1 more than the nontreated. Delaying the initial herbicide application from 7 to 42 DAE caused a rice yield loss of 1790 kg ha-1 with a net loss of $460 ha-1, or $13 ha-1 loss per day. Field studies were conducted at the RRS and a GL in drill-seeded rice to evaluate Nealley's sprangletop infestation densities in rice and the impact on rice yield. Analysis indicated significance for Nealley's sprangletop density on rice yield where the linear effects of density were significant (P < 0.0064). Based on economic evaluations, Nealley's sprangletop at densities of 5 to 10 plants m2 are sufficient threshold levels for treatment.

<p> Agriculture in the Midwest United States (Illinois, Indiana, Iowa, Michigan, Minnesota, Ohio, and Wisconsin) is a critically important component of the United States economy and also for world exports of food grain. This is well reflected in the 2012 Census of Agriculture which showed that these states had a market value of crop and livestock products sold in excess of $80,000,000,000 (USDA, 2012). Within the U.S. the three Midwest states, Illinois, Iowa, and Minnesota are ranked 2nd, 3rd, and 4th for the economic value of crops sold. This economic value of agriculture in the Midwest encompasses not only corn, soybeans, livestock, vegetables, fruits, tree nuts, and berries but also nursery and many greenhouse plants. Soil is the one common underlying platform for agriculture and if agriculture has to remain profitable and sustainable, a scientific understanding of soils and their relationship to plant productivity is critical. </p><p> Soils harbor probably the most diverse microbial ecosystems on Earth (Delmont et al., 2011) and we are just beginning to understand the full extent of this diversity and how it influences agricultural productivity and how in turn agricultural practices influence the microbial diversity. Estimations indicate that approximately 1,000 Giga base pairs (Gbp) of microbial genomic sequences exist per gram of soil (Vogel et al., 2009). Microorganisms occupy almost every available niche on Earth and directly affect the environment and agricultural systems by a range of mechanisms that include biological nitrogen fixation (Hungria, Franchini, Campo, &amp; Graham, 2005), suppression of diseases (Mendes et al., 2011), decomposition of organic components (Schmidt et al., 2011), plant growth promotion (Bhattacharya &amp; Jha, 2012), soil nutrient cycling (Brussard, 2012) and bioremediation (Ali et al., 2012). Soil microbial community structure and its associated and interdependent biological processes can be affected by the way land is used and managed. Since a vast majority of soil microorganisms do not respond to "traditional" culturing techniques (Delmont et al., 2011), it has been difficult to study and characterize the functional and phylogenetic diversity of these important ecosystems until recent advances in next-generation DNA sequencing which have begun to unravel what is beneath our feet (Caporaso et al., 2010). According to Food and Agricultural Organization (FAO), the amount of land used for agriculture is about 11% (http://www.fao.org/docrep/005/y4252e/y4252e06.htm) and the emissions which can have serious environmental and health effects from agricultural food production far outweigh the total emissions from all the other industries combined (Bauer, Tsigardis, &amp; Miller, 2016). Thus, any steps to fine-tune the management practices and the way the agricultural land is utilized can go a long way in sustaining our way of life while maintaining a healthy environment. </p><p> The purpose of this study is to examine the shifts in the taxonomic diversity of bacteria in soils at phylum, class and order level between two distinct agricultural practices&ndash;Conventional Tillage (CT) and Conservation Tillage (NT) in Southern Illinois along with changes in soil compaction and soil phosphatase activity. The larger idea, based on results reported here and elsewhere, is to encourage conservative tillage practices using a combination of diverse cover crop systems and continuous soil cover which seem to enhance functional microbial diversity in the soil (Ajay &amp; Ngouajio, 2012; Verzeaux et al., 2016). Research also indicates the presence of higher numbers of bacteria of varied trophic groups, as well as increased species richness in bacteria in well-managed soils with minimal tilling and this, may correspond to more resilience to drying and rewetting disturbances in the soil (Anne et al., 2006). </p><p> This research may be the first to reconstruct the entire soil bacterial community in agricultural fields of Southern Illinois and will also hopefully be a precursor for more studies aimed at not only understanding soil from a biological bacterial perspective but also in deciphering interesting patterns that can help correlate changes in land management practices and how they impact bacterial communities. It may help us in developing a methodology to use bacterial taxa as indicators of soil management practices. The study will also detect previously unreported rare bacterial taxa-specific for this region and regional geochemistry.</p><p>

Proper nitrogen (N) management is essential to optimize crop production. This study was conducted to evaluate different N fertilizer management strategies to improve N use efficiency and yield in sugarcane production in Louisiana. This research was initiated in 2013 at the Sugar Research Station in St. Gabriel, LA and was arranged in a randomized complete block design with four replications consisting of different N rates (0, 45, 90, and 135 kg N ha-1) and sources (urea-46% N, ammonium nitrate [AN]-34% N, and urea-ammonium-nitrate solution [UAN]-32% N dribbled and knifed-in) as treatments. Sensor readings were taken from different N response trials to validate the sugarcane yield potential prediction and N response index (RI) models based on normalized difference vegetation index (NDVI). Soil nitrate (NO3-) and ammonium (NH4+) at 0-15 and 15-30 cm depths were also measured at different dates after N fertilization. At the grand growth stage, plots which were knifed-in with UAN showed a more even distribution of NO3- and NH4+ compared to urea- and AN-treated plots for both depths. Among the treatments, the highest sugarcane yield was achieved from plots treated with 90 kg N ha-1 as UAN knife-in and 135 kg N ha-1 as AN. Yield potential prediction models established in 2012 and 2015 could be used to estimate sugar and cane yield using NDVI readings collected at 21 (r2=0.30 and r2=0.51) and 60 (r2=0.41 and r2=0.52) days after N fertilization (DANF), respectively. Both RI and modified RI models demonstrated a better level of precision when RI was predicted at 60 DANF (r2=0.30) for both cane and sugar yield compared to 21 DANF (r2=0.15). The outcomes of this study demonstrated the effectivity of UAN knife-in as N source and the current N recommendation, but there were indications that application of higher N rate may further maximize yield. This study also revealed some limitations of the models used for predicting the components of remote sensor-based N recommendations for Louisiana sugarcane production. Apart from strengthening the yield and sensor readings database, areas of focus for future research include the use of different vegetation indices and reflectance readings from different wavebands.

Loss of phosphorus (P) from soil may degrade water quality. The problem exists where soil has been heavily fertilized with P, including use of poultry litter as fertilizer for pastures on the Coastal Plain. This research proposed that amending a P-enriched soil with a material that has a relatively high capacity to sorb P would decrease such loss in runoff or subsurface drainage. The P sorption behavior of two adsorbent materials, naturally occurring soil ironstone and bauxite refining residue (red mud), was examined in laboratory studies, with results guiding the design of a greenhouse experiment using these materials mixed with P-enriched Ruston soil (fine-loamy, siliceous, semiactive, thermic Typic Paleudults) used to grow common bermudagrass (Cynodon dactylon). The Langmuir P sorption maxima of ironstone and red mud were about five-times greater than that of Ruston but sorption was affected by kinetics. Miscible displacement studies confirmed reduced P mobility in these materials compared to Ruston, and reduced mobility of P in Ruston when mixed at a 9 to 1 ratio, with red mud being more effective than ironstone. The greenhouse experiment compared Ruston mixed with the P adsorbents at 0, 5, 10 and 20% with 4 replicates in a completely randomized design. Bermudagrass yield was greatest in the red mud treatments but variability among replicates led to no significant treatment effect in mass of P leached. Decreased infiltration with red mud led to ponding lasting longer than one day, which therefore represented potential loss of desorbed soil P in runoff. However, under simulated rainfall later in the experiment losses of P were numerically least from the red mud treatments, suggesting that the shorter-term results reflected transient behavior and that red mud may have potential as a soil amendment to reduce P losses.

A field study was conducted in 2015 and 2016 at the H. Rouse Caffey Rice Research Station (RRS) to evaluate mixture interactions of quizalofop and ALS-inhibiting herbicides. Quizalofop was applied at 120 g ai ha-1. Mixture herbicides included penoxsulam at 40 g ha-1, penoxsulam plus triclopyr at 352 g ha-1, halosulfuron at 53 g ha-1, bispyribac at 34 g ha-1, orthosulfamuron plus halosulfuron at 94 g ha-1, orthosulfamuron plus quinclorac at 491 g ha-1, imazosulfuron at 211 g ha-1, and bensulfuron at 43 g ha-1. All ALS herbicides mixed with quizalofop indicated antagonistic responses for weedy rice or barnyardgrass control at either 14 or 28 days after treatment (DAT). At 28 DAT, quizalofop mixed with penoxsulam or bispyribac controlled barnyardgrass 33 to 38%, compared with an expected control of 91 to 92%. A study was conducted at the RRS to evaluate interactions of quizalofop applied in mixtures with contact herbicides. Quizalofop was applied at 120 g ha-1. Mixture herbicides included carfentrazone at 18 g ha-1, propanil at 3360 g ha-1, saflufenacil at 25 g ha-1, or thiobencarb at 3360 g ha-1. Propanil severely antagonized quizalofop activity on weedy rice and barnyardgrass at all evaluations. At 28 DAT, barnyardgrass treated with quizalofop mixed propanil indicated an observed control of 16%, compared with an expected control of 93%. A study was conducted at the RRS evaluating sequential applications of quizalofop at 120 g ha-1 and propanil plus thiobencarb at 672 g ai ha-1. A prepackage mixture of propanil plus thiobencarb was applied for each timing treatment when ACCase-R rice was at the 2- to 3-leaf growth stage (day 0). Application timing treatments consisted of quizalofop applied at 7, 3, and 1 days before (DBPT) and after (DAPT) the propanil plus thiobencarb application at day 0. Additionally, quizalofop was applied alone and in a mixture with propanil plus thiobencarb at day 0. Quizalofop activity was reduced on weedy rice and barnyardgrass when applied at 1 and 3 DAPT or mixed with propanil plus thiobencarb at day 0; however, quizalofop activity was not reduced when applied before propanil plus thiobencarb.

Crop residue plays an important role in improving soil fertility. Crop residue affects soil biological and chemical properties by increasing soil organic matter, nutrient status and availability, and microbial activity. The degree of the effects of crop residue on soil fertility depends on the crop residue management practice. Samples were collected in 2014 in wheat (Triticum spp.) stubble and corn (Zea mays) stubble residue. A second soil sample collection under wheat stubble residue was taken in 2015 in the prescribed fire and no-till sections. A total of 342 soil samples (0-2.5cm) were collected across conventional tillage, no-till, and prescribed fire treatments of wheat stubble and corn stubble residue located on the Macon Ridge Research Station in Winnsboro, LA. Samples were collected pre-management (0 hr) and at 1, 24, 168, 720, and 4320 hr intervals post-management and analyzed for soil chemical (macronutrients and soil organic matter) and biological (microbial community structure and enzyme activities) properties. In 2015, additional samples were taken in wheat stubble residue 6 hrs and 168 hrs (1 week) post-management. Additional samples were collected in corn stubble residue 6 hrs post-management. Prescribed fire increased NO3--N relative to no-till and conventional tillage in wheat stubble. Prescribed fire increased β-glucosidase activity relative to conventional tillage but was similar to β-glucosidase activity observed in no-till. Short term changes in organic matter, nutrients, and enzyme activity were observed in prescribed fire, no-till, and conventional tillage. Shifts in microbial communities were observed in wheat stubble residue with Gram negative, total bacteria, and actinomycetes dominating the prescribed fire soil and abundance of arbuscular mycorrhizal fungi, saprophytic fungi, and fungi:bacteria dominated no-till and conventional tillage soil. The effects of management practices on microbial community structure was unable to be determined in corn stubble residue based on the fatty acid profiles tested in this study. While prescribed fire increased NO3--N and β-glucosidase activity, similarities between management were observed in NH4+-N, soil organic matter, and N-acetyl-β-D-glucosaminidase activity. Therefore, further research needs to be done in order to determine the most efficient crop residue management practice to optimize soil fertility.

The mineral nutrient density of vegetables has fallen in the past fifty years. As a result, some people are suffering chronic diseases due to shortage of mineral elements in these foods. The causes of this decline in nutritive value of vegetables have been attributed to a depletion of soil fertility and to a decrease in nutrient concentration in modern cultivars of vegetables. Lettuce (Lactuca sativa L.) is the most widely used leafy vegetable around the world. Research is needed to develop a nutrient content of lettuce that was help to supply adequate mineral nutrition to people. The objectives of the study are to determine if the mineral nutrient densities of lettuce can be increased through cultivar selection and soil fertility practices and to assess genetic diversity of the selected cultivars with use of molecular markers. This experiment was conducted with lettuce grown in organic and conventional fertility management practices in a greenhouse and in field sites. Butterhead, Romaine, and Loose-leaf phenotypes were selected in Heritage and Modern groups of lettuce. Eighteen lettuce cultivars were used from among three phenotypic groups with half of the varieties being Heritage and half being Modern cultivars. Commercial organic and water-soluble nutrient solutions (including Hoagland No. 1 Solution and 20-10-20 Peat Lite) were used in the greenhouse experiments. In the field, compost, organic, and conventional fertility regimes were used. Molecular diversity tested phenotypes and cultivars of lettuce through use of EST-SSRs markers. Growth parameters of height and fresh and dry weights were reported for the experiment. Elemental analysis of P, K, Ca, Mg, S, Mn, Fe, Cu, and Zn were conducted by ICP spectrophotometry. Generally, no differences or only small differences in nutrient accumulation were noted between Heritage and Modern cultivars in the greenhouse or field. Differences among phenotypes were small with somewhat higher accumulations of nutrients occurring with the Loose-leaf and Romaine cultivars than with the Butterhead cultivars. However, large differences in nutrient accumulation occurred among cultivars. 'Red Deer Tongue', 'Forellenschluss', 'Winter Density', 'Coastal Star', 'Simpson Black-Seeded', and 'Tom Thumb' were high in P, K, Ca, Mg, and Zn contents. 'Two Star, 'Tropicana', 'Red Rosie', 'Simpson Elite', 'Focea', and 'Claremont' were low in these elements. Overall, in the field, the conventional fertility regime showed higher produce yield than compost or organic fertility regimes. Modern and Loose-leaf types of lettuce showed higher weight yields than Heritage or Butterhead varieties. In the greenhouse, higher elemental accumulation occurred in conventional organic and Hoagland no. 1 fertility regimes than with a conventional fertilizer (20-10-20 Peat Lite), and accumulation was higher in Loose-leaf and Romaine lettuce than in Butterhead cultivars. In molecular assessment, higher heterozygosity was observed in Loose-leaf than in Romaine or Butterhead types. These studies allowed assessments of cultivars and management of conventional fertilizers on the accumulation of nutrients in lettuce and determination of genetic diversity. It is clear that varietal differences occur among cultivars of lettuce and that accumulation of nutrients can be controlled by management of the fertility regimes. Organic and conventional management might be equally effective as long as adequate plant nutrition is provided by each regime.