The practice of planting cover crops during fallow periods has increased due to the benefits provided to the soil system including improved nutrient cycling, addition of organic matter and a more diverse soil fauna resulting in better crop yield and an overall improvement of soil health. Research has shown that microbial activity is sensitive to changes in management practices and is a good indicator of whether the changes are benefiting the production system. To study the effects of cover type on corn (Zea mays L.) harvest parameters and soil chemical and biological properties a field trial consisting of a split plot design was established at LSU Agcenters Macon Ridge Research Station in northeast Louisiana. Treatments consisted of 8 covers: fallow, cereal rye (Secale cereal L.), forage radish (Raphanus sativus var. longipinnatus), berseem clover (Trifolium alexandrinum), crimson clover (Trifolium incarnatum L.), winter pea (Pisium sativum L.) and hairy vetch (Vicia villosa Roth) and 4 N rates (0, 235, 268 and 302 kg ha-1). Corn grain yield decreased by 20% after cover crop but responded to the addition of N both seasons. Cover crops had a positive effect on soil C:N over time, indicating active mineralization, and NO3- - N decreased almost three-fold between fall 2014 and spring 2015 (p<0.05). Cycling of C, N and S was also affected by cover crops; β-glucosidase and arylsulfatase activity were highest in spring 2015 (after cover crop termination) and averaged 73 and 32.9 mg p-nitrophenol kg-1 soil h-1, respectively. Microbial community structure shifted after cover crop with soil microbial communities under leguminous covers (hairy vetch, crimson clover, winter pea and berseem clover) separating from the brassica (forage radish) and grass (cereal rye) covers. Arbuscular Mycorrhiza Fungi (AMF) was higher (9.07 mol %) under the 0 N rate compared to the 263-302 kg ha 1 N rates (average 7.28 mol %) indicating the establishment of symbiotic relationship between plants and AMF as a response to nutrient deficient conditions. Cover crops established under Mid-South corn production systems show potential for improving the chemical and biological properties of soil.

End rot development in sweetpotato is caused by several pathogens and exacerbated by unfavorable environments. A critical need exists to know what factors in the environment trigger end rot development and how to manage the crop to minimize the incidence of end rots which are the overall objectives of this study. This research was divided into three studies: 1) Effect of environmental factors on expression of end rot in sweetpotato roots. Factorial combinations consisted of flooding/non-flooding; skinned/non-skinned; cured/non-cured; recommended storage/ambient storage are environmental variables not tested previously together in a systematic way. Results showed that curing at 29oC and 85-90% RH for five days and storage at 13oC and 85-90% RH were the critical factors mitigating end rot incidence. 2) Understand the role of calcium deficiency on end rot incidence. Relationship was observed between calcium and ethephon. Ethephon induced proximal and distal end rot incidences and decayed areas in sweetpotato. End rot symptoms are akin to blossom end rot in tomato caused by calcium deficiency. Increased rates of calcium in hydroponic solution increased calcium content in storage roots and reduced incidence of end rot. Calcium deficiency had impact on end rot incidence. 3) Identify expressed genes in storage roots treated with ethephon and 1-MCP. Molecular mechanisms triggered by the onset of end rot are unknown and may provide insight into plant protective mechanisms to exploit in a breeding program. This study identified differentially expressed genes (DEGs) using the annealing control primers (ACPs). DEGs identified are involved in protective mechanisms, transcriptional regulation, and an expressed protein (unknown). All 5 genes expressed in sweetpotato with end rot were confirmed by semi-quantitative reverse transcription polymerase chain reaction (sqRT-PCR) analysis. Genes differentially responded to 3.9 mM ethephon and 1 ppm 1-MCP. 1-MCP induced higher expression of TH2 and ATG8 than ethephon treated storage roots and minimized end rot incidence. This study furthered our knowledge of the role environment plays in inciting end rot development and how to minimize the incidence of end rots. Also, new genes were found that putatively lessen end rot and may have value as markers in breeding programs.

Sweet sorghum [Sorghum bicolor (L.) Moench] (SS) has been grown in the southern United States to produce syrup for many years. There is an interest in SS as a biofuel feedstock due to its high sugar content and high total biomass. Currently, little is known about the nutrient demand for SS or how it responds to tillage and fertilization. The objectives of this study were to: 1) evaluate the effects of tillage and phosphorus (P) and potassium (K) fertilization on SS agronomics, 2) evaluate nitrogen (N), P, and K uptake and nutrient partitioning in SS, 3) determine P and K maintenance fertilization rates for sugar and cellulosic ethanol production, and 4) evaluate the effects of tillage and maintenance fertilization on soil test extractable P and K at three depths after four years of a monocrop system. A split-plot, randomized complete block design with four replications was used to evaluate the effects of two tillage treatments (no-till system (NT) and conventional tillage (CT)) and two fertilization treatments (with maintenance (MF) and without maintenance (NMF)) on SS production from 2012 to 2015. The MF applied 45 and 67 kg ha-1 of P2O5 and K2O, respectively. The CT decreased days to 50% heading and increased the initial plant population. The NT increased the number of harvestable stalks which were derived from tillers. The MF increased plant height, stalk diameter, total biomass, and stalk biomass. The NT increased the P removal rate in green leaves. The MF application increased K concentration of stalk, green leaves, and the total K removal rate of the whole plant. The MF increased the P removal rate in the stalk. A 75 Mg ha-1 of SS would remove 40 and 145 kg ha-1 of P2O5 and K2O, respectively, when only the stalk is harvested. When the whole plant is removed, approximately 78 and 193 kg ha-1 of P2O5 and K2O would be removed, respectively. The MF application increased soil test exactable P at the 15 to 30 cm soil depth. Soil test extractable K was not affected by tillage and fertilization across the different soil depths.

While silicon (Si) fertilization is widely practiced in paddy rice production, the establishment of critical soil Si levels has remained understudied. This study was undertaken to: 1) determine the critical soil Si level for rice production in Louisiana using different extraction procedures, and 2) document the relationship between plant-available Si and select essential plant nutrients in soil and their uptake by rice. Field trials were established at 12 sites across Louisiana from 2013 to 2015. Si was applied as silicate slag (SiO3, 14% Si) at the rates of 0, 1, 2, 4, 6, and 8 Mg ha-1. Agricultural lime was also applied at (2 and 4 Mg ha-1) to evaluate the liming effect of slag in the main treatments. Treatments were arranged in a randomized complete block design with four replications. Soil samples collected at harvest were analyzed for pH, soil Si, heavy metals and plant-essential nutrients. Rice straw and panicle were analyzed for Si content; while panicle was analyzed for heavy metals and plant-essential nutrients. Analysis of variance and correlation analysis were performed for all measured variables using SAS 9.4. Slag application significantly increased the soil pH up to 1.4 units (p<0.05) in several sites. Rice grain yield was significantly (p<0. 1) increased in several sites by slag application, with the highest average grain yield obtained at application rates ranging between 1-4 Mg ha-1. The critical Si levels in soil ranged from 11.8 mg kg-1 (0.01 M CaCl2) to 771 mg kg-1 (0.1 M citric acid). The Si content in rice straw was negatively correlated with the panicle P (r = -0.25), S (r= -0.38), As (r = -0.33) and Cd (r = -0.39) but positively correlated with its Mn (r = 0.35) content. In general, soils with high initial Si and pH gave minimal responses to Si fertilization, while the Si content of soils with low initial Si was increased. Soil Si did not interfere with the uptake of most plant-essential nutrients, but the decrease in As and Cd contents of panicle shows that Si fertilization could be essential for improving grain quality of rice.

Ambrosia beetles have been a challenge to profitable nursery production for decades, with management recommendations focused on population monitoring and properly-timed insecticidal applications. Beetles disperse from forests starting in early spring, but few studies have determined the extent of this flight period, or how far they will fly into a nursery. And while the use of semiochemicals by ambrosia beetles has been widely examined, their use of visual cues including colors represents another gap in our knowledge. In addition to these under-studied behavioral traits, the available chemical control measures for ambrosia beetles are not completely effective, and repeated applications become costly for growers. Additional options are needed to reduce treatment frequency and to provide acceptable protection. The first experiment from 2012-13 determined beetle response to thirteen different trap colors. Mean beetle capture from opaque and red traps was significantly higher than from yellow or white traps, but we recommend that industry-standard black traps are adequate for ambrosia beetle monitoring. The second experiment from 2013-14 determined the timing of beetle flights and dispersal distance, as well as optimal trap and crop location. In addition to the well-documented spring flight, southeastern nursery managers need to be aware of a second, late-summer flight. Captures from traps placed at various distances (-25 to 200 m) from the forest/nursery interface showed a significant decreasing trend in numbers of beetles captured over increasing distance from the forest. Susceptible tree cultivars may gain added protection when placed deeper within nursery interiors and when baited traps line adjacent nursery edges. The third experiment from 2014-15 tested four treatments (kaolin clay, bifenthrin, kaolin + bifenthrin, and an untreated control) applied to ethanol-baited trees, with counts of new ambrosia beetle galleries compared roughly every other day for two weeks. While kaolin trees were better-protected than untreated trees at one day after treatment, subsequently there was no significant difference from untreated controls. And while there was a numerical reduction in attacks on kaolin + bifenthrin trees vs. bifenthrin trees, the effect was not statistically significant at any time.

Prickly sida (Sida spinosa L.) is widely distributed in the southern U.S. and is a troublesome weed in many agronomic crops. In northeastern Louisiana on silty clay loam and clay soils, prickly sida seedling emergence began in early March when soil temperature reached 13.8 C and ceased in mid-October. Seasonal peaks in emergence were associated with rainfall events and variability in prickly sida emergence was observed between soil types and years. Total emergence was as high as 3,000 prickly sida plants m-2. In shade studies, prickly sida was able to emerge and persist under a heavy shade environment and to produce a significant amount of seed when exposed to both increasing and decreasing shade levels as the growing season progressed. Under a season-long 30% shade environment, around 3,000 prickly sida seed were produced per plant. With exposure to 90% shade in the early season followed by a gradual decrease in shade to full sun, total seed production was around 8,100 seed per plant. In a weed control programs study, late season prickly sida control was 93% when glyphosate was applied both at-planting in late April/early May and postemergence (POST) in mid-May/late June. Soybean yield was increased an average of 10% when the residual herbicides chlorimuron-ethyl and tribenuron-methyl were applied with glyphosate plus 2,4-D preplant in mid-March compared with glyphosate plus 2,4-D alone. Yield was equivalent when glyphosate or glyphosate plus the residual herbicides flumioxazin, chlorimuron-ethyl, and thifensulfuron-methyl were applied at-planting and averaged approximately 25% greater than when no herbicide was applied at-planting. Application of 2,4-D or glyphosate plus 2,4-D to prickly sida reduced total seed production 78% compared with glyphosate alone. Herbicide treatments most effective for control of prickly sida present after crop harvest included diuron and linuron applied with glufosinate, paraquat, or glyphosate (75 to 85% control); diuron, atrazine, or 2,4-D ester applied with paraquat (74 to 77%); and 2,4-D ester and dicamba applied with glyphosate (75%).

To provide for a weed-free seedbed, Louisiana crop producers typically apply a burndown herbicide four to six wk prior to seeding summer annual crops; however, these treatments often provide inadequate henbit (Lamium amplexicaule L.) control. Research was conducted in Louisiana to evaluate henbit emergence from north to south, compare growth of henbit accessions based on emergence date, and control with fall-applied residual herbicides. For the emergence study during the weeks of Oct 17 to Dec 12 at all locations in all years, soil temperatures at 2.5 cm averaged between 10 and 18.5 C. Henbit at densities of at least 50 m-2 emerged each week from approximately Oct 20 through Dec 20, for the three northern most sites which included the Northeast Research Station, a growers field in Concordia Parish, and the Dean Lee Research and Extension Center.. At all three northern most locations counts in excess of 1000 henbit m-2 were observed in November, indicating potential for high henbit density at these locations. Henbit emergence was more sporadic from 2012 through 2015 for the three northern locations, with densities not exceeding 40 henbit m-2 at the Dean Lee Research and Extension Center, although large single week increases in the number of henbit did occur between mid-October to mid-December at those locations. Regardless of year, densities at the Ben Hur Research Farm, the southern location, were less overall. Averaged across emergence date leaf area ratio (LAR) for September and October was 0.012 and 0.010 cm2 g-1, respectively, and although not significantly different was greater than henbit emerging in November. Specific leaf weight (SLW) for henbit emergence in November was 119.0 g cm-2, greater than September and October populations at 54 and 89 g cm-2, respectively. Additionally, relative growth rate (RGR) for September emerged henbit averaged across harvest intervals was 0.194 g g-1 d-1, and greater than for both October and November emerged henbit with 0.121 and 0.092 g g-1 d-1, respectively. Results suggest that September emerged henbit could be larger and more difficult to control than November emerged henbit. However, October populations had similar trends and were not different than September emerged henbit, conceding that any competitive advantage September may have over October is slight. For fall applied residual herbicides study variability in henbit control, across years was observed. Overall, application Nov 1 through Dec 1 provided more consistent henbit control compared with oxyfluorfen applications controlled henbit at least 76% 100 DAT regardless of herbicide date. For flumioxazin and rimsulfuron: thifensulfuron, greater than 70% henbit control 100 DAT was obtained only when applied Nov 1 through Dec 15.

Aflatoxins are toxic and potent carcinogenic metabolites produced by Aspergillus flavus and A. parasiticus. Aflatoxins can contaminate cottonseed under conducive environmental conditions. Much success has been achieved by the application of atoxigenic strains of A. flavus for controlling aflatoxin contamination in cotton, peanut and maize. Development of aflatoxin-resistant cultivars overexpressing resistance-associated genes and/or knocking down aflatoxin biosynthesis of A. flavus could be an effective strategy for controlling aflatoxin contamination in cotton. In this study, differentially expressed genes (DEGs) were identified in response to infection with both toxigenic and atoxigenic strains of A. flavus pericarp and seed of cotton through genome-wide transcriptome profiling. The genes involved in antifungal response, oxidative burst, transcription factors, defense signaling pathways and stress response were highly differentially expressed in pericarp and seed tissues in response to A. flavus infection. The cell-wall modifying genes and genes involved in the production of antimicrobial substances were more active in pericarp than seed. Genes involved in defense response in cotton were highly induced in pericarp. The DEGs will serve as the source for identifying biomarkers for breeding, potential candidate genes for transgenic manipulation, and will help in understanding complex plant-fungal interaction for future downstream research. The increasing volume of sequence data generated by the rapidly decreasing cost of RNA sequencing (RNA-Seq) necessitates the development of software pipeline(s) that can analyze the massive amounts of RNA-Seq data in an efficient manner. Through the present study, a comprehensive and flexible Standalone RNA-Seq Analysis Pipeline (SRAP) implemented with the parallel programming approach was developed, which can analyze transcriptome for any genome. SRAP consists of high-level modules, including sequence reads filtering, mapping to reference genome (or transcriptome), sequence assembly, gene expression analysis and variant discovery along with low-level modules for other common NGS utilities. The high-level modules, unlike low-level modules, require intense computation in terms of memory and processor. SRAP is developed with in-house developed scripts (Python), parallel computing and open source bioinformatics tools. It can be executed as a batch and/or individual mode for single or multiple sample files. SRAP generates RNA-Seq data analysis output files with statistical summary and graphic visualization.

There are so many people who have helped me throughout my graduate studies and for whom I am grateful. I would like to take this opportunity to first and foremost thank God for his always guidance throughout my life and giving me the wisdom and the patience I needed to finish my thesis. I would like to thank Dr. Brenda Tubana for taking me in and providing me with guidance and knowledge. I also would like to thank my committee members, Prof. Brian D. LeBlanc who guided me, encouraged me and provided me with knowledge about sustainable agriculture and Dr. Paul Price for his encouraging words and kind assistance in this project. I would like to thank Prof. David Blouin for providing me with assistance and knowledge in designing the statistical model and conducting statistical analyses. I thank Ms. Emily Frank for her kind assistance in Middleton library. I would like to thank soil fertility group for all the times they have helped me in completing this project. Thank you Prof. Lawrence Datnoff for all of yours words of encouragement. I thank Prof. Maud Walsh for her kind guidance. I thank STPAL laboratory for their always assistance in running our experiment. My acknowledgement would be incomplete without thanking the biggest sources of my strength, my father, my mother, and my brothers who always inspires me by their fervent support, kindness, prayers and blessings. I would finally like to thank all of my friends who, I feel fortunate to write, are too numerous to name. You gave me the will to go on, and you made me motivated when I needed to.

The established sugarcane industry in Louisiana is perceived as an advantage for biofuel industry because of the similarities of energy cane and sugarcane by way they are cultivated, harvested, and processed. This study was conducted at the LSU AgCenter Sugar Research Station in St. Gabriel, LA from 2013-2015 to evaluate the influence of planting scheme, N rate, and harvest date on energy cane yield, quality parameters, nutrient uptake, and biomass chemical composition. The relationship of vegetation indices (VI) with stalk, fiber yield, and N uptake of energy cane harvested at different dates was also evaluated. The experiments consisted of variety (Ho 02-113, US 72-114), N rate (0, 56, 112, and 224 kg N ha-1) and harvest date (one- and two- months earlier harvest and scheduled harvest) as treatments arranged in split-split plot in a randomized complete block design with four replications. Another experiment was conducted with planting scheme (whole stalks vs. billets) and variety (Ho 02-113, US 72-114, Ho 06-9001, Ho 06-9002, L 01-299, and L 03-371) as factors arranged in split plot in randomized block design with four replications. Energy cane yield, quality parameters, chemical composition, and nutrient concentration and uptake were significantly affected by harvest date only. Both N rate and planting scheme did not affect biomass yield and quality. The nutrient removal rates between planting scheme were similar but not among harvest dates and varieties suggesting that the fertilizer recommendation will remain virtually the same for whole stalk- and billet-planted energy cane. The Pearson correlation analysis showed a strong dependence between VIs (i.e., simple ratio, normalized difference vegetation index) computed from reflectance readings at 670 (red) and 705 (red-edge) nm and stalk yield, N uptake, and fiber yield across cane age. The outcomes of this study show the: a) applicability of sugarcane cultural management practices for energy cane production, b) potential use of optical remote sensing in energy cane stalk and fiber yield prediction, and c) several areas of research emphasis to pursue for future studies on energy cane.