Doctor of Philosophy / Department of Agronomy / Charles W. Rice / Atmospheric concentrations of the greenhouse gases (GHG) carbon dioxide (CO2), nitrous oxide, and methane have been increasing since the Industrial Revolution. An expanding human population, increased fossil fuel use, extensive ecosystem disturbance, and intensive production agriculture have contributed to this increase. Storing carbon (C) in soil in natural and agricultural ecosystems has the potential to offset a portion of the future atmospheric increases in CO2 levels. Laboratory and field studies were conducted to evaluate basic mechanisms of C sequestration. The research reported here focuses on identifying strategies to reduce C loss from soil by (1) slowing plant residue decomposition rates, or (2) increasing soil fungal dominance and physical protection of soil C. Grain sorghum (Sorghum bicolor) hybrids were used in a laboratory experiment to determine the effect of varied amounts of lignin on plant residue C mineralization. The different levels of lignin in the hybrids was not strongly correlated with plant residue C mineralization. Another laboratory experiment investigated larger differences in lignin content between crop plants. Plant residue exhibiting the natural mutation referred to as brown midrib (bmr) also had lowered total lignin and different lignin chemistry. The bmr plants decomposed faster than the normal isolines, and the addition of nitrogen lowered overall mineralization. Nitrogen additions also significantly impacted the microbial community by lowering total phospholipid fatty acids (PLFA) and shifting fungal energy storage physiology. A field experiment was conducted to measure the soil microbial response to adding grain sorghum residue in both tillage (CT) and no-tillage (NT) agricultural ecosystems. The residue mineralized similarly in both systems, but the NT microbial population was stimulated significantly greater than CT. The fungal PLFA in NT 0-5 cm was higher than NT 5-15 cm, CT 0-5 cm, or CT 5-15 cm. A significantly greater amount of plant residue C was found in soil macroaggregates, as compared to microaggregates, at the conclusion of the experiment, regardless of tillage. More N was found in NT macroaggregates than in CT macroaggregates. The experiment identified two mechanisms for increased C storage in NT soils, as compared to CT soils.

Doctor of Philosophy / Department of Agronomy / Johanna A. Dille / This dissertation has two complementary components: educational, in a survey of students in Weed Science and their perception of the Kansas State University Agronomy Learning farm, and research, regarding interactions between mesotrione and sulfonylurea herbicides. The Learning Farm serves as a resource where undergraduate students at KSU can develop agronomic skills through hands-on field site experiences and investigations. Students’ perceptions of experiential learning activities in the development of problem-solving and critical thinking skills were studied as a result of the Learning Farm. Activities included: undergraduate students in Weed Science (AGRON 330) developing a weed management recommendation, and Undergraduate Research Assistants (URAs) conducting weed science research projects at the Learning Farm. Students stated that experiential learning activities increased their critical thinking skills, required effective time management, and presented concepts that could be used in other situations. Pre- and post-project evaluation questionnaires showed that URAs had an increased interest in agronomy, weed science, and research following the completion of their project. For the research project, field and greenhouse studies were conducted from 2003 to 2006 to evaluate the efficacy of various sulfonylurea herbicides when applied with mesotrione or mesotrione + atrazine. Research demonstrated that the addition of mesotrione to sulfonylurea herbicides decreased efficacy of sulfonylurea herbicides on green foxtail, yellow foxtail, and shattercane. The addition of atrazine to the tank mix, or increased mesotrione rates, resulted in additional decrease in sulfonylurea herbicide efficacy on shattercane and foxtail species. Additional studies were performed to determine if absorption, translocation, or metabolism was the basis for the reduction in sulfonylurea herbicide efficacy when mixed with mesotrione or mesotrione + atrazine. Results indicated that the cause of antagonistic interaction between mesotrione and sulfonylurea herbicides in green and yellow foxtail was reduced absorption and translocation of the sulfonylurea herbicides. Producers who choose to apply mesotrione and sulfonylurea herbicides to corn should apply the herbicides sequentially to achieve maximum control of weedy grass species.

Doctor of Philosophy / Department of Agronomy / Michel D. Ransom / Upland soils in east central Kansas have a complex genesis, often contain one or more paleosols, and form in multiple parent materials including loess, colluvium, residuum, and alluvium. Quaternary loess/paleosol investigations have largely ignored this region of Kansas, as the total loess thickness on uplands is <2 m thick. In this study, the objectives are to examine the morphology and genesis of the soils of interest and how these characteristics vary within soil profiles, across landscapes, and throughout the current series mapping extent. The series of interest include the Irwin, Konza, Dwight, and Ladysmith soil series. Methods used in this study include field descriptions and sampling, terrain analysis, micromorphological investigations, and laboratory characterization, including silt and clay mineralogy. Accelerator mass spectrometry (AMS) was used for numerical dating and determination of stable carbon isotope values (δ13C) for selected paleosols. Radiocarbon ages ranged from 24,000 to 19,000 yr BP and δ13C values were between -19 and -17 ‰ (PDB), indicating that the paleosols were formed in Gilman Canyon loess or the Severance formation, under a mix of C3 and C4 vegetation. Terrain analysis results illustrated that, in given drainage areas, the soil series were mapped on a wide range of slope positions. Field observations and terrain analysis confirmed no relationships between mollic epipedon thickness, solum thickness, paleosol thickness, or depth to the paleosol with respect to landform. Micromorphological investigations revealed increasing soil development with depth, i.e., the presence of two paleosols beneath the modern soil. Mean particle size and mineralogy vary geographically within individual series. Pedogenic carbonate accumulations and redoximorphic concentrations are common features of the soils of interest, and less common features include sodium and gypsum accumulations, slickensides, and redoximorphic depletions. Results from this study will be provided to the USDA-NRCS for use in future soil survey updates, and will contribute to Quaternary loess/paleosol knowledge in Kansas and the Great Plains.

Doctor of Philosophy / Department of Agronomy / Johanna A. Dille / Palmer amaranth is a competitive weed and has caused variable corn yield losses in diverse environments of Kansas. The objectives of this study were to 1) determine corn and Palmer amaranth growth, development, and grain (seed) production, 2) determine soil water content throughout the growing season, and 3) evaluate the performance of the modified ALMANAC model for simulating monoculture corn yield and corn yield loss from Palmer amaranth competition when corn and Palmer amaranth were grown alone or in competition under dryland and irrigated environments. For the first objective, field experiments were conducted in 2005 and 2006 with whole-plots of dryland and furrow irrigation arranged in a side-by-side design. Within each soil water environment, sub-plot treatments were monoculture Palmer amaranth at one plant m-1 of row, and corn with zero, one, and four Palmer amaranth plants m-1 of row. Corn height, leaf number, LAI, and total plant dry weight were reduced with increasing water stress and were reduced further in the presence of Palmer amaranth. Corn yield losses were similar with increasing Palmer amaranth density across soil water environments in each year, except for 2006 dryland corn. Palmer amaranth growth and development were negatively impacted by corn interference and weed density. For the second objective, Time Domain Reflectometry measurements documented seasonal trends of volumetric soil water content at the 0 to 15 and 0 to 30 cm soil profile depths for treatments in dryland and irrigated environments each year. The soil water depletion rate increased as water received prior to a drying period increased at the 0 to 30 cm soil depth in the dryland and irrigated environments. For the third objective, the modified ALMANAC model was parameterized based on monoculture corn and Palmer amaranth growth data. The model underestimated monoculture corn yield but overestimated corn yield with Palmer amaranth competition. The model performance was not consistent when comparing simulation results to dryland and irrigated experiments conducted across Kansas. Overall, the experiment provided an improved understanding of corn yield loss risks associated with water management and Palmer amaranth competition.

Master of Science / Department of Agronomy / Kassim Al-Khatib / Field experiments were conducted near Manhattan, KS in 2005 and 2006 and Sabetha, KS in 2005 to determine the efficacy of S-metolachlor tank mixed with fomesafen on common waterhemp in soybean. Preemergence treatments included S-metolachlor + fomesafen at 0.91 + 0.22, 1.21 + 0.28, 1.52 + 0.36, and 1.82 + 0.43 kg ha-1 and S-metolachlor + metribuzin at 0.55 + 0.14 kg ha-1. These treatments were applied alone or followed by a postemergence glyphosate application at 0.88 kg ha-1. Ratings were taken 2, 4 and 8 weeks after treatment. The study showed that S-metolachlor + fomesafen gave excellent early season control of common waterhemp at both Sabetha and Manhattan. S-metolachlor + fomesafen at the 1.52+0.36 kg ha-1 rate gave greater weed control than S-metolachlor + metribuzin. A separate study was conducted to determine the competitiveness and fitness of a protox-resistant common waterhemp biotype. Protox-resistant and protox-susceptible biotypes of common waterhemp were grown under noncompetitive and competitive arrangements in the greenhouse. In the noncompetitive study a single plant of both biotypes was planted in 15-cm-diam pots. Photosynthesis, leaf area, and plant biomass were measured 10, 20, 30, and 40 day after transplanting (DATP). In general, photosynthesis rate and plant biomass was similar between biotypes. However, the protox-resistant biotype had higher leaf area then the susceptible biotype at 20, 30, and 40 DATP. Under competitive conditions, a replacement series study, photosynthesis, leaf area, plant height, and plant biomass were measured 7, 14, 21, and 28 DATP. In general protox-resistant and –susceptible common waterhemp values were similar 28 DATP. Relative crowding coefficient values 28 DATP were 0.86, 0.89, 1.09, and 1.13 for photosynthesis, leaf area, plant height, and plant biomass, respectively. Suggesting, protox resistance did not change the ability of common waterhemp to grow normally under competitive conditions.

Master of Science / Department of Agronomy / John P. Fellers / Allan K. Fritz / Water availability is commonly the most limiting factor to crop production, especially in drought prone areas like the Midwest. This study was conducted to map quantitative trait loci (QTL) involved in drought tolerance in wheat (Triticum aestivum L.) to enable their use for marker assisted selection (MAS) in breeding. A population of 122 F[subscript]7 derived recombinant inbred lines from a cross between Dharwar Dry and Sitta, spring wheat lines with contrasting drought tolerances, was analyzed using the amplified fragment length polymorphism (AFLP) technique and Diversity Array Technology (DArT) markers to create a QTL map. Of the 256 AFLP primer combinations evaluated, 151 were found to be polymorphic between the parents and were used to screen the population. A linkage map of 48 groups was created from the combined DArT markers, AFLP data, and SSR markers. This was used to create a QTL map which identified QTL in 24 of these groups. Using these markers for MAS in a breeding program could overcome the difficulties of selecting for drought tolerance. Another serious limitation to wheat production is leaf rust caused by the pathogen Puccinia triticina. Leaf rust causes between 1% and 20% yield loss on average and tends to be the worst in years with high yield potential. PI 289824 contains a single, dominant gene for seedling resistance mapping to chromosome 5BS and thought to be different from Lr52. An F[subscript]2 mapping population from a cross between PI 289824 and Jagger was used to try to identify markers very closely linked to the gene and therefore useful for MAS. The population presented some mapping challenges, but with the use of SSR and EST-STS markers, the gene was flanked. However, the markers were at too a great distance to be useful for mapping.

Doctor of Philosophy / Genetics Interdepartmental Program-Agronomy / William T. Schapaugh Jr / The soybean aphid (Aphis glycines Matsumura) has been one of the major pests of soybean [Glycine max (L.) Merr.] in soybean-growing regions of North America since it was first reported in 2000. The objectives of this study were to screen for soybean aphid resistant genotypes, determine the inheritance of resistant genes, and map and validate the resistance gene in the moderate resistant genotype K1621 using simple sequence repeat (SSR) markers. A mapping population of 150 F2:3 families from the cross between K1621 and susceptible genotype KS4202 were evaluated for aphid resistance. Phenotyping was conducted on the basis of total aphid number per plant 7 days following infestation with 4 aphids. Inheritance study indicated that one major dominant gene controls soybean aphid resistance in K1621. After SSR markers for polymorphism were screened between parents, a total of 133 polymorphic markers distributed across the soybean genome were used for genotyping. One quantitative trait loci (QTL) controlling antibiotic resistance was found by using the composite interval mapping method. This QTL localized on chromosome 13 (linkage group F) between markers Sat_234 and S6814 and explained 54% of the phenotypic variation. The putative QTL was further validated by single marker analysis using an independent population derived from the cross of K1621 and Dowling. The locus for soybean aphid resistance in K1621 was named [Rag]_K1621. The markers identified and validated in this study could be useful for marker-assisted selection of [Rag]_K1621.

Doctor of Philosophy / Department of Agronomy / Allan K. Fritz / In this research, a recombinant inbred line (RIL) population derived from cross between a leaf rust- and stripe rust-susceptible spring wheat ‘Avocet S’ and a slow leaf- and stripe-rusting resistant spring wheat ‘Amadina’ was used to postulate and map leaf rust seedling resistance genes, identify quantitative trait loci (QTL) for slow-rusting resistance against leaf and stripe rust, and study slow leaf-rusting components, latent period and infection frequency. Two known Lr genes (Lr23, and Lr26) were identified to be present in ‘Amadina’ through gene postulation, pedigree, cytogenetic, and polymerase chain reaction analyses. One unknown gene associated with seedling resistance was also mapped on chromosome 1BL. In greenhouse experiment, it was estimated that at least five genes conditioning final disease severity (FS) and latent period (LP), and four genes conditioning infection frequency (IF), segregated in the population. Correlations between LP and FS, and LP and IF were moderately negative, and that between IF and FS was moderately positive, indicating inter-dependence of the traits. Two QTL on chromosomes 1BL and 6BL were associated with LP and FS, and three QTL on chromosomes 1BL, 6BL and 2DS were associated with IF. Segregation of the RIL population in field experiment indicated that there were at least four and three adult plant resistance (APR) genes involved in resistance for leaf and stripe rust. Six QTL on chromosomes 3AL, 4AL, 1BL, 5BL, and 7BL were associated with APR for leaf rust, and seven QTL on chromosome 4AL, 5AL, 1BL, 2BL, 4BL, 5BL, 2DL, and 4D were associated with APR for stripe rust. Our results indicated that the major portion of genetic variability for slow-rusting resistance was additive gene action, and, to some extent, epistasis. In this research, we also explored the utility of remote sensing and geographic information systems (GIS) and analytical operations to discriminate leaf rust pustules from other parts of leaf and to accurately determine pustule size in ‘Amadina’ and ‘Avocet S’.

Master of Science / Department of Agronomy / Walter H. Fick / Kevin Price / Caucasian bluestem [Bothriochloa bladhii (Retz) S.T. Blake] is a perennial, C4 warm-season bunchgrass that was first introduced in 1929 from Russia as a potential forage crop in the Great Plains. Due to its invasiveness and tolerance of drought and grazing pressure, Caucasian bluestem can out-compete native prairie species. Research has shown that this species, when compared to native tallgrass species in the Flint Hills of Kansas causes decreased cattle weight gains because of its poor forage quality relative to tallgrass prairie species. Traditional methods of plant data measurements and mapping are costly and time consuming. Use of remotely sensed data to map and monitor the distribution and spread of this plant would be most useful in the control of this aggressive invader. Spectroradiometer data were collected over the 2009 growing season to determine if and when Caucasian bluestem was spectrally unique from native tallgrass prairie species. Observations were made from June through September as the plants were going into a senescent state. Reflectance data were measured approximately every two weeks or when clear/near clear sky conditions prevailed. Statistical analyses for differences in spectral characteristics were conducted to determine the optimal spectral bands, indices and timing for discriminating Caucasian bluestem from native tallgrass species. Difference in reflectance for spectral reflectance of bands 760 nm, 940 nm, 1,070 nm, and 1,186 nm were found to be statistically significant on the June 17th and June 30th sampling dates. The following band ratios and indices were found to be significantly different between Caucasian bluestem and native range on the June 17th collection date: Simple Ratio, Modified Normalized Difference Index, Normalized Phaeophytinization Index, Plant Index 1, Normalized Water Difference Index, Water Band Index, Normalized Difference Nitrogen Index, and the Normalized Difference Lignin Index. Findings of this study suggest that Caucasian bluestem can be spectrally discriminated from native tallgrass prairies of the Flint Hills in Kansas if the measurements are collected in mid to late June. Statistical analyses also showed differences between treatments for percent litter, grass, and forb basal cover.

Doctor of Philosophy / Department of Plant Pathology / Barbara S. Valent / Rice blast caused by the ascomycetous fungus Magnaporthe oryzae remains a threat to global sustainable agriculture and food security. This pathogen infects staple cereal crops such as rice, wheat, barley and millets, as well as turf grasses, in a distinct way among fungal plant pathogens, which we described in the first chapter. In addition to economical importance, rice blast is a model pathosystem for difficult-to-study biotrophic fungi and fungal-plant interactions. We are studying proteins that fungi secrete inside living cells to block plant defenses and control host cell processes; these proteins are called effectors. To date mechanisms for secretion and delivery of effectors inside host cells during disease establishment remain unknown. This step is critical to ensure the successful infection. So far, the only commonality found among all unique small-secreted blast effector proteins is their accumulation in a novel in planta structure called the biotrophic-interfacial complex (BIC). Identifying effectors and understanding how they function inside rice cells are important for attaining durable disease control. In the second chapter, we presented one approach to address this challenge. We characterized four candidate effector genes that were highly expressed specifically during the rice cell invasion. Using transgenic fungi that secrete fluorescently-labeled versions of each protein allowed me to follow them during invasion in vivo by live cell imaging. These candidates show distinct secretion patterns suggesting a spatially-segregated secretion mechanism for effectors. Results revealed a BIC-located strong candidate cytoplasmic blast effector, two putative cell-to-cell movement proteins and a putative extrainvasive hyphal membrane (EIHM)-matrix protein, which has become a valuable tool for assessing successful infection sites. In the third chapter, we test if normal secretion components of filamentous fungi are involved in accumulation of effectors into BICs. We report localization studies with M. oryzae orthologs of conserved secretion machinery components to investigate secretion mechanisms for effectors showing preferential BIC accumulation and for non-BIC proteins such as BAS4. Especially bright fluorescence adjacent to BICs from Mlc1p (Myosin Light Chain, a Spitzenkörper marker), from Snc1p (a secretory vesicle marker), and from Yup1p (a putative t-SNARE endosomal protein) suggest secretion actively occurs in the BIC-associated cells. Localization of Spa2p (a polarisome marker), as a distinct spot at the tips of the bulbous invasive hyphae (IH) in planta, suggests the existence of two secretion complexes after the fungus switches growth from the polarized filamentous primary hyphae to bulbous IH. In the final chapter on future perspectives, we present some strategies towards the molecular understanding of the M. oryzae secretion mechanism during biotrophic invasion, which will lead to novel strategies for disease control.