Master of Science / Department of Agronomy / Guihua Bai / Stem rust, caused by Puccinia graminis f. sp. tritici, has successfully prevented rust epidemics by Deployment of resistant cultivars in the past several decades. Unfortunately, race TTKS (termed Ug99) has defeated most stem rust resistance genes existing in commercial cultivars. Sr40, a stem rust resistance gene from Triticum timopheevii ssp. araraticum, was transferred to wheat and provides effective levels of seedling and adult plant resistance against Ug99. To characterize Sr40 in wheat, two mapping populations were developed from the crosses RL6088 / Lakin and RL6088 / 2174. RL6088 is an Ug99-resistant parent with Sr40. Since race TTKS is a quarantined pathogen, a US stem rust isolate RKQQ that is avirulent to Sr40 was used to evaluate the rust resistance in the F[subscript]2 and F[subscript]2:3 populations at the seedling stage. A total of 83 simple sequence repeats (SSR) primers on chromosome 2B were used to screen the parents for polymorphism. Each F[subscript]2 population was analyzed with the markers polymorphic between two parents. Marker Xwmc344 was the most closely linked to Sr40, at 0.7 cM proximal, in the linkage map constructed from the population RL6088 / Lakin, while Xwmc474 and Xgwm374 were also tightly linked. Xwmc474 was mapped 2.5 cM proximal to Sr40 in the RL6088 / 2174 population. Xwmc474 and Xwmc661 were flanking markers for Sr40 in both populations. Markers linked to Sr40 will be useful for marker-assisted integration of Sr40 into elite wheat breeding lines. In addition, a unknown stem rust resistance gene from another source, OK01307, a breeding line from Oklahoma State University shows partial resistance to Ug99, and was characterized using SSRs in this study. Two mapping populations were developed from cross OK01307 / Chinese Spring and OK01307 / LMPG-6. A total of 1300 SSR primers were screened for polymorphism between OK01307 and Chinese spring, and 1000 SSR primers were screened for polymorphism between OK01307 and LMPG-6. Polymorphic primers between parents and between bulks were used to screen the corresponding population. One Sr gene in OK01307 was mapped on chromosome 1BS of the both populations, which was closely linked to Sr24. Whether the gene is Sr24 per se or a new Sr gene that closely linked to Sr24 needs further investigation.

Master of Science / Department of Electrical and Computer Engineering / Steven Warren / The greenhouse in Throckmorton Hall at Kansas State University (KSU) has a temperature and humidity monitoring system. The system updates its measurements every thirty minutes online, and air temperature is controlled by an automated system. Each room has one temperature and humidity sensor box, which provides a suitable reference but is insufficient for more detailed plant research. To provide a distribution of temperature and humidity, a sensing system should be composed of a collection of sensors that gather data simultaneously. The new multi-point greenhouse monitoring system presented here can be helpful for plant research on a low budget. The demonstration system uses 27 sensor boxes in a 3x3x3 sensor grid (nine sensors at the same height and three different heights). Each sensor box contains temperature, humidity and light sensors that record data once per minute. MATLAB plots of these data indicate that temperature varied between 20 and 25 °C at night. Daytime temperatures are increased by sunlight, and rise to a maximum around noon. Sun-lit areas have higher temperatures than shaded areas, and during cloudy days all areas were almost the same temperature. Relative humidity is inversely related to temperature changes; when the temperature is stable, humidity is also stable. Humidity drops at noon because of increasing temperature and rises again at night. When researchers water the plants, humidity increases immediately. Greenhouse light intensity depends on the room design and the angle of the sunlight. Direct sunlight makes an obvious difference in shaded areas, and cloudy days promote even light distribution. Lighting at night time diffuses well at lower heights.

Master of Science / Department of Agronomy / David B. Mengel / Anhydrous ammonia (AA) is one of the most commonly used nitrogen (N) fertilizer sources for corn (Zea mays L.) in the US. Traditional knife applicators are slow, have high power requirements and create substantial soil disturbance. Thus, there is considerable interest in high speed, shallow placement, and low draft AA applicators like the newly introduced JD 2510 series, particularly for no-till production systems. The objective of this project was to compare a prototype high speed, low draft applicator (JD) with a traditional knife type AA applicator (TRAD) for irrigated and dryland corn production in the Kansas River Valley. Field studies were conducted from 2007 through 2009. Six N rates ranging from 0 – 224 kilograms N per hectare, in 45 kilogram increments, were applied at 3 application timings, Fall (FALL), Preplant (PRE), and Sidedress (SD) with both type applicators. Gaseous AA emissions were collected over a seven to nine day period after each application for both the TRAD and JD applicators for all application timings. The impact of applicator, timing and N rate was also measured on plant stand, earleaf N content, total N uptake, nitrogen use efficiency and grain yield. Statistically higher post application losses of ammonia at high N application rates were seen at all application timings with the JD applicator. However, these N losses were not of agronomic significance, and did not affect grain yield in 2007 or 2008. In 2009, there did appear to be a significant difference between applicators in grain yield, however this was primarily due to a significant yield decrease at the JD SD 224 kilograms N per hectare treatment from high application loss and resulting plant tissue damage. A significant response to N application was seen every year. Optimum N rate varied between years. FALL and PRE treatments had significantly higher grain yield than SD applications in 2008. However, in 2009 there was no significant difference in N application timing.

Master of Science / Department of Agronomy / Loyd R. Stone / Corn (Zea mays L.) yields are often reduced by limited pumping capacity of irrigation wells drawing from the High Plains Aquifer. As a result of decreased well capacities in this region, many irrigation systems no longer have the ability to meet peak irrigation (water) needs during the growing season. The purpose of this study was to measure easily identifiable plant characteristics of corn hybrids and relate those characteristics with the ability to maintain yield under water-limited conditions. This study involved measuring several plant characteristics of 18 corn hybrids grown under irrigated and dryland conditions near Tribune, KS during the growing seasons of 2005, 2006, and 2007. During each year, hot and dry conditions occurred during silking which resulted in large differences, and many poor yields, in the dryland plots. The number of days and growing degree days (GDD) to initiation of silking were the variables most strongly correlated with grain yield in the dryland environment. The shorter the time it took to reach initiation of silking the greater the grain yield. The number of days, or the GDD, to initiation of silking in irrigated environments did not have a significant correlation with corn grain yield. Other characteristics including canopy temperature, PAR (photosynthetically active radiation), color, leaf angle, number of internodes, number of leaves, and leaf N had no significant correlation with corn grain yield for either dryland or irrigated environments in 2005 and 2006. In this study using hybrids with maturity ratings between 98 and 118 d, there were no significant differences in grain yield in the irrigated environment. In the dryland environment, the hybrids used (98 – 118 d) in this study resulted in a decrease in grain yield with an increase in maturity. By considering the maturity of a hybrid, a producer will potentially be able to better select a variety that will perform well in a growing season with potential or likely severe water cutbacks as a result of limited water supply or reduced well capacity.

Master of Science / Department of Agronomy / Scott A. Staggenborg / Current demand for ethanol production is stressing feedstock production. Previous research has shown sweet sorghum and photoperiod sensitive sorghum [Sorghum bicolor (L.) Moench] as viable feedstocks which may supplement or replace current feedstocks. Studies were conducted at two dryland locations in north central and northeast Kansas in 2008 and 2009 to determine the effects of cultivar, nitrogen fertilizer rate, plant density, and harvest date on sweet sorghum juice and biomass yields. The cultivar study indicated the cultivar ‘M81E’ generally had the greatest yield. Other cultivars were not well suited for this region. No significant results were found in the nitrogen rate trial, indicating sweet sorghum may be insensitive to nitrogen fertilizer applications. The plant density trial results indicated that sweet sorghum possess a great ability to compensate for plant spacing. No differences were found in juice yields across densities, and the only difference found in total dry biomass was at the highest plant density. Results from the harvest date study indicate that sweet sorghum harvest should be delayed until at least the grain soft dough stage and can be continued for at least 10 days after a killing freeze without a yield penalty. Delaying harvest allowed for an increase in total dry matter and fermentable carbohydrates without a decrease in juice yield. Two studies were conducted at two dryland locations in northcentral and northeast Kansas in 2008 and 2009 to determine the effects of plant density on photoperiod sensitive sorghum yields, with an additional study to determine the effects of winter weathering. Photoperiod sensitive sorghum was found to be similarly insensitive to plant density, with few differences found in total dry biomass yield. Yields were found to decrease significantly due to winter weathering. A final study was conducted to examine a variety of sorghums as biofuel feedstocks. Photoperiod sensitive sorghum yielded the greatest in 2008 while sweet sorghum yielded less. In 2009, sweet and photoperiod sensitive sorghum yielded less than the cultivar TAMUXH08001. Sweet sorghum yields are generally the greatest with ‘M81E’ and when harvested after soft dough. Yields of both sorghums are occasionally influenced by plant density.

Doctor of Philosophy / Department of Agronomy / Jianming Yu / Knowledge of the genetic bases of grain quality traits will complement plant breeding efforts to improve the end use value of sorghum (Sorghum bicolor (L.) Moench). The objective of the first experiment was to assess marker-trait associations for 10 grain quality traits through candidate gene association mapping on a diverse panel of 300 sorghum accessions. The 10 grain quality traits were measured using the single kernel characterization system (SKCS) and near-infrared reflectance spectroscopy (NIRS). The analysis of the accessions through 1,290 genome-wide single nucleotide polymorphisms (SNPs) separated the panel into five subpopulations that corresponded to three major sorghum races (durra, kafir, and caudatum), one intermediate race (guinea-caudatum), and one working group (zerazera/caudatum). Association analysis between 333 SNPs in candidate genes/loci and grain quality traits resulted in eight significant marker-trait associations. A SNP in starch synthase IIa (SSIIa) gene was associated with kernel hardness (KH) with a likelihood ratio–based R[superscript]2 (R[subscript]L[subscript]R[superscript]2) value of 0.08. SNPs in starch synthase (SSIIb) gene (R[subscript]L[subscript]R[superscript]2 = 0.10) and loci pSB1120 (R[subscript]L[subscript]R[superscript]2 = 0.09) was associated with starch content. Sorghum is a crop well adapted to the semi arid regions of the world and my harbor genes for drought tolerance. The objective of second experiment was to identify quantitative trait loci (QTLs) for yield potential and drought tolerance. From a cross between Tx436 (food grain type) and 00MN7645 (drought tolerant) 248 recombinant inbred lines (RILs) was developed. Multi-location trials were conducted in 8 environments to evaluate agronomic performance of the RILs under favorable and drought stress conditions. The 248 RILs and their parents were genotyped by genotyping-by-sequencing (GBS). A subset of 800 SNPs was used for linkage map construction and QTL detection. Composite interval mapping identified a major QTLs for grain yield in chromosome 8 and QTL for flowering time in chromosome 9 under favorable conditions. Three major QTLs were detected for grain yield in chromosomes 1, 6, and 8 and two flowering time QTLs on chromosome 1 under drought conditions. Six QTLs were identified for stay green: two on chromosome 4; one each on chromosome 5, 6, 7, and 10 under drought conditions.

Master of Science / Department of Agronomy / Dorivar Ruiz Diaz / Corn (Zea mays) response to fertilization and placement methods has been studied extensively; however studies on soybean [Glycine max (L.) Merr.] response to placement have been limited. Three studies were completed to evaluate different aspects of crop response. The objective of the first study was to evaluate the effect of starter and broadcast fertilizer application on corn and soybean, in a typical corn-soybean rotation in Kansas. Treatments were unfertilized control, starter (N, P and K), broadcast P and K using mono ammonium phosphate (MAP) and potassium chloride (KCl) and the combination of starter and broadcast. Corn and soybean yield generally was not affected by starter and broadcast treatments. Thus fertilization may be recommended only under specific conditions. The objectives of the second study were (i) to evaluate the effect of residual and direct fertilization on soybeans after corn under a corn-soybean rotation system, and (ii) study the effect of fertilizer P and K application on soil test P (STP) and soil test K (STK) changes over time. Direct fertilization increased soybean yield while residual fertilizer did not. Therefore maintenance rates may be effective to improve soybean yield and likely maintain STP and STK levels. Application of P and K fertilizer generated significant increases in STP and STK after one year of application. The rate of P and K fertilizer required to increase 1 mg kg-1 yr-1 was between 2.8 - 5.1 kg ha-1 for P and between 1.0- 2.5 kg ha-1 for K, respectively. The objective of the third study evaluate both corn and soybean response to direct P fertilization including starter and broadcast. The treatments were a control, two starter fertilizers (with N-P and N only), five P rates (9.8, 19.6, 29.3, 39.1, 48.9 kg P ha-1) and one treatment with starter fertilizer in addition to the broadcast fertilizer application. Corn grain yield was not significantly affected by any broadcast or starter treatments. Broadcast application rates significantly increased soybean yield on low STP levels. Results of this study show that large corn or soybean yield response to starter and broadcast P application are likely with low STP levels.

Master of Science / Department of Agronomy / William T. Schapaugh / Recent results from a genetic gain study have illustrated the contribution of plant breeding to the improvement in seed yield of soybean (Glycine max (L.) Merr.). The objective of this research was to characterize the changes in several physiological parameters that have occurred in the released cultivars with improvement of seed yield. Sixty maturity group III and 54 maturity group IV cultivars, released from the 1920's through 2010, were evaluated in dryland and irrigated environments at Manhattan, KS in 2010 and 2011. Genotypes were planted in four-row plots, 3.4 m long, spaced 76 cm apart, arranged in a randomized complete block design with four replications. Genotypes were evaluated for canopy temperature, leaf chlorophyll content, pollen germination, leaf chlorophyll fluorescence, leaf antioxidants, and yield components. Canopy temperature measurements were captured between 1000h and 1400h using an infrared camera multiple times from R1 continuing through R6. Leaf chlorophyll content was measured using a SPAD meter several times from R1 through R6. In vitro pollen germination was measured using incubation temperatures of 28 and 34° C, beginning at late R1 through the end of flowering. Leaf chlorophyll fluorescence was measured beginning at R1 through R6. Leaf antioxidants were analyzed for total antioxidant capacity and electrolyte leakage by collecting leaves from the top 3rd to 5th trifoliate at R4 and R6. Yield components were analyzed from a hand harvested 0.33 m section of one border row. Genotypes differed significantly for canopy temperature, leaf chlorophyll content, pollen germination, and yield components. No significant differences were found for leaf chlorophyll fluorescence or leaf antioxidants. Seed yield increased with year of release. Canopy temperature was negatively correlated and leaf chlorophyll content was positively correlated with year of release in both maturity groups. No significant correlation with year of release was found for in vitro pollen germination or electrolyte leakage. Leaf chlorophyll fluorescence, yield components, and total antioxidant capacity was positively correlated in the maturity group IV genotypes with year of release. Evaluation of these parameters may serve as a basis to select for seed yield, or to assess the abiotic stress tolerance of a genotype.

Doctor of Philosophy / Department of Agronomy / Scott A. Staggenborg and Alan J. Schlegel / Previous work in the High Plains with alternative planting geometries of corn and grain sorghum has shown potential benefits in dryland production. Studies conducted in 2009-2011 at Tribune, KS evaluated five planting geometries in corn and grain sorghum: conventional, clump, cluster, plant-one skip-one (P1S1), and plant-two skip-two (P2S2). Geometries were evaluated at three plant densities in corn: 3.0, 4.0, and 5.1 plants m[superscript]-2. Every measured corn production characteristic was affected by planting geometry, seeding rate, or an interaction in at least one of the years. Corn planted in a P2S2 configuration produced the least above-ground biomass, kernels plant[superscript]-1, kernels ear row[superscript]-1, and the highest kernel weight. Conventionally planted corn minimized harvest index and maximized stover production. Alternative geometries produced similar harvest indices. Grain yield response to seeding rate varied by geometry and year. Responsiveness and contribution of yield components were affected by geometry. Yield and yield components, other than ears plant[superscript]-1, were the least responsive to seeding rate in a cluster geometry. Clump planting consistently maximized kernels plant[superscript]-1. Prolificacy was observed in the cluster treatment and barrenness in the skip-row treatments. Light interception at silking was highest for clump and conventional geometries and lowest for the skip-row treatments. Corn in a P2S2 configuration did not fully extract available soil water. Conventionally planted corn had the lowest levels of soil water at tassel-silk indicating early-season use which potentially affected kernel set. In the lowest yielding year, grain water use efficiency was highest for clump and P2S2. Across-years, grain yields were lower for corn planted in a P2S2 geometry. Across-years corn yields were maximized when planted in clump at low or intermediate plant density, conventional and P1S1 at low plant density, P1S1 at high density, or cluster at any density. Planting grain sorghum in a P1S1 or P2S2 configuration reduced total biomass, grain yield, water use efficiency for grain production (WUEg), and water use efficiency for biomass production (WUEb) compared to conventional, clump, or cluster geometries at the yield levels observed in this study. Total water use was unaffected by planting geometry although cumulative water use at flower / grain fill was higher for conventional, clump, and cluster than for skip-row configurations. Sorghum planted in a conventional geometry was always in the highest grouping of grain yields. Grain yields from sorghum in either a cluster or clump geometry were each in the top yield grouping two of three years. When evaluated across-years, sorghum planted in a clump, cluster, or conventional geometry resulted in similar levels of above-ground biomass, grain yield, WUEg, and WUEb. Clump or cluster planting appear to have substantially less downside in a high yielding year than skip-row configurations. A comparison of corn and sorghum reinforced the findings of others that the relative profitability of the crops is largely dependent on the environment for any given crop year. Relative differences in grain yield, WUEg, WUEb, and net returns varied by year. Net returns over the three year study were maximized by conventional, cluster, and clump planted sorghum as well as clump planted corn.

Doctor of Philosophy / Department of Grain Science and Industry / Dirk E. Maier / Increased mandates for the production of transportation fuels from renewable resources have thrust the conversion of lignocellulosic biomass, e.g., energy crops and agricultural residues, to ethanol into commercial production. The conversion of biomass to ethanol has been implemented; transportation and storage logistics are still obstacles to overcome by industry. Limited harvest windows throughout the year necessitate extended periods of biomass storage to maintain a consistent, year-round supply to the biorefinery. Sorghum biomass stored with no coverage (NN), covered with tarp (NT), wrapped in plastic (PN) and covered with a tarp and wrapped in plastic (PT) for six months was analyzed for changes in biomass components—cellulose, hemicellulose and lignin, cellulose and hemicellulose degrading enzymes, and conversion to ethanol yields. Treatment NN had increased enzyme activity, and reduced cellulose content and ethanol yields; while biomass covered maintained enzyme activity, cellulose content and ethanol yields. Sequencing of the Large SubUnit (LSU) region and the internal transcribed spacer (ITS) regions of ribosomal RNA gene gave consistent results of fungal community dynamics in biomass stored as previously described. Fungal community richness and diversity increased, while evenness decreased in uncovered biomass during storage. Covered and uncovered storage treatments and over time were found to exhibit distinctly different fungal communities. In contrast, bacterial communities were found to be unresponsive to storage treatments and durations. Cladosporium, Alternaria and Cryptococcus were found to be the most abundant in the stored biomass. Covering of biomass strongly limits the arrival and establishment of new fungal propagules in stored biomass, reducing biomass degradation by these often pathogenic, saprobic or endophytic communities. Overall, covering of biomass during storage is essential for optimal substrate retention for downstream processing into ethanol. In addition, storage and transportation logistics of three real-world scenarios were evaluated for the conversion of wheat straw, corn stover and sorghum stalks residues to ethanol at a biorefinery located in Southwest Kansas. Economic evaluation revealed that transport and storage of residues at satellite storage facilities was most economical for farmers and would create opportunity for the operation of profitable facilities that would supply the local biorefinery on demand throughout the year.