Doctor of Philosophy / Department of Agronomy / Phillip W. Stahlman / Saflufenacil is an experimental herbicide for control of broadleaf weeds in various crops including several herbicide resistant weed biotypes. Wheat is highly tolerant to preplant and preemergence applications of saflufenacil, but winter wheat growers prefer to apply herbicides postemergence (POST) in early spring. Objectives of this research were to (1) evaluate winter wheat and four common broadleaf weed species response to POST treatments of saflufenacil applied alone and in combination with bentazon or auxin herbicides at various rates both with and without adjuvants, and to (2) determine the possible mechanism(s) responsible for crop safening observed when saflufenacil is applied with 2,4-D amine or bentazon in winter wheat. Growth chamber, greenhouse, and field studies showed saflufenacil at a minimum rate of 25 g/ha controlled blue mustard and flixweed >85% when saflufenacil was applied alone or mixed with dicamba, 2,4-D amine, 2,4-D ester, or MCPA ester. Also, mixtures of bentazon with 13 g/ha of saflufenacil resulted in death of kochia, but increasingly higher rates of 2,4-D amine were needed to achieve 90% growth reduction when saflufenacil rates were decreased from 50 to 25 to 13 g/ha. In general, most of the saflufenacil combinations tested controlled henbit <85%. Leaf necrosis and stunting of winter wheat were reduced by tank mixing saflufenacil with dicamba, 2,4-D amine, or bentazon, but not with MCPA ester or 2,4-D ester. Including nonionic surfactant (NIS) in mixtures of saflufenacil plus 2,4-D amine resulted in significant wheat injury similar or greater than injury caused by saflufenacil plus NIS. Finally, 2,4-D amine enhanced saflufenacil absorption into winter wheat plants, whereas bentazon reduced absorption of saflufenacil. No more than 11% of applied saflufenacil translocated out of treated leaves to other plant parts when applied alone or when saflufenacil was mixed with 2,4-D amine or bentazon. Metabolism of saflufenacil by wheat plants was not affected by tank mixing with bentazon, but saflufenacil metabolism was slowed by mixing with 2,4-D amine. Overall, these studies indicate saflufenacil can potentially be used POST in wheat at an optimum rate of 25 g/ha plus 2,4-D amine or dicamba to effectively control blue mustard and flixweed.

Master of Science / Department of Agronomy / Jianming Yu / Tan spot, caused by Pyrenophora tritici-repentis (Ptr), is an economically important foliar disease worldwide. Race 1 of the fungus, which produces the necrosis toxin Ptr ToxA and the chlorosis toxin Ptr ToxC, is the most prevalent race in the Great Plains of the United States. The purposes of this study are to 1) identify and map novel quantitative trait loci (QTL) involved in resistance to tan spot race 1 in common wheat (Triticum aestivum L.) and 2) explore the inverse gene-for-gene interaction in the wheat-P. tritici-repentis pathosystem. A population of 288 F2:6 recombinant inbred lines (RILs) developed from the cross between Chinese landrace WSB (resistant) and Ning7840 (highly susceptible) was firstly used to identify genomic regions harboring novel sources of resistance. Two QTLs associated with resistance to chlorosis were mapped to the short arm of chromosome 1A and 2B in the WSB/Ning7840 population. No interaction was found between the two QTL. To further explore the specific wheat-ToxC model, three other populations were developed based on two susceptible parents, Ning7840 and Wheaton. QTL analysis revealed that common QTL were detected in populations shared with the same susceptible parents. The observations suggested that susceptibility rather than resistance for tan spot chlorosis is specific and presented evidence for the inverse gene-for-gene theory in the WSB-ToxC pathosystem. Leaf rust, caused by Puccinia triticina Eriks., is another important foliar disease of common wheat worldwide. The rust-resistance genes Lr41 and Lr42 from T. tauschii accessions TA2460 (Lr41) and TA2450 (Lr42) have been used as sources of rust resistance in breeding programs. Molecular markers linked to these genes are essential tools for gene pyramiding. Two BC3F2:6 mapping populations were evaluated for leaf rust resistance at both seedling and adult plant stages and analyzed with simple sequence repeat (SSR) markers. Both genetic and physical mapping confirmed that markers linked to Lr41 and Lr42 were on chromosome arm 2DS and 1DS, respectively. Marker analysis in a diverse set of wheat germplasm indicated that tightly linked markers for Lr41 and Lr42 can be used for marker-assisted selection (MAS) in breeding programs.

Doctor of Philosophy / Genetics Interdepartmental Program-Plant Pathology / James Nelson / The goal of quantitative-trait locus (QTL) mapping is to understand the genetic architecture of an organism by identifying the genes underlying quantitative traits. It targets gene numbers and locations, interaction with other genes and environments, and the sizes of gene effects on the traits. QTL mapping in plants is often done on a population of progeny derived from one or more designed, or controlled, crosses. These crosses are designed to exploit correlation among marker genotypes for the purposes of mapping QTL. Reducing correlations between markers can improve the precision of location and effect estimates by reducing multicollinearity. The purpose of this thesis is to propose an approach for developing experimental populations to reduce correlation by increasing recombination between markers in QTL mapping populations especially in selfing species. QTL mapping resolution of recombinant inbred lines (RILs) is limited by the amount of recombination RILs experience during development. Intercrossing during line development can be used to counter this disadvantage, but requires additional generations and is difficult in self-pollinated species. In this thesis I propose a way of improving mapping resolution through recombination enrichment. This method is based on genotyping at each generation and advancing lines selected for high recombination and/or low heterozygosity. These lines developed are called SA-RILs (selectively advanced recombinant inbred lines). In simulations, the method yields lines that represent up to twice as many recombination events as RILs developed conventionally by selfing without selection, or the same amount but in three generations, without reduction in homozygosity. Compared to methods that require maintaining a large population for several generations and selecting lines only from the finished population, the method proposed here achieves up to 25% more recombination. Although SA-RILs accumulate more recombination than conventional RILs and can be used as fine-mapping populations for selfing species, the effectiveness of the SA-RIL approach decreases with genome size and is most valuable only when applied either to small genomes or to defined regions of large genomes. Here I propose the development of QTL-focused SA-RILs (QSA-RILs), which are SA-RILs enriched for recombination in regions of a large genome selected for evidence for the presence of a QTL. This evidence can be derived from QTL analysis in a subset of the population at the F2 generation and/or from previous studies. In simulations QSA-RILs afford up to threefold increase in recombination and twofold increase in accuracy of QTL position estimate in comparison with RILs. The regional-selection method also shows potential for resolving QTL linked in repulsion. One of the recent Bayesian methods for QTL mapping, the shrinkage Bayesian method (BayesA (Xu)), has been successfully used for estimating marker effects in the QTL mapping populations. Although the implementation of the BayesA (Xu) method for estimating main effects was described by the author, the equations for the posterior mean and variance, used in estimation of the effects, were not elaborated. Here I derive the equations used for the estimation of main effects for doubled-haploid and F2 populations. I then extend these equations to estimate interaction effects in doubled-haploid populations. These derivations are helpful for an understanding of the intermediate steps leading to the equations described in the original paper introducing the shrinkage Bayesian method.

Master of Science / Department of Grain Science and Industry / Hulya Dogan / Viscoelastic wheat flour doughs are renowned for their ability to produce high quality aerated bread products. Dough exhibits extremely complex rheological properties which makes it capable of occluding and retaining gas cells. The ability of these bubbles to resist failure and remain stable throughout the proofing and baking process is critical to final bread structure and volume. Understanding these factors is important when creating the distinct structural and textural characteristics that consumers desire in baked products. In this study, a method was established for using X-ray microtomography (XMT) to study the microstructure of proving dough as well as bread made from three very different wheat flours. Doughs were prepared according to AACC Method 10-10B optimized straight-dough bread-making method. Sections from unproofed (0 min), underproofed (20 min) and optimally proofed (40 min) doughs were carefully cut and frozen at –80°C. Baked loaves were also prepared following standard test bake procedures. Small specimens were cut from two locations of both the proofed and baked loaves prior to microstructural analysis. A total of 96 dough and bread samples were scanned using a high resolution desktop X-ray micro-CT system Skyscan1072 (Skyscan, Belgium) consisting of an X-ray tube, an X-ray detector and a CCD-camera. X-ray images were obtained from 137 rotation views through 180° of rotation. Hundreds of reconstructed cross sectional images were analyzed using CTAn (v.1.7) software. 3-D analysis of the bubbles indicated that average dough void fractions increased dramatically over proof time from 30.9% for the unproofed dough (0 min) to 62.0% and 74.5 % for the underproofed (20 min) and optimally proofed (40 min) doughs respectively. Oven spring caused further expansion in the baked loaves which increased average void fraction to 84.3%. Gas cell size distributions were largely skewed to the right and shifted in that same direction as processing time increased. Differences in gas cell size seen among flour varieties were largely due to variations in the size of the largest cells caused by coalescence.

Master of Science / Department of Agronomy / Phillip W. Stahlman / Several weed species infest sunflower fields, but herbicidal options for broadleaf weed control are limited. In recent years, imazamox and tribenuron herbicides have been registered for POST use in imidazolinone-tolerant and tribenuron-tolerant sunflowers, respectively. Objectives of this study were to 1) investigate the effects of soil nitrogen level on Palmer amaranth control with imazamox in imidazolinone-tolerant sunflower and 2) evaluate crop response and weed control efficacy of single and sequential applications of tribenuron at two rates and the effectiveness of preemergence herbicides followed by postemergence tribenuron in tribenuron-tolerant sunflower. Greenhouse experiments were conducted in Manhattan, KS and field experiments were conducted near Hays, KS in 2007 and 2008. For the first objective, treatments consisted of a factorial arrangement of three soil nitrogen levels (28, 56, and 84 kg/ha) and two imazamox rates (26 and 35 g ai/ha) in a RCBD. Palmer amaranth growth rate increased with increasing soil nitrogen level. In all experiments, plants grown at the highest soil nitrogen level exceeded the maximum recommended plant height (7.6 cm) by >35% at the time of imazamox application. Generally, imazamox rates did not differ in control effectiveness at the 56 kg/ha soil nitrogen level, but the higher 35 g/ha rate was superior to the lower rate at the 84 kg/ha soil nitrogen level because of greater weed size. For the second objective, tribenuron was applied singly at 9 and 18 g/ha, sequentially in all combinations of those rates, and singly at those rates following PRE herbicide treatments. In general, tribenuron at 18 g/ha applied with methylated seed oil adjuvant before weeds exceeded 10 cm in height provided excellent control of most species with insignificant injury to the crop. The need for supplemental PRE herbicides for weed control in tribenuron-tolerant sunflower depends on weed species present and their size at the time of tribenuron application.

Master of Science / Department of Agronomy / David B. Mengel / This study was initiated to determine if potassium (K) deficiencies seen in soybeans (Glycine max (L.) Merr.) under no-till and strip-till production systems are impacting soybean yields, and if so, what fertilizer application practices including: rate of K application; broadcast or deep band methods of application; and the use of starter fertilizer at planting; could be used to correct the problem. The residual impacts of K fertilization and placement were also evaluated on corn (Zea mays L.) grown in rotation with soybeans. This research was conducted on-farm in cooperation with local producers. Soybeans sites in 2007 were near Harris, Ottawa and Westphalia, Kansas with corn planted in 2008 at the sites near Ottawa and Westphalia. Soybean sites in 2008 were located near Ottawa and Welda, Kansas. Selected sites were generally near or below the current soil test K critical level of 130 mg per kg extractable K, based on sampling histories provided by the cooperators. Sampling in the spring of 2007 confirmed these soil test (ST) K levels. Soybean leaf tissue potassium levels in 2007 were less than the critical level of 17 mg per kg in the unfertilized control plots, and were significantly greater when potassium fertilizer was deep banded or a high-rate of K fertilizer was broadcast. No significant difference in yield of soybeans due to K fertilization was seen, likely due to significant water stress during the grain fill period, which severely limited soybean yield in 2007. Soil test K levels at all the research sites increased dramatically between 2007 and 2008, even where no K was applied. Different weather conditions experienced these two years may have contributed to this occurrence. No residual impacts of K fertilization in 2007 on soybeans were seen in soil tests, corn leaf tissue K levels or corn yield in 2008. Soybean sites in 2008 also showed a dramatic increase in K ST levels in 2008 as compared to farmer records. No effects of K fertilization on soybean growth or yield were seen in 2008. The 2008 Ottawa soybean site had very low P soil tests. A significant response to P fertilization contained in the starter treatments was observed. This suggests that the dominant farmer practice of applying P and K fertilizer to corn, and not applying fertilizer directly to soybeans, even at low soil test levels, may not be supplying adequate P to soybeans, and is likely costing farmers yields and profits.

Master of Science / Department of Agronomy / Jianming Yu / Tannin, a second metabolic product in sorghum, has been directly related to resistance to insects and birds. Tannin also impacts sorghum nutritional value. Previous studies have shown tannin content has a positive correlation with early season cold tolerance, an important agronomic trait. Sorghum contains condensed tannins in testa layer below the pericarp. The testa layer tannin is controlled by two complementary genes B1 and B2: tannins are present when both genes are dominant but absent when only one or none of these two is dominant. The purpose of this research is to identify and map QTLs associated with the presence of condensed tannins, analyze interaction of QTLs, and provide a potential path to dissect the more complex trait of early season cold tolerance in future studies. A population of 109 F6:7 recombinant inbred lines (RILs) developed from the cross of a high tannin sorghum Shan Qui Red (SQR) and non-tannin line Tx430 was used in the mapping study. Two QTLs related to condense tannin presence in testa layer were mapped to chromosome 2 and 4, respectively. Strong epistatic interaction of these two QTLs was detected. The two QTLs together with their interaction explained 74% of the phenotypic variation. Sorghum grain quality traits, including kernel size, kernel hardness, protein and starch content, are complex traits which are directly related to sorghum nutritional value and market value. Association mapping is a promising method for complex quantitative traits analysis and dissection in plant science. Sorghum grain quality trait association analysis research is purposed to analyze large amount of grain quality data based on a diversity panel. A sorghum bicolor panel of 300 lines including germplasm derived from sorghum conversion program and elite commercial lines were established and served as diversity population for the association study. Phenotypic data of grain quality traits were collected by single kernel characterization system (SKCS) and near infrared reflectance spectroscopy (NIRS). Data analysis proved high diversity within the SB panel. A correlation between tannin presence and kernel hardness was also observed. Quality traits showed high consistence across years and environments.

Master of Science / Department of Agronomy / David B. Mengel / The increasing price of phosphorus (P) fertilizers has created interest among producers in ways to enhance the efficiency of applied P fertilizers. Research has long focused on increasing phosphorus efficiency through the use of fertilizer placement techniques (banding, strip applications, and in furrow placement with the seed). Recently, various products have been introduced and marketed claiming to increase efficiency of applied P or increase availability of native soil P. The objective of this study was to test the use of two such widely advertised products: Avail®, a long chain, organic polymer created to reduce the fixation of fertilizer P by aluminum and calcium, and JumpStart®, a seed inoculant containing a fungus (Penicillium bailii), which is said to increase the availability of fertilizer and native soil P to plant roots through the colonization of the root system and producing organic acid exudates. This study was conducted at multiple locations across Kansas with corn (Zea mays L.) in 2008 and 2009 and winter wheat (Triticum aestivum L.) in 2009. Selected sites varied in soil test P, with a majority of the locations having a Mehlich III P test of < 20mg kg-1, where a P response would be expected. Treatments consisting of P rates from 0 to 20 kg P ha-1 with and without the addition of Avail were applied at planting. At many locations, each of the fertilizer/Avail treatments were planted with and without Jumpstart seed treatment. Plant samples were collected at early and mid-season growth stages. Harvest data consisting of grain yield, grain moisture content at harvest, test weight or bushel weight and grain P content also were collected to measure treatment response. Plant samples for both trials failed to show consistent responses to the addition of either product. Excellent corn grain yields were obtained at seven of eight site years with location averages above 12,500 kg ha-1. One location displayed a significant grain yield response to P in both 2008 and 2009. There were no significant responses to enhancement products where a response to P was seen. At two of the five wheat trials, a significant tissue P response to the addition of P was seen. At one location with very low soil test, 6 mg kg-1, P fertilization increased rate of maturity. No effect on growth or yield at either P responsive or unresponsive sites was seen in wheat due to the use of enhancement products. A series of 20 single replications sites were conducted with the JumpStart product in cooperation with County Extension Agents as a part of wheat variety demonstrations. Analysis of this data showed a significant decrease in wheat yield with the addition of JumpStart in 2009. Overall, this study showed a lower than expected frequency of response to applications of P fertilizer based on soil test and the KSU P fertilizer recommendations. It also showed no response across locations, years and crops to the use of P fertilizer enhancement products.

Master of Science / Department of Agricultural Economics / Jeffery R. Williams / This study examines the economic profitability of reduced-tillage and no-tillage systems for corn, soybeans, and grain sorghum production in annual rotation with winter wheat, and monoculture wheat and grain sorghum in south-central Kansas. Net returns to land and management per acre for each of 13 production systems are calculated several different ways. Net returns are calculated using the 10-year average yield for each crop, the average crop price from 2009, and 2009 input prices. A distribution of net returns is also calculated using the actual historical yields and crop prices from 1997 to 2006 and 2009 input prices. This process is repeated, except average crop prices from 2006, 2007, 2008 and 2009 are now used. Finally, net returns are calculated using simulated yield and price distributions based on actual historical yields, four historical monthly price series, and 2009 input costs. Overall, the reduced-tillage wheat-soybean systems (RTWS) have the greatest net returns for each of the net return distributions. No-tillage wheat-soybean (NTWS) generally has the second highest net returns. Stochastic Efficiency with Respect to a Function (SERF) is used to determine the preferred management strategies under various risk preferences. SERF analysis indicates that RTWS is the system most preferred by all producers, regardless of their level of risk aversion. NTWS is typically the second most preferred system to RTWS. Using historical annual prices for 1997 to 2006 and the simulated monthly prices series for 2006 to 2009 and 2007 to 2009 to calculate the net return distributions, managers with higher levels of risk aversion prefer reduced-tillage wheat-grain sorghum (RTWG) over no-tillage wheat-soybean (NTWS). Sensitivity analysis shows that as the price of glyphosate falls, no-till systems become relatively more profitable. SERF analysis using the historic yields, 2006 to 2009 simulated monthly prices, and 2009 input costs with reduced glyphosate prices indicate that NTWS would be the system most preferred by producers at all levels of risk aversion. RTWS closely follows NTWS as the next preferred system with those conditions also for all levels of risk aversion.

Master of Science / Department of Agronomy / Johnathon D. Holman / Kraig L. Roozeboom / Replacing fallow periods with cover crops can provide many benefits including soil quality improvements and reduced nitrogen fertilizer requirements. Field experiments were established near Garden City, KS with winter wheat and fallow phases as main plots, thirteen legume or non-legume cover crops, continuous winter wheat, and fallow as subplots, and cover crop termination method as sub-subplots. Treatments containing triticale had greatest water use efficiency (19.9 kg ha[superscript]-1 mm[superscript]-1) and aboveground biomass (3550 kg ha[superscript]-1), but subsequent winter wheat yields were reduced due to a reduction in volumetric water content. Increased soil residue through greater cover crop biomass resulted in increased precipitation storage efficiency during the fallow period, but water requirements to produce biomass depleted soil moisture more than growing a low biomass crop or fallow. In years of above-average precipitation, low biomass cover crops might be grown with little to no negative effect on subsequent wheat yields. A second field experiment was established near Manhattan, KS with fallow, double crop soybean, and four cover crop treatments planted after wheat harvest in a winter wheat-grain sorghum-soybean no-till cropping system, with five nitrogen treatments applied to the sorghum crop to estimate nitrogen contribution of the cover crops. Greatest above ground biomass production and nitrogen accumulation was observed with sorghum-sudan grass. At the 0 kg ha[superscript]-1 N rate, grain sorghum yields were reduced 1200 kg ha[superscript]-1 following sorghum-sudan grass, while all other cover crop treatments provided a 20-30 kg ha[superscript]-1 N equivalent benefit. Sorghum yields might be reduced following large biomass producing cover crops when nitrogen is limiting, but a small nitrogen benefit might be realized following low C:N ratio cover crops. Cover crop productivity and their subsequent effects on grain sorghum performance were evaluated in field studies established near Manhattan and Hutchinson, KS in 2008 and 2009. Sixteen summer or fall cover crop species were planted in no-tillage winter wheat stubble and evaluated for biomass production, nitrogen concentration, and nitrogen accumulation. Summer annual grass species produced the greatest biomass, 3392 kg ha[superscript]-1 and greater, and legume species accumulated the greatest amounts of nitrogen, averaging 43 kg ha[superscript]-1. Grain sorghum yields were 867 kg ha[superscript]-1 greater following summer cover crops compared to fall cover crops. Cover crops had a significant effect on sorghum performance, with yields 1240 kg ha[superscript]-1 greater following legume cover crops.