Master of Science / Department of Agronomy / Charles W. Rice / The sequestration of atmospheric CO[subscript]2 into soil through no-till management is an economic and viable method for reducing greenhouse gases, but maintaining no-till practices are necessary to sequester C in the long-term. Our study focused on the effects of a single tillage operation on soil organic C and N and aggregation in no-till soils when no-till practices are immediately resumed after tillage. Three locations in western Kansas were selected that had been in continuous dryland no-till for at least 5 years – Wallace, Tribune, and Spearville. Tillage treatments were administered in 2004 and consisted of no-till (NT), disk plow (DP), sweep plow (SwP), and chisel plow (CP). Treatments were arranged in a randomized complete block design with four replications. Soil samples were taken at 0-5, 5-15, and 15-30 cm depths. Composite samples were taken from each block prior to tillage and tested for whole soil organic C and N. Further soil samples were collected in spring 2005 at approximately nine months after tillage (MAT) and again in fall 2005 at approximately 12 MAT and tested for whole soil organic C and N and aggregate size distribution. Bulk density was measured for each plot and depth prior to sampling at 12 MAT. Twelve MAT samples were also tested for aggregate-associated C and N. The DP tillage had a greater C concentration than NT and CP when averaged over depth and time, but C mass did not vary between tillage systems. Changes in whole soil C and N over time varied by location, but the differences were similar between tillage treatments. Tillage treatments DP and SwP also had a greater mass of macroaggregate (250-1000 [Mu]m) associated C relative to CP (but not to NT) for Wallace in the surface 0-5 cm at 12 MAT. No other differences between tillages in aggregate-associated C were observed. A single tillage event did not have a significant impact on aggregate size distribution. The greatest amount of aggregate-associated C and N existed in the large microaggregate (53-250 µm) fraction. Changes in aggregate distribution or aggregate-associated C or N did not directly correlate to changes in whole soil C and N. We therefore conclude that a single tillage operation using these implements will not result in a measurable loss in sequestered C over time for dryland soils in a semi-arid climate such as western Kansas.

Master of Science / Department of Agronomy / David B. Mengel / Grain Sorghum (Sorghum bicolor) is one of the most drought and stress tolerant crops grown in Kansas. For this reason, much of the sorghum is grown in high risk environments where other crops are more likely to fail or be unprofitable. Efficient sorghum cropping systems should not only produce high yields and use inputs such as nitrogen efficiently, but they should also remove as much risk as possible for a successful crop, and give farmers more flexibility in making input decisions. The price of nitrogen (N) fertilizer has increased substantially in recent years. Current retail prices for commonly used N fertilizers range from $0.88 to $1.50 per kilogram of N in Kansas. Thus, a farmer could easily invest $50-$100 per hectare in N, depending on the rate of N needed and the source used. Practices which allow farmers to assess crop potential as late as possible after planting before applying costly inputs like fertilizer, can increase the potential for a profitable return on those inputs in risky environments. Currently, most sorghum growers routinely apply all the N fertilizer prior to planting, sometimes as much as 6 months prior. The current Kansas State University (KSU) nitrogen recommendation is yield goal based and performs well when the grower is able to predict yield six months or more in advance of harvest. However, yield is quite variable and difficult to predict. Because long range weather and yield predictions are not very reliable, could deferring making N application decisions until later in the season when yield can be more accurately predicted reduce risk? Can the use of active sensors provide a better estimate of yield potential and nitrogen needs sometime after planting? If they can, how late can the decision be made and how best should the fertilizer N be applied? Several studies were conducted throughout Kansas to look at the effect of N rate, N application timing (pre-plant, side dress, or combinations of the two) and method of application on sorghum yield and N use efficiency. The studies were also designed to examine the potential of using optical sensors to predict optimum N rate for post-planting applications as a means of avoiding the use of soil tests to estimate soil N contributions. The objectives of this research were: a. to validate the KSU N fertilizer recommendations for grain sorghum grown in rotation with crops such as soybeans and wheat, b. to determine the effect of both preplant and midseason N applications on the growth and yield potential of grain sorghum, and to determine the optimal timing and method for midseason N applications on grain sorghum, and, c. to assess the potential of optical sensing of the growing crop to refine N recommendations using in-season applications during the growing season. This thesis will summarize the results from the various experiments we completed to achieve these objectives. The KSU N fertilizer recommendations for grain sorghum may need some revisions. This research suggests that including coefficients relating to N use efficiency may be necessary to get more accurate N recommendations. Both pre-plant and midseason N applications increased the yield of grain sorghum whenever a response to N was observed. There was no negative effect of applying all the nitrogen midseason at 30-40 days after planting when compared to pre-plant applications. Injecting nitrogen fertilizer below the soil surface had higher yields than other methods of midseason N applications such as surface banding or surface broadcasting, especially when a significant rainfall event did not occur within a few days of application. The optical sensors used in this study were very effective at making N recommendations 30-40 days after planting. These sensors will provide for more accurate N recommendations compared to the current soil test and yield goal method.

Master of Science / Department of Agronomy / P. V. Vara Prasad / Grain sorghum (Sorghum bicolor L. Moench) is the fourth most important cereal crop grown throughout the semi-arid regions of the world. It is a staple food crop in Africa and Asia, while it is an important feed crop in the United States (US). More recently it is increasingly becoming important as a potential bioenergy feedstock crop around the world. The state of Kansas is the largest producer of grain sorghum in the US and contributes 40% of the total production. Drought is one of the major environmental factors limiting sorghum production in the semi-arid regions of the US, Asia and Africa. It is estimated that global crop losses due to drought stress exceed $10 billion annually. In crop production, drought stress can be classified into pre- or post-flowering. Even though the world collections of sorghum contain over 35,000 accessions, the genetic base currently used in breeding programs is very small (about 3%). Thus, it is important to identify diverse breeding lines for crop improvement. The diversity (association) panel consisting of 300 sorghum lines from all over the world was assembled for trait evaluation and association mapping. In this research these lines were grouped into the five major races (Figure 1) and 10 intermediate races of sorghum. The objectives of the research are to: (i) quantify the performance of the diversity panel under field conditions in Kansas, (ii) identify critical physiological traits affected by drought at both pre- and post-flowering stages of sorghum development, (iii) identify the most sensitive stage to drought stress during the reproductive phase of sorghum development and, (iv) test the feasibility of using a chlorophyll fluorescence assay (CVA) as a tool for identifying stay-green lines in grain sorghum during early stages of crop development. Field experiments were conducted in 2006 and 2007 in two locations in Kansas (Manhattan and Hays) under rain fed and irrigated conditions for the association panel. Objectives (iii) and (iv) were achieved with controlled environment experiments conducted in the greenhouse at the agronomy department, Kansas State University in 2006 and 2007. Results showed that there was large genetic variability among and within different races in the diversity panel for growth, physiological traits and yield components. Some genotypes showed yield stability across the different environments that were investigated. Drought significantly decreased seed number and harvest index across genotypes and races. In grain sorghum the period prior to flowering (panicle initiation) was the most sensitive stage to drought stress, in terms of its effect on seed-set, during reproductive development. A cell viability assay showed that there were significant differences in the loss of cell viability between leaf sample of stay green and non-stay green genotypes when leaf samples are collected in the morning and subjected to high respiratory demand. Therefore the chlorophyll fluorescence assay has potential as a tool for stay green trait screening at early stages of growth in grain sorghum.

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.