Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2006. / Source: Dissertation Abstracts International, Volume: 67-11, Section: B, page: 6119. Adviser: Robert G. Hoeft. Includes bibliographical references. Available on microfilm from Pro Quest Information and Learning.

Master of Science / Department of Biology / Brett K. Sandercock / Cattle-grazing is a dominant land use in the United States, with more than 300 million hectares of land grazed each year. The habitat changes facilitated by cattle grazing can influence resource availability and habitat selection for associated wildlife. To investigate the potential for changes in traditional livestock management to restore native grassland and riparian habitat, we evaluated biological community responses to winter-grazing and livestock exclusion at the Kansas Army Ammunition Plant in southeastern Kansas. In grassland habitats, we combined winter-grazing by domestic cattle and discontinued fertilization in an attempt to restore pastures dominated by tall fescue to native tallgrass prairie and improve habitat for grassland-breeding birds. We observed a decrease in tall fescue and an increase in native, warm-season grasses in winter-grazed pastures compared to fertilized, year-round grazed pastures. Grassland-breeding bird responses to winter-grazing were species-specific. Dickcissels preferred winter-grazed pastures, while Eastern Meadowlarks and Grasshopper Sparrows tended to prefer year-round grazed pastures. Dickcissels were negatively correlated with the presence of cattle during the breeding season and the abundance of tall fescue. Grasshopper Sparrows were negatively correlated with native, warm-season grass abundance and visual obstruction, but were positively correlated with forb abundance. Henslow’s Sparrows and Common Yellowthroats were detected breeding in low numbers on pastures that had been winter-grazed for five years. Our results suggest that winter-grazing and discontinued fertilization of agricultural grasslands can direct semi-natural plant communities toward tallgrass prairie and benefit some grassland-breeding birds. In riparian habitats, livestock were excluded from 1996 to 2005. We measured bird community responses in grazed and ungrazed sites using baseline data collected in 1996-97 and post-treatment data collected in 2004-05. Riparian bird community data were analyzed using robust design mark-recapture models that allowed us to evaluate changes in bird species richness while accounting for differences in detectability among species. We detected increases in species richness in both ungrazed and grazed treatments. We observed few differences in community vital rates between treatments; however, we did detect differences in guild responses. The changes observed within both grazed and ungrazed riparian bird communities were likely influenced by regional fluctuations in species richness and composition.

Doctor of Philosophy / Department of Agronomy / Charles W. Rice / Soil C sequestration in agricultural ecosystems is an immediate and significant option to mitigate the increase in the atmospheric CO2 concentration. The objectives of this study were to determine 1) the influence of crop and soil management practices applicable to Kansas (i.e., tillage, N fertilization, and crop rotations) on soil C and N, C sequestration rates, soil aggregation and aggregate-associated C and N; and 2) the influence of long-term tillage practices on SOC and total N, soil aggregation and aggregate-associated C and N in three soil types: an Oxisol (Brazil), a Vertisol (Argentina), and a Mollisol (Kansas, USA). The Kansas experiments included: tillage (conventional tillage (CT), reduced tillage (RT) and no-tillage (NT)) and native prairie; nitrogen (N) fertilization rates; and crop rotations comprising various combinations of winter wheat (Triticum aestivum L.), grain sorghum (Sorghum bicolor L. Moench), and soybean (Glycine max L. Merrill). The presence of a fallow period negatively affected C sequestration rates even under NT systems. Nitrogen fertilization generally increased C sequestration rates. Rotations that contained wheat or sorghum had the greatest C sequestration rates while continuous soybean had the lowest rates. Cultivation decreased the amount of macroaggregates with a concomitment increased in the amount of microaggregates. Wheat and sorghum increased total C in the macroaggregate fraction (>250 mm) under NT while soybean had the lowest C concentration. Cultivation reduced microbial biomass C and N and potentially mineralizable C and N. The combination of conservation tillage and rotations that produced a greater amount of residue had greater C sequestration rates. In the Oxisol, NT had greater amounts of large macroaggregates (>2000 mm) than CT, however no differences between tillage practices were detected in the Vertisol and Mollisol. Cultivation of native grassland reduced the amount of macroaggregates and the associated C and N concentration; however NT tended to be more similar to the native grassland. Overall, our results indicated that the use of conservation tillage could be an important strategy to sequester C in these agroecosystems. The adoption of management practices that enhance C sequestration would be important for reducing GHGs emissions and maintaining the sustainability of agricultural systems.

Doctor of Philosophy / Department of Agronomy / Guihua Bai / Growing resistant cultivars is an economically effective method to control wheat disease Fusarium head blight (FHB) caused by Fusarium graminearum. Ninety-five wheat lines mainly from China and Japan were evaluated for resistance to initial infection (type I), spread of symptoms within a spike (type II), and deoxynivalenol (DON) accumulation in infected grains (type III). Most of lines were resistant or moderately resistant, 15 lines had DON content lower than 2 ppm and six lines showed a high level of resistance for all the three types. Deoxynivalenol content was significantly correlated with type II, but not type I resistance. Fifty-nine of the ninety-five lines were evaluated for genetic diversity on the basis of amplified fragment length polymorphism (AFLP) and simple sequence repeats (SSRs). Genetic relationships among these lines were consistent with pedigrees and their geographic distribution. Chinese lines had broader genetic diversity than Japanese lines. Sumai 3 is a widely used Chinese variety for FHB-resistant breeding in the US and elsewhere. Haplotype patterns of the SSR markers linked to FHB resistance quantitative trait loci (QTL) on chromosomes 3BS, 5AS and 6BS of Sumai 3 indicated that only a few Sumai 3 derivatives carry all of these Sumai 3 QTL. SSR data also suggested that these QTL in Sumai 3 were derived from Chinese landrace Taiwan Xiaomai. Some highly resistant lines may carry novel QTL for FHB-resistance QTL, and need further investigation. A mapping population of 139 recombinant inbred lines derived from the cross of Wangshuibai (resistant Chinese landrace)/Wheaton (susceptible cultivar) was genotyped with more than 1300 SSR and AFLP markers. Five QTL for type I resistance were detected on chromosome arms 3BS, 4BS, 5DL, 3AS, and 5AS; seven QTL for type II resistance on 3BS, 1AL, 5AS, 5DL, 7AL, and 3DL; and seven QTL for type III resistance on 3BS, 5AS, 1AS, 5DL, 1BL, and 7AL. These QTL together explained 31.7%, 64%, and 52.8% of the phenotypic variation for FHB type I, II, and III resistance, respectively. QTL on 5AS, the distal end of 3BS, and 5DL contributed to all three types of resistance. FHB resistance QTL identified in Wangshuibai can be used in developing wheat cultivars with enhanced FHB resistance by pyramiding FHB resistance QTL from other sources.

Doctor of Philosophy / Department of Plant Pathology / James C. Nelson / The aim of quantitative trait locus (QTL) mapping is to identify association between DNA marker genotype and trait phenotype in experimental populations. Many QTL mapping methods have been developed to improve QTL detecting power and estimation of QTL location and effect. Recently, shrinkage Bayesian and penalized maximum-likelihood estimation approaches have been shown to give increased power and resolution for estimating QTL main or epistatic effect. Here I describe a new method, shrinkage interval mapping, that combines the advantages of these two methods while avoiding the computing load associated with them. Studies based on simulated and real data show that shrinkage interval mapping provides higher resolution for differentiating closely linked QTLs and higher power for identifying QTLs of small effect than conventional interval-mapping methods, with no greater computing time. A second new method developed in the course of this research toward increasing QTL mapping efficiency is the extension of multi-trait QTL mapping to accommodate incomplete phenotypic data. I describe an EM-based algorithm for exploiting all the phenotypic and genotypic information contained in the data. This method supports conventional hypothesis tests for QTL main effect, pleiotropy, and QTL-by-environment interaction. Simulations confirm improved QTL detection power and precision of QTL location and effect estimation in comparison with casewise deletion or imputation methods.

Doctor of Philosophy / Department of Agricultural Economics / Andrew P. Barkley / Previous studies show that there has been a deceleration in world wheat yield growth, specifically in irrigated areas, which has led some to believe that the potential for genetic gains is slowing. Some reports claim that the Centro Internacional de Mejoramiento de Maiz y Trigo (CIMMYT) breeding program "reached a plateau" in the 1980s. Such a breeding plateau would have global ramifications, since it is often poor consumers who benefit the most from yield enhancement of staple crops including wheat. CIMMYT estimates that by 2020, the developing world will need 40% more wheat than it consumes today. Because of the lack of involvement by private breeders in most low-income countries, CIMMYT, whose germplasm is used extensively in the developing world, will need to ensure that modern varieties that they release are increasing in yield to meet the rising wheat demand in the developing world. CIMMYT, a non-profit organization, distributes improved germplasm to national agricultural research systems (NARS) for worldwide utilization. CIMMYT has consistently invested a large amount of public expenditures in wheat breeding research each year for several decades. Estimates of the impact of the wheat breeding program on increasing wheat yields provides information to scientists, administrators, and policy makers regarding the efficacy and return to these investments. Quantitative estimates of yield improvements due to the wheat breeding program provide important information for future funding decisions. Wheat lines released by CIMMYT during 1962-2002 were analyzed to estimate genetic yield increases associated with the CIMMYT breeding program using test plot data from the Yaqui Valley in Mexico from 1990-2002. Using several econometric techniques including a Just-Pope production function to account for multiplicative heteroscedasticity across the different varieties, results indicate that through the release of modern varieties CIMMYT has contributed 53.77 kg/ha to yield annually in Mexico’s Yaqui Valley during 1962-2002. Estimates of the gains attributed to CIMMYT’s breeding program on a global scale equal 481.47 million (2002) USD annually from 1990-2002. CIMMYT’s average total wheat breeding cost in from 1990-2002 was roughly 13.95 million USD making the average cost-benefit ratio approximately 1:34.

Master of Science / Department of Agronomy / Johanna A. Dille / Corn yield potential is limited by water deficit stress and limited soil nitrogen. Field and greenhouse experiments were conducted near Manhattan, KS in 2005 and 2006. The field experiment evaluated the influence of nitrogen (N) rate and increasing Palmer amaranth (PA) density grown alone and in competition with corn in two moisture environments. In 2006 the dryland environment was very drought stressed, while 2005 had more intermediate conditions. Weed-free corn yields were approximately half in dryland environments compared to the irrigated environment across years. Increasing PA density increased corn yield loss similarly in both 2005 environments and in 2006 dryland environment across all N rates. In the 2006 irrigated environment corn yield loss was increased by decreasing N rate and increasing PA density. Maximum predicted yield loss at high PA densities in both 2005 environments was 20-54% while in 2006 dryland environment, maximum yield loss was 95% and in the irrigated environment was 62%. In general, soil moisture environment was more critical than N rate or PA density when determining potential corn yield. In the greenhouse study a factorial arrangement of two irrigation methods and five crop-weed combinations (corn, PA, GF, corn/PA, and corn/GF) was established with two replications and three runs conducted. Two plants were grown in 25.4 cm diameter PVC pipe cut into 91.5 cm lengths. Irrigation application method included a surface and subsurface application. Plants were harvested at the V10 corn growth stage. No differences were detected between irrigation methods with respect to above- or below ground biomass production. Corn aboveground biomass was decreased by the presence of corn or PA but not GF. Below ground biomass information was presented as column totals because species could not be separated. There was no impact on root to shoot ratio, total below ground biomass, rooting depth, or root area across the crop-weed combinations except for the GF monoculture columns which were lower than all other crop-weed combinations. Future research needs to examine the light interception of corn and PA when grown at different N rates along with examining the influence of surface and subsurface irrigation practices on crop weed interactions and weed seed germination in a field setting.

Master of Science / Department of Statistics / Shie-Shien Yang / In fitting linear models, R[superscript]2 statistic has been wildly used as one of the measures to assess the goodness-of-fit and prediction power of the model. Unlike fixed linear models, at this time there is no single universally accepted measure for assessing goodness-of-fit and prediction power of a linear mixed model. In this report, we reviewed seven different approaches proposed to define a measure analogous to the usual R[superscript]2 statistic for assessing mixed models. One of seven statistics,Rc, has both conditional and marginal versions. Association mapping is an efficient way to link the genotype data with the phenotype diversity. When applying the R[superscript]2 statistic to the association mapping application, it can determine how well genetic polymorphisms, which are the explanatory variables in the mixed models, explain the phenotypic variation, which is the dependent variation. A linear mixed model method recently has been developed to control the spurious associations due to population structure and relative kinship among individuals of an association mapping. We assess seven definitions of R[superscript]2 statistic for the linear mixed model using data from two empirical association mapping samples: a sample with 277 diverse maize inbred lines and a global sample of 95 Arabidopsis thaliana accessions using the new method. R[superscript]2[subscript]LR statistic derived from the log-likelihood principle follows all the criterions of R[superscript]2 statistic and can be used to understand the overlap between population structure and relative kinship in controlling for sample relatedness. From our results,R[superscript]2[subscript]LR statistic is an appropriate R[superscript]2 statistic for comparing models with different fixed and random variables. Therefore, we recommend using RLR statistic for linear mixed models in association mapping.

Doctor of Philosophy / Department of Agronomy / Jay M. Ham / Land management practices such as burning and grazing may affect evapotranspiration (ET) and water balance of the tall grass prairie in the Flint Hills of eastern Kansas. Experiments were designed to estimate or measure the water balance of a stock-watering pond, and compare energy balance parameters and ET between grazed and ungrazed prairies. The hydrology of the native tallgrass prairie also was compared with mature stand of eastern red cedar (Juniperus virginiana), a site that was formerly prairie but converted to woodland when prescribed burning was discontinued. Data were collected to encompass the seasonal and yearly changes in weather variability. A host of micrometeorological sensors were used to measure surface atmosphere exchange and water losses, including: eddy covariance towers on prairie and woodland sites, specialized through fall and stem flow equipment at the woodland site, and an instrumentation raft at the stock watering pond. Results of the stock pond study showed that, on average, evaporation accounted for 64% of the water loss, followed by seepage at 31%, cattle use at 3% and transpiration at 2%. Comparisons of grazed and ungrazed areas showed that grazing caused only small, 3 to 6 %, reductions in seasonal ET compared with ungrazed pastures despite large differences in vegetative cover. In the woodland study, the 50-yr-old cedar canopy intercepted 54% of the precipitation received, thus decreasing the amount of precipitation reaching the soil. Evapotranspiration from woodland and prairie sites were similar, but net carbon exchange was greater on the prairie. Thus, the apparent water use efficiency during he summer months was 3 times greater on the prairie. Net radiation at the woodland site was 100 W m-2 higher compared with the prairie. This caused an increase in the woodland sensible heat flux and midday Bowen ratios, yet woodland latent heat flux and ET was similar to the prairie during the study, factors that could affect regional climate. Land management decisions regarding grazing, prescribed burning, and stock pond design will impact the watershed hydrology and productivity of the tallgrass prairie.

No description available.