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.

In the southwestern United States, rising costs and limited availability of water have lead to irrigation scheduling based on plant stress indicators in an effort to conserve water. This research was conducted to better define the recovery rates of transpiration, stomatal resistance, and leaf water potential in field grown extra long staple cotton (Gossypium barbadense cv. Pima S-6) following varied durations of water stress. Three water stress treatments were maintained by scheduling irrigations at different Crop Water Stress Index (CWSI) values. Plants irrigated at 0.19 and 0.68 CWSI units needed 72 hours for plant water potential to recover, while plants irrigated at 0.41 CWSI units needed only 24 hours. Water stress had a smaller effect on the recoveries of stomatal resistance and transpiration. Stomatal resistance recovered within 24 hours for all plants regardless of water treatment. Transpiration recovered within 24 hours for plants irrigated at 0.19 CWSI units, and within 48 hours for plants irrigated at 0.41 and 0.68 CWSI units.

Carbon sequestration in small-scale farming systems in semi-arid regions offers the possibility to increase local soil fertility, improve crop yields, enhance rural people's wellbeing, and strengthen the resilience of agricultural systems while reducing CO2 accumulation in the atmosphere and, thus, contributing to climate change mitigation. A variety of management practices and land use options have been proposed to increase carbon uptake and reduce system losses. So far, less attention has been paid to local smallholders, the ultimate agents of anticipated community carbon projects, and the complexity, diversity, and dynamics of their livelihoods in a highly variable and risk-prone environment. A hybrid research approach, combining biophysical, economic, cultural, and institutional analysis, was used to assess the potential for soil carbon sequestration in the Old Peanut Basin of Senegal. In situ soil and biomass measurements provided current carbon accounts. Historic carbon changes and future sequestration rates under various management practices were simulated with CENTURY, a biogeochemical model. The simulation results well represented general historic trends and carbon storage potential. However, they did not accurately reflect variable and flexible site-specific management strategies as farmers adapt to stress, shock, and crises over time. To account for these, distinct pathways of agricultural and environmental change were examined in Wolof and Serer villages and viable options for carbon sequestration were evaluated. Systems analysis was used to explore the various components that influence farmers' perceptions, choices, and decisions with respect to land management. Results showed that resource endowment and institutional and policy incentives determine which carbon sequestration activities might be most appropriate for different groups of farmers. Finally, a cost-benefit analysis and a cash-flow analysis (using STELLA) were performed to assess the financial profitability and economic feasibility of proposed management strategies. The study reveals large differences in these measures between farmers with low and high resource endowments. In most cases, local smallholders are not likely to have the investment capital necessary to implement the alternative management practices. A farmer-centered approach to carbon sequestration, as proposed by the study, can be used to more effectively address the needs and capacities of smallholders in dryland carbon offset programs.

Elongation factor 1A is one of the lysine-rich proteins increased in o2 mutants, and its concentration is highly predictive of the protein-bound lysine content of the endosperm. Understanding the biological basis of this relationship could help to explain the mechanisms of lysine accumulation in the endosperm, providing new insights for developing maize genotypes with better nutritional quality. Three different eEF1A isoforms were purified from developing endosperm and investigated in their accumulation, structural and functional activities. The accumulation of the isoforms appears to be developmentally regulated and independent of the o2 mutation. The purified proteins differed in their ability to bind F-actin in vitro, suggesting they are functionally distinct. The isoform that binds actin most effectively was the most predominant in high eEF1A genotypes, which may be related to enhanced cytoskeleton formation, and therefore increased synthesis of cytoskeleton-associated proteins in these genotypes. Tandem mass spectrometry revealed each isoform is composed of the four same gene products, which are modified post-translationally by methylation and phosphorylation. The chemical differences that account for their different actin binding activities could not be determined. Recombinant inbred lines varying in eEF1A content were developed from a cross between a high (Oh51Ao2) and a low (Oh545 o2) eEF1A inbred. The parental inbreds and RILs with the highest and lowest eEF1A content were used to investigate patterns of gene expression and protein synthesis. Transcript profiling with an endosperm EST microarray identified about 110 genes coordinately regulated with eEF1A. These genes encode proteins involved in several biological structures and processes, including the cytoskeleton, the endoplasmic reticulum and the protein synthesis apparatus. The content of alpha-zein and several cytoskeletal proteins was measured in high and low eEF1A inbred lines, and the levels of these proteins were found to correlate with that of eEF1A. Thus, higher levels of eEF1A may be related with a more extensive cytoskeletal network surrounding the rough ER and increased translation of mRNAs encoding cytoskeleton-associated proteins, all of which contribute significantly to the lysine content of the endosperm.

Withholding irrigation to alfalfa (Medicago sativa L.) during summer, a management strategy referred to as summer irrigation termination (SIT), has been suggested as a way to conserve water in desert environments. SIT may decrease productivity of alfalfa stands, although such negative effects may be reduced if cultivars with improved tolerance to SIT could be developed. This research was undertaken to determine how improved tolerance to SIT could be achieved through plant breeding. Single spaced plants of an extremely nondormant alfalfa population were grown in a field trial in Tucson, AZ and exposed to SIT in 1994 and 1995. These plants were used to identify traits associated with tolerance to SIT and represented parental material in a selection experiment. Direct selection for minimal reduction of forage yield following SIT was conducted under two stress intensities (lengths of SIT) and compared to indirect selection for characteristics potentially associated with dehydration avoidance. None of these selection criteria improved post-SIT forage yield relative to a random sample of plants from the parental population. This lack of response from selection was attributed to stress intensities that were not sufficiently high to fully expose genetic variation for yield following SIT. Physiological studies showed that high concentrations of total nonstructural carbohydrates (TNC) in crown tissue are positively associated with tolerance to SIT. Using TNC concentrations as an indirect selection criterion may therefore represent a more promising approach in improving tolerance to SIT than direct selection for post-SIT yield. Crown tissue was shown to die if the tissue moisture content fell below about 42%. This threshold value was used to predict whole-plant mortality of alfalfa grown in solid-seeded plots comparable to commercial fields. Crown samples were taken at five locations within the field along a soil gradient that caused whole-plant mortality to vary from 0.5 ± 0.5 to 48.7 ± 4.1%. Predicted values closely followed this change in observed mortality rates (r² = 0.97*) but tended to overestimate actual mortality on average by 4.2%. Alfalfa growers may be able to minimize mortality using this simple method to predict mortality during SIT and to reschedule irrigation accordingly.

Collaborative plant breeding (CPB) is an approach to crop improvement incorporating close attention to local biophysical and sociocultural environments and interaction between farmers and plant breeders. CPB may have particular potential for improvement in highly stress-prone environments and for low-resource, traditionally based agricultural communities, situations where more conventional approaches have not been effective. However, CPB will require methodological adjustments or innovations relevant to the smaller scale of its target area and its participatory approach. This study investigated methodologies useful to CPB, working with maize farmers from two communities in the Central Valleys of Oaxaca, Mexico. A method for rapid estimation of broad sense heritability (H) was applied in farmers' maize fields. H estimates for morphophenological traits were compared with narrow sense heritability (h2) from half sib family analysis of five of the same populations and with published estimates. Absolute values of H were larger than h2 from this study and the literature, however trait ranking was the same as in the literature, but differed from h2 rankings from this study. With an understanding of their limitations, these rapid, economical estimations provide useful information for CPB work on-farm, where empirical information is frequently lacking. Collegial interaction based on the knowledge and skills of farmers and breeders will depend upon understanding those in terms relevant to each group. Methods from social and biological sciences were integrated to understand selection and its consequences from farmers' perspectives but based on concepts used by plant breeders. Information was elicited regarding farmers' perceptions of their maize populations, growing environments and expectations for response to selection. Farmers' decisions about varietal repertoires imply assessments of local genetic and environmental variation. Traits of high and low heritability are distinguished, as reflected in expected selection response. Farmers' selection practices were not always effective yet they understood the reasons for this and had no expectations for selection response in some traits given the methods available. Farmers' statements, practices and perceptions regarding selection and the genetic response of their maize populations to their selection indicate selection objectives different than may be typically assumed, suggesting a role for breeder and farmer collaboration.