Master of Science / Entomology / Ming-Shun Chen / Robert "Jeff" J. Whitworth / MicroRNA (miRNA) plays a role in nearly all the biological pathways and therefore may provide opportunities to develop new means to combat the Hessian fly, Mayetiola destructor, a destructive pest of wheat. This study presents a comprehensive analysis of miRNA species via deep-sequencing samples from Hessian fly second instar larvae, pupae and adults. A total of 921 unique miRNA species were identified from approximately 30 million sequence reads. Among the 921 miRNA species, only 22 were conserved among Hessian fly and other insect species, and 242 miRNA species were unique to Hessian fly, the remaining 657 share certain sequence similarities with pre-miRNA genes identified from various insect species. The abundance of the 921 miRNA species based on sequence reads varies greatly among the three analyzed stages, with 20 exclusively expressed in adults, two exclusively expressed in pupae and two exclusively expressed in second instar larvae. For miRNA species expressed in all stages, 722 were with reads lower than 10. The abundance of the remaining 199 miRNA species varied from zero to more than eight-fold differences among different stages. Putative miRNA-encoding genes were analyzed for each miRNA species. A single putative gene was identified for 594 miRNA species. Two putative genes were identified for 138 miRNA species. Three or more putative genes were identified for 86 miRNA species. The three largest families had 14, 23 and 34 putative coding genes, respectively. No gene was identified for the remaining 103 miRNA species. In addition, 1516 putative target genes were identified for 490 miRNA species based on known criteria for miRNA targets. The putative target genes are involved in a wide range of processes from nutrient metabolism to encoding effector proteins. Analysis of the expression patterns of miRNA and pre-miRNA for the miRNA family PC-5p-67443, which contains 91 genes, revealed that miRNA and pre-miRNA were expressed differently in different developmental stages, suggesting that different isogenes are regulated by different mechanisms, or pre-miRNAs had other functions in addition to as an intermediate for miRNA biogenesis. The large set of miRNA species identified here provides a foundation for future research on miRNA functions in Hessian fly and for comparative studies in other species. The differential expression patterns between a pre-miRNA and its encoded mature miRNA in a multigene family is an initial step toward understanding the functional significance of isogenes in dramatically expanded miRNA families.

Master of Science / Agricultural Economics / Vincent R. Amanor-Boadu / Ghana is the first Sub-Saharan African country to meet the Millennium Development Goals (MDG) of halving extreme poverty by 2015 and has made great improvement in four of the total eight MDG. Supporting by several aid programs, Ghana is right in the middle of an economic boom through agriculture with the stock exchange listing of the Ghanaian Agricultural Development Bank the 3rd of July 2015. However, many Ghanaian producers, specifically in the northern part, cannot take full advantage of this “boom” as they are dealing with poor soil quality and suboptimal levels fertilizer use. By increasing fertilizer use, producers can improve their field’s soil quality and achieve higher crop yields. The purpose of this study is to gain a better understanding of factors influencing the fertilizer use decision among smallholder producers in northern Ghana. A two-part model is estimated and takes into account number of important demographic, production and marking factors affecting producer’s decision on fertilizer adoption and amount used. Findings from this study have implication for designing private initiatives and public policies on improving smallholder producers’ agricultural productivity through the adoption of fertilizer.

Doctor of Philosophy / Department of Animal Sciences and Industry / J. S. Drouillard / The main goal of this dissertation was to evaluate different methods to protect polyunsaturated fatty acids (PUFA) against biohydrogenation by ruminal microorganisms. The first chapter is a review of literature pertaining to fat and fatty acid metabolism by ruminants and why these fats are relevant in human nutrition. The second chapter discusses effects of supplementing high concentrations of dietary copper to feedlot cattle to assess impact on PUFA profiles in tissues. Two levels of copper (10 or 100 mg/kg) were supplemented to diets with or without flaxseed during the finishing period for beef heifers. Added copper did not affect performance (P > 0.15). Final body weights were similar for cattle fed with or without flaxseed (P > 0.05), but cattle fed diets with flaxseed consumed less feed (P < 0.05), and therefore were more efficient (P < 0.01). Carcass traits were unaffected by treatment. Feeding elevated levels of copper did not appreciably alter proportions of PUFA in plasma, but plasma concentrations of omega-3 fatty acids were greater for heifers fed flaxseed (P < 0.05). Chapter 3 describes the evaluation of 3 novel methods to protect PUFA from microbial biohydrogenation activity within the rumen, including a) coextrusion of flaxseed with molasses; b) mixing with soybean meal followed by induction of a non-enzymatic browning reaction; and c) encapsulation of ground flaxseed within a matrix consisting of dolomitic lime hydrate (L-Flaxseed). The resulting products were evaluated using in vitro methods to estimate resistance to biohydrogenation or in 12- to 14-d feeding studies in which plasma concentrations of [alpha]-linolenic acid (ALA) were measured. Our processing strategies a) and b) did not improve efficiency of omega-3 fatty acid utilization (P > 0.1). The in situ study of L-flaxseed revealed a 2-fold increase in resistance of ALA to ruminal biohydrogenation, and the concentration in plasma after 14 d on feed was more than 4 times that observed in cattle fed ground flaxseed, suggesting the dolomitic lime hydrate was effective as a protective matrix. Chapter 4 evaluated performance, carcass traits, and meat quality of finishing beef heifers in response to feeding diets containing L-Flaxseed. Animals were blocked by weight, randomly assigned to individual pens, and pens to 6 dietary treatments: Control (high concentrate finishing diet), ground flaxseed fed at 3 or 6% of diet DM, L-Flaxseed fed at 2, 4, or 6%. Concentration of ALA in meat increased linearly in response to the level of flaxseed fed (P < 0.05); Moreover, transfer of dietary ALA to tissues increased by 47% when flaxseed was encapsulated within the dolomitic lime matrix. Cattle that were fed diets with 4 or 6% L-Flaxseed consumed less feed than other treatments (P < 0.05), which adversely affected feedlot performance and carcass traits.

Master of Science / Entomology / C. Michael Smith / The bird cherry oat aphid, Rhopalosiphum padi, and one of the viruses it vectors, barley yellow dwarf virus (BYDV), form a very damaging pest unit on cereals. Understanding how people can better manage crops to prevent damage or recognize environmental or geographic factors that put their crops at risk for BYDV could lead to improved virus aphid management strategies. One of the most successful methods for mitigating pest damage is using pest-resistant varieties of crops. Seven candidate wheat varieties were screened for resistance to R. padi, by testing aphid population densities and aphid host choice. Results of this research identified six varieties of wheat that show resistance to R. padi. One of the major knowledge gaps in BYDV management is forecasting potential damage. Our objective was to create viral presence maps, to start building the foundation of correlations between persistent and changing frequency of viruliferous R. padi. The results of BYDV assays in R. padi in wheat fields across Kansas indicated that the amount of BYDV infection in viruliferous aphids changes rapidly from year to year, and differs considerably between geographic regions and field landscape characteristics in Kansas. Neonicotinoid wheat seed treatment is a management technique that reduces R. padi populations. However, a common question among producers is whether or not seed treatments stop viral transmission. Results of greenhouse seed treatment experiments with plants from neonicotinoid treated and untreated seed infested with viruliferous R. padi indicated no significant difference in viral transmission due to seed treatment. This new information about R. padi wheat varietal resistance, geographic distribution of BYDV in Kansas, and neonicotinoid seed treatment creates a better understanding of aphid-virus-wheat interactions. Results from this thesis directly enhance producer ability to forecast risk from BYDV, select wheat varieties that effectively reduce R. padi as a BYDV vector, and to make better decisions about the use of insecticide to reduce BYDV infection.

Doctor of Philosophy / Department of Agricultural Economics / Dalton, Timothy J. / Essay one evaluates two farmer field schools aimed at promoting conservation agricultural practices. The field schools were conducted and offered to approximately 1/3 of all individuals surveyed in a baseline in 2010. These same farmers were resurveyed in 2012 in order to determine whether their knowledge of conservation agriculture practices had changed using a double-difference approach. The approach was also used to determine whether innate perceptions and biases against conservation agriculture have changed over time due to training in the field schools. These findings are supported with enterprise budgets of conservation practices to determine whether knowledge or on-farm economics limit adoption of conservation practices. The data showed that farmer-to-farmer communications are effective tools for raising knowledge. Essay two examines the interdependence of sustainable agricultural intensification practices (SAIPs) in order to better understand the constraints and incentives for the adoption of components and “packages” of components. The impact of accumulated knowledge score on the adoption of SAIPs was assessed using data from 168 participant and non-participant farm households that completed a survey in 2014 and 2012 from the Upper West region of Ghana. From a three-step regression, our findings show knowledge of participant household improved with evidence of knowledge spillover to non-participant. Participation, age and gender of the head of household and experience were factors impacting farm household knowledge score change on SAIPs. The study found that, knowledge score through the treatment effect impacts adoption of SAIPs which are complementary. Younger household heads and experience in farming are also found to likely impact adoption. Essay three estimates technical efficiency (TE) scores for millet and sorghum and evaluates the impact of soil and water conservation methods on TE scores. The paper also examines the sensitivity of TE scores on the distributional assumptions of the one-sided error using data from 518 and 754 farm households producing millet and sorghum respectively from a random national household survey in Niger. A Cobb-Douglas stochastic frontier model was used. The mean TE scores range from 52% to 66% and 35% to 60% respectively for adopters and non-adopters of soil and water conservation methods in millet production based on the distributional assumptions of the one-sided error. For sorghum production, the mean TE scores range from 47% to 63% and 39% to 63% respectively for adopters and non-adopters of soil and water conservation methods based on the distributional assumptions of the one-sided error. This suggests inefficiencies in the production of millet and sorghum and hence, the potential to improve output using existing technology. Adopters are relatively more efficient than non-adopters of soil and water conservation methods. The TE score differences in millet production are explained by location of household (rural), educational level and adoption of soil and water conservation. The efficiency score differences in sorghum can be explained by household size, educational level and soil and water conservation adoption. We also found TE scores are sensitive to the distributional assumptions of the one-sided error using the farm household level data.

Master of Science / Animal Sciences and Industry / Micheal J. Brouk / Study 1 was performed to assess the effect of an evaporative cooling system (ECS) on core body temperature (CBT) and lying times in lactating dairy cows. Respiration rates and rear udder temperatures (T[subscript u]) were also measured. Trial 1 contained 3 environmental treatments while trial 2 contained 2 environmental treatments. Treatments were: OFF (Cyclone fans and fog shut off), FAN (Cyclone fans only, no fog), and FANFOG (Cyclone fans and fog on) and cows exposed to these 3 environments were housed in a bedded pack barn (PACK) equipped with an ECS or a tie-stall barn (TIE). TIE and PACK cows moved between barns every 8 h for milking and both groups moved opposite of each other. Ambient, barn temperature and relative humidity (RH) measurements in addition to vaginal temperatures and lying times were recorded by sensors which took measurements at 1 min intervals. Respiration rates (BPM), for PACK cows during FANFOG were reduced (P < 0.05) when compared to TIE (53 ± 2.0 vs 64 ± 2.0, respectively) in trial 1. Similar results were found in trial 2. Rear udder temperature was measured and found to be decreased (P < 0.05) in PACK cows while housed under FANFOG vs TIE in trial 1. These results could not be repeated in trial 2 because of greater ambient temperatures. Core body temperature (CBT) was reduced during each trial as shown by less time spent above 39.0°C during FANFOG. During trial 2, PACK spent 5.7 and 8.5 h/d less over a CBT of 39.0°C compared to TIE cows. Total daily lying time was tracked and found to increase for cows exposed to the ECS during PACK but no difference between PACK and TIE. In study 2, the same ECS was used but its effects on nonlactating dairy cows were studied. There was a treatment by h interaction for vaginal temperature showing the greatest effects during the afternoon h where FANFOG had numerically decreased CBT vs FAN. FANFOG cows spent reduced time over a CBT of 39.0°C and greater time < 38.0°C. FANFOG cows also had increased lying times of 1.7 h/d compared to FAN.

Master of Science / Department of Agricultural Economics / Vincent Amanor-Boadu / Food insecurity affects 16 percent of the population in northern Ghana, making food security a major focus for many of the development programs in the country. A major initiative to overcome food insecurity may involve the development of effective storage systems to help farmers control the flow of their production to markets and, thus, have higher control over the price they receive. While the poor storage infrastructure in the region is known, there is lack of knowledge about the factors motivating farmers to utilize storage in spite of these conditions. The purpose of this paper is to increase understanding about storage behavior of smallholder maize farmers in northern Ghana. A review of the literature indicates credit plays a large role in storage behavior. The purpose of this thesis is to bridge the gap between literature on storage as a bank, and on storage as a way to ensure food security. Specific objectives include: i) estimating formal and informal credit’s effects on storage behavior of smallholder maize growers, and ii) examining the effect of credit at various levels of storage. This analysis is based on data collected on 527 farmers in Ghana’s four northernmost regions obtained from an agricultural production survey conducted in 2013 and 2014 by USAID-METSS – a project funded by the Economic Growth Office of the USAID mission in Ghana. Ordinary Least Squares modeling was employed to determine the marginal effects of formal and informal credit on storage. Additionally, quantile regression modeling estimated the marginal effects at different levels of storage, including the median. The results indicate that formal credit and on-farm storage had statistically significant negative effects on maize storage at both the mean and median, but only farm output proved to be statistically significant at different levels across the storage distribution. On-farm storage had a statistically significant negative effect on storage when compared to storing off-farm at facilities like local store rooms. Carryover storage from the previous year tested to have statistically significant negative effects on storage. Under the conceptual framework utilized for this study, the results suggest that using formal credit increases a household’s food security.

Master of Agribusiness / Department of Agricultural Economics / Ted Schroeder / Selection of a herd sire has always been of paramount importance given the initial financial investment and their contribution and effect on the genetic make-up of a beef herd. Data was collected from the nation’s longest consecutively run bull test conducted at the University Farm of Oklahoma Panhandle State University (OPSU). The Bull Test and Bull Sale data utilized were collected from 2008-2013. Performance data was collected over a 112 day test period with data collection occurring at 28 day intervals. The top seventy bulls from each year’s test were selected based upon a performance index of ½ ADG and ½ weight per day of age (WDA), and a semen quality and motility score of excellent and sold at auction. Angus bulls were the focus of the study as they represented the vast majority of individuals sold. Three hedonic pricing models were created to try to determine what attributes buyers at the OPSU bull test sale were placing emphasis on. The initial hedonic model contained production data that included BW, ADG, WDA, Julian age, final test weight ultrasound data, and a dummy variable for sale year. The second model utilized all production data and added genetic variables in the form of production EPDs (Calving Ease Direct (CED), BW, Weaning Weight and Yearling Weight) and maternal EPDs (Calving Ease Maternal, Maternal Milk). The third model included the variables from the first and second models with the inclusion of carcass EPDs (Marbling, Ribeye Area (REA) and FAT). Year was significant in all three models however there was less of an effect on price as more variables were included. In model one, the production facts that were of significance were: ADG (P<0.01), BW (P<0.01) and final test weight (P<0.01). In the second model, ADG, BW and final test weight retained their significance at the P<0.01 level. The only production EPD that was significant (P<0.05) was CED. In the third model, years, ADG and BW were still significant (P<0.01). Final test weight (P=0.70) and CED (P = 0.132) had substantial changes. The carcass EPD ribeye area had a P value of 0.057. Producers who are placing bulls on test can utilize the given information to assist with their selection. It cannot go unsaid that while single trait selection can be very detrimental; ADG was significant across all models. The study indicates that performance and growth are of utmost importance to buyers, followed by birth weight consideration.

Master of Agribusiness / Department of Agricultural Economics / Allen M. Featherstone / Farm Credit Mid-America is experiencing strong growth due to the success of the farming sector in our four state territory of Tennessee, Kentucky, Indiana, and Ohio. The company is well positioned to meet the financial demands of its customers and they have an aggressive growth plan to increase total assets from $18 billion to $25 billion in five years. They also plan to add 600 new employees in that time period. Determining the appropriate level of capital to sustain growth and meet the demands of its customers will be a primary objective of the organization over the next five years. Permanent capital is viewed as a percentage of total assets at Farm Credit Mid-America with the ideal amount between 14% and 16%. A detailed analysis of the current capital level, regulatory requirements, and the projected future financial position of the company was completed to: · Define and understand capital as it applies to Farm Credit Mid-America; · Research the current capital levels for Farm Credit Mid-America; · Compare capital levels of Farm Credit Mid-America to capital levels of other Farm Credit Associations and other banks; · Understand Basel III Accords and how it applies to Farm Credit Mid-America’s capital requirements; · Complete sensitivity analysis with multiple scenarios applied to the current Farm Credit Mid-America loan portfolio to determine the effect certain events may have on capital levels; · Determine if Farm Credit Mid-America is appropriately capitalized based on the other objectives. When looking at the results, it is determined that current capital levels are in line with other Farm Credit associations and competitors. Also, Farm Credit Mid-America has met the Basel III guidelines for minimum capital requirements. The sensitivity analysis included a wide range of scenarios from normal growth rates to extreme loan portfolio distress and the effects those scenarios would have on permanent capital. The permanent capital ratio exceeded the minimum standard of 12% on all sensitivity analysis scenarios. Therefore, based on the objectives of this thesis Farm Credit Mid-America appears to be adequately capitalized.

Master of Agribusiness / Agricultural Economics / Kevin Gwinner / House-Autry Mills is a food manufacturing company located in Eastern North Carolina. It produces a variety of products including corn meals, breaders, hushpuppies and biscuits. House-Autry Mills has been producing these types of products for over 200 years and is always looking for ways to promote and expand its business. Before House-Autry Mills decides to add a new line of products, it must conduct a lot of research and evaluate the success in this potential market. The purpose of this thesis is to look at the data available, and determine if grits will be a good fit for House-Autry, and for the market in general. Chapter I is an introduction to the entire thesis project. Much of the literature I reviewed deals with successfully bringing new products to the market. It also goes through an eight-step decision making process when determining if the project should be worked on, or if the project should be dropped at various stages. This is Chapter II of the thesis. The Methods and Data Collection section of this thesis is located in Chapter III. This chapter will go through the process of forming a focus group, screening the participants, and determining what types of questions should be asked, based on the feedback that the firm wants to receive. I also look at several data sets collected through Infoscan Resources, Inc. There are two chapters that contain the results. Chapter IV looks at the results found from the data collected, and chapter V looks at the results that were observed during the two focus groups findings. The final chapter is where my conclusion and recommendations are listed. I included the action that House-Autry Mills took, and also my thoughts on that action. The section goes through different recommendations including the market first approached, risk involved in the new product, the benefit of keeping the price competitive, and the eventual expansion of the line.