Agroforestry production methods present one option for addressing growing concerns about the long term sustainability of intensive coffee production techniques. A study was designed to compare the effects of fertilization and shading from two leguminous species, Erythrina poeppigiana and Chloroleucon eurycyclum, on coffee grown at a Costa Rican research site. Coffee below biannually pruned, conventionally fertilized Erythrina exhibited the highest photosynthetic performance under both low and high light levels as well as greater biomass and higher N concentration. Soil P did not affect coffee performance, although shade trees on sites with higher soil P fixed more N compared to trees grown on low P sites, most of which were not found to be fixing. Results suggest shade mechanisms are the most important drivers of coffee adaptation in coffee agroforestry systems, though proper soil nutrient management and legume species pairing also appear to augment coffee response to microclimate conditions.

Agroforestry production methods present one option for addressing growing concerns about the long term sustainability of intensive coffee production techniques. A study was designed to compare the effects of fertilization and shading from two leguminous species, Erythrina poeppigiana and Chloroleucon eurycyclum, on coffee grown at a Costa Rican research site. Coffee below biannually pruned, conventionally fertilized Erythrina exhibited the highest photosynthetic performance under both low and high light levels as well as greater biomass and higher N concentration. Soil P did not affect coffee performance, although shade trees on sites with higher soil P fixed more N compared to trees grown on low P sites, most of which were not found to be fixing. Results suggest shade mechanisms are the most important drivers of coffee adaptation in coffee agroforestry systems, though proper soil nutrient management and legume species pairing also appear to augment coffee response to microclimate conditions.

The root systems of five tree species (Populus deltoides × nigra clone DN-177, Juglans nigra, Quercus rubra, Picea abies, and Thuja occidentalis) are described following non-intrusive imaging using ground penetrating radar (GPR). This research aimed to 1) assess the utility of GPR for in situ root studies and 2) employ GPR to estimate tree root biomass and distribution in an agroforestry system in southern Ontario, Canada. The mean coarse root biomass estimated from GPR analysis was 54.1 ± 8.7 kg tree-1 (± S.E.; n=12), within 1 % of the mean coarse root biomass measured from matched excavations. The vertical distribution of detected roots varied among species, with T. occidentalis and P. abies roots concentrated in the top 20 cm and J. nigra and Q. rubra roots distinctly deeper. I evaluate these root systems based on their C storage potential and complementary root stratification with adjacent crops.

The root systems of five tree species (Populus deltoides × nigra clone DN-177, Juglans nigra, Quercus rubra, Picea abies, and Thuja occidentalis) are described following non-intrusive imaging using ground penetrating radar (GPR). This research aimed to 1) assess the utility of GPR for in situ root studies and 2) employ GPR to estimate tree root biomass and distribution in an agroforestry system in southern Ontario, Canada. The mean coarse root biomass estimated from GPR analysis was 54.1 ± 8.7 kg tree-1 (± S.E.; n=12), within 1 % of the mean coarse root biomass measured from matched excavations. The vertical distribution of detected roots varied among species, with T. occidentalis and P. abies roots concentrated in the top 20 cm and J. nigra and Q. rubra roots distinctly deeper. I evaluate these root systems based on their C storage potential and complementary root stratification with adjacent crops.

Master of Science / Department of Animal Sciences and Industry / Michael Tokach / In 3 experiments, 4,720 pigs were used to determine the effects of: 1) dietary fat and feeding duration on growth performance and fat quality in finishing pigs; or 2) a novel protease or 3) increasing levels of Zn amino acid complex (ZnAA) or ZnO on finishing pig performance. Experiment 1 tested the effects of feeding tallow, soybean oil, or a blend of the two for various feeding durations (d 0 to 42, 42 to 84, or 0 to 84). Overall, pigs fed added fat for the entire 84 d had improved G:F compared to those fed a control diet. Additionally, pigs fed additional fat for the entire study had improved ADG and G:F as well as increased d 84 BW compared to pigs fed additional fat for 42 d. Increasing the feeding duration of soybean oil lowered monounsaturated fatty acids and increased polyunsaturated fatty acid concentrations while these values remained relatively unchanged by the addition of tallow. There were feeding period by fat source interactions for fatty acid composition and iodine value for belly and backfat, but not jowl fat, indicating a longer turnover rate for jowl fat compared to belly or backfat. In Exp. 2, adding a protease to a nutrient deficient diet increased ADFI and tended to increase ADG compared to pigs fed a negative control diet. There were no differences observed in ADG, ADFI, or G:F between pigs fed a positive control diet, formulated to 90% of the pigs SID lysine requirement, and those fed a negative control diet plus the protease, which would suggest the release values attributed to the enzyme were accurate. In Exp. 3, supplementing additional Zn from either ZnAA or ZnO at 25, 50, or 75 ppm in finishing diets for commercial finishing pigs was evaluated. Overall, no differences were observed in ADFI, but a Zn source by level interaction was observed for ADG and G:F, as pigs fed increasing ZnO were observed to have similar performance, while pigs fed added levels of 25 and 50 ppm Zn from ZnAA had decreased performance compared to those fed the highest level of ZnAA.

Doctor of Philosophy / Department of Plant Pathology / Frank White / The genus Xanthomonas consists of bacterial species causing economically important plant diseases in major crops. In a wide variety of Xanthamonas species, the transcription activator-like (TAL) effectors (proteins) are synthesized and secreted into host cells, whereby they enter the plant nucleus. TAL effectors bind specific host gene promoters, inducing the expression of the targeted genes, which in some cases leads to either resistance or an enhanced state of disease susceptibility. The TAL effectors in individual Xanthomanas species and their targets in host plants have been characterized in relatively few cases. The premier example is the induction of any one member of a clade of sugar transporter genes in rice by TAL effectors of the bacterial blight pathogen X. oryzae pv. oryzae, where induction of the susceptibility (S) genes was shown to be required for the disease process. TAL effector genes are present in a wide variety of Xanthomonas species other than X. oryzae pv. oryzae. My dissertation focuses on the characterization of the TAL effectors in the citrus bacterial canker (CBC) and soybean bacterial pustule pathosystems. In CBC, CsLOB1 was identified as the S gene targeted by multiple major TAL effectors from CBC causal strains. Furthermore, another two members in family of citrus LBD family, although not identified as targets in the field, can serve as S genes in CBC. Initial analysis of bacterial pustule disease of soybean indicates that the TAL effector TAL2 of X. axonopodis pv. glycines is a virulence effector and associated with the expression of two candidate S genes, which encode a member of the ZF-HD transcription factors and a member of aluminum activated malate transporter family. These studies will enhance our understanding of plant-bacterial interactions and evolution of disease susceptibility, and also inform development of durable disease resistant crop varieties.

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.