Drought stress was studied in rice (Oryza sativa) and maize (Zea mays) to identify drought-responsive genes and associated biological processes. One experiment with rice examined drought responses in vegetative and reproductive tissues and identified drought-responsive genes in each tissue type. The results showed that brief periods of acute drought stress at or near anthesis reduced photosynthetic efficiency and ultimately lowered grain yield. Yield was reduced as a result both of fewer spikelets developed and of lower spikelet fertility. Affymetrix arrays were used to analyze global gene expression in the transcriptomes of rice vegetative and reproductive tissue. Comparative analysis of the expressed genes indicated that the vegetative and reproductive tissues responded differently to drought stress. An experiment was conducted with maize, using GS-FLX pyrosequencing to identify differentially expressed genes in vegetative and reproductive tissues; and these results were compared with those from the just-described rice transcriptome. Some of the drought-responsive genes in the maize reproductive tissue were validated by quantitative real time polymerase chain reaction (qRT-PCR). The differentially expressed genes common to both maize and rice were further analyzed by gene ontology analysis to reveal core biological processes involved in drought responses. In both species, drought caused a transition from protein synthesis to degradation, and photosynthesis was one of the most severely affected metabolic pathways. In a validating experiment, a drought-responsive transcription factor found in rice and dubbed HIGHER YIELD RICE (HYR) was constitutively expressed in rice, and the transgenic HYR plants were studied. Under well-watered conditions, the HYR plants developed higher rates of photosynthesis, greater levels of soluble sugars (glucose, fructose, and sucrose), more biomass, and higher yield. They also exhibited a drought-resistant phenotype, with higher water use efficiency, photosynthesis, and relative leaf water content under drought stress. Taken together, these studies demonstrate the potential value of newer technologies for identifying genes that might impart drought resistance and for using such genes to make crops more productive either in the presence or in the absence of drought stress. / Ph. D.

<p>Vertical farming (VF) as a newer sector of controlled-environment agriculture (CEA) is proliferating as demand for year-round, local, fresh produce is rising. However, there are concerns regarding the high capital expenses and significant operational expenses that contribute to fragile profitability of the VF industry. Enhancing resource-use efficiency is a strategy to improve profitability of the VF industry, and different approaches are proposed in the three chapters of this dissertation. LEDs are used for sole-source lighting in VF, and although they recently have significantly improved electrical efficiency and photon efficacy, the Lambertian design of the illumination pattern leads to significant loss of obliquely emitted photons beyond cropping areas. In chapter 1, close-canopy lighting (CCL) is proposed as one effective energy-saving strategy, through which unique physical properties of LEDs were leveraged, and two CCL strategies (energy efficiency and yield enhancement) were characterized at four different separation distances between light-emitting and light-absorbing surfaces. Dimming to the same light intensity at all separation distances resulted in the same biomass production while significant energy savings occurred at closer distances. Significantly higher light intensity and yield were achieved under closer separation distances in the yield-enhancement strategy for the same energy input. The energy-utilization efficiency (g fresh/dry biomass per kWh of energy) was doubled in both scenarios when the separation distance between LED emitting surface and crop surface was reduced maximally. At reduced separation distances, the chance of photon escape from growth areas is less, and canopy photon capture efficiency is improved.</p><p>Optimizing environmental conditions for indoor plant production also helps improve resource-use efficiency for the nascent vertical-farming industry. Although significant technical advancements of LEDs have been made, use of efficient far-red (FR) LEDs has yet to be exploited. As a recent proposed extension to traditional photosynthetically active radiation (PAR, 400-700 nm), FR radiation (700-750 nm) contributes to photosynthesis as well as photomorphogenesis when added to shorter wavelengths of traditional PAR. However, the interaction of FR with other environmental parameters such as CO2 is less studied. In chapter 2, the interaction effect of four FR fluxes (as substitution for red) in combination with three different CO2 concentrations were investigated at three distinctive stages of young-lettuce production. The highest biomass achieved at all stages occurred at 800 mmol mol-1 CO2 compared to 400 and 1600 mmol mol-1. A photomorphogenic effect of FR to promote leaf length was pronounced at the earliest stages of development, at which FR did not contribute to higher biomass accumulation. At more developed stages, 20 mmol m-2 s-1 of FR substituting for red contributed to biomass accumulation similar to shorter wavelengths of traditional PAR, whereas higher fluxes of FR in the light recipe resulted in undesirable quality attributes such as longer leaves.</p><p>Optimizing environmental conditions for indoor production with emphasis on light intensity and CO2 concentration at four distinctive stages of lettuce production was investigated in chapter 3. Utilizing the Minitron III gas-exchange system, light and CO2 dose-response profiles were characterized at four distinctive crop-development stages through instantaneous gas-exchange measurements at crop level. At all developmental stages, as CO2 concentration increased, photosynthesis increased up to 500 mmol mol-1, above which the incremental rate of photosynthesis was reduced. Light-dose response profiles were characterized at 400 or 800 mmol mol-1 CO2, and as light intensity increased, photosynthesis increased up to 650 mmol m-2 s-1. However, when instantaneous power (Watts) consumed for lighting was taken into consideration, power-use efficiency as the ratio of output photosynthesis increment to input power increment (to increase light intensity), decreased at higher light intensities. Vertical farming as a nascent and growing industry is facing limitations including marginal and even elusive profitability. Optimizing environmental conditions for indoor plant production such as these will help improve resource-use efficiency and profitability of the vertical farming industry.</p>

Short rotation woody crops (SRWC) are bred for rapid growth properties. Knowledge of how varying environmental conditions and endophytic bacteria impact physiology are needed to make planting recommendations. Three eastern cottonwood (EC) and three hybrid poplar (HP) varietals were planted in replicate blocks at upland and alluvial sites. Whole-tree water use and water use efficiency (WUE) were measured using heat-dissipation sap flow and related to overall productivity. Productivity measurements were higher at the upland site. Sap flow was higher at the upland site and for endophyte treated individuals. WUE was higher at the alluvial site and for EC. WUE and leaf area index (LAI) were significantly correlated with biomass (negatively and positively respectively). Overall, HP performed better at the upland site, EC at the alluvial site. These results are beneficial in further testing of optimal site and genotype pairings for SRWC.

No description available.

Flooding is a major environmental stress that damages agricultural production worldwide. Using the key regulator of submergence tolerance in rice, SUB1A, as a model, we have advanced our understanding of how plants coordinate transcriptional, hormonal, and metabolic responses to submergence. However, the contribution of SUB1A to recovery from sublethal submergence is still unknown. This study revealed SUB1A's additional role in the recovery phase: promotion of a rapid return to normal metabolic status upon desubmergence through quick recovery of photosystem II photochemistry and carbon fixation. We also investigated how SUB1A differentially regulates adaptive responses in two functionally distinct leaves, growing and mature leaves, under submergence. This study revealed that rice plants promote rapid carbohydrate and nitrogen remobilization and transport in mature leaves, supporting quick elongation growth of growing leaves. In the presence of SUB1A, these metabolic processes were suppressed in mature leaves, resulting in the avoidance of energy starvation in the source tissues. In growing leaves, SUB1A enhanced the accumulation of abscisic acid, but repressed the level of ACC, a precursor of ethylene, contributing to the restriction of elongation growth and leaf senescence in the sink tissues. Application of nitrogen fertilizers is a necessary step to maintain high grain yield in cereals, but plants absorb only 30-50% of supplied N. Wheat, one of the most widely grown crops in the world, requires a high level of nitrogen application to maintain grain yield and protein content. In this study, we investigated how nitrogen input affects the accumulation of major N and C compounds and expression of genes associated with N and C metabolism in flag leaves of wheat. We used two genotypes with distinct nitrogen use efficiencies (NUE), VA08MAS-369 and VA07W-415. VA08MAS-369 displayed higher grain yield, stover biomass, and stover N content at low N, which results from greater N-uptake efficiency in this genotype. Consistently, high N-uptake efficiency was reflected by increased mRNA accumulation of nitrate transporters and their transcriptional regulator, NAC2, in flag leaves at the post-anthesis stage. Overall, this study advanced our knowledge of the important mechanisms in plant response to flooding and N limitation in these key staple cereals. / PHD

Increasing drought and salinity tolerances in economically important trees adapted to dry land areas is key challenge for maintaining the socioeconomic welfare of dry land areas. Strategies to improve drought and salt tolerance must examine the tree physiological mechanisms that link to the trees survival and growth. This study examined physiological adaptive traits allowing Senegalia senegal to grow better in both saline and dry lands. We conducted two greenhouse experiments and one field study to characterize growth, photosynthetic capacity, water use efficiency (WUE) and gum arabic yield potential among different Senegalia senegal provenances. In the first experiment, we tested early growth and photosynthetic response of seed sources to a cyclic drought treatment. The second greenhouse study examined seed source response to drought, salinity and fertility conditions. Gum yield assessment, growth and WUE of mature trees were determined from a field trial. In general, results showed a high intra genetic variability of Senegalia senegal on gum yield, biomass accumulation and growth. Ngane provenance presented superior growth characteristics as both mature trees and seedlings and exhibited a more conservative water use strategy under drought. Both greenhouse studies revealed similar photosynthetic capacity among Senegalia senegal genotypes when conditions are not limiting. However, when factors such as salinity, fertility and severe drought are involved, different physiological and morphological responses appear and at times this was dependent on seed source. But, at moderate drought stress (chapter 2), no drought by provenance interaction was found. Results of chapter 3 revealed that Ngane has larger stomata with low density in comparison with Diamenar and Kidira provenances. With the exception of Ng21B1, all seed sources displayed similar adaptations to salt stress in term of biomass accumulation. Fertilizer increased total biomass of all seed sources from 63% to 213% for Ng21B1 and K17B19, respectively. However, salinity reduced the fertilizer effect on biomass increment. Leaf gas exchanges were affected by salinity and fertilizer within various responses among seed sources. Results of chapter 4 revealed that gum yield was found to be positively correlated with tree height, crown width, stem volume index and crown area index. Ngane and Diamenar appeared the best provenances in term of annual gum yield per hectare. Diamenar had a higher survival rate than Ngane. This finding reveals the need to consider the tradeoff between tree survival rate and individual tree gum yield in Senegalia senegal stands. In addition to being more sensitive to salinity, Ngane also seems to be more susceptible to low soil pH in terms of survival, but this result needs to be tested further. This study suggests that improvement of gum arabic production can be possible through genetic selection. But, for the best adapted genotypes, research should explore new genetic combination and investigate physiology and genetic diversity. Moreover, the findings on the relationship between soil pH and tree survival rate suggests a need for care in selecting appropriate sites for Senegalia senegal stands. Therefore, silviculture practices as well as genetic selection appear critical in improving gum arabic production. / Ph. D.

The PROTEOLYSIS 6 (PRT6) branch of the N-end rule pathway is a well-characterized negative regulator of flooding and low oxygen tolerance in plants. This study investigated the role of this pathway in adaptation to salinity stress in Arabidopsis and maize via physiological and molecular characterization of Arabidopsis prt6-1 and maize prt6 MU insertion mutants, respectively. Our study demonstrated that the loss of function mutation of prt6 in Arabidopsis activated hormonal and transcriptional responses associated with adaptation to salinity stress, enhancing high salt tolerance at seed germination, seedling, and adult plant stages. Our data also indicated that salinity tolerance conferred by the prt6 mutation is attributed to increased mRNA abundance of key transcriptional factors in ABA-dependent (AREB/ABFs) and independent (DREBs) pathways, together with the dominant expression of downstream dehydrins. Furthermore, this study revealed that the prt6 mutation enhances ethylene and brassinosteroid responses, resulting in restricted Na+ accumulation in roots and shoots as well as increased expression of dehydrin genes such as RD29A and RD29B. Maize prt6 mutant plants, contrary to our observation in Arabidopsis, showed lower seed germination, primary root elongation, and shoot biomass growth along with increased malondialdehyde (MDA) accumulation under high salt. Moreover, maize prt6 mutants exhibited reduced grain yield and yield-related components under high salt. These results indicate that PRT6 functions as a negative regulator for salinity tolerance in Arabidopsis, whereas this gene plays a positive role in salinity tolerance in maize. In wheat, we compared two genotypes with contrasting nitrogen-use-efficiency (NUE), VA08MAS-369 and VA07W-415, to dissect physiological and molecular mechanisms underlying NUE regulation. Our agronomic data revealed that line 369 maintained yield and yield-related parameters and exhibited greater NUE indexes relative to line 415 under N deficient conditions. Furthermore, our analyses suggested that the significantly higher nitrogen use efficiency (NUE) in line 369 could be attributed to the greater N uptake efficiency in this genotype. In fact, line 369 was able to maintain the development of root systems under N limitation. Consistently, genes encoding high-affinity nitrate transporters such as TaNRT2.1 and TaNRT2.2 were expressed more abundantly in the roots of line 369 than line 415 at limited N. Overall, the results of this study characterized physiological and molecular phenotypes associated with high N uptake efficiency in line 369. This is useful information for the development of new wheat accessions with improved NUE. / Doctor of Philosophy / In coastal areas, sea-level rise increases the chances of saltwater intrusion into cultivable lands, making a hostile environment for crop growth and production by imposing flooding and salinity stresses simultaneously. Identification of central regulators that regulate the adaptation to both flooding and salinity is a critical step for the development of new crop genotypes with enhanced tolerance to these stresses. Previous studies have characterized the function of the PROTEOLYSIS 6 (PRT6) gene in adaptation to flooding stress in plants. This study assessed whether this gene is involved in adaptation to salinity stress in Arabidopsis and maize by evaluating the growth and survival of their respective prt6 mutants under high salt. Consistent with the flooding tolerance data, our study showed that the PRT6 gene also functions as a negative regulator of salinity stress tolerance in Arabidopsis. The prt6 mutation in Arabidopsis activated the key transcriptional and hormone response pathways associated with adaptation to both salinity/osmotic stress and sodium toxicity, expressed as enhanced tolerance to excess salt at seed germination, seedling, and adult plant stages. In maize, disruption of the PRT6 gene decreased seed germination, primary root elongation, and shoot biomass growth under high salt, which is opposite to our observations in Arabidopsis. Additionally, the maize mutant plants encountered more oxidative stress, as demonstrated by the higher accumulation of malondialdehyde (MDA) under high salt. Moreover, maize prt6 mutants exhibited reduced grain yield under high salt. Overall, these results indicate that disruption of the PRT6 gene confers increased tolerance to high salt in Arabidopsis, whereas it conversely reduced salinity tolerance in maize. In wheat, we compared two genotypes with distinct nitrogen use efficiency (NUE), VA08MAS-369 and VA07W-415, to determine critical traits involved in NUE regulation. Our study showed that grain yield and yield-related parameters were significantly higher in line 369 than line 415 under low N. Moreover, high NUE in line 369 was attributed to efficient N uptake in this genotype under limited N. Our root architecture analysis demonstrated that line 369 was able to maintain root depth, volume, and thickness even under N limitation. Consistently, line 369 highly induced expression of genes associated with nitrogen transport at low N. Altogether, this study identified key traits involved in high NUE in wheat, facilitating the breeding of new wheat genotypes with enhanced NUE.

Master of Science / Department of Agronomy / David B. Mengel / Nitrogen fertilizers play an essential role in agricultural production in Kansas, particularly in row crops such as corn (Zea mays L.) and grain sorghum (Sorghum bicolor (L.) Moench). A good portion of the corn and grain sorghum grown in Kansas is typically grown using no-till production systems. These systems leave a large amount of surface residue on the soil surface, which can lead to ammonia volatilization losses from surface applied urea-containing fertilizers and immobilization of N fertilizers placed in contact with the residue. Leaching and denitrification can also be a problem on some soils. Current nitrogen prices, as well as concerns over environmental stewardship, are forcing producers to make smarter choices in the fertilizer products used as well as when and how the materials are applied, to optimize their nitrogen use efficiency. A common practice throughout Kansas is to apply N fertilizers prior to planting, sometimes up to 6 month prior to planting. What affect does this practice have on nitrogen availability to the growing crop? Current Kansas State University (KSU) soil test fertilizer recommendations assume 50% nitrogen use efficiency. This means of every pound of nitrogen applied only half will be utilized by the plant and turned into valuable grain. Possible solutions to help increase nitrogen use efficiency are the use of nitrogen additives which are currently on the market and claim to reduce nitrogen loss through denitrification and volatilization as well as the use of timing and application of fertilizers to further increase nitrogen use efficiency. The objective of this study is to evaluate different N fertilizer products, as well as additives and application practices and determine whether specific combinations can improve yield and N use efficiency of no-till corn and grain sorghum. The long-term goal of this study is to quantify some of these relationships to assist farmers in selecting specific combinations that could enhance yield and profitability. In this study five tools for preventing N loss were examined: fertilizer placement, or placing N below the soil surface or in bands on the residue-covered soil surface to reduce immobilization and/or volatilization; use of a urease inhibitor Agrotain (NBPT) that blocks the urease hydrolysis reaction that converts urea to ammonia and potentially could reduce ammonia volatilization; the use of a commercially available additive, Agrotain Plus, that contains both a nitrification inhibitor (DCD) and a urease inhibitor to slow both urea hydrolysis and the rate of ammonium conversion to nitrate and subsequent denitrification or leaching loss; use of a commercial product NutriSphere-N, which claims urease and nitrification inhibition; and the use of a polyurethane plastic-coated urea to delay release of urea fertilizer until the crop can use it. The ultimate goal of using these practices or products is to increase N uptake by the plant and enhance yield. An important measurement that was developed for this research was the use of a greenleaf firing index which used the number of green leaves below the ear at pollination as a key measurement in determining the effectiveness of fertilizer placement, application method, application timing and the use of nitrogen additives. If significant differences in lower leaf nitrogen stress are found, the potential exists to further develop this index and correlate differences observed with key parameters of nitrogen uptake such as ear-leaf nitrogen concentration, total nitrogen uptake and grain yield. Results observed from this research show that the potential to increase nitrogen use efficiency and reduce nitrogen loss do exist with the use of certain nitrogen additives, application methods and application timing. When conditions are conducive for nitrogen loss the use of currently available tools to protect nitrogen from volatilization, immobilization and/or denitrification loss significantly increased yields in the corn experiments. Results from the grain sorghum research indicate that when N losses limit yield, the use of products and practices enhance yield. In locations where nitrogen loss is minimal or low yields limit nitrogen response, the use of these practices was not found to be helpful.

Nitrogen use efficient (NUE) wheat varieties have potential to reduce input costs for growers, limit N runoff into water ways, and increase wheat adaptability to warmer environments. Previous studies have done little to explain the genetic basis for NUE and components, nitrogen uptake efficiency (NUpE) and nitrogen utilization efficiency (NUtE). Four studies were conducted to 1) determine genotypic stability of NUE under high and low N regimes and under warming 2) determine effect of warming on NUE 3) indentify QTL associated with NUE components 4) assess the utility of canopy spectral reflectance (CSR) as a high-throughput phenotyping device for NUE. Genotypic response to N stress or warming varied. Uptake efficiency was found to be more important than utilization efficiency to genotypic performance under high and low N environments and under warming. Selection under low N for NUpE and under high N for NUtE most efficiently identified NUE varieties. Uptake and utilization were lower under warming due to quickened development. No strong correlations between the CSR indices and NUE existed. No QTL were found to be significantly associated with NUE components. Further research into the mechanisms controlling NUE and to reveal plant response to N stress and under warming is necessary.

This thesis presents a more in-depth understanding of global root responses of contrasting tomato genotypes to cadmium-induced stress. Tomato genotypes growing in media containing 35 &mu;M CdCl2 over seven days showed metal accumulation in roots and shoots of both genotypes, but with increased Cd allocation over time mainly in roots. PR (tolerant) accumulated lower levels of Cd in the shoots, exhibiting higher growth rate and higher levels of MDA in roots compared to CR (sensitive). Therefore, the PR genotype appears to have a more efficient mechanism to cope with Cd-induced stress. Enzymatic analysis revealed that the presence of Cd altered GSH content in roots of both genotypes, whilst increased the activities of APX, GR and GST, which in turn, together may be the main players against oxidative stress in the tolerant genotype. Following the characterization of tomato roots systems against Cd challenge the second chapter brings the root morphology parameters analysis. Cd exposure decreased the root length, the surface area and the volume in both genotypes, being more severe in the CR genotype. Tomato roots exposed to Cd showed NUE for many macro and micronutrients in the CR genotype lower than verified for the PR. These findings reinforce the explanation that the tolerant phenotype observed in PR plants could be related to a better nutrient management and minor damages in root morphology under Cd stress. Finally, the last chapter brings a large scale quantitative proteomic approach employed to determine alterations in the protein profile of tomato roots exposed to Cd. Tomato genotypes were grown in hydroponics and exposed to Cd over four days. The spectral counting revealed a total of 380 differentially accumulated proteins (DAP), which 62 were shared between both genotypes and showed similar alterations after metal exposure. In general, CR genotype presented higher number of DAP compared to PR. DAP showed alterations in diverse pathways, including proteins involved in cell wall, stress response, and redox activities. The results obtained in this study contributed to increase the understanding of Cd-tolerance in tomato plants. / Esta tese apresenta um aprofundamento do conhecimento global sobre as respostas radiculares de genótipos contrastantes de tomateiro ao estresse induzido por cádmio (Cd). Os genótipos cultivados em hidroponia em meio contendo 35 &mu;M de CdCl2 durante sete dias exibiram acúmulo de metal tanto em raízes como em parte aérea em ambos genótipos, mas com um aumento da alocação de Cd principalmente nas raízes. PR (tolerante) acumulou menores níveis de Cd na parte aérea, exibindo maiores taxas de crescimento e acúmulo maior de MDA comparado ao CR (sensível). No entanto, o genótipo PR parece ter um sistema mais eficiente para lidar com o estresse induzido pelo Cd. Os ensaios enzimáticos revelaram que a presença de Cd alterou o conteúdo de GSH nas raízes de ambos os genótipos, com aumentos nas atividades de APX, GR e GST, que em conjunto podem ser os principais elementos responsivos na defesa contra o estresse oxidativo no genótipo tolerante. Seguindo a caracterização dos sistemas radiculares dos genótipos de tomateiro, o segundo capítulo contém as análises morfológicas. A exposição ao Cd provocou decréscimos nos parâmetros avaliados como comprimento radicular, área superficial e volume, sendo mais severos no genótipo CR. As raízes de tomate expostas ao Cd mostraram alterações na eficiência do uso de nutrientes para vários macro e micronutrientes, sendo menor no CR em comparação com PR. Esses resultados reforçam a explicação de que o fenótipo tolerante observado no genótipo PR pode estar relacionado a um melhor gerenciamento nutricional aliado aos menores danos na morfologia da raiz sob estresse. Finalmente o último capítulo contém dados de proteômica quantitativa, uma abordagem que foi empregada para determinar as alterações provocadas pelo Cd no perfil proteico das raízes de tomateiro. As plantas cresceram em hidroponia e foram expostas ao metal por quatro dias. A contagem espectral revelou um total de 380 proteinas diferencialmente acumuladas (DAP), das quais 62 foram compartilhadas entre os genótipos e apresentaram alterações similares após exposição ao metal. Em geral, CR apresentou maior número de DAP comparado ao PR. DAP foram alteradas em diversas vias, incluindo proteínas envolvidas em parede celular, resposta a estresse e atividades redox. Os resultados obtidos neste estudo contribuíram para aumentar o entendimento da tolerância ao Cd em tomateiro.