Ph.D. - Tropical Plant and Soil Sciences

Permanent URI for this collectionhttps://hdl.handle.net/10125/20042

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Pedogenesis, soil fertility, and indigenous adaptation: The formation of Hawaiian volcanic soils across climate, time, and parent material
(University of Hawai'i at Manoa, 2025) Haensel, Thomas; Lincoln, Noa K.; Tropical Plant and Soil Sciences
Soils exist at the interface of the critical zone, hosting many of the chemical reactions that regulate the Earth’s biogeochemical cycles. The formation of soils, or pedogenesis, is a key process in understanding soil functioning and is controlled by environmental drivers (climate, parent material, topography, and biota) over time. The Hawaiian Islands are considered a “model system” for ecological and pedological studies because they contain broad gradients in substrate age and climate while simultaneously having relatively consistent parent material and biotic components. Many pedological studies have utilized Hawai‘i as a study system to see how soils evolve across climate and time, and have observed that soil properties, including soil nutrients, behave in response to a series of pedogenic thresholds and soil process domains. Pedogenic thresholds and soil process domains have been observed and quantified in Hawaiian soils along three different-aged climosequences (20, 150, and 4,100 ky). However, the age component in understanding how pedogenic thresholds and soil process domains occur over time is limited. A broadened chronosequence of climosequences would support a better understanding of the evolution of pedogenic thresholds in Hawaiian soils and could potentially allow for modeling pedogenic thresholds across climate and time. Modeling the development and evolution of pedogenic thresholds over time could have implications for understanding how soil nutrients accumulate and deplete in Hawaiian soils, which could support soil fertility spatial models. But this type of modeling assumes that the parent material component in Hawaiian soil formation is consistent, which it may not be.Through this dissertation, I sought to understand the connections between soil fertility, pedogenesis, and the adaptation of traditional Hawaiian agroecology by modeling the evolution of pedogenic thresholds and soil process domains of Hawaiian volcanic soils across a broadened chronosequence of climosequence and implementing this work into generating geospatial models for traditional Hawaiian rainfed agroecological systems. I then questioned the pedogenic consistency of Hawai‘i’s parent material by examining the influence of parent material geochemistry on soil heterogeneity along a lithosequence. In Chapter 2, I sampled and analyzed hundreds of soils across the Hawaiian archipelago to construct a broadened chronosequence of five climosequences (5, 15, 120, 450, and 1,400 ky), which I then used to observe the evolution of pedogenic thresholds and soil process domains across time. I was able to quantify a pedogenic threshold along each substrate climosequence that represents the exhaustion of primary mineral inputs and found that this threshold shifts to drier climates as soil substrates get older. I then modeled the occurrence of this pedogenic threshold with an empirical equation, which predicts the exhaustion of primary mineral inputs as a function of climate and substrate age. In Chapter 3, I used this empirical soil threshold equation to predict soil fertility and generate geospatial models for traditional Hawaiian rainfed agroecology. These models predicted the extent of Intensive Rainfed, Marginal Rainfed, and Agroforestry agriculture in ancient Hawai‘i, which were ancient rainfed agroecological systems characterized by unique crops and cultivation methods. I also validated these empirically-constructed models with archaeological remnants and historical accounts, which suggested that my models were more accurate at predicting dryland rainfed agriculture but were less accurate at predicting agroforestry than previously constructed rainfed geospatial models. In Chapter 4, I looked at soil heterogeneity across a geochemical lithosequence of Hawaiian lava flows in order to address the consistency of Hawai‘i’s parent material. Across the lithosequence, soil geochemical composition and nutrient concentrations were significantly different. Through correlation analysis, I also observed that soil geochemical concentrations were inherited from the parent material, suggesting that Hawai‘i’s parent material is not consistent from a pedogenic perspective and needs to be taken into account in future studies.
EXPLORING PHYTOPHTHORA PALMIVORA PARTIAL RESISTANCE IN CARICA PAPAYA FOR CROP IMPROVEMENT
(University of Hawai'i at Manoa, 2024) Domingo, Ryan S.; Kantar, Michael; Tropical Plant and Soil Sciences
Papaya root rot caused by Phytophthora palmivora is a destructive disease threatening Hawaii’s papaya industry, resulting in crop damage, decreased production, and plant death. The surveillance of P. palmivora isolates from commercial papaya farms through the use of molecular techniques and evaluation of root rot resistance of commercially grown papaya cultivars will help estimate how much variation exists for potential use in breeding programs. This will help examine the geographic distribution of pathogen diversity, identify alternative cultivars with increased root rot resistance, and aid in developing new cultivars with increased resistance to P. palmivora. Extensive production loss and mortality of Carica papaya is associated with Phytophthora palmivora in Hawaii and other papaya growing regions of the world. Currently no commercial papaya cultivar is fully resistant to Phytophthora root rot. However, it is important to identify those that show partial resistance. Partial resistance is defined as reduced pathogen proliferation and spread in a plant, while tolerance is the ability of a plant to maintain yield in the presence of disease. Here we present a novel rapid papaya phenotyping assay with three quantification methods to assess P. palmivora resistance. Three papaya varieties of varying resistance (i.e., ‘Waimanalo’, RS-1, and ‘SunUp’) were used to validate the assay, which confirmed that the ‘Waimanalo’ cultivar exhibited increased resistance over RS-1, and the susceptible ‘SunUp’. Differential responses to P. palmivora infection were observed as early as three days post-inoculation. This assay will help to shorten the breeding process by quickly and cheaply identifying potential sources of resistance genes in seedlings, thus expediting the selection process compared to current conventional phenotyping protocols.
Protecting the Exceptional: Challenges and Opportunities to Enhance Hawai‘i's Exceptional Tree Program with Implications for Global Standards
(University of Hawai'i at Manoa, 2024) Ritchie, Myles T.; Kaufman, Andrew; Tropical Plant and Soil Sciences
“Exceptional trees” have long been recognized for the unique characteristics that set them apart from other trees. While the terms used to identify exceptional trees can vary based on geographic location (e.g., “significant,” “heritage,” “champion,” “monumental,” etc.,), these trees embody similar traits that represent important attributes valued by humans. However, anthropogenic activities often conflict with exceptional trees, threatening their existence and the benefits they provide to society and the local environment. Exceptional trees are recognized in various locations worldwide through urban forestry conservation programs, which are designed to identify and sometimes offer legal protections to these valued specimens. For example, Hawai‘i’s “Exceptional Tree Program” began in 1975 with the enactment of Act 105 by the Hawai‘i State Legislature, conferring legal protections to exceptional trees. However, in the intervening five decades, the program has become stagnant and remains relatively unknown by the public and practitioners due to ineffective programmatic components, which have also seen few improvements since the program’s inception. This three-paper dissertation examines the current state of Hawai‘i’s Exceptional Tree Program to identify its known weaknesses and provide suggested improvements to enhance this urban forestry conservation program. The first paper explores current challenges associated with Hawai‘i’s Exceptional Tree Program based on the lived experiences of exceptional tree practitioners through the use of the Reflexive Thematic Analysis methodology. The second paper is based upon an analysis of exceptional tree case studies in Hawai‘i and South Australia in order to provide suggested improvements to the widely-used Delphi methodology, while also providing methodological context for the third paper. The third paper uses the Delphi method to achieve expert consensus on the ideal program components that should be include in Hawai‘i’s Exceptional Tree Program. Together, these three papers provide a template on how an exceptional tree program in Hawai‘i and elsewhere can be improved, in addition to urban forestry conservation programs more broadly. The collective findings of these papers also help to better understand the knowledge exchange preferences of urban forestry practitioners and experts. Finally, the study’s recommended Delphi methodological improvements could be used to aid future research utilizing this method, particularly studies focusing on exceptional tree and urban forestry topics.
Anthocyanin Profile of Euphorbia Pulcherrima (Poinsettia) and the Effects of High Temperature on Anthocyanin Content and Dihydroflavonol 4-Reductase (DFR) Gene Expression
(University of Hawai'i at Manoa, 2024) Teng, Emily Shih-wen; Amore, Teresita D.; Tropical Plant and Soil Sciences
Poinsettias are a symbol of the Christmas season worldwide and the most popular holiday plant in the United States. Breeders of this commercially valuable commodity are continuously creating new and improved cultivars for the market, and the color of the bracts is one of the most important traits targeted in their breeding programs. Poinsettia growers face difficulties in production when plants do not color in time for Christmas sales, an issue that can be caused by high temperatures delaying flower initiation and bract coloration, termed heat delay. Color in poinsettia bracts is conferred by anthocyanins, a group of water-soluble flavonoids contributing to the color of a wide range of plant tissues. The goal of this research was to expand the knowledge base of anthocyanins in poinsettia bracts by examining the physical aspects of their spatial location and distribution, conducting a quantitative and developmental profile of modern cultivars including the newer E. pulcherrima × E. cornastra interspecific hybrids (EIH), investigating the role of the dihydroflavonol 4-reductase (DFR) gene in anthocyanin production, and determining how high night temperatures affect anthocyanin accumulation and DFR gene expression. Microscopic examination of the cross-sections of bracts of 11 cultivars infiltrated with polyethylene glycol revealed anthocyanin accumulation in both adaxial and abaxial epidermal layers, with some pigmentation within the mesophyll in red and pink E. pulcherrima cultivars and pink EIH. White cultivars did not show any anthocyanins in the cross-sections. Epidermal cell shape in all cultivars were domed with varying amounts of cell elongations. EIH had the most elongated epidermal cells and white E. pulcherrima cultivars had the flattest epidermal cells. Spatial location of pigmented cells in bracts of modern poinsettia and EIH cultivars has not been previously reported. High-performance liquid chromatography (HPLC) analysis was conducted on anthocyanidins extracted and purified from poinsettia bracts to identify and quantify the pigments contributing to their color. Cyanidin and pelargonidin were identified in red, pink, and white bracts of six of the seven E. pulcherrima cultivars examined (‘Premier Red’, ‘Premier White’, ‘Premier Pink’, ‘Freedom Red’, ‘Polly’s Pink’, ‘Orange Spice’), with the total amounts of each component and the proportions of the two compounds influencing not only the color of the bracts, but the darkness/lightness of that color and where on the color spectrum it falls. Red bracts can shift towards purple or orange and pink bracts can shift towards red or orange. The genetic and breeding background of the cultivars were explored and related to the amounts and proportions measured in the different cultivars. No anthocyanidins were detected in ‘Polar Bear White’, ‘Princettia Max White’, or E. cornastra, and very small amounts of cyanidin were found in the pink EIH cultivars 'Princettia Dark Pink’ and ‘Luv U Pink’. The anthocyanin profiles of a range of modern poinsettia cultivars is reported while the main contribution to the bright pink color of EIH cultivars remains unclear. Chlorophyll content measured using the Soil Plant Analysis Development (SPAD) meter, anthocyanin content measured using HPLC analysis, and DFR relative gene expression measured using Real-Time Quantitative PCR (qPCR) in ‘Prestige Red’ poinsettias throughout development from the beginning of inductive short-days to post-anthesis after 10 weeks were used to build a developmental profile and quantify the relationship between these parameters. The timing of DFR expression increases paralleled anthocyanidin production increases with peak DFR activity at 8 weeks and total anthocyanidin amounts reaching highest concentrations at 10 weeks. These results support previous evidence that the DFR gene is critical to anthocyanin synthesis in poinsettia bracts under short-day conditions. Temperature effects on these same parameters were studied by applying high night temperatures of 28 °C at the start of inductive short-days to induce heat delay of flower initiation and bract coloration. Anthocyanin accumulation and DFR expression increase were slightly delayed in the high night temperature treatment plants, and the overall levels of expression were lower throughout development. However, quantity of anthocyanidins measured in the high night temperature treatment were greater than those in the moderate temperature treatment, in contrast to the DFR expression levels in the two treatments. These results imply that other factors may be involved in anthocyanin accumulation in poinsettia bracts that are more critical than DFR. Overall, the results of this research begin to illuminate the underlying molecular mechanisms of heat delay temperature conditions on anthocyanin synthesis gene expression in poinsettias. The anthocyanin research undertaken in this study will inform breeders on how anthocyanins operate in poinsettias and assist in producing new and improved cultivars both for growers facing anthocyanin related production issues and for consumers to enjoy during the holiday season or even year-round.
Breeding Scheme Development and Optimization During Neo-Domestication and Wide Hybridization
(University of Hawai'i at Manoa, 2023) Fumia, Nathan; Kantar, Michael B.; Tropical Plant and Soil Sciences
Global food systems are under increasing pressure. There is an increasingly stochastic climate with future projections showing declines in major food crop production across the major growing locales. In the future, the geographic regions that are projected to be suitable for staple production are expected to shift, which may lead to the need to abandon current production regions and/or shift to new species for cultivation. Many of the potential new species to replace current systems or fill novel niches include ∼30,000 edible plants worldwide; however, currently ∼150 are cultivated at large scale across the world. These domestic and semi-domestic plant species span 160 taxonomic families with a total of ∼2,500 species having undergone some extent of domestication. Domestication is a process by which a wild organism shifts to a form more adapted for human use, typically through the acquisition and subsequent fixation of traits, commonly termed the domestication syndrome. Neo-domestication is the attempt to re-domesticate or newly domesticate wild and semi-wild species leveraging modern breeding techniques in a strategic framework. These programs use large phenotypic and/orgenotypic data sets to efficiently select breeding parents to maximize progeny gain of typically quantitative traits. Neo-domestication foci include fixation of simple traits, via variance reduction, that typically hinder cultivation and breeding for complex traits that improve marketability. The increasing pressure on food systems and breadth of options creates a situation of strategic uncertainty, specifically two questions: 1) Which species do we choose?2) How do we increase the adaptability of said species to the agroecosystem? This dissertation aims to systematically answer the second question to understand the impact of breeding schemes on the pace of adaptation. Specifically breeding scheme development encompasses the parametrization in breeding cycle components (Crossing, Evaluation, Selection) by leveraging empirical data to train stochastic models. First, empirical data are integrated with simulation output to test specific use-cases, this is followed by optimization of genetic gain. The empirical case study chapters (1-3) rely upon the concepts of population improvement through artificial selection: an iterative process of generational selection to increase in favorable alleles in the population. The goal is to increase the probability of extracting a superior cultivar from the population. The increase in favorable allelesdrives genetic gain, which is a product of additive genetic variation within the population, selection intensity, and selection accuracy. Optimizing breeding cycle components has beneficial effects on the genetic gain components. However, this framework has not been applied to wild and semi-domesticated breeding towards domestication. The last chapter (4) integrates the effects of these case studies to create a framework for understanding the expected rate of gain for potential species with known biological characteristics. In Chapter 1, the first breeding cycle component addressed is crossing. Crossing includes the following parameters: number of parents, number of crosses, number of progeny, type of cross, and mate allocation. To parse parametric effects in crossing on gain, the wild-endemic tree species Acacia koa (koa) was used. Koa is an excellent system for understanding crossing parameters of number of parents and number of progeny effects on gain in seedling vigor with disease resistance constraint. The koa system provides a clear set of experiments to validate the influence of breeding population size and number of progeny on phenotypic gain in simulation results of seedling vigor when constrained by varying levels of disease. The second chapter focuses on the next component of the breeding cycle, evaluation. This component includes the following parameters: number of locations, levels of replication, number of checks, experimental design, and subsampling. To parse parametric effects in evaluation on gain, the tropical tree species Theobroma cacao (cacao) is used. Cacao production spans the globe, but production varieties vary from developed (hybrids) to semi-domesticated (open-pollinated landrace). The cacao system provides a clear set of experiments to understand the precision necessary to observe significant differences between varieties within different domestication status groups. The investigation into the deviation of phenotypic measurements from the most precise (full sub-sampling of plot) to least precise (single sample of plot) will facilitate an understanding of the appropriate level of precision needed when using different types of germplasm in a neo-domestication breeding program. The last aspect of the breeding cycle, selection, is addressed in chapter 3. This component includes the following parameters: percentage selected (intensity), selection method (culling, index), selection unit (families, lines, parents), and selection criteria (phenotypic, genotypic, breeding values, index). To parse parametric effects in selection on gain, the subtropical herbaceous shrub species Stevia rebaudiana (stevia) is used. Stevia production spans the globe, but production varieties are considered non-adaptable to the agroecosystem (semi-domesticate) and lack classic domestication syndrome traits, including reduced dormancy, branching, and photoperiod sensitivity. The stevia system provides a clear set of experiments to understand the influence of phenotypic recurrent selection on domestication traits across multiple generations. Although these systems differ by life-history and domesticated status, they provide key insight into the components of the breeding cycle with varying trait complexities. The simulation varying crossing parameters can take the empirical estimates from Koa and expand intuition around other parameters during crossing (e.g., varying number of crosses). The simulation varying evaluation parameters can take the empirical estimates from Cacao and expand intuition around other parameters during evaluation (e.g., level of replication or environmental evaluation). The simulation varying selection parameters can take the empirical estimates from Stevia and expand intuition around other parameters during selection (e.g., alternative selection criteria). Each variable is therefore grounded in crucial empirical estimates derived from experiments in each case-study crop. The input for these case studies provides the knowledge and intuition for the final chapter, which synthesizes these expectations into species agnostic neo-domestication breeding schemes. This synthesis uses replicated and varying stochastic simulations across the breeding cycle components to provide an estimate of potential gain for any domestication scenario. These new breeding schemes are returned to reality by applying known cost structures to key parameter decisions (e.g., cost of phenotyping versus genotyping; cost of subsampling versus plot level analysis). Mixed-model analysis is then applied to estimate breeding cycle component parameter values which maximize the return on investment for given traits and targets.
Anthurium Flower Color: Histology And Genetic Manipulation
(University of Hawaii at Manoa, 2022) Toves, Peter J.; Amore, Teresita D.; Tropical Plant and Soil Sciences
Anthurium is the most important cut flower in the Hawaii floriculture industry. Conventional breeding for desirable vase life, shape, and color has been the mainstay for keeping growers in Hawaii competitive in the global market. No blue anthuriums exist and cannot be made via conventional breeding since anthuriums lack the genes to produce delphinidin-derived anthocyanins. The objectives of this research were to expand our understanding of the biochemical and histological aspects of flower color that are essential for developing strategies for breeding, conduct transient gene expression in anthurium spathes, and to explore genetic engineering of the anthurium flavonoid pathway for novel color development. Flower color is influenced by pH, since anthocyanins exist in different forms depending on the pH of the vacuole. A survey of spathe pH in 50 hybrid selections and cultivars revealed that green spathes had the highest average pH (6.14), followed by whites (5.96), purples (5.82), pinks (5.78), corals (5.72), reds (5.46), and oranges (5.40). Flower color is influenced by the distribution and combinations of anthocyanins in the floral tissue. Anthocyanins were distributed in the hypodermis and mesophyll in red, pink, orange and coral anthurium spathes, with some hybrid selections having very few pigmented cells in the epidermal layer. The spatial distribution of anthocyanins was more expansive in purple anthurium spathes, and was observed in the adaxial and abaxial epidermis, and in the adaxial and abaxial hypodermis of some selections/cultivars. White and green spathes lacked anthocyanins; however green spathes contained substantial amounts of chlorophyll. The pH and spatial distribution data can help to make informed decisions when using the surveyed anthurium cultivars/selections for breeding, since pH can affect color and spatial distribution of anthocyanins can affect the perceived color intensity. Since the development of stable transformants with genes for novel flower color is a lengthy process with low transformation efficiency, we tested agroinfiltration-mediated transient expression to assess functionality of the structural gene F3’5’H and the transcription factors Delila and Rosea1 in 18 selections/cultivars. The effects of detached and attached spathes, older and younger spathes, the effect of full spectrum and enhanced LED, and sonication were tested in addition to agroinfiltration with the color constructs. The transient transformation results obtained were inconsistent and not conclusive for positive transient expression, since some spathes infiltrated without the color gene or transcription factors developed blue coloration despite the lack of F3’5’H or transcription factors Delila and Rosea1 . In this study, calli of seven hybrid selections or cultivars were co-cultivated with Agrobacterium tumefaciens AGL0 with one of the following plasmids with the NPTII selection gene: 1) pJAM1983 with the gene F3'5'H from petunia, 2) pJAM1889 with the gene Delila from Antirrhinum majus, 3) pJAM1463 harboring the gene Roseal from A. majus. Of the 372 samples tested via Polymerase Chain Reaction (PCR) (some made by Hawaii Agriculture Research Center (HARC), others made in this research), eight ‘Marian Seefurth’ samples from HARC tested positive for the NPTII antibiotic resistance gene and six of those samples tested positive for F3’5’H.
Shading Of Coffee Plantations For Induced Epizootics Of The Entomopathogenic Fungus Beauveria Bassiana (Bals.) Vuill. On The Coffee Berry Borer, Hypothenemus Hampei Ferrari
(University of Hawaii at Manoa, 2020) Caraballo Ferrer, Jeffrey; Wright, Mark G.; Tropical Plant and Soil Sciences
The use of shade has generated a debate on whether shade trees are beneficial to coffee culture. This topic has lacked a clear consensus in the scientific literature. In this research we addressed the effect of shade from a pest management perspective focusing on the impacts of shade on the entomopathogenic fungus Beauveria bassiana and the main insect pest, the coffee berry borer (Hypothenemus hampei (Ferrari), Coleoptera; Curculionidae, CBB) in the field and on green coffee quality following Specialty Coffee Association standard (SCA). The effect of irrigation, artificial and natural shade on the efficacy of B. bassiana, CBB infestation and damage to green coffee were evaluated. The irrigation treatments consisted of a high, low aerial irrigation and no irrigations regimes. The artificial and natural shade treatments consisted of 30% shade cloth, 50% shade cloth, full sun, shade under the canopy of a shade tree and shade beside the canopy of a shade tree. In addition, distance from the shade was used as a surrogate measure of shade in a separate experiment. The 5 distances or coffee tree positions were: 1, coffee trees right next to the shade tree trunk; 2, coffee trees located at the edge of the canopy of the shade tree; 3, coffee trees located halfway between the edge of the canopy and the farthest projected shade; 4, coffee trees located at the farthest projected shade and 5 located farther away where no shade was received. These distances were oriented according to the eastern and western cardinal directions from the shade tree. CBB mortality by B. bassiana, CBB field infestation, CBB parchment infestation, lost green bean yield, percentage of severely and slightly bored beans (in green coffee). In 2016, artificial and natural shade treatment significantly increased CBB mortality by B. bassiana, but not in 2015. Aerial irrigation did not affect CBB mortality by B. bassiana nor CBB field infestation. Artificial and natural shade did not affect the CBB field infestation in 2015, but in 2016 dense shade increased the CBB field infestation. The CBB parchment infestation was affected by artificial and natural shade where in 2015 the infestation decreased with increasing shade and in 2016 CBB parchment infestation increased with increasing shade. The shade cloth treatments and shade beside the canopy had less green coffee yield loss and percentage of severely bored beans than full sun and shade under the canopy. Distance from the shade did not affect CBB mortality by B. bassiana. Distance from the shade tree significantly affected CBB parchment infestation, green coffee yield loss and percent of severely bored beans where the coffee trees beside the canopy of the shade tree that received cardinal shade had the lowest infestation, yield loss and percentage of severely bored beans. Cardinal direction also had a significant impact on CBB parchment infestation, yield loss and percent of severely bored green beans but the actual difference between the eat and west was small. In summary, no adverse effect of shade nor irrigation on CBB mortality by B. bassiana were recorded. Although, shade is capable of increasing CBB mortality by B. bassiana, this effect was not consistent. In addition, shade beside shade trees and lighter shade percentages reduce CBB damage to coffee green coffee quality.
Morphological And Molecular Approaches To Disentangling The Taxonomy Of Plumeria Species (apocynaceae)
(University of Hawaii at Manoa, 2019) Perez, B. Kauahi; Manshardt, Richard M.; Tropical Plant and Soil Sciences
This dissertation investigated the taxonomy of Plumeria, a popular ornamental plant in the Apocynaceae. A brief introduction to the plant and its current taxonomy is provided in Chapter 1 along with a proposal for research to identify Plumeria spp. by morphological and molecular approaches. The overall goal of this research was to evaluate morphological and molecular characters that are useful for identifying Plumeria spp. so that we can delineate species boundaries, verify our taxonomic understanding of Plumeria, and begin to understand their evolutionary history. The use of qualitative and quantitative morphology to diagnose Plumeria spp. from the literature is difficult because of the multitude of descriptions given by various authors, even for the same species. Furthermore, the criteria for delineating currently recognized Plumeria spp. is unclear. Hence, in Chapter 2 the use of descriptive morphology is evaluated to determine its effectiveness at identifying Plumeria spp. Using iterative principal component analyses, it was found that a combination of descriptive vegetative characters was useful for identifying most Plumeria spp. However, other species could not be identified based solely on descriptive morphology, due to morphological variation of descriptors used. Instead, it would require the use of quantitative measurements and the use of other morphological characters, such as fruits and flowers, to properly diagnose these species. Chapter 3 explores molecular approach to delineating species and investigates the phylogenetic utility of five candidate loci. Some regions were able to identify operational taxonomic units as true species, but no single region could be used to identify all the putative species in our sampling. In fact, not all species could be recovered as distinct clusters even with a data set that combined four molecular regions. On the other hand, it did result in a well resolved phylogeny that agrees with prior findings, notably that most Plumeria are distinguishable by molecular means and that some Plumeria form a species complex comprised of morphologically variable members that share very similar molecular characters. Chapter 4 concludes with a synthesis of morphological and molecular findings and future directions in the realm of disentangling the taxonomy of Plumeria spp.
Molecular Analyses Of Papaya Viruses In Bangladesh: Detection, Characterization, And Distribution
(University of Hawaii at Manoa, 2019) Hamim, Islam; Hu, John S.; Tropical Plant Pathology
Aphid-transmitted PRSV is the greatest disease threat to commercial papaya production worldwide. Specific, ultrasensitive assays are important for the early detection of PRSV in the field. I developed a single-tube nested PCR (STNP) assay to address this need. Two nested PCR primer sets were designed to target the P3 gene of the virus. The concentrations and annealing temperatures of both primer pairs were optimized to avoid potential competition between primer sets during STNP. The assay was more sensitive than regular RT-PCR as determined by serial dilutions of cDNA and RNA templates and sample extracts from infected plants. RT-PCR and ELISA were capable of detecting PRSV 14 to 21 days post-inoculation, whereas STNP detected PRSV in plants 7d post-inoculation. This new STNP assay also detected PRSV from virus-infected asymptomatic plants. This system could assist epidemiological studies in the field and in quarantine protocols by enabling early detection of very low PRSV titers in the field and in imported plant samples. As in other countries, PRSV is the major limitation to papaya production in Bangladesh. Full-length coding genomes of PRSV strains from severely infected papaya plants were determined using the Illumina NextSeq 500 platform, followed by Sanger DNA sequencing of viral genomes obtained by reverse transcriptase polymerase chain reaction (RT-PCR). The genome sequences of two distinct PRSV strains, PRSV BD-1 (10,300 bp) and PRSV BD-2 (10,325 bp) were 74% and 83% identical to each other at the nucleotide and amino acid levels, respectively. PRSV BD-1 and PRSV BD-2 were 74 to 75% and 79 to 88% identical to other full-length PRSV sequences at the nucleotide level, respectively. Based on phylogenetic analysis, PRSV BD-2 was most closely related to PRSV-Meghalaya (MF356497) from papaya in India. PRSV BD-1 formed a distinct branch from the other PRSV sequences by nucleotide as well as amino acid sequence comparisons. Comparisons of the genome sequences of these newly identified PRSV strains with other sequenced PRSV genomes indicated two putative recombination events in PRSV BD-2. One recombinant event contained a 2,766-nucleotide fragment with the highest identity to PRSV-Meghalaya (MF356497) and the other contained a 5,105-nucleotide fragment with the highest identity to PRSV-China (KY933061). The occurrence of PRSV BD-1 and PRSV BD-2 in the sampled areas of Bangladesh was approximately 19% and 69%, respectively. Plants infected with both strains (11%) exhibited more severe symptoms than plants infected with either strain alone. The new full-length genome sequences of these PRSV strains from Bangladesh and their distribution provide important information on the dynamics of papaya ringspot virus infections in papaya in Bangladesh. Forty-five papaya samples with severe leaf curl symptoms were tested by PCR using a degenerate primer set for virus species in the genus Begomovirus. Of these, 29 were positive for tomato leaf curl Bangladesh virus (ToLCBV). The complete genome sequences of ToLCBV (GenBank accession no. MH380003) and its associated tomato leaf curl betasatellite (ToLCB) (MH397223) from papaya isolate Gaz17-Pap were determined and characterized. Defective betasatellites were found in ToLCBV-positive papaya isolates Gaz19-Pap, Gaz20-Pap and Gaz21-Pap. This study confirmed that papaya is a host of ToLCBV, ToLCB, and other defective and recombinant DNA satellites in Bangladesh. The complete genome sequence of tomato leaf curl Joydebpur virus (ToLCJoV) and its associated tomato leaf curl Joydebpur betasatellite (ToLCJoB) were determined and characterized from papaya isolate J1-Pap. ToLCJoV infecting papaya was most closely related to ToCJoV reported from Gazipur, Bangladesh, causing tomato leaf curl disease of tomato. ToLCB infecting papaya had the highest homologies at nucleotide and amino acid levels to ToLCB from tomato in India. The complete genome sequences of the DNA A and DNA B components of tomato leaf curl New Delhi virus (ToLCNDV) were determined and characterized from papaya isolate ND-71. ToLCNDV infecting papaya was most closely related to ToLCNDV reported from Gazipur, Bangladesh, causing tomato leaf curl disease of tomato. DNA B of ToLCNDV infecting papaya had the highest homologies at nucleotide and amino acid levels of DNA B of ToLCNDV from tomato in India.
Management Of Plant-parasitic Nematodes And Soil Health Using Oil Radish (Raphanus sativus) And Brown Mustard (Brassica juncea) Cover Crops
(University of Hawaii at Manoa, 2019) Waisen, Philip; Wang, Koon-Hui; Tropical Plant Pathology
This dissertation is composed of five chapters. Chapter one reviews factors that affect efficacy of biofumigation on management of plant-parasitic nematodes, focussing on Meloidogyne spp. in cropping systems and highlights two challenges. First, a number of literatures highlighted that susceptibility of biofumigant crops to target plant-parasitic nematodes could be an important management challenge and second, biofumigation being biocidal could have non-target impacts on free-living nematodes as bioindicators of soil health. Chapter two takes an alternative approach and elucidates the challenge of susceptibility as an opportunity to capitalize on as a trap crop arguing that using a good brassica host to a target nematode would be more effective as a conventional trap crop than using a poor host. When comparing trap cropping effects of ‘Sodbuster’ oil radish (OR; Raphanus sativus) as a poor host and ‘Caliente 199’ brown mustard (MS; Brassica juncea) as a good host against Meloidogyne spp. and R. Reniformis, MS showed potential as a trap crop depending on how long the trap crop was grown. MS suppressed soil population densities of Meloidogyne spp. in first and second trials by 60 and 50%, respectively where the cover crop was terminated within 42 days after planting (DAP; P ≤ 0.05) but not in third trial when terminated 49 DAP. However, population densities of R. reniformis were not suppressed by MS in the first two trials where it was terminated 42 DAP but were suppressed by 61% (P ≤ 0.05) in the third trial when the MS was terminated 49 DAP. Chapter three confirmed with previous studies that tissue maceration is necessary to activate myrosinase-glucosinolate system in brassica tissues to release bioactive isothiocyanates (ITC), soil tillage is required for the tissues to be in contact with the nematodes, and covering black plastic mulch is important to retain ITC from volatilization loss, together to maximize biofumigation effect on Meloidogyne spp. and R. reniformis. In three field trials conducted using OR and MS, soil populations of Meloidogyne spp. were suppressed by OR or MS if the biofumigant crops were macerated (M), tilled (T) into the soil and covered with black plastic (BP) in all the trials, and reduced zucchini root galls in Trials I and II. However, suppression of Meloidogyne spp. was stronger when using MS than OR in the MTBP treatment. Regardless, MTBP suppressed R. reniformis in Trial I but not in Trials II and III. None-the-less, the trend appeared that MTBP reduced R. reniformis by 33.9 and 54.9% in Trials II and III, respectively. MTBP also stimulated zucchini growth in Trials I and III, but not in II. Chapter four investigated whether biofumigation could have non-target impacts on free-living nematode as indicators of soil health. Both OR and MS did not compromise soil health but instead OR enhanced nutrient enrichment throughout zucchini growth while MS did transiently for up to 1 month after biofumigation. Terminating both OR and MS by MTBP enhanced soil health indicators but suppressive to plant-parasitic nematodes. As indicators of biofumigation, Myr activity (based on soil glucose analysis) and soil sulfate analysis were conducted to establish relationships with soil health indicators and other response variables. Myrosinase activity had a strong positive relationship with soil health indicators when toluene (methylbenzene) was added in soil samples to arrest microbial degradation of glucose. However, sulfate was stable in the soil without toluene and even had a stronger positive relationship with the soil health indicators, thus a good indicator of biofumigation in the field. Chapter five concludes the findings and provide recommendations and future directions to enhance biofumigation effects of brassicaceous cover crops against plant-parasitic nematodes.
Determining Potassium (K+) Release, Crop Availability and Uptake from Three Red Algal (Rhodophyta) Species
(University of Hawaii at Manoa, 2017-05) Gangaiah, Chandrappa; Tropical Plant and Soil Sciences
As a result of increasing fertilizer costs associated with rising oil prices, many growers in the Pacific region have become interested in locally available resources that can be used as low cost inputs to improve crop health and productivity. In recent years, use of algae and their extracts have gained in popularity due to their potential use in sustainable farming and may be used as an alternate to synthetic fertilizers. In Hawaii efforts are underway to control the most commonly found invasive algae species; Eucheuma denticulatum, Gracilaria salicornia, and Kappaphycus alvarezii. These are dominant invasive, non-indigenous species on Hawaiian reefs. The average potassium (K+) dry matter content in these species is around 14 -20%. Although these seaweeds were used in the past for crop production, not much is understood about application rates, yield performance, species efficacy for crop nutrition, nutrient release pattern and mechanisms of release. To address these gaps, greenhouse and laboratory experiments were conducted to: 1) determine the efficiency of the cardy meter as a rapid, low-cost tool for evaluating the tissue K status of pak choi from fresh sap, 2) describe effect of three invasive algae species on growth (yield) and K nutrition (tissue K+) of pak choi at different K fertilizer rates, 3) to evaluate algae biomass as a replacement for K+ synthetic fertilizers, 4) compare the two buffers to minimize ionic interference using a K+ selective electrode, and 5) to understand the K+ nutrient release pattern and mechanics of these three species. Our data show that the invasive algae species increased the yield and growth of pak choi and the response was greater when algae was applied to provide K+ at the rate of 224-284 kg.ha-1. Results of the algae comparison with synthetic K+ showed no significant differences between them for yield; e.g. Plants grown with K. alvarezii, KCl and KNO3 had an average dry weight of 7.5 g when K+ was provided at 280 kg.ha-1. Only K+ rates, not K+ source were significant for yields and tissue K concentrations in all trials. Although the values between rapid electrode and ICP measured tissue K+ values were well correlated, ICP was identified as the preferred method of K+ quantification in tissue. However, in soil solution, ion strength adjustment buffers (ISAB) were able to significantly mask the other ionic interferences when measuring K+ and with a selective electrode. No notable difference was observed among the two buffers, NaClO4 and NaCl (slope near 1) with a strong correlation (r =0.99). This is the first report of such a comparison in the literature. Based on the results from the leachate study, we conclude that the total amount of K+ released from algae was lower than synthetic K fertilizers applied at equivalent rates of K+. Results from the both the whole plant and polysaccharides leachate studies show that there is a difference in K release pattern among the algae with the cumulative recovery of K+ from both whole plant G. salicornia and extracted agar were significantly lower (10-12%) than whole plant K. alvarezii and extracted carrageenan at both K application rates. These differences in release among algal species may be explained in part by differences in cell wall composition, chemical properties including sulfate groups differences and physical properties such as higher gel strength of Gracilaria agar. To our knowledge, this work is the first detailed report of these red algae species as significant sources of K+. This is also the first report in the literature of the less expensive NaCl buffer being an effective substitute for NaClO4, allowing for cost effective, high-throughput analysis of soil solution K+. We propose that carrageenan containing species may be more efficient sources of K+ than those containing agar, but future studies are needed to elucidate the mechanisms for these differences. Our study may also provide the established protocols for further investigation of the functional properties of naturally extracted agar and carrageenan from these species and at different locations.
Predicting Sediment Export into Tropical Coastal Ecosystems to Support Ridge to Reef Management
(University of Hawaii at Manoa, 2016-05) Falinski, Kim
Sediment, a principal land-based source pollutant, can negatively affect coral reef ecosystems and impact the services they provide to society, such as recreation and fishing. Watershed managers interested in evaluating options and trade-offs require decision support tools that predict sediment export and retention. However, sediment load has previously been difficult to model in Hawaii because 1) observed annual sediment load data is not widely available and 2) Hawaii’s volcanic hydrology makes it difficult to use models designed on the continent. One method to estimate annual sediment loads is by measuring deposition rates in reservoirs. As of 2013, Hawaii had 140 regulated water storage reservoirs that perform as retention basins, yet the extent of their functionality had not been analyzed. I conducted a state-wide survey of reservoir capacity. Results demonstrated that only 15% of the total water storage capacity of Hawaii’s reservoirs is currently used, and 40% of all reservoirs are affected by sedimentation, representing a significant maintenance cost and potential risk. I also investigated spatial patterns of a broader array of ecosystem services including sediment retention, nitrogen retention, water yield, carbon sequestration, and agricultural production in West Maui. Between 1778 and 1920, I determined that sediment export increased by 18 times, while nitrogen export increased by 11 times over the same period. I demonstrated that past impacts from agriculture were more severe than predicted future development and climate change. Lastly, to calculate the first state-wide estimates of annual sediment export, I used a RUSLE-based model coupled with an estimate of the sediment delivery ratio (SDR), and adapted input datasets, including the erodibility and cover factors. To calibrate the model, I analyzed 60 watersheds with observed data for annual sediment load. I calculated that only 42% of the total land area contributes to sediment export, and that Hawaii and Maui export 57% of the total sediment load. Annual specific sediment yields ranged from 26 to 273 tons km-2 yr-1 across all islands, with Kahoolawe and Maui having the highest rates. These projects combined provide a base for watershed managers to identify management strategies to mitigate sediment export within an ecosystem context.
Characterization of Dormancy, Establishment and Seed Production of Waltheria indica and Panicum torridum
(University of Hawaii at Manoa, 2015-08) Lukas, Scott
Biochar as an Amendment to Acid Soils
(University of Hawaii at Manoa, 2015-05) Berek, Arnoldus Klau
The capacity of biochar to improve acid soil productivity and enhance nutrient retention was the main focus of this study. The specific objectives were to characterize six wood-derived biochars, to assess biochars’ liming effects on Hawaiian and Indonesian acid soils, and to study nutrient retention of biochars. Six and another two biochars were collected, characterized, and then were used to evaluate their liming effect on a Hawaiian and two Indonesian acid soils with Desmodium intortum and soybean (Glycine max) as test plants, respectively. Two biochars in combination with two composts (both at 2%) as nutrient sources were used to investigate their nutrient retention with pak choi (Brassica rapa) as the test plant. The results showed that six wood-derived biochars were different in their properties, including ash content, pH, cation exchange capacity (CEC), CaCO3 equivalent, basic cations and surface functional groups. Based on their CaCO3 equivalent, leucaena (Leucaena leucocephala) and lac tree (Schleichera oleosa), Hilo mixed wood and she oak (Casuarina junghuhniana), and mahogany (Sweitenia mahagoni) and mountain gum (Eucalyptus urophylla), were grouped into the highest, moderate, and lowest liming potential biochars, respectively. Additions of six biochars at 2% and 4% with or without 2 cmolc/kg of lime to a Hawaiian acid soil increased soil pH and CEC, reduced exchangeable Al, enriched plant nutrients and enhanced Desmodium growth with lac tree and leucaena being most effective, followed by she oak and Hilo mixed wood biochars. Similar results were obtained from lac tree wood and rice husk biochars (4 and 8%) applied to two Indonesian acid soils. Addition of lac tree wood and Hilo mixed wood biochars in combination with vermicompost or thermocompost to a Ultisol and a Oxisol of Hawaii showed a positive interaction effect on EC, P and K, cabbage fresh and dry matters. Biochars increased soil pH, plant tissue Ca, retention of K, Ca and Mg, and reduced exchangeable Al in both soils. Overall, the liming capacity and nutrient retention potential of selected biochars have been positive.
Seed dormancy, smoke-stimulated germination and harvest timing of pili grass (Heterpogon contortus), a native Hawaiian grass with potential for expanded re-vegetation use
(University of Hawaii at Manoa, 2013-12) Baldos, Orville Caldo
Pili grass (Heteropogon contortus (L.) P. Beauv. ex Roem. & Schult.) is a culturally and ecologically important native species in Hawaiʻi that has been used for re-vegetation of severely degraded land. Currently, it is being evaluated for expanded use on roadside and streambank stabilization, water efficient landscaping and agricultural buffer strip plantings. Despite efforts to increase its use on a variety of re-vegetation applications, planting materials such as seeds are still in limited supply. In order to develop large scale seed production protocols, studies on seed dormancy and seed harvest timing need to be conducted. The three main objectives of this dissertation were to: 1) elucidate the mechanisms involved in pili grass seed dormancy loss through the use of scarification and germination stimulants (i.e., gibberellic acid [GA], fluridone, food grade liquid smoke [FGLS], pili grass smoke infused water, xylose smoke infused water, karrikinolide and cyanide); 2) assess the effect of storage factors (i.e., seed moisture content and temperature) on pili grass seed dormancy loss and viability; and 3) determine an average cumulative growing degree unit (ACGDU) correlated indicator which has potential use for determining the optimum seed harvest timing. Studies on seed scarification, germination with stimulants and dormancy loss under different storage conditions support the placement of pili grass under the non-deep physiological dormancy class of seeds. The observed partial germination with scarification (i.e., exposure of the embryo) suggests the presence of both physical and physiological dormancy controls. Germination assays with the plant growth regulators, fluridone and GA, as well as with FGLS suggests that the abscisic acid (ABA):GA balance plays an important role in pili grass seed dormancy. Seed germination response to chemical stimulants across a gradient in dormancy relief supports the theory of increased effective levels of GA as storage duration increases. Short term seed storage studies (i.e., 1 year or less) show that dormancy and seed viability loss is affected by storage temperature and equilibrium relative humidity (eRH) (i.e., seed moisture content). Storage at 10°C, regardless of eRH, maintained seed dormancy and viability for one year. To optimize dormancy loss while maintaining seed viability, fresh seeds must be stored at either 12% eRH (6% seed moisture content, dry weight basis) at 30°C for 12 months or at 50% eRH (11% seed moisture content, dry weight basis) at 30°C for 9 months. As storage temperature was increased from 20 to 30°C and storage relative humidity was increased from 50 to 75% eRH (11 to 14% seed moisture content, dry weight basis), loss in seed viability became more pronounced over time. The viability of pili grass seeds, relieved of dormancy, can be maintained for at least 6 months with storage at 12% eRH (6% seed moisture content, dry weight basis) and 5°C. FGLS, pili grass smoke infused water and xylose smoke infused water were effective in stimulating germination of dormant pili grass seeds. FGLS and pili grass smoke infused water provided consistent germination stimulation in two batches of seed that represented two levels of dormancy relief. Xylose infused smoke water was less effective since its ability to stimulate germination was not consistent across the two seed batches. Assays which evaluated two bioactive compounds found in smoke (i.e., karrikinolide and cyanide) indicated that only cyanide stimulated germination (20 to 29% germination) of dormant pili grass seeds. Cyanide stimulated germination suggests the role of reactive oxygen species in dormancy loss of pili grass seeds under warm, dry conditions. The presence of cyanide was confirmed in pili grass smoke, but not in FGLS or xylose smoke infused water. Germination observed in these non-cyanide containing smoke sources indicates the presence of other bioactive compounds in smoke. Germination assays conducted throughout this dissertation indicated differences in depth of dormancy with time of year harvest. March seeds exhibited the lowest levels of dormancy compared to seeds harvested in June, July and October. Seasonal dormancy in pili grass seeds can be attributed to differences in growing conditions during seed development. Finally, harvest timing studies identified ACGDU, spike moisture content and the onset of seed head tangling as useful harvest timing indicators for pili grass seed production. Results indicate that maximum seed harvests can be obtained between 768 to 778 ACGDUs (79 to 82 days after cutting) under irrigated conditions. Spike moisture for optimum seed harvest timing was determined to be between 0.68 to 0.72 grams H2O per gram of dry weight. The onset of seed head tangling provided a visual cue which coincided with the optimum seed yield and range of spike moisture content. A decline in seed production over four harvest cycles (spanning two years) was recorded with possible causal factors such as stand age, cutting height and thatch accumulation.
Development of papaya chromosome-specific cytogenetic markers and cytogenetic map of papaya sex chromosomes
(University of Hawaii at Manoa, 2011-12) Wai, Ching Man
Papaya (2n =2x =18) is a tropical and subtropical fruit tree grown worldwide. In recent years, the papaya genome has been sequenced and genetic maps have become available for analyzing genomic structure of the male-determining region of Y chromosome (MSY). However, research in the cytological aspect lags behind the model crops. One reason for slow cytological progress is because the papaya condensed chromosomes are small and similar in size, making it difficult to distinguish among them based on chromosomal morphology or staining pattern. By probing nine microsatellite marker-tagged BAC clones on papaya chromosome spread using fluorescence in situ hybridization (FISH) techniques, individual papaya metaphase chromosomes were distinguished and integrated with a genetic map. Then, a detailed cytogenetic map was constructed for the papaya sex chromosome (chromosome 1) by probing 15 microsatellite marker-tagged and 2 cytological-feature associated BAC clones on highly resolved papaya pachytene chromosomes. This cytogenetic map integrated the chromosomal features with genetic and physical data. Analysis of recombination rates along chromosome 1 revealed a small non-recombining region (12.2% of chromosome length) where the MSY is located, suggesting that papaya has a pair of young evolving homomorphic sex chromosomes. Sequence analysis of euchromatic and heterochromatic regions on the X chromosome showed an uneven distribution of genes and transposable elements. This cytological information enhances our understanding on the relationship between genome composition and chromosomal structure.
Vermicompost tea: effects on pak choi (Brassica rapa cv. bonsai, Chinensis group) growth and yield, phytonutrient content and soil biological properties
(University of Hawaii at Manoa, 2011-08) Pant, Archana Pandey
Vermicompost tea, an aqueous extract of vermicompost has been reported to improve plant health, yield and nutritional quality. Most of the previous research on compost tea has investigated the potential of compost tea for control of plant disease. Very limited data exists on the use of vermicompost tea for improving the yield and nutritional quality of vegetable crops and altering soil biological properties. Therefore, laboratory, greenhouse and field experiments were conducted in order to identify and describe: 1) the effects of vermicompost tea extraction methods [(i) non-aerated (NCT), (ii) aerated (ACT), and (iii) aerated with additives (ACTME)], fertilizer types (Osmocote and vermicompost), and three growth media (Oxisol, Mollisol and a peat-perlite medium) on yield and nutritional quality of pak choi (Brassica rapa, Chinensis) as well as soil biochemical properties; 2) the effects of the ratio of vermicompost to water and different fertilizers on yield and nutritional quality of pak choi as well as soil biological properties; 3) the effect of compost quality on biochemical properties of compost tea; and 4) mechanisms involved in the effects of compost tea on plant growth. The results showed that applications of vermicompost tea, regardless of extraction method, increased plant yield, mineral nutrients and phytonutrient content of pak choi. The microbial activities of two soils and a peat-perlite medium were also increased. This effect was most prominent under organic fertilization. These findings suggest that vermicompost tea serves both as a supplemental source of plant nutrients and an enhancer of soil biological properties. Similarly, application of vermicompost tea with compost to water ratios of 1:10-1:100 (v:v) increased yield, total carotenoids, total glucosinolates and N content of pak choi; and microbial activities in soil. The responses of these parameters to vermicompost to water ratio was positive and linear. The results also indicated that biochemical properties of compost determined biochemical properties of compost tea, and variability in quality of tea explained differences in the magnitude of effect of compost tea on plant growth and tissue mineral nutrient. The positive effect of vermicompost tea or compost tea on plant growth was largely associated with N (NO3-) and gibberellin (GA4) present in the tea and nutrient uptake by plants.
Aluminum tolerance in Medicago truncatula Gaertn
(University of Hawaii at Manoa, 2012-05) Srimake, Yawadee
Aluminum (Al) toxicity in acid soils is one of the major problems in agricultural production worldwide. In this study, we investigated Al tolerance in a legume crop, Medicago truncatula. Ninety-one ecotypes and 62 ethylmethylsulfonate (EMS)-generated mutants were screened for their Al-sensitivity using three different methods: 1) Al-containing agarose media; 2) hematoxylin staining; and 3) Al-toxic soil. Root lengths and Relative Root Growth (RRG, i.e. ratio of root elongation of seedlings grown with Al at a particular level to that of seedlings grown without Al) were measured. We found significant differences in response to Al-toxicity among the ecotypes and EMS mutant lines, and the results correlated positively between each method. We identified 3 Al-tolerant, 3 sensitive ecotypes, and 1 sensitive mutant. The Al-tolerant and sensitive lines were cross-pollinated to generate segregating populations. The F2 population of PI 577633 (Al-tolerant ecotype) and S69 (sensitive mutant) were screened using the Al-containing agarose assay. Genomic DNA of extremely tolerant and sensitive seedlings was extracted for Restriction site-associated DNA (RAD) analysis. We identified 11 candidate alleles that might be associated with Al tolerance. This information could be useful in breeding or selecting for improved Al tolerance in the model legume M. truncatula, as well as other crop legume species.
The impacts of evolutionary and human mediated dispersal mechanisms on invasion success in Solanaceae
(University of Hawaii at Manoa, 2014-12) Gauthier, Martha Jane
Understanding the mechanisms behind the dispersal and evolution of agricultural weeds is critical for the development of appropriate weed management strategies and protection of the world's food supply. However, little is known about the evolution of weed species in agricultural environments or the impacts of human-mediated dispersal on the evolutionary potential of these species. To gain a deeper understanding of the evolution and evolutionary potential of weeds in agricultural environments, I use a population genetics approach to investigate the genetic diversity of two non-native, invasive Solanum species that are problematic in agricultural systems (Solanum elaeagnifolium and S. torvum). I focus on three key questions: 1) do population structure and differentiation exist, 2) what is the level of genetic diversity present, and; 3) has the evolutionary potential of these species been diminished in non-native regions post introduction? Overall, results indicate the level of genetic diversity was comparable throughout each species' range; genetic population differentiation and structure existed; and adverse effects due to founding events were not evident. To address the need for appropriate weed management and protection of the world's food supply I explore two practical strategies. First, I examine non-native Solanum species found in agricultural settings. Specifically, I assess whether Silverleaf nightshade (Solanum elaeagnifolium), a non-native agricultural weed, is more likely associated with a specific crop type than other non-native Solanum species in California. To answer this question, I utilize cropland data layers (CDLs) and a geographical information system-based (GIS) spatial correlation approach to determine weed-crop correlations. I describe these associations as likely indicators of primary dispersal mechanisms of unwanted species. Second, I utilize the premise of DNA barcoding to develop a molecular means of distinguishing between four Solanum species on the Hawaii Noxious Weed List and their close relatives. I suggest two molecular techniques that provide easily recognizable patterns that represent a unique DNA profile for each of the four focal species examined.
Quantifying and mapping soil organic carbon in Mali, West Africa using spatiotemporal methods
(University of Hawaii at Manoa, 2008) Querido, Antonio Luis Evora Ferreira
The Kyoto protocol recognized the importance of the terrestrial sink of carbon and proposed schemes that allow countries to treat sequestered carbon as a commodity that can be traded for global environmental benefit. Carbon sequestration can be a win-win scenario because it also introduces a set of new benefits into dryland farming communities particularly in Sub-Saharan Africa. The possibility, however, for agricultural producers to participate in the emerging market for tradable carbon-credits requires a reliable verification mechanism. Soil carbon inventories of many developing nations rely on a broad scale assessment. These approaches do not account for the spatial and temporal variability of soil carbon nor do they provide a measure of uncertainty associated with these assessments. This study proposed the use of Bayesian Maximum Entropy (BME) to quantify and map soil organic carbon at field scale in four agroecological zones of Mali, Sub-Saharan Africa. The prediction model comparisons using the mean error (ME) indicated that BME performed better than did the kriging methods (0.033, 0.41, respectively). BME prediction also provided a lower MSE representing a 25% reduction compared with Kriging, and 10% compared with cokriging. This study also demonstrated potential use of space---time covariances as tools to improve our understanding of spatial and temporal variability of soil organic carbon. Based on the temporal and spatial models maps were generated to predict mean trends. The estimation of tree biomass in Sub-Saharan Africa is important for an accurate assessment of the potential of these systems to capture and store carbon. The results show that tree carbon represented as much as 34% of the amount of organic carbon stored in soil surface (0-20 cm). Data from 2000 to 2006 indicated a net increase of soil organic carbon, which varied between 2.6 to 13.9 Mg ha-1. Despite the complexities that characterize the spatial and temporal distribution of most environmental processes, BME provides a framework to analyze both space and time components.

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