399 research outputs found
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Towards understanding the genetics of pre- and post- harvest traits bitter pit in apple and chilling requirement in pear
No full textCrops from the Rosaceae family are very important for Washington agriculture but many factors can decrease yield and quality of the main tree fruit species of this family. One of the biggest problems in apple is bitter pit, a nutritional disorder. The main cause is a calcium deficiency that results in localized cell death which develops into black, corky pits. It is hard to define the stages and the mechanisms behind its development because many different factors influence its occurrence. The genetic and phenotypic characteristics define the generation of the pits, but also agronomical practices can have an important effect. A previous study in the Dhingra lab identified two homologs of a putative bitter bit associated gene (MdPBAG) in apple. These genes have been cloned and sequenced to detect genetic variability among eight commercial cultivars and eight seedlings with differing susceptibility to bitter pit. This genetic analysis was the first step in a larger genomic screen to detect QTLs for bitter pit in apple. Several QTL regions were identified and one of the two MdPBAG homologs was found to be approximately located 1cM apart from a QTL on linkage group 3. The QTL regions were also analyzed to identify candidate genes and their expression was evaluated to determine if they might be involved in the genetic mechanism inducing the disorder. Consumers find pear fruit problematic; 'ripe and ready-to-eat' pears are difficult to source. Many cultivars of pear only start to mature after a cold storage period which switches on the autocatalytic production of ethylene. Previous reports indicate that the gene family ACS seems to have a major function in determining the length of the required cold treatment. In this project, three cultivars, with different chilling requirements were analyzed to identify specific alleles for the genes of the ACS family. New ACS alleles, compared to the previously reported ones, were identified in both Anjou and Comice. In order to advance this study further, a segregating population was created, making reciprocal crosses of the three selected cultivars to create new genetic recombinants with differing cold requirements and to analyze their segregation
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Establishing a foundation for the identification and initiation of clonal variation in Vitis vinifera
No full textCompared to other valuable fruit crops, there is minimal focus on genetic improvement of varietal quality of fruit produced from the world‟s major wine grapes, with current breeding programs focusing on traits such as resistance to biotic or abiotic stresses. To produce the highest quality fruit, viticulturists give attention to the best utilization of existing varieties with relationship to vineyard location and cultural practices. The existence of “clones”, assumed to be natural genetic variants within existing varieties, provides viticulturists with vines and fruit that fit their needs. The overarching goal of this project is to further the understanding of clonal variation of Vitis vinifera. The first objective of this project was to assess the importance of clonal variation to the Washington wine industry and develop a sense of the knowledge and interest in clonal variation among wine consumers. To achieve this, two surveys were conducted and results indicate that clonal variation is important to the industry and consumers, and there is a need for a resource in Washington that could genetically confirm clonal identity. To address the need identified by the survey studies, a new genetic test was investigated as part of the second objective. The method tested in this study yielded similar results as in all past DNA-based studies where varieties could be clearly differentiated, but clonal identification remains a challenge. The final objective of this project focused on developing a lab-based resource for the generation of clones to enable further studies. The Vitis genome has been sequenced and functional genomics studies are being conducted which are expected to reveal the genetic basis of clonal variation. Thus, a need has arisen for an in planta system to test gene function in V. vinifera. A prerequisite for such studies is an efficient regeneration system in Vitis. This has been accomplished using plant material from the dwarf cultivar V. vinifera „Pixie‟, an excellent model Vitis system
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Evaluation of pre-breeding resources for Pyrus spp.
No full textIn the U.S. there is an urgent need for dwarfing, precocious, cold tolerant, and disease resistant rootstocks for efficient production of pear (Pyrus communis L.). A key challenge is finding locally acclimated and genetically diverse parental material for breeding desirable rootstocks suitable for pear production in the U.S. To address this genetic resource gap, Pyrus communis L.cultivars, acclimated to the U.S environment, were utilized to develop two types of populations. A traditional population was developed in 2012 and consisted of 132 individuals derived from reciprocal crosses between 'Bartlett', 'D'Anjou', and 'Comice'. A putative mutant population was developed in 2013, utilizing gamma-irradiated pollen, comprising of 49 individuals recovered from crosses between 'Abbé Fetel', 'D'Anjou', 'Bartlett', and 'Comice'. In addition, a genetically diverse set of Pyrus germplasm was sourced from the USDA-ARS Corvallis Germplasm Repository as a pre-breeding resource for Pyrus rootstock development. Progeny from both types of populations were phenotyped for segregation of traits including, branch density, caliper, height, bark type, branch angle, and blind wood. Within the traditional population, ten of the individuals were potentially dwarfing and two individuals exhibited precocity as they flowered within four years after germination. Within the putative mutant population, four individuals were found to be potentially dwarfing. Target Region Amplification Polymorphism (TRAP) molecular markers were used to evaluate the extent of genetic interrelatedness, and diversity, within both types of populations and the germplasm collection. This analysis revealed that individuals in the traditional population formed two distinct groups. The individuals in the putative mutant population exhibited unpredictable grouping, perhaps as a consequence of gamma-irradiation of the pollen or to their true paternal lineage in case of any outcrossing, which is common during hybridization. The USDA germplasm collection separated into two groups, with no clear subgroups, most likely due to the inclusion of a genetically diverse set of individuals. Phenotypic and genetic diversity information generated for these pre-breeding resources is expected to enable appropriate selection of individuals for use as parental material for breeding experiments aimed at developing pear rootstocks for efficient pear production in the United States
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Population structure analysis of parental material in hop and pear breeding programs
No full textHops and pears are important agricultural commodities in the United States, particularly in Washington State. Hop, Humulus lupulus, is a cone-bearing plant that produces essential oils and organic acids that contribute to the flavor, aroma, and bitterness of beer. Washington hop production exceeded 205 million) of the United States pear production value, followed by Oregon State and California with 30% and 20%, respectively. To maintain and improve the viability of these industries in Washington State, hop and pear breeding programs must continue to create disease resistant and desirable cultivars using diverse parental material. Evaluating genetic relationships among new parental material for these breeding programs is critical for helping breeders make crosses between diverse v individuals. This thesis presents information on genetic diversity in breeding parents for hops and advanced rootstock selections for pear, and helps to resolve genetic relatedness between genotypes. Genetic relationships among hop parental genotypes used in th
Effects of hormones on sweet cherry seed germination
No full textAcknowledgements/Funding: CAHNRS Undergraduate Research and Creative Projects Awards, Washington State Tree Fruit Research Commission, David Allan and Yakima Valley Orchards, Auvil Fruit Research Fellowship, NSF CURE Program and grant money.Increasing seed germination translates to higher success of finding the next best sweet cherry variety.Washington State University, Molecular Plant Sciences; Department of Horticulture and Landscape Architecture.Allan, M, Koepke, T, Oraguzie, N. & Dhingra A. (2012) Effects of hormones on sweet cherry seed germination. Presented at the 2012 Washington State University Academic Showcase. Available at: http://hdl.handle.net/2376/365
Self-assembled strained nanostructures for light emission grown using molecular beam epitaxy
No full textIII-V nanostructures are widely researched for applications in dislocation-resistant light emitters for photonic integrated circuits, quantum computing and single photon emitters. The 0D nanostructures include quantum dots (QDs), dot in a well (DWELLs), sub-monolayer QDs and droplet epitaxy QDs, while 1D elongated structures include quantum dashes and nanowires (NWs). The optical properties of nanostructures can be controlled through size, composition, strain and band-offsets during epitaxial growth and can be tailored precisely to emit light with photon energies suited to the application, spanning 0.2-2.0 eV. This thesis explores two novel QD based light emitters in the visible and near-infrared wavelength regime. In the first part of the thesis, we demonstrate the growth and characterization of tensile strained Ge QDs and Ge NWs phase segregated in the III-V matrix via Volmer-Weber growth mode emitting at 1200 nm. The second part of the thesis demonstrates the dislocation tolerance of compressively strained InP QDs grown on lattice-matched GaAs and lattice-mismatched Si substrate via Stranski-Krastanov growth mode emitting at 713 nm.
The first part of the thesis explores the growth of tensile strained Ge QDs and NWs phase segregated in the III-V matrix. Epitaxial growth of phase segregated Ge nanostructures embedded within III-V compound semiconductors is a promising way to achieve a high biaxial tensile strain along with precise control of nanostructure density, size and morphology. Here we demonstrate growth of phase-segregated Ge quantum dots (QDs) and compare them to our previously reported Ge nanowires (NWs); both are strained to an In0.52Al0.48As matrix with a high biaxial tensile strain of 3.6%. Despite the similar growth conditions, there exist pronounced differences in the lateral size and planar density of Ge QDs and Ge NWs, with Ge QDs showing significantly larger size, lower density and structural anisotropy along the in-plane [1-10] direction. In addition to the difference in morphology, Ge QDs are shown to be more prone to plastic relaxation by formation of dislocations and stacking faults, which we attribute to their larger in-plane size. Finally, tensile Ge QDs are shown to exhibit strong room-temperature photoluminescence at 1176 nm, which is blueshifted from the case of Ge NWs.
In the second part of the thesis, we demonstrate epitaxial InP QDs on GaAs on Si virtual substrates with room-temperature photoluminescence (PL) intensity nearly identical to those grown on GaAs substrates. The similarity in PL characteristics is remarkable considering that the active region on the GaAs/Si virtual substrate has a threading dislocation density (TDD) of ~3×10^7 cm-2, as compared to the bulk GaAs substrate with TDD 50× improvement in the luminescence intensity of InP QDs annealed at ~700⁰C for 100 minutes without observable structural degradation or blue-shift in the PL spectrum.Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2021-05-01The student, Pankul Dhingra, accepted the attached license on 2019-04-25 at 12:06.The student, Pankul Dhingra, submitted this Thesis for approval on 2019-04-25 at 12:16.This Thesis was approved for publication on 2019-04-25 at 14:10.DSpace SAF Submission Ingestion Package generated from Vireo submission #13914 on 2019-08-22 at 16:23:56Made available in DSpace on 2019-08-23T20:48:26Z (GMT). No. of bitstreams: 2
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Understanding the role of biochar in agriculture
No full textBiochar (BC) is the carbon-rich product derived from pyrolysis of plant biomass. While currently gaining traction for agro-ecosystem services, it was utilized by ancient farmers to improve soil health. BC, based on its recalcitrance index, can be retained in the soil for several hundred years, thereby aiding in long-term carbon sequestration. Several recent studies have demonstrated BC's ability to positively impact soil health by changing its physical, chemical and biological properties. BC has also been shown to positively impact plant growth and development, and yields; however, contradictory results have also been reported. The variation in the results could be attributed to several variables like type of feedstock used to produce the biochar, pyrolysis conditions, preexisting conditions of the soil and type of crop. In this study, the impact of wheat-derived BC on the agronomic performance of tomato (Solanum lycopersicum) var 'Oregon Spring' was evaluated. BC was added to the organic Palouse soil on the Washington State University Eggert Organic Farm at a rate of 1 and 2 ton/ha. The control and treatment plants were identical in their agronomic performance based on the quantification of above ground shoot biomass, yield and fruit quality. The addition of BC resulted in carbon sequestration in an organic production system, which represents healthy soils with adequate organic content. These observations in the context of other published studies indicate that BC may have a significant influence on soil health and crop performance when used in water depleted conditions or when soil health is marginal. In healthy soils, it is able to aid in carbon sequestration. However, the long-term effects of BC amendment in organic soils remains to be determined
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Metabolic engineering of oleaginous yeast Yarrowia lipolytica for the production of fatty alcohols
No full textFatty alcohols are long-chain aliphatic hydrocarbons with one hydroxyl group usually attached to their terminal carbon. These important oleaginous chemicals are widely used in detergent, lubricant, personal care, and pharmaceutical industries. The use of oleaginous yeasts as a cell factory to produce fatty alcohols from renewable resources is a sustainable and promising alternative to traditional approaches relying on plant oils or petrochemicals. In this thesis project, the expression levels of multi-copy insertion of tafar1 gene in a model oleaginous yeast Yarrowia lipolytica was quantitatively measured first. Then the possibility of knocking out negative regulators of INO1 in this yeast to increase its fatty alcohol productivity was explored. Through NCBI protein BLAST, gene deletion targets, mot1, pah1, rpd3, and isw2, were selected, and each gene was then deleted separately from yeast genome by homologous recombination. Engineered strains were cultivated in shake flasks for 5 days using the YPD medium with 40g/L glucose (YPD4). Every 24 hours, the OD600 value of each strain was measured with a UVspectrophotometer, and concentrations of fatty alcohols produced by engineered strains were detected using GC-FID. The growth curve showed that the deletion of RPD3 gene significantly inhibited cell growth while no obvious change was observed for other gene deletions. Among the knockout strains, the RPD3 knockout strain produced the highest titer of hexadecanol 278.5 mg/L. However, no single gene knockout was found to enhance fatty alcohol production in comparison to the control strain. The results highlight the complexity and uncertainty of manipulating both structural and regulatory genes. Finally, based on these findings, future metabolic engineering strategies to increase fatty alcohol production in Y. lipolytica were proposed
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Performance of 'Bartlett' and 'd'Anjou' Pear Grafted on Cold-Hardy Quince Accessions
No full textPear is widely grown worldwide, with production estimated at 22.6 million tons. Washington state leads in US production of the European (Pyrus communis L.) pear and grows most of the fresh and canning pears in the Pacific Northwest for the commercial market. Orchard designs and training systems have been changing from traditional low-density plantings to modern high-density plantings in tree fruit areas around the world to maximize production through high yields; reduce labor costs and challenges, and improve overall orchard efficiency. To have a sustainable and successfully productive high-density orchard, dwarfing rootstocks are needed to control vigor and tree size, increase precocity, and produce high-quality large fruit for the market. Unlike with apples, the US has been hesitant about adopting high-dwarfing rootstocks for pear production mainly because the currently available rootstocks are more susceptible to harsher environments than are found in the PNW. Further research evaluating dwarfing rootstocks for high-density pear orchards is crucial to improving the current state of the US pear industry. This research addressed the improvement of European pear production in the PNW utilizing rootstock selection, emphasizing the use of quince as a dwarfing rootstock for ‘Bartlett’ and ‘d’Anjou’ pear cultivars. Overall performance and growth characteristics were determined for all nine CYD quince rootstock graft combinations, using a ‘Comice’ interstem for both cultivars. Specifically, this research identified 4 promising CYD quince accession rootstock combinations for WA pear production based on adequate vegetative growth and vigor, physiological performance, fruit productivity, and fruit quality. These combinations included ‘Bartlett’ and ‘d’Anjou’ grafted with a ‘Comice’ interstem to quince rootstocks 22.001, 23.001, 57.001, and 65.001. These findings allow the US pear industry to move more confidently into the direction of high-density pear production using a promising dwarfing quince rootstock for pear
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