Search results
(1 - 20 of 133)
Pages
- Title
- Genomics of beta vulgaris crop types : insights into tap root development and storage characteristics
- Creator
- Galewski, Paul John
- Date
- 2020
- Collection
- Electronic Theses & Dissertations
- Description
-
Cultivated Beta vulgaris L. (beet) is a species complex composed of several distinct crop types developed for specific end uses. The crop types include sugar beet, fodder beet, table beet and leaf beet/chard. The evolution of each crop type appears to have resulted from interactions between selection, drift, gene flow, recombination, and the sorting of ancestral variation. Beets are generally heterozygous and contain self-incompatibility mechanisms. Therefore, reproducing and maintaining the...
Show moreCultivated Beta vulgaris L. (beet) is a species complex composed of several distinct crop types developed for specific end uses. The crop types include sugar beet, fodder beet, table beet and leaf beet/chard. The evolution of each crop type appears to have resulted from interactions between selection, drift, gene flow, recombination, and the sorting of ancestral variation. Beets are generally heterozygous and contain self-incompatibility mechanisms. Therefore, reproducing and maintaining the genetic constitution of a single individual for genetic and phenotypic analysis is a challenge. Beet populations are the fundamental unit of improvement and contain the evolutionary and adaptive potential of the species. This research used several approaches which explore the utility of pooled population genomic sequencing to survey the organization and distribution of genetic diversity within cultivated B. vulgaris lineages, and give context and clarity to the genetics underlying important agronomic characters.Whole genome sequence data was produced for important varieties and germplasm releases which represent the B. vulgaris crop type lineages. Using population genetic and statistical methods, relationships were determined between populations. Lineage-specific variation, or variation unique to specific crop types, was uncovered and used to quantify the level of support for these groups as discrete units. Allele frequency was able to differentiate between crop types using Principle Components Analysis (PCA), suggesting positive selection for end use was a major driver of crop type divergence. PCA carried out on a chromosome-by-chromosome basis showed the relative contributions of specific chromosomes to crop type diversification. Gene diversity (e.g., expected heterozygosity) and FST proved powerful indicators of selection along the chromosome at nucleotide resolution. In total, 12.13% of loci within the genome were differentiated with respect to crop type. Interestingly, this corresponds to levels of divergence observed in studies of incipient speciation. Differentiated regions, indicated by FST outliers, contained 472 genes, or 1.6% of the 24,255 genes predicted in the reference genome assembly. Respectively, sugar beet, table beet, fodder beet, and chard genomes contained 16, 283, 2, and 171 genes characterized as differentiated between crop types. Cryptic relationships were observed between crop types due to a high degree of genetic variation shared between crop type lineages. Specific instances of common ancestry, sorting of ancestral variation, and admixture and introgression were identified, which explain the degree of substructure observed between specific crop types.The content and organization of diversity in beet genomes reflects a complex history related to B. vulgaris crop type diversification. With the exception of chard, much of the species' historical selection has focused on the improvement of root characters (e.g., root enlargement, biomass, dry matter content, and sucrose concentration). As a result, major differences in root morphology and physiology can be observed between these lineages. Measures of root development and physiology between crop types were compared, and interestingly, much of the phenotypic variation partitioned between crop types corresponds to candidate genes identified from analyses of genome-wide variation using FST and 2pq. Admixture and introgression appear to have shared specific variation involved in the reduction of lateral roots (e.g., Root primordium defective 1), root enlargement (e.g., Brevis radix-like 4, putative NAC domain-containing protein 94, cytokinin dehydrogenase 3), and biomass accumulation (e.g., 6-phosphofructo-2-kinase). High relationship coefficients and high correlations in allele frequency for this variation were observed, indicating the genetic variation influencing these characters may have been derived from a single origin. The development of beet into an economically viable sugar crop required both an enlarged root and an increase sucrose concentration. Genes were identified that may explain these physiological changes within the root (e.g., decrease in water concentration, increase in dry matter content and increase in sucrose concentrations). These genes correspond to shared variation, distributed among crop types, as well as lineage-specific variation, restricted to sugar beet lineages. Integrating selection, drift, and admixture into a putative demographic history of beet provides evidence for the role of specific genes in the development of beet crop types and the expression of novel phenotypic characters.
Show less
- Title
- Genome-wide association study reveals genes associated with mite recruitment phenotypes in the domesticated grapevine (vitis vinifera
- Creator
- LaPlante, Erika R.
- Date
- 2020
- Collection
- Electronic Theses & Dissertations
- Description
-
Plants in the grape genus Vitis have varying densities of trichomes and mite-domatia on their leaves, which facilitate the recruitment, retention, and reproduction of beneficial mites. By increasing the abundance of mites on grape leaves, these phenotypes promote a defense mutualism contributing to the control of grape pests and pathogens. Identification of the genes controlling these phenotypes would inform our understanding of the genetics underlying mite-plant mutualistic interactions and...
Show morePlants in the grape genus Vitis have varying densities of trichomes and mite-domatia on their leaves, which facilitate the recruitment, retention, and reproduction of beneficial mites. By increasing the abundance of mites on grape leaves, these phenotypes promote a defense mutualism contributing to the control of grape pests and pathogens. Identification of the genes controlling these phenotypes would inform our understanding of the genetics underlying mite-plant mutualistic interactions and could lead to breeding domesticated Vitis vinifera L. varieties that are naturally defended against pathogens. Little is known about the genetics underlying mite recruitment phenotypes in Vitis. We conducted a GWAS to determine the genetic architecture of mite recruitment traits in V. vinifera using 399 cultivars from a common garden diversity panel. We investigated eight traits previously established in the literature associated with an increase in beneficial mite abundance. We found single nucleotide polymorphisms (SNPs) significantly associated with each mite recruitment trait investigated. Corresponding gene annotations of SNP genetic coordinates revealed notable gene associations, including a trichome development gene, and a physiological defense response gene, suggesting these genetic regions may have a large impact on mediating mite-plant interactions in this species. Our findings are among the first to investigate which genes underly ecologically important mutualisms between plants and beneficial mites and suggest promising candidate genes for breeding and genetic editing to increase naturally occurring predator-based defenses in grapes.
Show less
- Title
- Characterization of cyclic-GMP-AMP signaling and novel gene networks in the Vibrio Seventh Pandemic Islands of El Tor Vibrio cholerae
- Creator
- Severin, Geoffrey Blaine-Graessley
- Date
- 2020
- Collection
- Electronic Theses & Dissertations
- Description
-
Vibrio cholerae is the causative agent of the diarrheal disease cholera, for which there have been seven pandemics. The first six pandemics (1817-1923) have been attributed to strains of the classical biotype while the seventh pandemic (1961- current) is being perpetuated by circulating strains of the El Tor biotype. It is hypothesized that El Tor's acquisition of two unique genomic islands of unknown origins, Vibrio Seventh Pandemic Island 1 & 2 (VSP-1 & 2), potentiated its displacement of...
Show moreVibrio cholerae is the causative agent of the diarrheal disease cholera, for which there have been seven pandemics. The first six pandemics (1817-1923) have been attributed to strains of the classical biotype while the seventh pandemic (1961- current) is being perpetuated by circulating strains of the El Tor biotype. It is hypothesized that El Tor's acquisition of two unique genomic islands of unknown origins, Vibrio Seventh Pandemic Island 1 & 2 (VSP-1 & 2), potentiated its displacement of classical strains in both environmental and clinical reservoirs prior to the seventh pandemic. Despite their connection to the pandemic evolution of the El Tor biotype and the likelihood they encode a wealth of novel biological functions the majority of the 303036 ORFs in the VSP islands have remained uncharacterized. The works presented in the thesis represent examples of our collective efforts to understand the unique traits afforded to the El Tor biotype by the VSP islands. .In 2012, ten years after the initial discovery of the VSP islands, the cyclic di-nucleotide synthase DncV was identified in VSP-1 and shown to synthesize the novel second messenger cyclic-GMP-AMP (cGAMP). Despite this significant discovery, cGAMP remained an orphan second messenger in bacteria for six years. In Chapter 2, I present our identification of the first cGAMP signaling network in bacteria by connecting the synthesis of cGAMP to the allosteric activation of the VSP-1 encoded patatin-like phospholipase vc0178, now named CapV. This finding helped catalyze the revelation that homologous cyclic-dinucleotide signaling networks contribute to bacteriophage-immunity and are distributed widely across the bacterial phyla.dncV and capV represent just two of the 103031 ORFs encoded in VSP-1, therefore we hypothesized that cGAMP signaling may extend to include additional genes within the island. Bioinformatic analysis of VSP island genes performed in collaboration with the laboratory of Eva Top at the University of Idaho predicted that dncV was likely to share a biological pathway with the VSP-1 encoded putative deoxycytidylate deaminase vc0175, we have now named DcdV. In Chapter 3, I describe our ongoing efforts to understand the biological function of DcdV and the discovery of its novel negative regulator DifV.The work presented in this thesis has made fundamental contribution to understanding the pandemic evolution of the El Tor biotype and the utility homologous genes afford to their bacterial host while providing a roadmap for further exploration of the biological role of the VSP-1 and VSP-2 islands in pandemic V. cholerae.
Show less
- Title
- Deconstructing the correlated nature of ancient and emergent traits : an evolutionary investigation of metabolism, morphology, and mortality
- Creator
- Grant, Nkrumah Alions
- Date
- 2020
- Collection
- Electronic Theses & Dissertations
- Description
-
Phenotypic correlations are products of genetic and environmental interactions, yet the nature of these correlations is obscured by the multitude of genes organisms possess. My dissertation work focused on using 12 populations of Escherichia coli from Richard Lenski's long-term evolution experiment (LTEE) to understand how genetic correlations facilitate or impede an organism's evolution. In chapter 1, I describe how ancient correlations between aerobic and anaerobic metabolism have...
Show morePhenotypic correlations are products of genetic and environmental interactions, yet the nature of these correlations is obscured by the multitude of genes organisms possess. My dissertation work focused on using 12 populations of Escherichia coli from Richard Lenski's long-term evolution experiment (LTEE) to understand how genetic correlations facilitate or impede an organism's evolution. In chapter 1, I describe how ancient correlations between aerobic and anaerobic metabolism have maintained - and even improved - the capacity of E. coli to grow in an anoxic environment despite 50,000 generations of relaxed selection for anaerobic growth. I present genomic evidence illustrating substantially more mutations have accumulated in anaerobic-specific genes and show parallel evolution at two genetic loci whose protein products regulate the aerobic-to-anaerobic metabolic switch. My findings reject the "if you don't use it, you lose it" notion underpinning relaxed selection and show modules with deep evolutionary roots can overlap more, hence making them harder to break. In chapter 2, I revisit previous work in the LTEE showing that the fitness increases measured for the 12 populations positively correlated with an increase in cell size. This finding was contrary to theory predicting smaller cells should have evolved. Sixty thousand generations have surpassed since that initial study, and new fitness data collected for the 12 populations show fitness has continued to increase over this period. Here, I asked whether cell size also continued to increase. To this end, I measured the size of cells for each of the 12 populations spanning 50,000 generations of evolution using a particle counter, microscopy, and machine learning. I show cell size has continued to increase and that it remains positively correlated with fitness. I also present several other observations including heterogeneity in cell shape and size, parallel mutations in cell-shape determining genes, and elevated cell death in the single LTEE population that evolved a novel metabolism - namely the ability to grow aerobically on citrate. This last observation formed the basis of my chapter 3 research where my collaborators and I fully examine the cell death finding and the associated genotypic and phenotypic consequences of the citrate metabolic innovation.
Show less
- Title
- The consequences of gene duplication by DNA transposons and their interaction with host genomes and retrotransposons
- Creator
- Cerbin, Stefan
- Date
- 2020
- Collection
- Electronic Theses & Dissertations
- Description
-
DNA is the ultimate genetic information carrier. These sequences of nucleotides hold enormous coded data controlling all aspects of functions, including growth, development, and defense of an organism. Genes are the protein coding units that support cellular function. While gene number is similar across species, genome size varies dramatically. One source of this variation is due to transposable elements, which are DNA sequences that are capable of moving from one locus to another in the...
Show moreDNA is the ultimate genetic information carrier. These sequences of nucleotides hold enormous coded data controlling all aspects of functions, including growth, development, and defense of an organism. Genes are the protein coding units that support cellular function. While gene number is similar across species, genome size varies dramatically. One source of this variation is due to transposable elements, which are DNA sequences that are capable of moving from one locus to another in the genome. These sequences are ubiquitous and provide sources of mutations for evolution. Transposable elements are classified into two classes: DNA and RNA elements (retroelements). The elements are further classified into autonomous and non-autonomous elements according to their capability to transpose. Specific elements have been shown to duplicate gene fragments and amplify in the genomes. These elements carrying genes have regulatory, evolutionary, and phenotypic effects. This dissertation illustrates examples of gene duplications by DNA transposons and their interactions with the remainder of the genome. The first entails GingerRoot: A novel DNA transposon encoding integrase-related transposase in plants and animals. This study reveals a unique DNA transposon located in the heterochromatic regions of the genome. The capability of duplicating gene fragments may have allowed them to be retained longer in genomic regions enriched with retrotransposons. The second comprises a study of Nucifera nelumbo landscape of transposable elements. In this basal dicot species, the genic regions have been significantly expanded by the insertion of transposable elements. Interestingly, genes involved in epigenetic pathways are enriched with insertions, suggesting the co-evolution between the transposable elements and the genome surveillance machine. The third study investigates Pack-MULE SlPM37 in Solanum lycopersicum and its relatives. This Pack-MULE element has achieved a higher copy number than any other Pack-MULE elements, and the possible mechanism underlining its amplification has been proposed through detailed characterization of this element and the relevant parental genes. These chapters show how genomes are comprised of varying transposons, how their context influences gene duplication, and the interactions with other genomic components including genes and other transposons. The dynamic interactions between transposable elements and their host genomes suggest the composition and abundance of transposons not only influence the genome size and genome structure, but also the path of evolution.
Show less
- Title
- Introducing sparsity into selection index methodology with applications to high-throughput phenotyping and genomic prediction
- Creator
- Lopez-Cruz, Marco Antonio
- Date
- 2020
- Collection
- Electronic Theses & Dissertations
- Description
-
Research in plant and animal breeding has been largely focused on the development of methods for a more efficient selection by altering the factors that affect genetic progress: selection intensity, selection accuracy, genetic variance, and length of the breeding cycle. Most of the breeding efforts have been primarily towards increasing selection accuracy and reducing the breeding cycle.Genomic selection has been successfully adopted by many public and private breeding organizations. Over...
Show moreResearch in plant and animal breeding has been largely focused on the development of methods for a more efficient selection by altering the factors that affect genetic progress: selection intensity, selection accuracy, genetic variance, and length of the breeding cycle. Most of the breeding efforts have been primarily towards increasing selection accuracy and reducing the breeding cycle.Genomic selection has been successfully adopted by many public and private breeding organizations. Over years, these institutions have developed and accumulated large volumes of genomic data linked to phenotypes from multiple populations and multiple generations. This data abundance offers the opportunity to revolutionize genetic research. However, these data sets are also increasingly heterogeneous, with many subpopulations and multiple generations represented in the data. This translates into potentially heterogeneous allele frequencies and different LD patterns, thus leading to SNP-effect heterogeneity. Genomic selection methods were developed with reference to homogeneous populations in which SNP-effects are assumed constant across the whole population. These methods are not necessarily optimal for the contemporary available data sets for model training. Therefore, a first focus of this dissertation is on developing novel methods that can leverage the large-scale of modern data sets while coping with the heterogeneity and complexity of this type of data. In recent years, there have also been important advances in high-throughput phenotyping (HTP) technologies that can generate large volumes of data at multiple time-points of a crop. Examples of this include hyper-spectral imaging technologies that can capture the reflectance of electromagnetic power by crops at potentially thousands of wavelengths. The integration of HTP in genetic evaluations represents a great opportunity to further advance plant breeding; however, the high-dimensional nature of HTP data poses important challenges. Therefore, a second focus of this dissertation is on the development of a novel approach to efficiently incorporate HTP data for breeding values prediction. Thus, this dissertation aims to contribute novel methods that can improve the accuracy of genomic prediction by optimizing the use of large, potentially heterogeneous, genomic data sets and by enabling the integration of HTP data. We present a novel statistical approach that combines the standard selection index methodology with variable-selection methods commonly used in machine learning and statistics, and developed software to implement the method. Our approach offers solutions to both genomic selection with potentially highly heterogeneous genomic data sets, and the integration of HTP in genetic evaluations.
Show less
- Title
- MODELING AND PREDICTION OF GENETIC REDUNDANCY IN ARABIDOPSIS THALIANA AND SACCHAROMYCES CEREVISIAE
- Creator
- Cusack, Siobhan Anne
- Date
- 2020
- Collection
- Electronic Theses & Dissertations
- Description
-
Genetic redundancy is a phenomenon where more than one gene encodes products that perform the same function. This frequently manifests experimentally as a single gene knockout mutant which does not demonstrate a phenotypic change compared to the wild type due to the presence of a paralogous gene performing the same function; a phenotype is only observed when one or more paralogs are knocked out in combination. This presents a challenge in a fundamental goal of genetics, linking genotypes to...
Show moreGenetic redundancy is a phenomenon where more than one gene encodes products that perform the same function. This frequently manifests experimentally as a single gene knockout mutant which does not demonstrate a phenotypic change compared to the wild type due to the presence of a paralogous gene performing the same function; a phenotype is only observed when one or more paralogs are knocked out in combination. This presents a challenge in a fundamental goal of genetics, linking genotypes to phenotypes, especially because it is difficult to determine a priori which gene pairs are redundant. Furthermore, while some factors that are associated with redundant genes have been identified, little is known about factors contributing to long-term maintenance of genetic redundancy. Here, we applied a machine learning approach to predict redundancy among benchmark redundant and nonredundant gene pairs in the model plant Arabidopsis thaliana. Predictions were validated using well-characterized redundant and nonredundant gene pairs. Additionally, we leveraged the availability of fitness and multi-omics data in the budding yeast Saccharomyces cerevisiae to build machine learning models for predicting genetic redundancy and related phenotypic outcomes (single and double mutant fitness) among paralogs, and to identify features important in generating these predictions. Collectively, our models of genetic redundancy provide quantitative assessments of how well existing data allow predictions of fitness and genetic redundancy, shed light on characteristics that may contribute to long-term maintenance of paralogs that are seemingly functionally redundant, and will ultimately allow for more targeted generation of phenotypically informative mutants, advancing functional genomic studies.
Show less
- Title
- GENETIC VARIABILITY AND MAPPING OF COOKING TIME AND SENSORY ATTRIBUTES IN ANDEAN DRY BEANS
- Creator
- Bassett, Amber Nichole
- Date
- 2020
- Collection
- Electronic Theses & Dissertations
- Description
-
Cooking time, flavor, and texture of dry beans (Phaseolus vulgaris L.) are valued by consumers but are not major considerations of dry bean breeding programs. The aim of this research is 1) to investigate mechanisms underlying fast cooking times of select genotypes, 2) to characterize the genetic control of cooking time, flavor, and texture of cooked beans in a diversity panel and a recombinant inbred line population, and 3) to evaluate how fast-cooking bean genotypes process into canned...
Show moreCooking time, flavor, and texture of dry beans (Phaseolus vulgaris L.) are valued by consumers but are not major considerations of dry bean breeding programs. The aim of this research is 1) to investigate mechanisms underlying fast cooking times of select genotypes, 2) to characterize the genetic control of cooking time, flavor, and texture of cooked beans in a diversity panel and a recombinant inbred line population, and 3) to evaluate how fast-cooking bean genotypes process into canned products. The genetic mechanism of fast cooking time was assessed via the physical and compositional seed characteristics in a set of 8 genotypes. Faster cooking beans had thinner cotyledon cell walls and seed coat layers and lower seed coat percentage, seed weight, and total and insoluble fiber. To identify genomic loci underlying cooking time, flavor, and texture, genome-wide association (GWA) and quantitative trait loci (QTL) mapping approaches were used with 430 lines of the Andean Diversity Panel and 242 yellow recombinant inbred lines. Sensory attributes included total flavor, beany, vegetative, earthy, starchy, sweet, and bitter intensity as well as seed coat perception and cotyledon texture. SNPs and QTL were identified for most of the attributes, with QTL for earthy intensity having the most phenotypic variation explained. In both populations, sweet and starchy intensity were positively correlated and associated via PCA, but other trait associations were minimal. A subset of lines from the RIL population were evaluated for canning quality following different retort processing durations. For fast-cooking lines, canning quality improved with reduced retort processing time, revealing a potential cost-saving benefit to the canning industry. This information lays a foundation for targeting fast cooking times and specific sensory profiles in breeding programs.
Show less
- Title
- IDENTIFICATION AND CHARACTERIZATION OF MOLECULAR TARGETS FOR DISEASE MANAGEMENT IN TREE FRUIT PATHOGENS
- Creator
- Peng, Jingyu
- Date
- 2020
- Collection
- Electronic Theses & Dissertations
- Description
-
Fire blight, caused by Erwinia amylovora, is a devastating bacterial disease threatening the worldwide production of pome fruit trees, including apple and pear. Within host xylem vessels, E. amylovora cells restrict water flow and cause wilting symptoms through formation of biofilms, that are matrix-enmeshed surface-attached microcolonies of bacterial cells. Biofilm matrix of E. amylovora is primarily composed of several exopolysaccharides (EPSs), including amylovora, levan, and, cellulose....
Show moreFire blight, caused by Erwinia amylovora, is a devastating bacterial disease threatening the worldwide production of pome fruit trees, including apple and pear. Within host xylem vessels, E. amylovora cells restrict water flow and cause wilting symptoms through formation of biofilms, that are matrix-enmeshed surface-attached microcolonies of bacterial cells. Biofilm matrix of E. amylovora is primarily composed of several exopolysaccharides (EPSs), including amylovora, levan, and, cellulose. The final step of biofilm development is dispersal, which allows dissemination of a subpopulation of biofilm cells to resume the planktonic mode of growth and consequentially cause systemic infection. In this work, we demonstrate that identified the Hfq-dependent small RNA (sRNA) RprA positively regulates amylovoran production, T3SS, and flagellar-dependent motility, and negatively affects levansucrase activity and cellulose production. We also identified the in vitro and in vivo conditions that activate RprA, and demonstrated that RprA activation leads to decreased formation of biofilms and promotes the dispersal movement of biofilm cells. This work supports the involvement of RprA in the systemic infection of E. amylovora during its pathogenesis. Bacterial toxin-antitoxin (TA) systems are small genetic loci composed of a proteinaceous toxin and a counteracting antitoxin. In this work, we identified and characterized a chromosomally encoded hok/sok-like type I TA system in Erwinia amylovora Ea1189. Ectopic overexpression of hok caused massive cell death in E. amylovora and its toxicity can be partially reversed through co-overexpression of the cognate sRNA sok. Phenotypic and transcriptomic examination of E. amylovora cells expressing hok at subtoxic levels demonstrated that hok causes membrane rupture and proton motive force dissipation, upregulates expression levels of ATP biosynthesis genes and consequently cellular ATP levels. Hok also positively affects phage shock protein genes to protect cells from further membrane damage. Taken together, the hok/sok TA system, besides being potentially self-toxic, appears to facilitate E. amylovora to manage various stress responses when the toxin gene is expressed in low levels. The succinate dehydrogenase inhibitor (SDHI) is a broad-spectrum fungicide class that has been widely utilized in agricultural fields. Blumeriella jaapii, the causative agent of cherry leaf spot (CLS), is the most important limiting factor for tart cherry production in the Midwestern United States. In the last decade, reduced efficacy in using SDHIs, i.e. boscalid, fluopyram, and fluxapyroxad, for management of CLS has been observed in many research and commercial orchard sites. Through whole-genome sequencing of B. jaapii using both PacBio long-reads and Illumina short-reads, we identified mutations in SdhB or SdhC that are correlative to resistance of this fungus to boscalid, fluopyram, and/or fluxapyroxad. SdhB and SdhC are components of the succinate dehydrogenase complex that contributes fungal respiration. In view of the widely conserved sequences of the SdhB and SdhC genes in phytopathogenic Ascomycete fungi, we expressed the wild-type or mutated alleles of the B. jaapii Sdh gene in the soybean white mold pathogen Sclerotinia sclerotiorum. We successfully validated the functions of the mutations in Sdh genes of B. jaapii in conferring resistance to several SDHIs examined in this study. The S. sclerotiorum heterologous expression system was also validated to be highly effective in characterizing the functions of other Sdh mutations of B. cinerea, C. homoeocarpa, and M. fructicola. The approach developed in this study can potentially be widely applied to interrogate SDHI fungicide resistance mechanisms in other phytopathogenic ascomycetes.
Show less
- Title
- Elucidating the genetic mechanisms of flowering and the repression of floral initiation by fruit in apple (Malus x domestica Borkh.)
- Creator
- Gottschalk, Christopher Charles
- Date
- 2020
- Collection
- Electronic Theses & Dissertations
- Description
-
Many tree fruit crops exhibit yearly cyclical fluctuations in flowering and fruiting, including apple (Malus × domestica Borkh.). This phenomenon, known as biennial bearing, is an intriguing biological problem, as well as a production limitation of many high-value apple cultivars. The current hypotheses to explain biennial bearing focus on the repressive effects of fruit on the initiation of floral primordia, which would develop into flowers the following year. This floral repressive response...
Show moreMany tree fruit crops exhibit yearly cyclical fluctuations in flowering and fruiting, including apple (Malus × domestica Borkh.). This phenomenon, known as biennial bearing, is an intriguing biological problem, as well as a production limitation of many high-value apple cultivars. The current hypotheses to explain biennial bearing focus on the repressive effects of fruit on the initiation of floral primordia, which would develop into flowers the following year. This floral repressive response could be the result of nutrient competition between the spur apex and the strong sink of the developing fruit, or flowering-inhibitory gibberellins (GAs) that are produced in the seeds of the developing fruit and exported to the spur apex. However, the molecular mechanism by which fruit load and/or GAs represses floral initiation is unknown.The first aim of my dissertation was to identify the genes involved in the floral initiation pathway. Utilizing transcripts assembled from a transcriptome of the biennial cultivar 'Honeycrisp' and the known flowering genes from Arabidopsis, I identified a comprehensive list of flowering-related homologs based on sequence homology, phylogenetic relationship, and syntenic organization. The second aim was to characterize the expression of the flowering-related homologs during the period of floral initiation under crop load conditions that either promote or repress flowering. Homologs of AGL24/SVP, AP1, FT, LFY, and SPLs were strongly expressed in apices of floral-induced trees, supporting their presumed role as floral promoters. In contrast, a homolog of the floral repressor TERMINAL FLOWER 1 (MdTFL1-2), was strongly up-regulated in apices of fruit-bearing, floral-repressed trees. Additionally, genes involved in the deactivation of bioactive GAs were strongly up-regulated in the floral-repressed trees. The timing of floral initiation is also known to vary between cultivars in apple. However, the diversity in flowering gene regulation that underlies this variation is unknown. The third aim of my dissertation was to investigate diversity of gene expression in six different apple species and cultivars. Generally, the expression profiles of the flowering-related genes were similar, suggesting a widely conserved mechanism. However, a few key genes involved in the regulation of floral initiation and development exhibited differential expression. For example, during the floral initiation period, five of the six genotypes were found to have differentially expressed MdTFL1s. This result implicates a potential role for the MdTFL1s in determining the timing of floral initiation in addition to a role in biennial bearing. Plant growth regulators (PGRs) offer the potential to control flowering and biennial bearing in established apple plantings. This final aim was to evaluate and improve the efficacy of foliar-applied GA regiments to repress flowering in apple. This study included the evaluation of application timings, GA formulations and concentrations, and cultivar-specificity. The most successful PGR trial used GA3 to inhibit flowering in 'Honeycrisp' when a strong return bloom was expected. As a result of the decreased flowering and fruit load, the harvested fruit in the year following GA application exhibited higher fruit-quality. The results from this collection of studies provide insight into the molecular control of flowering and biennial bearing while demonstrating a practical approach to managing flowering in a high-value apple cultivar.
Show less
- Title
- GENOME BIOLOGY OF THE CULTIVATED POTATO, SOLANUM TUBEROSUM
- Creator
- Pham, Gina Mai
- Date
- 2019
- Collection
- Electronic Theses & Dissertations
- Description
-
Cultivated potato is a highly heterozygous, clonally propagated autotetraploid. These traits make it a difficult crop to study and make genetic improvements. In the following dissertation, I present studies that aim to improve our knowledge of genetic complexity in potato and potato breeding strategies. First, I show that several thousand genes in cultivated potato varieties show evidence of preferential allele expression, a characteristic not expected for autotetraploids. This trend was...
Show moreCultivated potato is a highly heterozygous, clonally propagated autotetraploid. These traits make it a difficult crop to study and make genetic improvements. In the following dissertation, I present studies that aim to improve our knowledge of genetic complexity in potato and potato breeding strategies. First, I show that several thousand genes in cultivated potato varieties show evidence of preferential allele expression, a characteristic not expected for autotetraploids. This trend was observed in evolutionarily conserved genes, suggesting that cultivated potato may have preferential expression of functional alleles. Cultivated potato also has excessive copy number variation. The results indicate that ~16-18,000 genes are copy number variable, and are evolutionarily recent and related to adaptation to biotic and abiotic stress. They are also lowly expressed, with only 528 genes showing correlation between copy number and gene expression. Second, a common method of genome reduction in potato, interspecific crossing, is explored to determine possible mechanisms by which genome elimination occurs and somaclonal variation which arises during the process. The results show that haploid inducer line, IVP101, produces <1% somatic translocation event frequency in the Superior dihaploid population studied. The translocation events occurred in regions of open chromatin, suggesting that they may be driven by transcription-coupled DNA repair. Finally, I present an improved potato genome assembly and annotation using a combination of long-read sequencing methods. The new assembly, DM v.5, is 727 Mb, of which 91% is contained in 12 chromosome-scale scaffolds. DM v.5 presents a new opportunity for studies in comparative genomics and potato biology.
Show less
- Title
- Pervasive alternative RNA editing in Trypanosoma brucei
- Creator
- Kirby, Laura Elizabeth
- Date
- 2019
- Collection
- Electronic Theses & Dissertations
- Description
-
"Trypanosoma brucei is a single celled eukaryote that utilizes a complex RNA editing system to render many of its mitochondrial genes translatable. Editing of these genes requires multiple small RNAs called guide RNAs to direct the insertion and deletion of uridines. These gRNAs act sequentially, each generating the anchor binding site for the next gRNA. This sequential dependence should render the process quite fragile, and mutations in the gRNAs should not be tolerated. In the examination...
Show more"Trypanosoma brucei is a single celled eukaryote that utilizes a complex RNA editing system to render many of its mitochondrial genes translatable. Editing of these genes requires multiple small RNAs called guide RNAs to direct the insertion and deletion of uridines. These gRNAs act sequentially, each generating the anchor binding site for the next gRNA. This sequential dependence should render the process quite fragile, and mutations in the gRNAs should not be tolerated. In the examination of the gRNA transcriptome of T. brucei, many gRNAs were identified that are capable of generating alternative mRNA sequences, and potentially disrupting the editing process. In this work, the effects of alternative editing are characterized. This analysis revealed the role of gRNAs in developmental regulation of gene expression, showing a correlation between the abundance of the initiating gRNAs across two different points in the life cycle of T. brucei and their expression. This study also revealed the existence of mitochondrial dual-coding genes, which provide protection for genetic material that is not under selection at all points of the life cycle of T. brucei. The examination of these dual-coding genes showed that RNA editing patterns can shift between cell lines and under different energetic conditions. Examining the gRNAs involved in these editing pathways revealed that there is a high amount of mismatching base pairs that are tolerated for editing to function, and that gRNA abundance is not a reliable predictor for editing preference. Finally, a reexamination of the gRNA transcriptome revealed that many gRNAs are still unidentified and most likely are generating new alternatively edited sequences."--Pages ii-iii.
Show less
- Title
- Genetic analysis of glandular trichome development and metabolism in cultivated tomato
- Creator
- St. Aubin, Brian
- Date
- 2019
- Collection
- Electronic Theses & Dissertations
- Description
-
Morphological structures and associated chemical compounds serve important functions during the life cycle of plants, including deterrence of herbivores. Terpenoids represent a major class of compounds involved in defending plants from herbivores. Their differential accumulation in specific tissues and cell types is at present not well understood. In cultivated tomato (Solanum lycopersicum), terpenoids and flavonoids accumulate in type VI glandular trichomes that are found on most above...
Show moreMorphological structures and associated chemical compounds serve important functions during the life cycle of plants, including deterrence of herbivores. Terpenoids represent a major class of compounds involved in defending plants from herbivores. Their differential accumulation in specific tissues and cell types is at present not well understood. In cultivated tomato (Solanum lycopersicum), terpenoids and flavonoids accumulate in type VI glandular trichomes that are found on most above ground plant organs. Due to our ability to isolate them, these glandular trichomes of tomato are an attractive model system that can help us better understand how plants regulate the biosynthesis of terpenoids. The mutations in the odorless-2 (od-2) and the anthocyanin free (af) genes produce defective type VI glandular trichomes that fail to accumulate flavonoids and volatile terpenoids. Accordingly, these mutants provide useful genetic tools to study the relationship between the development and metabolic capacity of glandular trichomes.In this work, I determined the molecular basis of the od-2 mutation and showed that the wild-type Od-2 gene encodes an enzyme (designated LCB1A for long chain base 1A) involved in the biosynthesis of long-chain base precursors of sphingolipids. A functional LCB1A gene is necessary for type VI trichomes to produce high levels of volatile terpenoids. Transgenic expression of the wild-type LCB1A cDNA from the Cauliflower Mosaic Virus 35S promoter complemented both the leaf developmental and sphingolipid content phenotypes of the leaflets of the mutant but failed to rescue the terpenoid deficiency. Conversely, expression of LCB1A from a trichome-specific promoter restored terpenoid production in type VI trichomes of od-2 but did not complement the foliar sphingolipid profile or other leaf developmental defects. These results provide new insights into the tissue- and cell type-specific function of sphingolipid biosynthesis in tomato and establish an essential role for sphingolipids in trichome-borne specialized metabolism.In a similar fashion, I used the chalcone isomerase 1 (CHI1)-deficient af mutant to study the tissue and cell-type specific role of flavonoids. Specifically, I constructed transgenic lines in which CHI1 was expressed in the af mutant background from either the 35S or a trichome-specific promoter. Detailed biochemical and physiological characterization of these lines showed that CHI1 activity in type VI glandular trichomes, but not in other cell types of the leaf, is required for abundant production of volatile terpenoids. Expression of CHI1 in type VI trichomes was also required to restore resistance of af leaves to feeding by the two-spotted spider mite Tetranychus urticae. In summary, the results described in this thesis advance knowledge of how various metabolic pathways, including sphingolipid and flavonoid biosynthesis, operate to promote normal development and function of glandular trichomes.
Show less
- Title
- Developmental plasticity : early life environment, DNA methylation, and later life phenotype in spotted hyenas
- Creator
- Laubach, Zachary M.
- Date
- 2019
- Collection
- Electronic Theses & Dissertations
- Description
-
Animals, including humans, vary in their phenotypes. While this phenomenon is partially explained by genotype, an organism's environment (and its experiences within a given environment) also contributes to trait variability. Of particular relevance to my dissertation is the notion of developmental plasticity, or variability in an organism's phenotype due to specific environmental exposures experienced across ontogeny. In my dissertation, I discuss theory (Chapter 2) and test empirical...
Show moreAnimals, including humans, vary in their phenotypes. While this phenomenon is partially explained by genotype, an organism's environment (and its experiences within a given environment) also contributes to trait variability. Of particular relevance to my dissertation is the notion of developmental plasticity, or variability in an organism's phenotype due to specific environmental exposures experienced across ontogeny. In my dissertation, I discuss theory (Chapter 2) and test empirical hypotheses (Chapters 3-5) regarding the role of developmental plasticity via DNA methylation in the relationship between early life environment and adult phenotype. Leveraging a wild population of spotted hyenas in the Masai Mara, Kenya (The Mara Hyena Project), my analytical Chapters 3-5 specifically focus on social and ecological measures of the early life environment in relation to global (via the luminometric assay [LUMA] of %CCGG methylation) and genome-wide DNA methylation (via Enhanced Reduced Representation Bisulfite Sequencing [ERRBS]). I then explore associations of each with adult stress phenotype, as indicated by fecal corticosterone concentrations. In Chapter 3, I detected differences in %CCGG methylation across the hyena genome with respect to both social and ecological factors early in life, suggesting that these characteristics may impact future phenotype through epigenetic modifications like global DNA methylation. In Chapter 4, I found that higher maternal care and greater social connectedness during early life are associated with higher %CCGG methylation and lower fecal corticosterone concentrations during adulthood, both of which are indicators of positive health. Finally, in Chapter 5, I identified differential methylation in CpG sites involved in inflammatory processes that were associated with both early life maternal care and adult fecal corticosterone levels, thereby implicating these sites as possible mediators to the relationship between early life maternal care quality/quantity and future stress phenotype.These findings are an important extension to current understanding of developmental plasticity that stems from rodent models and studies of captive primates. Biomedical models of developmental plasticity often utilize laboratory rodents, which lack the natural social structure and intact life history involved in development of complex and variable phenotypes. Studies of captive primates typically focus on extreme measures of early life social deprivation that do not capture the naturally occurring spectrum of social experiences in wild mammals. In wild spotted hyenas, I was able to test hypotheses surrounding the concept of developmental plasticity in a gregarious mammal with a complex social structure that is also subject to natural selection. Furthermore, use of data and samples from The Mara Hyena Project enabled me to characterize multiple aspects of the early life environment, DNA methylation, and stress phenotypes in the same individuals - a feat rarely accomplished even in well-established human cohort studies.
Show less
- Title
- QTL mapping of post-processing color retention and other traits in two black bean populations
- Creator
- Bornowski, Nolan M.
- Date
- 2018
- Collection
- Electronic Theses & Dissertations
- Description
-
"When black beans are processed for consumption, they can lose their dark coloration due to the leaching of water-soluble pigments called anthocyanins. After hydrothermal processing, beans are commonly a faded brown color instead of the dark black color typical of the dry seed. The aim of this research was to develop mapping populations with different genetic sources of color retention in order to identify regions of the dry bean genome associated with canning quality traits. To this end, two...
Show more"When black beans are processed for consumption, they can lose their dark coloration due to the leaching of water-soluble pigments called anthocyanins. After hydrothermal processing, beans are commonly a faded brown color instead of the dark black color typical of the dry seed. The aim of this research was to develop mapping populations with different genetic sources of color retention in order to identify regions of the dry bean genome associated with canning quality traits. To this end, two half-sibling black bean recombinant inbred line (RIL) populations segregating for post-processing color retention were developed. These RIL populations were phenotyped for canning quality over two years and genotyped using the BARCBean6k_3 BeadChip. A novel phenotyping method using digital image analysis was shown to outperform current methods of quantitative color measurement. QTL for post-processing color retention were detected on six chromosomes, with QTL on Pv03, Pv08, and Pv11 being the most notable for their co-localization with QTL for quantitative measurements of color. In particular, QTL associated with color retention on Pv11 mapped to a very small physical interval and were consistent across years, populations, and phenotyping methodologies. Color retention QTL on Pv08 and Pv11 are good candidates for development of molecular markers that may be used in marker assisted selection (MAS) or early-generation screening to improve post-processing color retention in black beans."--Page ii.
Show less
- Title
- Carbon partitioning in engineered cyanobacterium for the study of feedback inhibition of photosynthesis
- Creator
- Abramson, Bradley William
- Date
- 2018
- Collection
- Electronic Theses & Dissertations
- Description
-
Cyanobacteria have promising potential to generate valuable compounds from light energy and atmospheric carbon dioxide (CO2). Many strains have been engineered to express pathways to generate a variety of products from pharmaceuticals to biofuels. Even with cyanobacteria’s high photosynthetic efficiencies most strains remain economically inviable. Many strains are grown in bioreactors where ample light and CO2 are provided, however, photosynthetic conversion of carbon and light to useful...
Show moreCyanobacteria have promising potential to generate valuable compounds from light energy and atmospheric carbon dioxide (CO2). Many strains have been engineered to express pathways to generate a variety of products from pharmaceuticals to biofuels. Even with cyanobacteria’s high photosynthetic efficiencies most strains remain economically inviable. Many strains are grown in bioreactors where ample light and CO2 are provided, however, photosynthetic conversion of carbon and light to useful compounds is limited. I propose photosynthesis is feedback limited, or sink limited, and the mechanisms of feedback inhibition can be alleviated in a Synechococcus elongatus PCC7942 strain engineered to export sucrose. By inducing expression of sucrose permease, in various salt conditions, the amount of sucrose can be tuned, which allowed us to measure a transient increase in the operating efficiency of PSII proportional to the rate of sucrose export. Concomitantly, an oxidized electron transport chain and lowered PSI acceptor side limitation were observed. These two photosynthetic parameters could be consequences of increased carbon fixation since the ratio of RbcL to PSII increases as well as greater accumulation of RbcS-GFP following sucrose export. These data suggest that sucrose export leads to greater carbon fixation and as a consequence increase light use efficiency within PSII. Furthermore, using this knowledge, we created strains that could partition carbon from growth and division to bioproduction and observed greater total and specific productivities for sucrose production. The ideas herein aid in the understanding of bioproduction strain inefficiencies and novel avenues for future genetic engineering for increased bioproduction.
Show less
- Title
- Elucidating the genetic control and mechanisms of cooking time differences in dry bean
- Creator
- Berry, Matthew (Graduate of Michigan State University)
- Date
- 2018
- Collection
- Electronic Theses & Dissertations
- Description
-
Dry bean (Phaseolus vulgaris L.) is a nutritious crop that is high in protein, fiber, vitamins and minerals and provides a large portion of dietary protein in the human diet. Beans require significant time to cook making them inconvenient for consumers potentially reducing the consumption rate. Considerable genetic variability exists for cooking time in P. vulgaris, but the underlying genetic causes of cooking time differences are largely unknown. To elucidate the genetic control of cooking...
Show moreDry bean (Phaseolus vulgaris L.) is a nutritious crop that is high in protein, fiber, vitamins and minerals and provides a large portion of dietary protein in the human diet. Beans require significant time to cook making them inconvenient for consumers potentially reducing the consumption rate. Considerable genetic variability exists for cooking time in P. vulgaris, but the underlying genetic causes of cooking time differences are largely unknown. To elucidate the genetic control of cooking time in dry bean, two Andean bean genotypes (TZ-27 and TZ-37) from Tanzania were identified with contrasting cooking times but similar seed color and plant growth habit. The average cooking time was 72.3 min and 33.1 min for TZ-27 and TZ-37, respectively, across nine growing locations globally. Additionally, TZ-37 had a 100 dry seed weight 1.2 to 1.5 times greater than TZ-27 in all test environments. The concentration of Ca and Mn were 1.7 and 1.3 times higher in TZ-27 than in TZ-37 respectively, while TZ-37 had 1.1 times the level of phytate than TZ-27.TZ-27 and TZ-37 were used to develop a biparental recombinant inbred line population (RIL) of 161 genotypes. The RIL population was evaluated for cooking time, hydration capacity, seed coat percentage, protein concentration, and other agronomic traits in Arusha and Morogoro in Tanzania in 2016 and 2017. Morogoro typically has higher temperatures, lower altitude, and lower soil fertility soil than Arusha. Significant variation was found for cooking time within the RIL population with a range of 21.4 min to 134.6 min across both years and locations. An environmental influence on cooking time was observed with the average cooking time in Morogoro being 15 min longer than Arusha. Five lines were identified that cooked faster than TZ-37 showing transgressive segregation for cooking time. Seed weight, hydration capacity, and protein concentration were inversely correlated with cooking time, while seed coat percentage was directly correlated.A quantitative trait loci (QTL) analysis was conducted using 2,427 single nucleotide polymorphism (SNP) markers discovered through genotyping by sequencing. Ten QTL were discovered for cooking time. A previously reported QTL, CT1.1, was found in Arusha in 2016 and 2017. CT3.2 was found in Arusha and Morogoro in 2017 and explained 20.5% of variation for the trait. CT6.1 was identified in both locations in 2017 and co-localized with multiple traits including hydration capacity, protein concentration, and 100 seed weight. CT10.1 was identified in Morogoro in both years. These 4 QTL, collectively, resulted in a reduction of cooking time by 16 minutes. Genes of interest within the cooking time QTL included one for polygalacturonase and another for the inhibitor of pectin methylesterase, which have previously been shown to affect cooking time. The QTL described serve as potential targets for improvement of cooking time in commercial dry bean genotypes and could be used to increase the efficiency in a breeding program by selecting for genotypes with multiple QTL for fast cooking. Developing faster cooking varieties would eliminate a major barrier for consumption. Faster cooking beans would be especially helpful in developing countries by reducing fuel burned as well as time required to gather firewood, which allows more time for other tasks.
Show less
- Title
- Rapid adaptation of floral phenotypes in weedy radish, R.r. Raphanistrum
- Creator
- Charbonneau, Amanda
- Date
- 2018
- Collection
- Electronic Theses & Dissertations
- Description
-
Agricultural weeds cause billions of dollars’ worth of damage worldwide as well as reducing yields, however we often know very little about where they came from, or how they adapt to farming techniques. Agricultural fields are human created environments quite unlike anything in nature and are relatively harsh environments that can exert strong selective pressures. Yearly tilling, for example, likely selects for plants that both quickly reproduce, and can survive in disturbed soils. While some...
Show moreAgricultural weeds cause billions of dollars’ worth of damage worldwide as well as reducing yields, however we often know very little about where they came from, or how they adapt to farming techniques. Agricultural fields are human created environments quite unlike anything in nature and are relatively harsh environments that can exert strong selective pressures. Yearly tilling, for example, likely selects for plants that both quickly reproduce, and can survive in disturbed soils. While some plants with generalist phenotypes might be well suited for thriving in these conditions, others, like Raphanus raphanistrum ssp. raphanistrum (weedy radish), have likely evolved to become weeds. To better understand how these agricultural weeds evolve, I have phenotypically and genotypically characterized weedy R.r. raphanistrum and it’s close relatives. In chapters one and two, I show that weedy R.r. raphanistrum is most closely related to native populations of R.r. raphanistrum, but that these two ecotypes have very different flowering phenotypes. Weedy R.r. raphanistrum flowers in approximately thirty days, while the native plants take fifty to one hundred and fifty days to flower. This demonstrates a likely adaptation to agriculture, and in chapter two I find several loci that may contribute to these phenotypic differences. In chapter three, I analyze differential expression patterns in two selection lines derived from weedy R.r. raphanistrum, to determine genes that underlie differences in floral morphology. These genes should contribute to differences in anther exsertion, which in turn controls how pollen is dispersed onto pollinators. Together, these studies answer basic questions about how evolution works on a short time scale and provide insights into the adaptations of one of the world’s most damaging agricultural weeds. More broadly, these studies demonstrate that weedy radish is a good system for studying rapid evolution in response to both natural and artificial selection and lay the groundwork for future work. In particular, chapters one and two will be useful for broad comparisons across agricultural weeds to determine whether weeds use similar strategies for invading croplands, which would tell us not only about the repeatability of evolution, but also be potentially useful in reducing agricultural losses due to weeds.
Show less
- Title
- Investigation into climatic effects on the growth and genetic structure of sky island ponderosa pine
- Creator
- Marquardt, Paula E.
- Date
- 2018
- Collection
- Electronic Theses & Dissertations
- Description
-
In the desert southwest, significant variations in moisture and temperature occur along steep altitudinal gradients. Ponderosa pine forests in the Santa Catalina Mountains, southeast Arizona, USA, consist of two partially sympatric species, the variable needle Pinus ponderosa var. brachyptera (3- and mixed-needle) that prefers cool and moist conditions, and the 5-needle P. arizonica that prefers hot and dry conditions. The objective of this research program is to determine how disturbance...
Show moreIn the desert southwest, significant variations in moisture and temperature occur along steep altitudinal gradients. Ponderosa pine forests in the Santa Catalina Mountains, southeast Arizona, USA, consist of two partially sympatric species, the variable needle Pinus ponderosa var. brachyptera (3- and mixed-needle) that prefers cool and moist conditions, and the 5-needle P. arizonica that prefers hot and dry conditions. The objective of this research program is to determine how disturbance–that is variations in climate–contributes to shifts in population structure. Data was collected along two south-facing slopes (of similar elevation and aspect) for average needle number per fascicle, tree-ring widths, and gene frequencies, to examine limiting factors to growth, climatic shifts in growth, and population genetic structure. Our data show that co-occurring ponderosa pine needle-types (3-, mixed-, and 5-needle) have filled different ecological niches; their growth is limited by seasonal water availability, which also controls the length of the growing season. Three distinct genetic groups are present in the Santa Catalina Mountains. Genetic variability is reduced for the 5-needle type suggesting a possible bottleneck or founding event. Results from this study about moisture limitations will help land managers to determine range limits for seed planting zones.
Show less
- Title
- Systematics of the genus Rhagoletis (Diptera : Tephritidae : new species, phylogeny, and justifications
- Creator
- Hulbert, Daniel Lloyd
- Date
- 2018
- Collection
- Electronic Theses & Dissertations
- Description
-
Flies of Rhagoletis (Diptera: Tephritidae) are economically important fruit pests (infesting specialty fruit crops including apples, blueberries and cherries), which also serve as models for studying modes of speciation and coevolutionary relationships with their hymenopteran parasitoids. There are new species within the genus which have not been previously formally described. One of these species is within the tabellaria species group. I describe the morphology of Rhagoletis bushi Hulbert &...
Show moreFlies of Rhagoletis (Diptera: Tephritidae) are economically important fruit pests (infesting specialty fruit crops including apples, blueberries and cherries), which also serve as models for studying modes of speciation and coevolutionary relationships with their hymenopteran parasitoids. There are new species within the genus which have not been previously formally described. One of these species is within the tabellaria species group. I describe the morphology of Rhagoletis bushi Hulbert & Smith, its geographic distribution, host association, phylogenetic relationships, and identify an associated species of parasitoid wasp. The new species infests the fruit of buffaloberry (Shepherdia argentea) in the Northern Great Plains of North America. There is a suite of morphological characters, and a unique host plant association, that are diagnostic of R. bushi. Further evidence for the validity of R. bushi and its placement within the tabellaria species group comes from DNA sequence data from multiple genetic loci. The phylogenetic relationships among Rhagoletis species groups remain unresolved despite analyses based on morphology, allozymes, and mitochondrial DNA. Most Nearctic Rhagoletis belong to one of five species groups (pomonella, tabellaria, cingulata, suavis , and ribicola groups), with two unplaced species (R. fausta and R. juniperina), all of which appear to be part of a larger monophyletic group that also includes some Palearctic taxa. Regarding the overall phylogeny of the genus, my goals were to 1) resolve phylogenetic relationships using mitochondrial (COI) and nuclear (28S, CAD, period, AATS) DNA sequences, and 2) to identify the monophyletic group containing these Nearctic species. Using Bayesian analysis of a combined dataset with 4399 aligned nucleotides, I inferred a well-supported monophyletic group containing the five Nearctic Rhagoletis species groups, plus R. fausta, R. juniperina, and two Palearctic species: R. batava and R. flavigenualis. Within this larger monophyletic assemblage, the five Nearctic species groups together are monophyletic as are four of the five individual species groups (not ribicola). Palearctic and Neotropical Rhagoletis were resolved into well-supported clades of taxa often sharing closely related host plants. A well-resolved phylogeny of Rhagoletis is a valuable tool for future work addressing questions pertaining to how history, geography and ecology have shaped the phylogenetic patterns we observe in the genus. It is often claimed that systematic biology is fundamental to all other areas of biology. I critically evaluate the acceptance of this claim by entomologists critically as it relates to the field of entomology. I also critically describe the justification and valuations for systematic biology using the framework of Boltanski and Thevenot's realms of worth and the philosophical framework for justification using virtues, desserts and outcomes. In order to accomplish these purposes, I critically analyze and review relevant entomological literature and interview practitioners of entomology and insect systematic biology. I find justification for systematic biology overwhelming takes the form of appeals to utilitarianism (both internally and externally focused) and are most relevant in the Industrial World. Additionally, some justifications given also pertain to the Civic World and to virtue. Evaluation of justification in systematic biology is important, especially as our globe becomes increasingly ecologically and politically unstable.
Show less