No description available.

<p>Examining the genetic basis across repeated origins of the same phenotypic adaptation allows us to address several questions pertaining to the genetic basis of adaptation. First, whether the genes and types of mutations that are involved in adaptation are predictable. Second, whether the underlying genetic changes can constrain future evolutionary trajectories. Here, I have focused on the genetics of blue to red flower color shifts, an adaptive shift that has repeatedly occurred across angiosperms. First, I review the literature and determine the relative contribution of functional vs. regulatory mutations to the evolution of red flowers can be predicted both on the mutational target size of each type of mutation and the degree of their associated deleterious pleiotropy. Chapter 2 characterizes the genetic basis of red flowers in Penstemon barbatus using a combination of gene expression and protein function assays. I demonstrated that multiple inactivating mutations to one anthocyanin pathway enzyme, F3'5'h, have occurred, but no mutations to any other component of the anthocyanin pathway have contributed to the evolution of red flowers. This suggests that F3'5'h may be a particularly favorable target for selection and also that evolutionary reversal to blue flowers would be highly unlikely. Chapter 3 investigates the genetic basis of an additional 12 origins of red flowers within Penstemon. Again, using a combination of gene expression and enzyme function assays, I found the genetic basis of these additional origins red flowers in Penstemon is highly predictable, involving redundant inactivating mutations to F3'5'h, and tissue-specific regulatory mutations to a second gene F3'h. Thus, the genetics of red flowers in Penstemon often involves inactivation of a non-pleiotropic gene, F3'5'h, but tissue-specific regulatory mutations to the pleiotropic gene F3'h. Furthermore, the presence of redundant inactivating mutations in many red-flowered Penstemon species indicates that the evolutionary reversal to blue flowers would be unlikely.</p> / Dissertation

Penstemon Mitchell (Plantaginaceae) is one of the largest, most diverse plant genera in North America. Their unique diversity, paired with their drought-tolerance and overall hardiness, give Penstemon a vast amount of potential in the landscaping industry—especially in the more arid western United States where they naturally thrive. In order to develop Penstemon lines for more widespread commercial and private landscaping use, we must improve our understanding of the vast genetic diversity of the genus on a molecular level. In this study we utilize genome reduction and barcoding to optimize 454-pyrosequencing in four target species of Penstemon (P. cyananthus, P. davidsonii, P. dissectus and P. fruticosus). Sequencing and assembly produced contigs representing an average of 0.5% of the Penstemon species. From the sequence, SNP information and microsatellite markers were extracted. One hundred and thirty-three interspecific microsatellite markers were discovered, of which 50 met desired primer parameters, and were of high quality with readable bands on 3% Metaphor gels. Of the microsatellite markers, 82% were polymorphic with an average heterozygosity value of 0.51. An average of one SNP in 2,890 bp per species was found within the individual species assemblies and one SNP in 97 bp were found between any two supposed homologous sequences of the four species. An average of 21.5% of the assembled contigs were associated with putative genes involved in cellular components, biological processes, and molecular functions. On average 19.7% of the assembled contigs were identified as repetitive elements of which LTRs, DNA transposons and other unclassified repeats, were discovered. Our study demonstrates the effectiveness of using the GR-RSC technique to selectively reduce the genome size to putative homologous sequence in different species of Penstemon. It has also enabled us the ability to gain greater insights into microsatellite, SNP, putative gene and repetitive element content in the Penstemon genome which provide essential tools for further genetic work including plant breeding and phylogenetics.

Penstemon is one of North America's largest endemic genera with over 280 described species. These species are distributed throughout most of North America from the Arctic northern latitudes to tropics of Central America. The genus has historically been divided into six subgenera, but has recently been reorganized into two subgenera following some recent phylogenetic studies. I made a comprehensive assessment of the Penstemon genus' geographic distribution utilizing herbaria databases by ecoregion to discuss the general ecologic adaptations of each historic subgenera. I also assessed the Penstemon genus' bee pollinator diversity utilizing online databases of bee specimen collections associated with Penstemon flowers. I investigated the efficacy of utilizing the plastid genomes (plastomes) of 29 species in the Lamiales order, including five newly sequenced Penstemon plastomes, for analyzing phylogenetic relationships and resolving problematic clades. I compared whole-plastome based phylogenies to phylogenies based on individual gene sequences (matK, ndhF, psaA, psbA, rbcL, rpoC2, and rps2) and concatenated sequences. I found that my whole-plastome based phylogeny had higher nodal support than all other phylogenies, which suggests that it provides greater accuracy in describing the hierarchal relationships among taxa as compared to other methods. I found that the genus Penstemon forms a monophyletic clade sister to, but separate from, the Old World taxa of the Plantaginaceae family included in our study. My whole-plastome based phylogeny also supports the rearrangement of the Scrophulariaceae family and improves resolution of major clades and genera of the Lamiales. I evaluated 16 accessions of P. cyaneus with 14 accessions of closely related Penstemon species in common garden in two distinct environments in Aberdeen, ID and Provo, UT during 2018 and 2019. I evaluated the accessions for key commercial seed production traits including survival, plant height, number of stems, and seed production. Both common gardens received supplemental irrigation during 2018, but I withheld irrigation during 2019. Plant survival in our Aberdeen, ID site was not significantly different between years, but survival was a significantly lower in 2019 than in 2018 at our Provo, UT site. The mean survival for P. cyaneus accessions ranged from 56% to 94%, and the mean seed production ranged from 91.2 kg/ha to 397.6 kg/ha. I recommend developing a commercial seed source derived from pooling germplasm of six accessions (PECY3-367, PECY3-371, PECY3-376, PECY3-443, PECY3-457, and PECY3-458). These accessions had mean survival rates of 82-94%, and seed production of 196.2-397.6 kg/ha.

Penstemon is the largest genus in North America with more than 270 reported species. However, little is known about the genome size of this genus and how this information may be useful in selecting species in developing hybrids for landscape use. Using flow cytometry, we estimated the genome size of approximately 40% of the genus (117 specimens from 104 different species.) Genome sizes for the putative diploids ranged from 2C = 0.94 – 1.89 pg (1C = 462 – 924 Mbp) and the putative polyploids ranged from 2.57 – 6.54 pg (1C = 1,257 – 3,156 Mbp). Chromosome counts were compiled and compared with the flow cytometry results for the species within this publication. Ploidy within the genus ranged from diploid to dodecaploid. These data were compared and contrasted with the current taxonomy of Penstemon and previously published ITS and cpDNA phylogenetic work. Based on genome size, reassigning P. montanus, P. cardinalis, and P. uintahensis to the subgenus Penstemon and P. personatus to the subgenus Dasanthera, would better reflect the phylogeny of the genus. Both auto- and allo-polyploidization are plausible mechanisms for increasing ploidy within the genus. The diploid species within the subgenus Saccanthera contain on average 1.09 pg (1C = 532 Mbp); however, two species within this subgenus are tetraploid and octaploid. The DNA content of subgenus Penstemon exhibits high plasticity and spans a six-fold increase. Our study found flow cytometry to be useful in species identification and verification. This represents the first published work on the genome size of Penstemon. This research will aid in future DNA sequencing experiments and breeding programs.

We evaluated the genetic diversity of Penstemon's Centromeric Histone 3 (CENH3), which localizes to chromosome centromeres in eukaryotes. From RNA extractions of 56 species, we successfully amplified two CENH3s (termed CENH3a and CENH3b), which share approximately 69% sequence homology across the length of the gene and about 85% across the histone fold domain (HFD). CENH3a is generally 72 bp longer than CENH3b and contains seven exons while CENH3b is made of five. Unlike studies of CENH3 in other plants, Penstemon's CENH3 N-tail was found to be highly conserved, indicative that the genus has undergone a short evolutionary history. Surprisingly, of the 99 CENH3 sequences obtained during this study, 32 appeared to be mis-spliced and contained premature stop codons. Of those aberrant transcripts, 84.4% originated from CENH3b genomic DNA. Most mis-spliced transcripts resulted from the retention of all or part of an intron. In some cases, all or portions of an exon were missing, including one that was missing the L1 motif. Second, we systematically cataloged interspecific breeding data in Penstemon, on which we then conducted a network analysis. The resulting network provides breeders with a better visualization of successful parental combinations and also identifies gaps in interspecific breeding. This method allowed for the identification of species with a high degree of interspecific compatibility, which we compared to the CENH3 sequencing data. Finally, we studied the performance of soil streaming in high tunnel production of tomatoes (Solanum lycopersicum L.). Our experiments revealed that soil steaming and mulch reduced weed coverage of Palmer amaranth (Amaranthus palmeri S. Watson), large crabgrass (Digitaria sanguinalis L.), and yellow nutsedge (Cyperus esculentus L.). Steam and mulch increased the tomato plant size, fruit size, fruit number, and fruit yield. Additionally, soil steaming reduced tomato southern blight, caused by Sclerotium rolfsii, by 5.8-fold. These findings provide promising results for high tunnel tomato producers, particularly those involved in organic production where pesticide and fumigation use is limited.

No description available.

Organometallic chemistry is highly dependent upon the ligands which are employed on a metal's surface. These ligands control steric bulk and electronics of the metal center which can change the reactivity of the organometallic complex. Ligands that are standard in organometallic chemistry include phosphine ligands. These phosphine ligands have been utilized in the field since the 1960's and have shaped the development of many key organometallic catalysts. Phosphine ligands are easily functionalized and highly reactive. This increased reactivity, however, causes severe limitations as phosphine ligands are often unstable under standard benchtop conditions and must be handled both air and moisture free environments. To combat some of these issues new ligand types have emerged such as N-heterocyclic carbene ligands. These ligands are found to possess similar reactivity in terms of electron and steric influences but can be prepared and used on the benchtop. In this work we highlight a dual N-heterocyclic carbene/phosphine ligand which is obtained from an accessible 2-phosphinoimidazole. These 2-phsophinoimidazole ligands can undergo a transformation in the presence of a proton source. The proton source will cause the disassociation of the C-P bond forming a NHC-phosphine complex. Addition of a metal source to the NHC-phosphonium complex causes a NHC/phosphine metal complex, which upon further investigation was found to be catalytically active. This activity was tested in various cross coupling reactions which include Suzuki, Heck, and Sonogashira. Highlights of these results include the extreme functionalization of these 2-phosphinioimidazole ligands which can produce new aryl groups on the NHC, a free N-H bond on the imidazole which can be deprotonated or influence intermolecular forces with substrates, replacing the moieties on the phosphine, and finally the ability to transform in situ with the addition of a common alcohol. Each of these functionalization's are explained below along with their reactivity to isolate a wide variety of substrates. In addition to the work above a collaboration with Rio Tinto and the Madsen Lab at BYU is discussed. This work involves the concerns of land managers and their ability to restore landscapes that have been destroyed through a variety of issues including fire, mining, and invasive species. These ecological pressures cause land managers to search for native plants to seed on a landscape. Issues arise when using natives, however, because of their inability to quickly germinate and establish on a landscape. This is caused by dormancy issues where an antagonistic relationship between gibberellic acid and abscisic acid where the overproduction of one over the other results in dormant native plants. We have invented a methodology to use slow releasing polymers to hijack this system and deliver gibberellic acid to a seed causing it to germinate regardless of external stimuli. Our results show significant improvement in native Penstemon species with no side effects to the plant growth and establishment.