Doctor of Philosophy, Case Western Reserve University, 2023, Biology

Tylosema esculentum (marama bean) is an underutilized legume, long considered as a local potential crop due to its rich nutritional value. The reference plastome and mitogenome were assembled using a hybrid method with both Illumina and PacBio data. The diversity was explored with the WGS data of 84 samples from various geographic locations in Namibia and Pretoria. Phylogenetic analysis revealed two cytotypes with distinct plastomes and mitogenomes with differing levels of variability. Deep sequencing has identified heteroplasmy with both types of organellar genomes present, albeit one at a very low frequency. The inheritance of this complex of organellar genomes appears to be fairly constant, providing a conundrum of how the two genomes co-exist and are propagated through generations. The type 1 mitogenome has two autonomous rings with a total length of 399,572 bp, which can be restructured into five smaller circular molecules through recombination on 3 pairs of long direct repeats. The type 2 mitogenome contains a unique 2,108 bp sequence, which connects distant segments to form a new structure consisting of three circular molecules and one linear chromosome. This increased the copy number of nad9, rrns, rrn5, trnC, and trnfM. The two mitogenomes differed at another 230 loci, with only one nonsynonymous substitution in matR. cpDNA insertions were concentrated in one subgenomic ring of the mitogenome, including a 9,798 bp long fragment that contains potential psbC, rps14, psaA, and psaB pseudogenes. The two types of plastomes range in length from 161,537 bp to 161,580 bp, differing at 122 loci and at a 230 bp inversion. The chloroplast genes rpoC2, rpoB, and ndhD were found to be more diverse than other genes in marama plastome. 21.6 Gb PacBio HiFi data was assembled using Canu v2.2 into an unphased assembly of 1.24 Gb. k-mer analysis indicated that marama may be ancient tetraploid with an estimated genome size of only 277 Mb. The generated assembly has an N50 v (open full item for complete abstract)

Committee: Christopher Cullis (Advisor); Hillel Chiel (Committee Chair); Peter Zimmerman (Committee Member); Jean Burns (Committee Member); Sarah Bagby (Committee Member) Subjects: Bioinformatics; Genetics; Plant Biology

Doctor of Philosophy, Miami University, 2021, Botany

Understanding plant adaptation mechanisms to prolonged water immersion provides options for genetic modification of existing crops to create cultivars more tolerant of periodic flooding. An important advancement in understanding flooding adaptation would be to elucidate the mechanism of aerenchyma air-space formation induced by prolonged immersion. Lysigenous aerenchyma formation occurs through programmed cell death (PCD), which entails the chemical modification of polysaccharides in root tissue cell walls. I investigated if a relationship exists between modification of pectic polysaccharides through de-methyl-esterification, xyloglucan through fucosylation, and the formation of root aerenchyma in select Fabaceae species. To explore this objective, I first characterized the progression of aerenchyma formation within the vascular stele of three different legumes - Pisum sativum, Cicer arietinum, and Phaseolus coccineus – through traditional light microscopy histological staining and scanning electron microscopy. I assessed alterations in stele morphology, cavity dimensions, and cell wall chemistry. Then I conducted an immunolabeling protocol to detect cellulose, hemicellulose (xylan, fucosylated and non-fucosylated xyloglucan), and specific degrees of de-methyl-esterified (DME) homogalacturonan (HG) among species during a 48-hour flooding time series. Additionally, I performed an enzymatic pretreatment to remove select cell wall polymers prior to immunolabeling for cellulose, hemicellulose and DME HG. I was able to determine that all species possessed similar aerenchyma formation mechanisms that begin with degradation of root vascular stele metaxylem cells. Immunolabeling results suggest de-methyl-esterification of HG, and degradation of xyloglucan, occurs prior or concurrent with aerenchyma formation in root vascular tissues. Furthermore, enzymatic pretreatment demonstrated that removal of cellulose and select hemicellulosic carbohydrates unmasks additional antigen (open full item for complete abstract)

Committee: Daniel Gladish Ph.D. (Committee Chair); Robert Baker Ph.D. (Committee Co-Chair); Richard Moore Ph.D. (Committee Member); Melany Fisk Ph.D. (Committee Member); Mitchell Balish Ph.D. (Committee Member) Subjects: Agriculture; Biochemistry; Biology; Botany; Developmental Biology; Plant Biology; Plant Sciences

Master of Science (MS), Bowling Green State University, 2016, Biological Sciences

Plants in the Fabaceae family are known for their ability to form symbiotic relationships with rhizobia, which provide nitrogen to plants. The formation and ecological outcome of this partnership depends on the genotypes of both symbionts, along with environmental factors. However, relatively few studies have examined the ecological factors that influence the distribution and abundance of this mutualistic relationship within natural ecosystems. Lupinus perennis is a native legume found on dry, sandy soils supporting globally rare oak savannas and tallgrass prairies. L. perennis seed coats are polymorphic in background color and speckling. These seed coat phenotypes, which are also correlated with changes in flavonoid biochemistry, vary in frequency, both within and between populations. The objective of this research was to investigate the effects of L. perennis seed coat phenotype variation, along with seed and inoculum source variation, on rhizobia recruitment in a controlled growth chamber. To determine how these factors affect seedling success and rhizobia recruitment, seeds from two populations were grown in each of four inoculum treatments, consisting of soil inoculums from each of the two native L. perennis populations, a positive control treatment consisting of a commercial rhizobia inoculum and a negative control treatment with no rhizobial inoculum added. We hypothesize that due to changes in flavonoid biochemistry, some of which are important in communication with rhizobia, dark and heavily speckled seeds will have higher nodulation rates and subsequently greater seedling fitness. In addition, we examined whether the distribution and abundance of L. perennis nodulating rhizobia differed within and between field populations, representing different environmental factors. We surveyed six L. perennis sites in northwest Ohio to determine if environmental factors, such as light levels, litter depth, and soil moisture affected nodule presence, as well as fruit (open full item for complete abstract)

Committee: Helen Michaels Ph.D. (Advisor); George Bullerjahn Ph.D. (Committee Member); Vipaporn Phuntumart Ph.D. (Committee Member); Moira van Staaden Ph.D. (Committee Member) Subjects: Ecology

Master of Science, The Ohio State University, 2010, Soil Science

Inclusion of a winter legume cover crop into a crop rotation has been suggested as method to provide a substantial portion of the nitrogen (N) requirement of a subsequent grass crop. While the benefits of winter cover crops such as reduced soil erosion, increased soil organic matter, and increased mulch cover have been well documented, the N contribution to the subsequent crop has shown to be variable. The objective of this study is to determine the N contribution from a red clover (Trifolium pretense, L.) cover crop following wheat (Triticum aestivum, L.) to a subsequent corn (Zea mays, L.) crop. The experiment was conduct at two western Ohio locations over three years. At both locations, red clover was either interseeded into wheat or seeded after harvest, the red clover cover crop was eliminated with tillage or herbicide application, and corn was planted with three N rates (0, 90, and 180 kg N ha-1). The data revealed that for three of the four site years (when the cover crop was successfully established) there was no N contribution attributable to the presence of red clover. The one site that did show an N contribution revealed that the amount of N contributed was less than 90 kg N ha-1. However, even when no N benefit was found, yields were improved by non-N related rotational effects. Significant reductions in N fertilization rates following a red clover cover crop are likely to result in lost corn yield opportunities in western Ohio.

Committee: Robert Mullen (Advisor); Nicholas Basta (Committee Member); P. Charles Goebel (Committee Member) Subjects: Agronomy

Master of Science, Miami University, 2006, Botany

The genus Maackia (Papilionoideae, Fabaceae) comprises trees and shrubs native to China, Japan, Korea, Russia, and Taiwan. Morphologically, Maackia appears most closely related to Cladrastis. However, molecular data indicate that Maackia is distantly related to that genus, being more closely allied to some Sophora species, Salweenia, and Euchresta, whereas Cladrastis is basal to the subfamily. Individual floras have mentioned the genus, but none have included all the species in Maackia, and no previous monograph exists. Over 600 specimens were obtained on loan from herbaria around the world. Separate analyses of fruiting and flowering specimens were conducted, because flowers and fruit do not occur simultaneously on one plant. From 130 specimens, 77 vegetative characters, 16 pod and seed characters, and 56 floral characters were measured. Data were analyzed using NTSYS – pc and MINITAB. Eleven species are recognized, one of which is new, another newly named, and a new subspecies combination made.

Committee: Michael Vincent (Advisor) Subjects: Biology, Botany