Potato genomics three ways: quantification of endoreduplication in tubers, a romp through the transposon terrain, and elucidation of flower color regulation
| dc.contributor.author | Laimbeer, Francis Parker Effingham | en |
| dc.contributor.committeechair | Veilleux, Richard E. | en |
| dc.contributor.committeemember | Saghai-Maroof, Mohammad A. | en |
| dc.contributor.committeemember | Bombarely Gomez, Aureliano | en |
| dc.contributor.committeemember | Tokuhisa, James G. | en |
| dc.contributor.department | Horticulture | en |
| dc.date.accessioned | 2018-08-03T08:01:00Z | en |
| dc.date.available | 2018-08-03T08:01:00Z | en |
| dc.date.issued | 2018-08-02 | en |
| dc.description.abstract | Investigations of potato (Solanum tuberosum) have been hampered by its complicated genetics and high genetic load. This dissertation applies genome reduction techniques to investigate a broad swath of genomic and physiological phenomena. It begins with the presentation and evaluation of a protocol to characterize endoreduplication within potato tubers, demonstrating substantial variation between tissue types and among wild species which may facilitate research into the genesis and growth of these starchy underground stems. Next, we transitioned to explore the distribution and consequences of a specific class of transposable element, Miniature Inverted Transposable Elements (MITEs), showing that they comprise approximately 5% of the potato genome, occur more frequently in genes with stress-related functions, and may be associated with changes, especially decreases, in gene expression. We then combined homology and sparsity based approaches to predict recent MITE activity, identifying five families as especially active. Finally, we expose the gene underlying the potato flower color locus, a homolog of AN2, while showing the effects it exerts on the flavonoid biosynthesis and fruit ripening pathways. This region was shown to be particularly dynamic, replete with MITEs and structural variants which we hypothesize to be the ultimate cause of differences in AN2 expression within the germplasm we examined. While the separate topics of this dissertation are quite disparate, each addresses an important topic in potato genetics, the in-depth study of which is only possible through the utilization of genomic reduction approaches to acquire homozygous genotypes for study and currently available genomic resources. | en |
| dc.description.abstractgeneral | Despite their humble appearance and routine consumption, potatoes have a complex genetic structure and a life cycle capable of both sexual reproduction through flowers, fruit and seed, and asexual reproduction through the tubers which also comprise the edible product. From an agronomic perspective, one of the most important qualities of a potato tuber is size, a feature influenced by genetics and environment. Cell-to-cell variation for the amount of DNA per cell, one component that influences tuber size, is known to occur, yet our ability to measure DNA content in starchy tuber cells has been obscured by debris generated through routine preparation techniques. We present and evaluate a new method for measuring the DNA content of potato tuber cells, which provides reliable results across a range of different potato varieties and species. ‘Jumping genes’ also known as transposons, first reported in maize but now known to occur in most advanced plant and animal species, have been found to comprise ~5% of the recently sequenced potato genome. We show that a particular class of transposons is more likely to occur adjacent or actually in certain types of genes, such as those which confer resistance to disease, where they may have meaningful effects on how those genes operate. We then proceed to predict the current activity of the various families of these jumping genes to understand how they continue to alter the genetic landscape of potato. Finally we identify a particular gene which dictates flower color in potato (purple vs. white). We demonstrate that several transposons occur in some forms of the flower color gene. Originally we hypothesized that transposons were associated with the turning off of the purple flower color form; however, on closer examination, we could express the white flower form in transgenic plants that were originally white-flowered and convert them to have purple flowers, demonstrating that even the white flower form was functional. While the separate topics of this dissertation are quite disparate, each addresses an important topic in potato genetics, the in-depth study of which is only possible through the availability of the special strains of potatoes with reduced chromosome number and the publication of the potato genome. | en |
| dc.description.degree | Ph. D. | en |
| dc.format.medium | ETD | en |
| dc.identifier.other | vt_gsexam:16698 | en |
| dc.identifier.uri | http://hdl.handle.net/10919/84480 | en |
| dc.publisher | Virginia Tech | en |
| dc.rights | In Copyright | en |
| dc.rights.uri | http://rightsstatements.org/vocab/InC/1.0/ | en |
| dc.subject | Solanum tuberosum | en |
| dc.subject | potato | en |
| dc.subject | endoreduplication | en |
| dc.subject | flow cytometry | en |
| dc.subject | ploidy | en |
| dc.subject | transposons | en |
| dc.subject | MITEs | en |
| dc.subject | anthocyanins | en |
| dc.title | Potato genomics three ways: quantification of endoreduplication in tubers, a romp through the transposon terrain, and elucidation of flower color regulation | en |
| dc.type | Dissertation | en |
| thesis.degree.discipline | Horticulture | en |
| thesis.degree.grantor | Virginia Polytechnic Institute and State University | en |
| thesis.degree.level | doctoral | en |
| thesis.degree.name | Ph. D. | en |
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