The field of functional genomics aims to understand the complex relationship between genotype and phenotype by integrating genome-wide approaches, such as transcriptomics, proteomics, and metabolomics. Large-scale "-omics" research has been made widely possible by the advent of high-throughput techniques, such as next-generation sequencing and mass-spectrometry. The vast data generated from such studies provide a wealth of information on the biological dynamics underlying phenotypes. Though functional genomics approaches are used extensively in human disease research, their use also spans organisms as miniscule as mycoplasmas to as great as sperm whales. In particular, functional genomics is instrumental in agricultural advancements for the improvement of productivity and sustainability in crop and livestock production. Improvement in soybean production is especially imperative, as soybeans are a primary source of oil and protein for human and livestock consumption, respectively. The research presented here employs functional genomics approaches – transcriptomics and metabolomics – to discern the transcriptional regulation and metabolic events underlying two economically important agronomic traits in soybean: seed phytic acid content and Soybean mosaic virus resistance. At normal levels, seed phytic acid content inhibits mineral absorption in humans and livestock, acting as an antinutrient and contributing to phosphorus pollution; however, the development of low phytic acid soybeans has helped mitigate these issues, as their seeds increase nutrient bioavailability and reduce environmental impact. Despite these desirable qualities, low phytic acid soybeans exhibit poor seed performance, which negatively affects germination rates and yield and has prevented their large-scale commercial production. Thus, part of the focus of this research was investigating the effects of mutations conferring the low phytic acid phenotype on seed germination. Comparative studies between low and normal phytic acid soybean seeds were carried out and revealed distinct differences in metabolite profiles and in the transcriptional regulation of biological pathways that may be vital for successful seed germination. The final part of this research concerns Rsv3-mediated extreme resistance, a unique mode of resistance that is effective against the most virulent strains of Soybean mosaic virus. The molecular mechanisms governing this type of resistance are poorly characterized. Therefore, the research presented here attempts to elucidate the regulatory elements responsible for the induction of the Rsv3-mediated extreme resistance response. Utilizing a comparative transcriptomic time series approach on Soybean mosaic virus-inoculated Rsv3 (resistant) and rsv3 (susceptible) soybean lines, this final study provides gene candidates putatively functioning in the regulation of biological pathways demonstrated to be crucial for Rsv3-mediated resistance. / Doctor of Philosophy / Soybeans are a crop of great economic importance, being a primary source of oil and protein for human and livestock consumption, respectively. Increasing demand for soybean calls for improvement in its production. An emerging field that has had tremendous impact on this endeavor is the field of functional genomics. Functional genomics approaches generate large-scale biological data that can aid in discerning how specific processes are regulated and controlled in an organism. The research presented in this work utilizes functional genomics approaches to elucidate the biological mechanisms underlying two economically important traits in soybean: seed phytic acid content and Soybean mosaic virus resistance. Phytic acid is a compound found in soybean seeds that causes nutrient deficiencies and phosphorus pollution. Soybeans with reduced to phytic acid content have been developed to mitigate these problems; they have poor seed germination and emergence. The studies in this work employ functional genomics approaches to compare unique sets of low and normal phytic acid soybeans to help establish the relationship between seed phytic acid content and seed performance. These studies resulted in new and promising hypotheses for future studies on investigating the low phytic acid trait. The final focus of this work used a functional genomics approach to discern the molecular mechanisms underlying a unique mode of resistance to Soybean mosaic virus. The study identified genes in soybean that are potentially critical to resistance against Soybean mosaic virus.
| Identifer | oai:union.ndltd.org:VTETD/oai:vtechworks.lib.vt.edu:10919/106739 |
| Date | 02 June 2020 |
| Creators | DeMers, Lindsay Carlisle |
| Contributors | Crop and Soil Environmental Sciences, Saghai-Maroof, Mohammad A., Pilot, Guillaume, Li, Song, Helm, Richard F. |
| Publisher | Virginia Tech |
| Source Sets | Virginia Tech Theses and Dissertation |
| Detected Language | English |
| Type | Dissertation |
| Format | ETD, application/pdf, application/vnd.openxmlformats-officedocument.spreadsheetml.sheet, application/vnd.openxmlformats-officedocument.spreadsheetml.sheet, application/vnd.openxmlformats-officedocument.spreadsheetml.sheet, application/vnd.openxmlformats-officedocument.spreadsheetml.sheet, application/vnd.openxmlformats-officedocument.spreadsheetml.sheet, application/vnd.openxmlformats-officedocument.spreadsheetml.sheet, application/vnd.openxmlformats-officedocument.spreadsheetml.sheet, application/vnd.openxmlformats-officedocument.spreadsheetml.sheet, application/vnd.openxmlformats-officedocument.spreadsheetml.sheet, application/vnd.openxmlformats-officedocument.spreadsheetml.sheet, application/vnd.openxmlformats-officedocument.spreadsheetml.sheet, application/vnd.openxmlformats-officedocument.spreadsheetml.sheet, application/vnd.openxmlformats-officedocument.spreadsheetml.sheet, application/vnd.openxmlformats-officedocument.spreadsheetml.sheet, application/vnd.openxmlformats-officedocument.spreadsheetml.sheet, application/vnd.openxmlformats-officedocument.spreadsheetml.sheet |
| Rights | In Copyright, http://rightsstatements.org/vocab/InC/1.0/ |
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