Biochemistry, Department of


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A DISSERTATION Presented to the Faculty of The Graduate College at the University of Nebraska In partial Fulfillment of the Requirements For the Degree of Doctor of Philosophy, Major: Biochemistry, Under the Supervision of Professor Gautam Sarath. Lincoln, Nebraska: April, 2015

Copyright (c) 2015 Nathan Palmer


Switchgrass (Panicum virgatum L.), a C4-perennial grass species, is being developed as a bioenergy crop. Although much is known from a breeding perspective, there is limited information on the functional genomics of this crop, specifically regarding molecular mechanisms controlling aerial senescence, winter dormancy, and traits that confer winter hardiness. Using functional genomics to generate a transcriptional roadmap underpinning senescence and winter dormancy will provide researchers with a molecular understanding that can be applied to improve switchgrass germplasm.

In an initial study, a de novo assembly of the crown and rhizome transcriptome from an upland cultivar Summer was performed. This study added about 30,000 new expressed-sequence tags to the public databases and provided the first details on the molecular aspects of switchgrass rhizome metabolism.

The acquisition and remobilization of minerals between plant tissues is an essential feature of plant development. For switchgrass, seasonal remobilization of minerals can impact rhizome health and overall sustainable production of biomass. A total of 520 putative mineral transporters were identified in the draft version of the switchgrass genome (Pvi0), and their expression patterns were queried in publically available transcriptome datasets from various tissues and developmental stages. These analyses suggested that some minerals more readily mobilized to the rhizomes at the end of the growing season. Transcripts for several mineral transporters were specifically enriched in rhizomes harvested at dormancy.

RNA-Seq analysis of field grown cv. Summer flag leaves resulted in the creation of a four-stage roadmap of flag leaf development and identified many genes specifically associated with expansion through senescence. Among these were two transcription factors homologous to a gene that regulates mineral remobilization from source to sink in wheat (Triticum aestivum) plants.

A related study established the molecular differences in rhizomes in contrasting cultivars of switchgrass. Results indicated that the latitudinally adapted cv. Summer was approaching a dormant state, whereas the rhizomes from the latitudinally non-adapted cv. Kanlow were actively growing. An improper timing of dormancy onset could negatively impact plant fitness.

These novel first results for any warm-season perennial grass species provide a robust molecular framework to understand winter dormancy in perenniating tissues.

Advisor: Gautam Sarath

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