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Abstract
Switchgrass is a sustainable perennial bioenergy crop with potential for the development of jet fuel. Lowland switchgrass, which is adapted to the southern U.S., accumulates greater amounts of biomass throughout its development than Northern-adapted upland accessions. It has been challenging, however, to expand cultivation of the high-yielding lowland switchgrass northwards while maintaining its high biomass yields due to reduced fitness in northern regions. The key traits that determine fitness are flowering time and freezing tolerance. Flowering time determines the length of the vegetative growing period and thus biomass production. Freezing tolerance determines survivorship of switchgrass at below-zero temperatures for prolonged periods in winter or post-emergence in Spring. In my dissertation, I focused on identifying key genes controlling differential flowering time as well as differential acclimation to cold between lowland and upland switchgrass. In Chapter 2, I identified quantitative trait loci (QTL) for flowering time in a biparental F2 population. PvHd1 was identified as causal to the Chr04K QTL using comparative sequence analyses, in silico protein structure modeling, in vitro thermal shift analysis and in vivo functional validation of the upland and lowland alleles in Arabidopsis. In Chapter 3, I identified genes that were differentially activated or repressed in temporal acclimation cascade processes over a 7-day period of cold treatment between a freezing-tolerant upland and freezing-sensitive lowland accession. Coexpression modules were built for the differentially expressed genes, and hub and connector genes in and among the modules were identified as potential regulators of other genes in the modules. The temporal transcriptome analysis was complemented with an expression QTL (eQTL) analysis in a lowland x upland F2 population. While the expression of most genes was controlled in cis, I also observed colocalization of cis eQTL for hub genes with trans eQTL of genes with correlated expression patterns, which could be indicative of the regulatory role of the hub genes. While the role of the putative regulatory genes in cold response needs to be validated, my research provides a source of potential novel genes for cold tolerance as well as a gene, PvHd1, that can be used to manipulate flowering time in switchgrass.