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Abstract
Production of second-generation lignocellulosic biofuel feedstocks on marginal lands will be limited by abiotic constraints, including low nutrient content of the soil. Therefore, we must utilize strategies to help these crops thrive under low inputs. Association with symbiotic soil fungi called arbuscular mycorrhizae (AM) influences a plants ability to access nutrition in low nutrient soils. Panicum virgatum (switchgrass), a candidate second-generation biofuel crop that has been the focus of research programs across the country, varies in its ability to form AM associations. Mapping experiments and transcriptomic studies suggest that AM colonization rate is under genetic control. Additionally, microRNAs (miRNAs) have been shown to be dynamically expressed during AM colonization in a range of plant species. MiRNAs target specific genes and downregulate them at the posttranscriptional level in a homology dependent manner. In this dissertation, I describe efforts to uncover miRNA-mediated regulation of AM colonization in switchgrass. In Chapters 2 and 3, I took a transcriptomic approach to analyze miRNAs that are responsive to AM colonization in the lowland accession Alamo and the upland accession Dacotah, and in two F1-sib lines, the parents of our F2 mapping population, which have been shown to differ in AM colonization rate. Through these efforts, I identified pvi-miR171 regulating Nodulation signaling pathway 2 (NSP2) in response to AM colonization, a miRNA-target pair previously shown to be active in AM interactions in model species. I observed downregulation of miRNAs that are part of a group known as the copper miRNAs in response to AM colonization which broadly targeted genes with oxidoreductase activity. In addition, I identified a set of known and novel miRNAs that target genes potentially controlling disease resistance and root morphology. I also identified AM responsive genes involved in disease resistance in both F1 parents and other genes that were upregulated in one parent compared to the other but not under apparent miRNA control. Lastly, in chapter 4, I mapped expression quantitative trait loci (eQTL) for the miRNAs identified in chapters 2 and 3 that were segregating in the F2 mapping population. This preliminary effort resulted in the identification of 22 miRNA-eQTL.