Li, Jingjia (2020-12). Functional and Evolutionary Dynamics of Genes Involved in Drought Tolerance in Loblolly Pine (Pinus Taeda L.). Doctoral Dissertation.
Thesis
Drought, a major threat to the health and productivity of both natural ecosystems and agriculture, is expected to increase in frequency and intensity across many regions as a consequence of climate change and repurposing of natural water resources. Loblolly pine (Pinus taeda L.) represents a major forest species across the southeastern US due to its widespread distribution, ecological prominence, and extensive utilization for industrial production. Thus, developing loblolly varieties with increased tolerance to aridity is a major goal of the forest industry. However, this will require a significant leap forward in our understanding of the genetic basis of drought tolerance in loblolly. The main goal of this project is to generate genomic resources and bioinformatic approaches to identify genes, regulatory regions, and genetic variants involved in drought tolerance in loblolly pine. In the first component, I analyzed transcriptomic (RNA-seq) data from two loblolly genotypes with divergent tolerance to aridity. I identified more than 4,000 drought-related transcripts in response to drought in the root of Pinus taeda. Genotype x Environment (GxE) interactions were prevalent, suggesting that very different cohorts of genes are influenced by drought in the tolerant vs. sensitive loblolly genotypes. In the second part, I identified nearly 9,500 unique sites representing 24 clusters of Transcription Factor Binding Sites (TFBSs) in the promoter region of 1,386 DRTs. All of the 24 TFBSs share homology with known motifs in flowering plants. A total of 1,046 unique DRTs linked to 16 TFBSs were associated with 213 overrepresented non-redundant GO terms, most of which are related to processes known to be involved in drought tolerance. In the third component of my research, I integrated the transcriptome data with extensive genetic variant (SNP) datasets in loblolly to determine the evolutionary dynamics associated with DRTs. I found that DRTs share higher rates of adaptive evolution and contain a higher than expected number of SNPs associated with aridity than other genes. Overall, these findings will assist the sustained effort to develop varieties of loblolly pine that can better sustain the projected increase in aridity along with the range of this key forest species.
