Analyzing genetic variation of the tussock cottongrass among ecotypes along a latitudinal gradient through transcriptomics

• Main Author: Webster, Carmen
• Format: Text
• Language: English
• Published: ScholarWorks@UTEP 2021
• Subjects: Bioinformatics; Biology; Ecology and Evolutionary Biology; Arctic; Climate change; Eriophorum; Alaska; Cottongrass
• Online Access: https://scholarworks.utep.edu/open_etd/3369; https://scholarworks.utep.edu/cgi/viewcontent.cgi?article=4368&context=open_etd

The Arctic is seeing some of the most extreme effects of climate change that induce environmental pressures, including warmer temperatures and longer growing seasons. Due to this, taxa may need to adapt or migrate in order to survive. The long-lived tussock cottongrass, Eriophorum vaginatum, is a foundation species in the Arctic, and little is currently known about the genetic constraints that could be playing a role in how this species will respond to the changing climate. Specific gene families that play an important role in signaling genetic pathways related to plant phenology and response to environmental stress are likely to be a key component to the performance of E. vaginatum under climate change in the Arctic. The purpose of this study was to investigate the genomics of adaptation, emphasizing the Phytochrome gene family and â??Response to Stressâ?? genes. Sanger sequencing was utilized to investigate evidence for selection among the Phytochrome gene family (PHYTA, PHYTB, and PHYTC) along a latitudinal gradient in northern Alaska. Analyses using Bayesian gene tree construction and nonsynonymous and synonymous (KA/KS) mutation rates showed that these genes are likely not under selection in relation to North/South ecotypes, but there is allelic variation in these genes and some evidence that is associated with specific populations. The E. vaginatum transcriptome, the program SciRoKo 3.4, and several Python scripts were used to identify genes that play a role in stress response and identify SSRs and SNPs associated with these genes for genetic marker development. Primers will be developed for these genetic markers to be used to examine the potential for ecotypic variation with stress response in future selection studies of E. vaginatum.