Sam Cassity
Samantha Cassity headshot
Year: 2023
Faculty Advisor: Andrew Nelson
Mentor: Kyle Palos

Investigating Conserved Transcriptional Responses to Salinity Stress in Arabidopsis and its Relatives

Salt stress is a prevalent obstacle in agriculture that can cause adverse effects in crops such as physiological drought and metabolic disruption The plant family Brassicaceae is a well-studied group that has species with various responses to salt. In the salt-sensitive species, Arabidopsis thaliana (Arabidopsis), salinity stress responses are well-documented and numerous genes have been characterized in mediating this stress response. However, this level of molecular characterization has not been performed on Arabidopsis’ salt tolerant relatives, such as Camelina sativa and Eutrema salsugineum (Camelina and Eutrema, respectively). If Camelina and Eutrema utilize conserved molecular mechanisms to tolerate salt stress, there should be overlapping responses that can be quantified through gene expression measurements (transcriptomics). However, if Camelina and Eutrema use species-specific mechanisms to tolerate salt stress, these transcriptional responses will be distinct. To explore this inquiry, I used the programming language R to extensively characterize the transcriptomic responses of Arabidopsis, Camelina, and Eutrema during control and salt stress treatment. This characterization included: (1) conducting differential expression to discern how genes undergoing statistically significant changes in gene expression vary between salt-sensitive species and salt-tolerant species. Further, (2) I assessed which genes are undergoing alternative splicing (differential isoform usage) due to salt stress. The culmination of these analyses identified numerous transcription factors and regulatory non-coding RNAs that may contribute to salt tolerance or sensitivity in Brassicaceae. With these findings, pathways involved in salt stress response for each species are better elucidated and can allow for a directed approach to tackling salt-sensitivity in agriculture.

My summer experience has been full of learning, meeting wonderful people, and enjoying everything upstate New York has to offer. Since I’m from Arizona, the best part about this summer has been the weather and the scenery. Ithaca is a beautiful and refreshing change of pace. I will deeply miss all of the greenery and wildlife that I don’t get to enjoy out in the desert. Aside from the beauty of campus, the workplace was also great. Being involved with the Nelson lab, I was met with hospitality, flexibility, and a great mentor, Kyle Palos. I learned so many new techniques within the realm of Rstudio and processing RNAseq data. He also did a great job of bolstering my professional development by helping me create a Github repository of code. Lastly, I am endlessly grateful for the friendships I’ve made along the way.