Lisa Yoo
Lisa Yoo_FeiLab
Year: 2016
Faculty Advisor: Zhangjun Fei

Identifying dynamically expressed genes during sweetpotato root development

Project Summary

The sweetpotato (Ipomoea batatas) is the seventh most important crop in the world. With its high nutritional quality and relatively low labor cost, it serves as a major food security crop for many sub-Saharan African nations. Though traditional breeding techniques have been implemented in order to boost the yield and quality of the sweetpotato, these have not been very effective. Therefore, it is necessary that we gain more genomic and genetic information about this crop to facilitate the development of next generation breeding tools.  There are three types of sweetpotato roots: fibrous roots (FR), pencil roots, and storage roots (SR), of which the storage roots are mainly consumed. For this project, we generated transcriptome profiles of total roots at 10 and 20 DAT (days after transplant) and fibrous roots and storage roots at 30, 40, and 50 DAT, for Beauregard, one of the world’s most popular varieties of sweetpotato. The RNA-Seq reads were mapped to the reference genome of I. trifida. To examine differential gene expression, we made comparisons between samples of different developmental stages in SR, and between FR and SR samples. We further evaluated these results using gene ontology and enzyme pathway analysis. Our results allowed us to identify candidate genes in the carbohydrate metabolism pathway that are important in storage root development, which is potentially useful in context of increasing the yield and quality of the sweetpotato.

My Experience

My summer at BTI was such an incredible learning experience. Coming into the program, I had almost no background in plant biology, research, or computer science. However, as the internship is drawing to a close, I can now say that I have developed knowledge and skills in all of these areas. Everyday, I was faced with new obstacles, whether it be writing my research proposal, or figuring out how to run a script on the server, or presenting my research in front of my lab. Through dealing with these tasks, I learned responsibility and independence. Working in a real laboratory has given me a higher level of appreciation for the challenges and excitement of conducting research.

I’d like to thank my mentor, Shan Wu, for helping me through every step of my research process. I’d also like to thank Dr. Fei, the whole Fei lab, the other interns, and Tiffany Fleming for making my experience so valuable and memorable.