Development of an eQTL database depicting SNP and expressional data analysis tools for tomato

A database was constructed to illustrate the RNA-seq data analyzed from the introgression lines parented by the domesticated tomato Solanum lycopersicum and the wild-type tomato S. pennellii. The purpose of this work is to organize large data sets in a comprehensible, efficient and convenient way for scientists to research expressional data and SNPs in tomato. Methods for the database construction included the making of the database schema, the use of the MySQL and phpmyadmin programs, and the manipulation of data through Perl scripts for appropriate upload to the database. Upon completion, Perl CGI scripts were written to allow viewing access to the data via HTML. This work allows differentially expressed genes and SNPs on tomato chromosomes to be analyzed in a more optimized and simplistic way. Following this, it is inferred that researchers would be more readily able to determine the importance of SNPs relative to desired phenotype traits in tomato. In turn, this helps to stimulate successful tomato production.

My Experience

Through my internship at the Boyce Thompson Institute, I have acquired the personal, professional and academic goals I set for myself upon arrival. I have been exposed to a new topic of interest for me: database design. I learned the procedures for designing a database schema and then implementing it, which also gave me a greater understanding of the Perl coding language. To complete my work, I often had to do a lot of self-learning, which helped to boost confidence in my ability to conduct research and overcome obstacles. The knowledge and experience that my mentors provided helped me through times where I had little direction. I thoroughly enjoyed the atmosphere that comes from working with a research team due to the sense of a team effort in pursuit of an overall goal. Additionally, I have earned experience that will prove invaluable towards my pursuit of graduate school studies.