Identification of Differentially Expressed Genes in F1 from the Cross between S. lycoperiscum M82 and S. pennellii LA0716

The modern cultivated tomato is characterized by a lack of genetic diversity due to extensive selective breeding. In contrast, wild tomatoes continue to display broad morphological and metabolic diversities including sugars, organics, and volatiles. Identifying genes with allele-specific expression (ASE) related to key agronomic traits in the F1 hybrid derived from the cross between the S. lycoperiscum M82 and the wild S. pennellii LA0716 could deepen our understanding of the regulation of tomato nutritional quality and flavor. This project used RNA sequencing (RNA-Seq) data from different fruit tissues at different developmental stages of the F1 cross. RNA-Seq reads were processed and mapped to the genomes of the two parents, respectively. Based on the mapping quality to each parent genome, the reads were assigned to one of the parents, and raw and normalized (FPKM) read counts for each of the two alleles were calculated for all genes. ASE genes were then identified and weighted gene co-expression analysis was performed. Gene ontology analysis for genes within the module with highly differential allele expression identified enriched biological processes, and genes with functions relevant to fruit flavor and nutrition were identified. The identification of these candidate genes could allow for future functional analysis that will deepen our understanding on how cross breeding with wild species could improve flavor and nutritional quality in cultivated tomatoes.

Through this experience at the BTI lab, I was able to gain invaluable knowledge about not only the tomato genome and the RNA-seq technology, but also in data analysis techniques and strategies. Throughout this process, I was able to learn about how to use the R, Linux, and Python programming languages for data analysis, and also used code management tools such as RPubs and Github. It was amazing to get to experience working in a laboratory environment and have access to the tools offered, and conduct an experiment with real-world applications. I did not come into this program with a lot of background in biology or plant science, so I was able to learn about both fields through my own research and the weekly seminars, which were a really great way for me to learn about current research in plant science.