“Genetics of Domestication in the Solanaceae“

Project Summary:

The Nightshade family (Solanaceae) contains approximately 98 genera and 2,700 species and includes a number of important domesticated plants such as tomato, pepper, potato, tobacco, and eggplant. Large amounts of genomic and transcriptomic sequencing data exist for many of these species, which can be mined using databases and bioinformatic approaches to answer evolutionary questions. This includes questions such as which genes have undergone selection in a specific lineage relative to other lineages in the clade. In this project, we will use comparative genomics and population genomics tools to find genomic and transcriptomic data from previous studies as well as publicly available data sets from wild and domesticated species pairs from subclades of the Solanaceae family to identify genes that may have been targets of selection during the process of domestication. While related genes may have comparable patterns of selection in many of the lineages, some targets of selection during domestication will vary depending on the trait considered desirable in a species (fruit size, tuber size, etc.). Through the use of these tools, we identified certain orthogroups with strong positive selection in tomato (Solanum lycopersicum) and regions of selective sweeps, and we hope to expand these methods into other important groups of domesticated plants. By identifying these targets of selection, we will be able to expand our understanding of domestication in the Solanaceae family and provide targets for future research, leading to more informed crop breeding.

My Experience:

From my experience as a PGRP intern, I was able to learn an extensive amount about bioinformatics in a professional environment, and gain invaluable experience. I really enjoyed working with a mentor, as they helped direct and teach a lot of background information and bioinformatic approaches that otherwise would have been a struggle to learn. I think the most important experience would be understanding how to use bioinformatic tools, especially through the UNIX command-line. I also developed much more advanced programming knowledge, and I learned research techniques like writing a proposal and creating a poster. Through my project, I learned so much about the Solanaceae family and primarily the tomato clade, and explored a wide range of research topics related to it. This experience ultimately expanded my knowledge of plant biology in general, and has made me seriously consider a career in scientific research.