Identification of copy number variations (CNVs) in wild and Eurasian cucumber populations

Project Summary

The Eurasian cucumber population has been domesticated in order to select for traits that improve growth and consumption. In doing so, the population has undergone a number of genetic changes. Discovering which genes vary between populations and which remain the same can help scientists understand the observable differences between the populations. It is valuable to investigate such differences in common fruits and vegetables because as a food source, it is necessary to ensure that they can be bred to be as nutritional as possible. In many cases, domestication has removed or altered genes with negative effects on crop traits and in the process may have also removed beneficial genes such as those that help with disease resistance or nutritional value. Discovering these inadvertently altered genes will allow breeders to be put back into the genome. In order to investigate the differences between the wild and Eurasian cucumber populations, the copy number variations (CNVs) were identified using cn.mops. The program distinguished 943 different regions in the cucumber genome, which contain CNVs. Among these regions was one containing the F locus, which is implicated as the region that causes gynoecious cucumbers. Many of the identified regions contain known genes, but other regions do not have any known genes. Discovering these genes in the CNV regions will provide useful knowledge for future genomics-based breeding that could improve important aspects of the plant.

My Experience

I have worked in two other Bioinformatics labs as an undergraduate, however, I have learned more from this experience at BTI than from either of the others. Working with a mentor for the first time, I had to adjust from working independently to collaborating with  a group of researchers.. While unsure of what to expect from the mentor-mentee relationship, this guidance enabled me to understand the work I was doing better than I had in any previous experience. As a result, I gained confidence in my ability to successfully conduct research. As my first experience working in the field of plant biology, this internship was a great success.  I have learned a lot about the dynamic of working in a research lab and about the impact and importance of plant biology research.