Building a genomic resource for a major African staple crop: the Cassava Expression Atlas
Cassava is a key staple crop for more than 500 million people across Africa, Asia and South America. Its ability to grow in poor and dry environmental conditions, as well as the high starch content in its roots, makes it a very desirable crop. Despite these benefits, cassava research has long been neglected in comparison to commodity crops such as wheat and rice. Additionally, its high heterozygosity level and low ability to flower are challenging biological features for research and breeding.
The Cassava Expression Atlas aims at developing resources for cassava genomics and offers an interactive tool to access and analyze cassava RNA-seq data. To implement the expression atlas we used an RNA-seq test dataset including three different cultivars of cassava, Arg7, SC124, and W14, under drought and control conditions, with a focus on the leaf and root organs of the plant. A Postgres database and various graphics were created to host and display the processed RNA-seq data.
While the dataset used in this work is relatively small, the Cassava Expression Atlas aims to provide an extensive data resource for the crop, including data on many biotic and abiotic conditions, plant organs, and cultivars. With such an available resource, ideally, any gene expression information can be retrieved and be made available to the international cassava research community.
My time spent during the summer as an intern at BTI has been an enjoyable and valuable experience for me. At the start of the program, I had no prior research experience, and while I enjoy both technology and science, I realized that there was a lot I didn’t know and would need to learn. Thanks to my mentors, I was able to find out more about UNIX and the Linux command line, how RNA-seq works, and the kinds of data one can retrieve and analyze using RNA-seq. More importantly, I was able to take the information that I learned and apply it to my research project effectively. This internship has been a truly invaluable experience for me, and the skills I have learned will hopefully help me in pursuing my future college and career goals.