How I spent my summer -- Undergraduate Research Program @ CSHL

By Daniel Burkhart, URP 2014

I spent this summer with the Ware Lab studying genetic variation between Sorghum bicolor cultivars implicated in drought resistance. As microbiology major at the University of Massachusetts Amherst, coming to work in plant genomics required some catching up. After spending a few days at the library and preparing a preliminary presentation, I was excited to get to work. My project focused on finding sites of genetic variation within the anthocyanin and dhurrin pathways. I searched for single nucleotide polymorphisms, which were present in stay-green sorghum—sorghum that is especially resistant to drought stress post-flowering—and were absent in non-stay-green sorghums.

I did most of this project using tools available on Gramene. Gramene scientists curated the SorghumCyc metabolic pathways from which I could find a list of genes in these two pathways. I used the Gramene Mart to find a list of genome coordinates for each of these 100+ genes. I used a previously curated set of SNPs and found a list of 17 that were within 2kb of my genes of interest. Going back to Gramene, I used the variant effect predictor to quickly determine if these SNPs were upstream, downstream, in introns, or in coding regions of these genes. I determined that in the stay-green sorghums, 5 out of 6 reactions in the dhurrin pathway contained at least one SNP. I also found that although fewer reactions in the anthocyanin pathway (6 out of 22) contained at least one SNP, one gene in the first reaction of the anthocyanin pathway contained 5 SNPs including the only missense variation. This gene has been computationally inferred to encode for an enzyme essential for the conversion of trans-cinnamate to 4-coumarate.

These results were exciting, and they may serve as the basis for further research. One could validate the product of this gene at the beginning of the anthocyanin pathway in order to determine if it encodes for the predicted enzyme. Future research might also entail a search for SNPs in a greater number of sorghum cultivars—I only looked at six. It would also be easy to expand the search to a greater number of genes and pathways. I won’t be continuing with this research, but some future URPs might. I had an incredible summer with the Ware Lab at Cold Spring Harbor. I learned a great deal of plant biology, and I left with a better understanding of the tools available for computational research.