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Alexander researching alfalfa genes for SRI grant

February 21, 2023

After transferring to Dakota State from the University of Arizona, Jay Alexander began talking to Dr. Andrew Sathoff about bioinformatics and any biology-related research they could be involved in.  

“I’m looking to get a Ph.D. in biochemistry,” Alexander said.

“Jay is a fixture in the offices, chatting about research and is very passionate about science,” Sathoff said.

Alexander, an Analytical Science major from Aurora, Ill., received a Student Research Initiative (SRI) grant this year to study the Functional Analysis of Differentially Expressed Genes in Alfalfa Inoculated with Aphanomyces. Aphanomyces root rot is a common, economically important alfalfa disease.

“There are several cultivars of alfalfa resistant to Aphanomyces and numerous susceptible to Aphanomyces,” Sathoff explained. “The idea is to inoculate the resistant and susceptible plants and then do an analysis to see what is going on inside the plants molecularly.”

This project will help determine what genes might play a role in resistance or susceptibility. Determining this can allow plant breeders to know the important gene that can be inserted in the plant to protect it from pathogens, he said.

Sathoff reached out to his former advisor at the University of Minnesota, Dr. Deborah Samac, who gave them an RNA-seq data set to work with to complete this research. “RNA-seq is sequencing all of the RNA that a plant produces,” he said.

Alexander is categorizing the different genes into biological processes. To do this, they utilize BLAST, a Basic Local Alignment Search Tool that finds areas of similarity between sequences. It uses databases with different genes to find the functions the genes perform.

“From there, you create a map, and you have to annotate them, which is something called gene ontology,” Alexander said.

“This is really complex research,” Sathoff said. “It’s bioinformatics 101, something a student would do in graduate school.”

Alexander utilizes Excel spreadsheets and software that creates graphs to disseminate their findings.

This work helps Alexander become independent in the lab, think critically, and be a problem solver, Sathoff said.

They hope to publish their findings this spring.

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