What’s lurking in your soil? Using BLAST to analyze DNA sequences

Shadybrook Farm is having soil trouble! A soil test report has identified several potential culprits. In a webinar sponsored by GrowNextGen and the Ohio Soybean Council, teachers helped identify the species by examining DNA sequences using BLAST. Presenter Dr. Zack Bateson led the group through the process of submitting samples and reading results from the National Center for Biotechnology Information website which hosts a database of genetic sequences.

Bateson is currently the lead research scientist at the National Agricultural Genotyping Center and a part-time instructor in the Biological Sciences Department at North Dakota State University in Fargo, North Dakota.

Many students are familiar with strawberry DNA extraction, but this real-world scenario demonstrates the next step: what do scientists do with this information?

Soils are complex, containing DNA from many different organisms, both good and bad. After getting a sample and extracting DNA, amplified PCR products are digitized into their nucleotide sequence. DNA sequencing and bioinformatics are used to identify differences in the barcodes which are areas that help to identify specific species.

Bioinformatics is a merger of several disciplines and it has many applications, such as genome sequencing and analysis, protein structure analysis, gene discovery (insect and disease resistance, improved nutritional quality, drought resistance), and pathogen and disease discovery and control. BLAST, Basic local alignment search tool, looks at specific pieces of a DNA sequence to find a match. Using the What is Bioinformatics? curriculum available on GNG, participants submitted five sequences and BLASTed them.

After identifying the species’ DNA in the sample, the final step is to help the farmer by making recommendations about certain resistant strains of soybeans or soil management techniques. Knowing the organisms within the soil will help farmers in the fight against diseases that destroy food crops around the US.

This webinar has been recorded so you can learn and share this information with your students!