Computers uncover how plants survive

MICHIGAN STATE (US) — Plant and computer scientists have teamed up to figure out how certain genes in a plant turn on and off to deal with environmental extremes.

Their work focused on the genome of Arabidopsis thaliana, a plant with more than 25,000 genes. Of those, about 3,000 to 10,000 are used to cope with extremes under just one particular stress.

The question is: What combination of factors has to occur to make the right genes switch on at precisely the right environment?

“Until now, we did not know how these genes were turning on and off at a genome-wide scale,” says Shin-Han Shiu, a plant biologist at Michigan State University. “Now we have a better idea of how these work, and that will give us more opportunity to control the genes to help them cope with extremes.”

The switches that essentially turn on and off the necessary genes are called cis-regulatory elements. By using the artificial intelligence of computers, Shiu and colleagues got a better handle on how they operate. The computers were able to run myriad switch combinations simultaneously to speed the research along.

“Suppose you have thousands and thousands of switches in front of you,” Shiu says, “and you want to know which combination will create the right kind of response in the plant. Don’t let humans do it. We rely on machines to find the combinations.”

It was through this work that the scientists were able to better understand which genes were relevant in coping with extreme environments and how they are controlled. Their findings are reported in the Proceedings of the National Academy of Sciences.

“Our work will contribute to improving crops so they can deal with environmental changes better,” Shiu says. “More broadly, what we find is important to better understand how global climate change may impact plant growth and food production.”

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