Nebraska team develops technique to speed identification of corn genes | Nebraska today

The genome of a corn plant contains nearly 40,000 genes, thousands more than the human genome. But 15 years after the publication of the first draft of the corn genome, the role that 98 percent of these genes play in making a corn plant or determining how corn responds to different growing conditions remains unknown.

Conventional methods for understanding the work of each gene have proven slow and expensive, but Husker scientists have taken a big step forward in identifying the function of corn genes. The work was led by Vladimir Torres-Rodriguez, a postdoctoral associate working with James Schnable, a professor and specialist in corn genetics in the department of agronomy and horticulture at the University of Nebraska-Lincoln.

Their results, recently published in The Plant Journal, could lead to faster creation of more resilient corn varieties and wider grower access to improved crops by identifying the functions of individual corn genes more quickly and accurately. Torres-Rodriguez is the lead author of the paper titled “Population-level gene expression can repeatedly link genes to functions in maize.”

The technique he developed and tested with the team of Schnable laboratory researchers specializing in corn uses RNA rather than DNA. This innovative approach identified approximately 10 times more maize genes affecting flowering time than widely used DNA-based methods for identifying genes.

Doing a better job of understanding the functions of genes could reduce the cost of bringing genetically modified corn varieties to market, leading to more competition and better prices for farmers, said Schnable, who contributed to the year latest in the historic completion of maize genome mapping.

Only a handful of large seed companies have the resources to invest hundreds of millions of dollars in developing new gene-driven products. But faster, more precise approaches, like the one demonstrated by UNL, could reduce costs and open up the market.

To make this project possible, the Husker team measured the RNA levels of more than 39,000 maize genes in each of approximately 700 maize varieties, using plants grown at the University of Lincoln's Havelock Farm. The researchers combined these RNA measurements with measurements of the corn plants themselves collected in Lincoln and by collaborators at Michigan State University.

Making the project work required new approaches not only on computers, but also in the field, said Schnable, presidential chairman of the Nebraska Corn Checkoff. The team had to collect samples from each corn plant in less than two hours and freeze them before environmental conditions could quickly break down the RNA that was key to Torres-Rodriguez's analysis.

Achieving these conditions required special equipment designed by Jonathan Turkus, a research director who works with Schnable at the university's Center for Plant Science Innovation. Turkus made equipment using 3D printers and other tools from the makerspace at the Nebraska Innovation Campus.

The result, Torres-Rodriguez said, is that “UNL has produced the largest dataset of corn gene expression measurements in the world.”

“Vladimir had to create a software pipeline to analyze this data,” Schnable said of Torres-Rodriguez's innovations. The work required “reusing other tools, finding other ways to process the data, and then figuring out all the new quality control steps to make sure everything was working correctly.” It was an incredible undertaking.

Torres-Rodriguez will continue the project with genetic analysis of additional corn traits. The goal, Schnable said, is to “ensure that decades from now, when a Nebraska farmer drives his tractor, the corn planted will have the genetics to perform well and tolerate harsher conditions.” Through projects like this, Schnable said, UNL is positioning itself as the go-to research institution that companies, from giants to small startups, can turn to for data sets, expertise or field support focused on corn.

A first example of such collaboration with the private sector contributed to the launch of this project. Schnable was working with Brad Zamft, a California scientist leading a team developing new artificial intelligence-based tools for agriculture.

“Brad asked me for a bigger data set,” Schnable said. “At the time, we were using the largest dataset of its kind that existed in the public sector. He thought about this for a while, then asked: How much would it cost to do this properly?

Ultimately, the two men worked together to secure a $650,000 grant for the project through the U.S. Department of Energy's Advanced Research Projects Agency-Energy program.

“There's no doubt in my mind that the University of Nebraska is an agricultural technology powerhouse,” said Zamft, project manager of a stealth plant biology project at X, Alphabet's “moonshot factory” division exploring a range of scientific innovations. “The expertise we’ve experienced and the collaborations we’ve engaged in have been delightfully productive and I believe could have a real impact on the world.” I'm not sure our team could have gotten this far without the support of the university's researchers.

Schnable said UNL has a real opportunity.

“We want to be, and we are becoming, the place where people from all over the country come to do cutting-edge corn research,” he said.