Nebraska team aids first mapping of corn genome

University of Nebraska–Lincoln scientist James Schnable and international colleagues have created the first complete map of the corn genome, a landmark achievement that can enable major long-term advances in crop health, resilience and productivity.

“These research findings can help us build tools to predict which new corn varieties will perform well in particular environments, because we will be better able to identify the functions of individual genes in corn,” said Schnable, Charles O. Gardner Professor of Agronomy.

Schnable and scientists from Iowa State University and China recently published their findings, titled “A Complete Telomere-to-Telomere Assembly of the Maize Genome,” in the journal Nature Genetics. Their findings come one year after the complete mapping of the human genome.

Scientists have devoted much effort this century to identifying the full breadth of the corn genome, the set of genetic material that plays a critical role in determining a corn plant’s physical characteristics, growth and health. Mapping the full breadth of corn’s genetic material has been a longtime challenge because the corn genome is large and immensely complex.

Technology used in the first draft of a corn genome, in 2009, identified a significant portion of corn’s wide variety of genetic material. Still, many genetic regions were too complex to be deciphered by the technology available at that time. In all, more than 100,000 gaps in the genetic sequence remained to be filled.

“Our team drew on the latest technology, plus the particular expertise of the individual team members, and that finally made possible the mapping of the complete corn genome,” Schnable said. In that first study, scientists had been able to map the centromeres — the complicated middle portions of chromosomes — for only two of corn’s 10 chromosomes, for example. Schnable and his colleagues were able to sequence all 10.

Schnable focused on regions of the corn genome containing genes called nearly identical paralogs: two or more genes located next to each other that are so similar it was hard or impossible to tell them apart in previous genomic-mapping efforts. Genetic repetition takes on extraordinary complexity in the corn genome, resulting in large areas of chromosomal material packed together in ways that have defied individual identification and analysis.

With this new complete analysis of a much-studied corn line known as Mo17, Schnable said, “we’re now able to resolve each of those individual genetic copies and start to do a better job of figuring out what individual genes do, rather than having all this combined into a mishmash where it’s hard to figure out which gene is doing what.”

The idea for this international project originated with Chinese researchers. Schnable has known Jinsheng Lai, a Chinese scientist and the paper’s lead author, for more than a decade, going back to when Schnable was a postdoctoral researcher at the Chinese Academy of Agricultural Sciences. “When he was putting this project together, he reached out to me to participate because of my expertise in this field,” Schnable said.

This new corn genome sequence has particular long-term value for developing improved corn varieties by strengthening the scientific understanding of how differences in corn genetics affect varieties. “Rather than conducting selection, we will have the potential to design and engineer corn varieties to adapt to changing climates and grow in more nitrogen-limited conditions,” Schnable said. “We can be more nimble in adapting corn to future challenges in terms of increasing yield and using less nitrogen and water.”

New opportunities also are possible, long term, for creating higher-value secondary products, such as additional value for dried distillers grains from ethanol plants.

This groundbreaking research connects to the university’s long history of cutting-edge study of corn genetics, Schnable noted. At the start of the 20th century, corn geneticist Rollins A. Emerson did pioneering work on the Nebraska faculty in rediscovering the laws of genetic inheritance established by Gregor Mendel.

Emerson later was a professor at Cornell University and in the 1920s was a mentor to doctoral student George Beadle, a Nebraska native and Husker alumnus who in 1958 received a Nobel Prize for his innovative work in genetics. The university’s Beadle Center, which facilitates research in biochemistry and biological sciences and includes the Center for Biotechnology, is named after him. Emerson also mentored another, later Nobel Prize recipient, Barbara McClintock, one of the 20th century’s central figures in corn genetic science.

In the 1960s and ’70s, Charles O. Gardner, the Husker scientist for whom Schnable’s professorship is named, was a leader in quantitative genetics and plant breeding. Gardner, a Regents Professor of Agronomy, served as president of the Crop Science Society of America and “developed new breeding methodologies and trained a whole generation of students,” Schnable said.

With the complete corn genome now sequenced, scientists will be able to proceed to important follow-up research to study and determine the function of individual genes that weren’t identified in previous corn genomic research. “Many of these genes are likely involved in corn’s ability to adapt to different environments and different stresses,” Schnable said.

The university “is well positioned to study this,” Schnable said, “because we have such a powerful research and Extension network and we’re able to grow corn varieties all across the state. One of my research groups here at the university is testing hundreds of corn hybrids across the 400-mile breadth of Nebraska and into Iowa.”

These Husker research initiatives, he said, “can help us build better models of how corn plants respond in different environments so we can develop those varieties that will thrive.”