The domestication of maize is one of the greatest examples of humankind’s impact on evolution. Early farmers’ pre-industrial plant breeding choices turned corn from a nearly inedible crop into the major global food source it is today.
Now, Cold Spring Harbor Laboratory Professors Rob Martienssen and Thomas Gingeras are uncovering the genetics behind choices farmers made 9,000 years ago. They aim to better understand how evolution works and to help today’s farmers update corn so it can grow in harsh conditions. To get there, they’ve launched a new genomic encyclopedia called MaizeCODE. The research project is based on the Encyclopedia of DNA Elements (ENCODE). ENCODE aimed to identify functional elements in the human genome. Gingeras was one of its principal investigators. He explains:
“The original purpose—and it’s copied in the MaizeCODE effort—is to find all the domains of the genome that encode operational and coding information that the cell uses to reproduce and carry out the functions the cell serves.”
In a new study, the Gingeras and Martienssen labs analyzed regulatory sequences across five different tissue types from three strains of maize and its ancestor teosinte. They found hundreds of thousands of regulatory regions, called enhancers, that help turn genes on and off in plants.
CSHL Professor & HHMI Investigator Rob Martienssen tells corn’s curious origin story.
They also saw that maize has a few thousand “super enhancers.” Each controls several genes at once. Incredibly, these super enhancers were very strongly selected when maize was domesticated 9,000 years ago. Martienssen explains:
“We can now say that maize domestication was really focused—unwittingly perhaps —by selection on this rather narrow set of super enhancers in maize ears.”
In addition to expanding our understanding of evolution, these findings could help point the way to new strains of maize. Martienssen and Gingeras have received a grant from the National Science Foundation to work on creating crops that can grow in soil with high levels of aluminum. Such conditions are common in South America. The scientists will use MaizeCODE “to find all the regulatory regions that are responsible for endowing both maize and sorghum with aluminum resistance,” Martienssen says.
But that’s not MaizeCODE’s only use. The genome database may one day help farmers further improve their maize crops. Imagine plants that are more resistant to disease or tolerant to droughts. Better still, imagine crops with higher yields that can feed more people. MaizeCODE may help make all of this possible. And because the data is publicly available, it can be accessed by plant biologists and breeders across the globe. “We’re only touching the tip of the iceberg,” Martienssen says.
Written by: Jen A. Miller | publicaffairs@cshl.edu | 516-367-8455
Funding
National Science Foundation, National Institutes of Health, Howard Hughes Medical Institute
Citation
Cahn, J., et al., “MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication”, Nature Communications, December 30, 2025. DOI: 10.1038/s41467-024-55195-w
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