MaizeCODE is a genomic project analyzing the genetic basis of maize domestication. Researchers identified key regulatory elements, including super enhancers, which were crucial in maize’s transformation.
The domestication of maize is one of the most remarkable examples of humankind’s impact on evolution. Early farmers’ pre-industrial plant breeding choices transformed 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 the choices farmers made 9,000 years ago. Their goal is to better understand how evolution works and to help modern farmers adapt corn to grow in harsh conditions. To achieve this, they have 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.”
Discovering the Genetic Blueprint of Maize
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.
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.
Reference: “MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication” by Jonathan Cahn, Michael Regulski, Jason Lynn, Evan Ernst, Cristiane de Santis Alves, Srividya Ramakrishnan, Kapeel Chougule, Sharon Wei, Zhenyuan Lu, Xiaosa Xu, Umamaheswari Ramu, Jorg Drenkow, Melissa Kramer, Arun Seetharam, Matthew B. Hufford, W. Richard McCombie, Doreen Ware, David Jackson, Michael C. Schatz, Thomas R. Gingeras and Robert A. Martienssen, 30 December 2024, Nature Communications.
DOI: 10.1038/s41467-024-55195-w
Funding: NIH/National Institutes of Health, U.S. National Science Foundation, Howard Hughes Medical Institute
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