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.
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.
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