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Corn 'dark matter' discovery to speed plant breedingCorn 'dark matter' discovery to speed plant breeding

Cornell and Florida State university researchers discover dark matter 'switches' to turn on and off corn traits and narrow down trait hunts.

John Vogel

May 18, 2016

2 Min Read

While digging through maize (corn) genes, geneticists at Cornell University and Florida State University uncovered what they call “dark matter” – 1% to 2% of the genome that turns genes on and off. These “switches” account for roughly half of observable corn traits and can substantially accelerate corn trait breeding.

The landmark finding “allows us to start pinpointing the single base pair changes small mutations that regulate or allow plants to adapt to their environment,” says Edward Buckler, USDA research geneticist at Cornell University. “It helps us narrow down the hunt dramatically.”


Most DNA is tightly coiled up to fit inside cell nuclei. But if you stretched DNA strands found in one corn cell all the way out, it would measure 2 meters [more than 6.5 feet]. But there are also cell DNA regions not tightly wrapped, known as open chromatin. That’s where the dark matter – 1% of the genome most important for turning genes on and off – was discovered.

Human gene-mapping assays pioneered the technology for many uses, including crops. This new assay is so efficient in pinpointing important DNA regions that the team expects it could be a transformative technique applicable to hundreds of crops. “It’s like finding a light switch on the wall,” adds Hank Bass, biologist at Florida State University and co-author if the study. “The chromatin profiling shows which parts of the genome are genetic switches.”

The research paper’s lead author was Eli Rodgers-Melnick, former postdoctoral researcher in Buckler’s lab, now with Dupont/Pioneer. The team used 15 years of corn data from Buckler’s lab to link phenotype traits such as yield, drought and stress tolerance or starch content with the mapped NA found in open chromatin.

With the new information, plant breeders will be able to use genetic markers linked to these key genomic areas and new genomic editing techniques to accelerate corn breeding to meet demands of growing populations and climate changes, say the researchers. The findings may open doors for discovering regulatory regions in other crops. The study was funded by the National Science Foundation and USDA.

About the Author(s)

John Vogel

Editor, American Agriculturist

For more than 38 years, John Vogel has been a Farm Progress editor writing for farmers from the Dakota prairies to the Eastern shores. Since 1985, he's been the editor of American Agriculturist – successor of three other Northeast magazines.

Raised on a grain and beef farm, he double-majored in Animal Science and Ag Journalism at Iowa State. His passion for helping farmers and farm management skills led to his family farm's first 209-bushel corn yield average in 1989.

John's personal and professional missions are an integral part of American Agriculturist's mission: To anticipate and explore tomorrow's farming needs and encourage positive change to keep family, profit and pride in farming.

John co-founded Pennsylvania Farm Link, a non-profit dedicated to helping young farmers start farming. It was responsible for creating three innovative state-supported low-interest loan programs and two "Farms for the Future" conferences.

His publications have received countless awards, including the 2000 Folio "Gold Award" for editorial excellence, the 2001 and 2008 National Association of Ag Journalists' Mackiewicz Award, several American Agricultural Editors' "Oscars" plus many ag media awards from the New York State Agricultural Society.

Vogel is a three-time winner of the Northeast Farm Communicators' Farm Communicator of the Year award. He's a National 4-H Foundation Distinguished Alumni and an honorary member of Alpha Zeta, and board member of Christian Farmers Outreach.

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