Genome 'dark matter' discovery a boon for corn breeders

Small portion of corn's chromatin holds vast amount of information accounting for traits such as plant size, shape, yield and stress response.

For astronomers, “dark matter” is the largely hypothetical substance that accounts for approximately 85% of the matter in the universe. Now, plant scientists have discovered a different kind of “dark matter” in the maize/corn genome: a tiny percentage of regulatory DNA that accounts for roughly half of the variation in observable traits found in corn.

In a landmark finding, Cornell University and Florida State University (FSU) researchers reported that they have identified 1-2% of the maize genome that turns genes on and off, so they may now focus their attention on these areas for more efficient plant breeding. Using a genetic mapping technique developed at FSU, the researchers have shown that this small percentage of the entire maize genome is responsible for almost half of a plant’s trait diversity.

Hank Bass, FSU associate professor of biological science, and Daniel Vera, director of the FSU Center for Genomics & Personalized Medicine, combined their expertise in maize genome mapping with the statistical genomics expertise of Cornell colleagues Eli Rodgers-Melnick and Ed Buckler.

Together, they found that a small portion of chromatin — the complex of DNA and its associated proteins — accounts for 40% of heritable trait diversity in maize. That means a small portion of the chromatin holds a vast amount of information that accounts for traits such as plant size, shape, yield and stress response.

“What blew me away about this work is how informative this chromatin profiling technique is at mapping the functionally important part of the maize genome,” Bass said.

The research was published in the May 16 issue of Proceedings of the National Academy of Sciences.

Identifying this part of the genome greatly narrows the area examined for maize breeding and genomic editing, which may greatly accelerate the pace for crop improvement. This means growers might be able to more quickly target areas of the genome that could help them develop crops that are more drought resistant or durable in adverse environments.

“It allows us to start pinpointing the single base pair changes (small mutations) that are regulating or allowing plants to adapt to their environment,” Buckler said. “It helps us narrow down the hunt dramatically.”

Maize is considered a model species for scientific research because it has exceptional genetic diversity and resources, underwriting decades of breakthrough research in mechanisms of heredity.

This new study helps explain how an organism can express different genes in different cell types despite the fact that the DNA must be compacted to nearly 1 millionth its length to fit inside the cell nucleus. Even when compacted, areas still exist — called open chromatin — that coordinate complex patterns of gene regulation. The researchers wanted to better understand what was happening in this space of open chromatin.

The study represents the first application of the chromatin profiling technique Vera and Bass developed as part of a National Science Foundation-funded project at FSU.

For this, Cornell sent 600 kernels to FSU. Bass and Vera grew the kernels into seedlings, collected tissue from the roots, stems and leaves and then isolated the cell nuclei. The nuclei were exposed to an enzyme that cuts specific portions of the DNA, and the data were computationally and statistically analyzed to identify the open chromatin in the genome.

“It’s like finding a light switch on the wall,” Bass said. “The chromatin profiling shows you which parts of the genome are genetic switches.”

The findings may open doors for discovering regulatory regions in other crops as well.

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