$5.5M NSF grant aims to improve rice crops with genome editing

A new project will harness the power of genome editing – a technique that allows researchers to precisely target, cut, remove and replace DNA in a living cell – to improve rice, a staple crop that feeds half the world’s people.

The project, led by Cornell researchers and funded by a four-year, $5.5 million National Science Foundation (NSF) grant as of May 1, will serve in part as proof of principle that genome editing can be used to address quantitative traits. These are traits, such as height or yield, that are expressed to varying degrees in different individuals. Very little is known about quantitative traits, as they require complex orchestration of many genes.

Scientists are also in a race against time to double the production of cereal crops on limited arable land by 2050, when the global population could reach 9.5 billion.

The editing technique will focus on such quantitative traits in rice as disease resistance and tolerance to acidic soils. Acidic soils hinder crop growth in 40 percent of the world’s arable land, according to Cornell researchers.

“We have the ability to open the genome like a book, go to a certain chapter and a specific word and change the word or correct its spelling,” said lead scientist Adam Bogdanove, where words are the DNA sequences that make up genes. Bogdanove, a professor of plant pathology and plant-microbe biology, is principal investigator of the NSF grant and a co-creator of TALENs, a key molecular tool used in genome editing.

The researchers already have identified particular stretches of DNA as candidates for the quantitative traits of interest, Bogdanove said.

While geneticists have made many advances in DNA sequencing, one grand challenge is defining the specific functions of each DNA sequence. Statistical analyses can determine whether particular stretches of DNA correlate with this or that trait, but the task remains to directly test whether a sequence in fact causes or contributes to a particular trait. That’s where genome editing comes in.

“We can test the hypothesis that these DNA sequences are important, and use them for crop improvement,” Bogdanove said. Traditional breeding is exceedingly difficult with quantitative traits that are linked to many genes. “Now, we don’t have to do years of breeding; we can just make the precise changes needed in a few short steps.”

For their work, the researchers will use a newly released dataset for 3,000 rice genomes, and they will test DNA sequences from this set and other rice genomes that are associated with beneficial traits. Rice geneticist Susan McCouch, a co-PI on the project, has been a key contributor to the rice genome dataset.

Along with developing a new system that employs genome editing for plant breeding, the researchers also hope to develop new lines of rice that breeders could use to address diseases and acid soils.

Additionally, the project team will develop related educational materials for middle and high school students and undergraduates, provide genome editing training workshops for plant biologists, and continually update a public project website, RiceDiversity.org.

The researchers are careful to note that genome editing should not be confused with genetic engineering; genome editing entails making precise changes, whereas genetic engineering is “akin to inserting a particular sentence somewhere at random into the book,” Bogdanove said.

Other co-PIs include Jan Leach, professor of bioagricultural sciences and pest management at Colorado State University; Erin Doyle, assistant professor of biology at Doane College; and Daniel Voytas, professor of genetics, cell biology and development at the University of Minnesota. Other Cornell team members include Jason Mezey, associate professor of biological statistics and computational biology, and Stefan Einarson, director of transnational learning.

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