Precise genome editing may improve rice crops

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. Funded by a four-year, $5.5 million National Science Foundation (NSF) grant, the project will serve, in part, as proof of principle that genome editing can be used to address quantitative 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.

University of Minnesota researcher Daniel Voytas co-created the TALENs, a key molecular tool used in genome editing, with Adam Bogdanove, professor of plant pathology and plant-microbe biology at Cornell University and principal investigator of the NSF grant. “The TALENs allows us to break and edit chromosomes at specific locations,” said Voytas, a co-author of the study who optimized the tool for use in the rice genome. 

“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 Bogdanove, where words are the DNA sequences that make up genes.

The researchers have already identified particular stretches of DNA as candidates for the quantitative traits of interest. "We now want to use the TALENs to identify genetic variation that is important for tolerance to acidic soils, disease and other stresses,” said Voytas.

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 acidic 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,

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 randomly into the book,” Bogdanove said.

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