Precise genome editing may improve rice crops,

Rice, a staple crop that feeds half the world’s people, may be improved by a new project that harnesses the power of genome editing.

$5.5 million NSF grant

The project, led by Cornell University researcher Adam Bogdanove and funded by a four-year, $5.5 million National Science Foundation grant, will serve as proof of principle that genome editing can be used to optimize quantitative traits, such as height, yield and disease resistance. Very little is known about quantitative traits expressed to varying degrees in different individual plants, as they require complex orchestration of many genes. Genome editing is a new technique that allows researchers to precisely target, cut, remove and replace DNA in a living cell.

Professor Jan Leach

Jan Leach, professor of Bioagricultural Sciences and Pest Management at Colorado State University, is one of the co-investigators working on the new study with principal investigator Bogdanove.

The editing technique will focus on such traits as disease resistance and tolerance to acidic soils. On average, 15 percent of rice yield is lost worldwide to rice diseases, according to Leach, who is also a University Distinguished Professor at CSU. Leach and her team will receive $930,000 for their contributions to the project.

In a race against time

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

“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, adding that in this case the words are the DNA sequences that make up genes. Bogdanove, a professor of plant pathology and plant-microbe biology, is also a co-creator of TALENs, a key molecular tool used in genome editing.

Disease resistance

The researchers already have identified particular stretches of DNA as responsible for the quantitative traits of interest. For example, CSU’s Leach, a plant pathologist, has identified several candidate sequences for disease resistance, and will use the genome editing process to test whether those sequences enable rice to survive diseases.

“What is so beautiful about genome editing is that we can relatively easily make very precise changes in the DNA sequences to test their importance and their usefulness for crop improvement,” said Leach. “Traditional breeding to select for quantitative traits is exceedingly difficult and slow. Genome editing would greatly expedite the process.”

3,000 rice genomes

For their work, the researchers will use a newly released dataset for 3,000 rice genomes. Brad Tonnessen, a CSU graduate student working on the project, will test this set and other rice genomes for sequences that are associated with beneficial disease resistance traits.

The researchers also hope to develop new lines of rice that breeders could use to address diseases and acid soils.

Educational outreach

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 at random into the book,” Bogdanove said.

Other co-investigators include 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 Susan McCouch, professor of plant breeding and genetics; Jason Mezey, associate professor of biological statistics and computational biology; and Stefan Einarson, director of transnational learning.