Hybrid rice engineered with CRISPR can clone its seeds

After more than 20 years of theorizing about it, scientists have tweaked a hybrid variety of rice so that some of the plants produce cloned seeds. No plant sex necessary. The feat, described December 12 in Nature, is encouraging for efforts to feed an increasingly crowded world.

Crossing two good varieties of grain can make one fabulous one, combining the best versions of genes to give crops desirable traits such as higher yields. But such hybrid grain marvels often don’t pass along those coveted genetic qualities to all seeds during reproduction. So farmers who want consistently higher yields have to pay for new hybrid seeds every year. This new lab version of hybrid rice would preserve those qualities through self-cloning, says study coauthor Venkatesan Sundaresan, a plant geneticist at the University of California, Davis.

Though 400 kinds of plants, including some blackberries and citruses, have developed self-cloning seeds naturally, re-creating those pathways in crop plants has “been harder than anyone expected,” Sundaresan says. He and his colleagues got the idea for the new research while studying “how a fertilized egg becomes a zygote, this magical cell that regenerates an entire organism,” as Sundaresan puts it.

The researchers discovered that modifying two sets of genes caused the japonica rice hybrid called Kitaake to clone its own seeds. First the team found that in a fertilized plant egg, only the male version of a gene called BABY BOOM1 found in sperm triggered the development of a seed embryo. So the scientists inserted a genetic starter switch, called a promoter, that let the female version of the same gene do the same job. No male would be necessary to trigger an embryo’s development.

But that tweak alone wasn’t enough to produce cloned hybrid seeds. That’s because a normal egg that had formed through meiosis — a type of cell division that produces eggs and sperm — would have only half a set of chromosomes.

A solution to the problem came from plant geneticist and study coauthor Raphael Mercier, based in Versailles with the French National Institute for Agricultural Research. His team had disabled three genes crucial for meiosis in rice, so mother plants then switched to reproducing asexually. Imtiyaz Khanday and Sundaresan updated the approach, using the CRISPR/Cas9 gene-editing tool to disable the genes.

Combining the two tweaks in Kitaake rice let a portion of the parents, so far about 30 percent at best, create viable clone seeds with their original hybrid genetics intact. Those seeds sprouted into plants that also could clone themselves, and so could the next generation. Now the challenge will be to make the process more efficient, Sundaresan says.

The research marks an important step toward cloning hybrid grains, says Anna Koltunow of the Commonwealth Scientific and Industrial Research Organization in Glen Osmond, Australia, who wasn’t involved in the study. “The study clearly shows one can re-engineer rice to switch it from a sexual to an asexual mode.”

Editor's note: This story was updated on December 12, 2018 to correct that Mercier's team used standard genetic tools, not CRISPR/Cas9, to disable the genes crucial for meiosis in rice. Khanday and Sundaresan then did so using CRISPR/Cas9.