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Deep-water rice can outgrow floods, as here, in Vietnam.

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New genes control plant height, could lead to flood-proof crops

Stature matters to plants. Short crops can carry more grain without bending under their own weight—a key trait that helped power the Green Revolution in the 1960s. But tall plants are better at surviving long floods. Now, researchers have found two genes that together help control the height of rice plants: one that accelerates the elongation of the stem and another that acts as a brake. If the system is similar in other plants, scientists say it could be useful in the breeding of many kinds of crops.

“This could be one more great tool in the toolbox,” says Julia Bailey-Serres, a rice biologist at the University of California, Riverside, who was not involved in the new research.

In the mid–20th century, plant breeders typically selected for wheat and rice varieties with short stems; these plants devoted more resources to grain and were less likely to fall over in heavy wind or rain. Biologists later discovered that these varieties, at certain times in their development, produce less of a hormone called gibberellic acid (GA) or can’t respond to its signals to elongate their stems. Side effects of those mutations can include young plants that sometimes emerge from the ground too soon in drought-prone regions.

Plant molecular geneticist Motoyuki Ashikari of Nagoya University and colleagues have been studying rice varieties that survive long, deep floods by growing taller—and quickly, if need be, up to 25 centimeters per day. So-called “deep-water rice” is grown in delta areas, mainly in Southeast Asia where slow seasonal floods can reach 1 meter or deeper. Previous work had shown that when plants are submerged, ethylene gas accumulates in their tissues and triggers GA production. Ashikari and his colleagues wanted to know how GA coaxes stems to grow in deep-water varieties of rice.

The team compared the DNA of one species of deep-water rice with another rice variety that can only grow in shallow water. They soon located the two genes, which they dubbed ACE1 (accelerator of internode elongation) and DEC1 (decelerator of internode elongation). Greenhouse experiments showed what the genes did: In deep-water rice, ACE1 turns on when plants are covered in water, stimulating cell division in their stems and helping them grow, the researchers report this week in Nature. But a typical shallow-water variety, which has a mutation in ACE1, did not lengthen its stem when flooded.

In other experiments, the team showed that DEC1 suppresses stem growth. DEC1 was active in the shallow-water variety, and it stayed active when those plants were flooded, essentially keeping the brakes on stem growth. In contrast, when deep-water rice was exposed to flooding, the brakes were lifted: DEC1 stopped expressing, further allowing for stem growth.

If plant breeders or molecular biologists can control those two genes, they might be able to adjust plant height without having to modify GA levels—perhaps even in crops other than rice—says Laura Dixon, a plant biologist at the University of Leeds. That means GA would continue to influence other parts of the plant normally. The two new genes could act like a simple “dimmer switch” for plant height, says Susan McCouch, a rice biologist at Cornell University, who was also not involved in the research.

The two genes also exist in sugarcane, barley, and the well-studied grass Brachypodium distachyon. They might occur widely in other agriculturally important grasses, Ashikari believes. Another important crop, corn, has an equivalent to ACE1, but it has a gene that only partially resembles DEC1. Still, the range of species with the two genes makes the new discovery “supersignificant,” McCouch says.

The genes might help rice breeders improve low-yield varieties that can already cope with seasonal flooding—or engineer new ones from productive shorter varieties. If this approach works in other plants, it could even help engineer flood-proof crops for areas experiencing more frequent flooding because of climate change, including the U.S. Midwest, Bailey-Serras says. Such efforts would depend entirely on whether the genes in the target crops are responsive, but, “It would make a heck of a lot of difference to the farmer.”