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A farmer inspecting a crop of deep water rice.

Rice survives long-term floods due to newly discovered genetic mechanism

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Lindsey Hadlock

Deepwater rice elongates with rising flood waters, up to 10 inches (25 centimeters) per day, and can reach up to 23 feet (7 meters) tall to keep shoots above water. The chart shows a comparison in growth between normal rice (top) and deepwater rice (bottom) when submerged over a week.

A team of Cornell and Japanese researchers has discovered a new genetic mechanism that allows certain rice plants to survive monthslong floods. When the plant becomes submerged, a rare form of a gene triggers rapid growth to keep shoots above rising water.

In a study published July 13 in Science, the team identified a rare allele (a mutation) of the semi-dwarf 1 (SD1) gene that orchestrates adaptation to deep water. By identifying the allele, breeders may target it to develop new varieties adapted to long-term flood conditions.

“If the water only rises one foot, the plant only grows one foot; if the water rises 20 feet, it can grow to stay ahead of that water,” said Susan McCouch, Cornell professor of plant breeding and genetics and a senior author of the study. Takeshi Kuroha, a plant biologist at Tokohu University, Japan, is the paper’s first author along with Diane Wang Ph.D. ’17, a former graduate student in McCouch’s lab, who is currently a postdoctoral associate at the University at Buffalo. Motoyuki Ashikari, a rice geneticist at Nagoya University, Japan, is also a senior author.

Researchers and breeders have been interested in understanding how to breed plants that naturally sense their environment and respond dynamically to changes in that environment; deep water rice provides an excellent example of that. The allele allows rice plants to grow rapidly under deep water, but only when they are submerged. Otherwise, the plants grow normally.

Through genetic analysis, the team determined that the allele evolved first in a wild rice, Oryza rufipogon, in Bangladesh and was domesticated there by ancient farmers who wanted to grow rice through sustained deep-water floods. To this day, farmers in Bangladesh, Thailand, India, Vietnam and other places that experience long seasonal floods grow cultivated varieties of O. sativa that survive in deep water. Farmers may wade chest-deep or take boats to harvest the grains from the top of the water.

“As climate change triggers radical shifts in weather patterns, other forms of cryptic genetic variation found in wild gene pools may offer adaptive solutions to help breeders fine-tune modern rice varieties to withstand the challenges of future growing conditions,” said McCouch.

During the genetic analysis, McCouch and colleagues were initially surprised to find the rapid elongation trait mapped to a region of the chromosome that was associated with dwarfed plant stature. Decades ago, researchers identified a “loss-of-function” allele of the SD1 gene that reduces stem and leaf elongation during the plant’s vegetative stage but does not affect growth during the reproductive stage. As a result, the plant puts less energy into producing leaf and straw material, and more energy into producing grain, which enhances yield. The “loss-of-function” SD1 allele was exploited by breeders to enhance grain yield during the Green Revolution – a period in the 1960s and 1970s where research and technology increased agricultural production worldwide. The flood-tolerant SD1 allele is a “gain-of-function” allele which directs increased expression of gibberellin, a hormone that promotes stem elongation, and allows the plant to grow rapidly to survive deep water conditions.

For plants with this “gain-of-function” mutation, SD1 gene expression is triggered by a build-up of ethylene gas in the water that occurs when a plant is submerged. The plant chemically senses the ethylene gas which triggers a genetic response that activates the expression of the SD1 gene; the protein the gene expresses then causes a rapid increase in a unique form of the hormone gibberellin, GA4, which promotes rapid stem elongation and growth of the plant.

The “gain-of-function” allele at SD1 is referred to as the deep-water haplotype. The researchers traced this haplotype to wild populations of O. rufipogon in Bangladesh, where it first evolved.

The study was funded by the Japan Science and Technology Agency, the Canon Foundation, the National Science Foundation and the U.S. Department of Agriculture.

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Krishna Ramanujan