BioEd Online

Biologists have found a gene that enables rice to live longer underwater. The new breed can survive underwater for up to two weeks, researchers say most rice plants die within days of being submerged.

The discovery could pave the way for flood-resistant rice, helping millions of the world's poorest farmers who lose their crops each year to flooding.

"We have known for a long time that there are varieties of rice that have this tolerance and we have tried to breed strains, but we didn't understand the genetics," says plant-breeding expert David Mackill, a co-author on the work from the International Rice Research Institute (IRRI) in Manila, the Philippines.

Researchers knew the rough location of the flood-resistant genes on the plant's chromosomes, but not the exact gene. This meant that every time they tried to breed flood-resistant strains, unwanted DNA was passed on along with the key genes, potentially affecting the rice's taste, colour or appearance.

Tiny change, big difference

Kenong Xu from the University of California, Davis, and his team first pinned down the key stretch of DNA in a flood-resistant plant. Within this region, they then found a cluster of genes that produce ethylene, a plant hormone that responds to environmental stress.

One variant of one of these genes, called Sub1A-1, is found only in plants that can live underwater, the team reports in Nature¹. The variant differs by one DNA letter from its flood-sensitive version, Sub1A-2.

"We knew the position on the chromosome that was causing the effect. Ten years later we found that exact gene," says Mackill.

The single DNA change in Sub1A-1 replaces a proline amino acid with serine. This triggers activity of other genes that help the plant to respire without oxygen.

Marie-Noëlle Ndjiondjop, a molecular biologist at the Africa Rice Center in Cotonou, Benin, says the discovery is a step forward for African rice farmers. Knowing the function and identity of the gene that confers water tolerance means that varieties already adapted to African conditions could be made flood-tolerant.

Pass it on

Xu and his team have already bred Sub1A-1 into a common Indian rice variety, using traditional breeding techniques rather than genetic manipulation. The results so far show that the plants have retained quality and high yields, as well as picking up the ability to survive drowning, they say.

Over the past decade scientists have identified hundreds of useful genes in rice, helping to boost disease resistance, yield, drought tolerance, and other useful qualities (see ' Heavy rice stands tall').

Thanks in part to these advances, rice production has doubled over the past 40 years. But the demand for rice still exceeds production, making this type of work invaluable, researchers say.

The team is now trying to identify genes in other varieties of flood-tolerant plants, such as maize and soy bean, to improve other crops.

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