Scientists find key ingredients in genetic recipe for hardier rice

As rice genes go, SNORKEL1 and 2, and SUBMERGENCE1a, b, and c have more evocative names than most. Not so much with pi21.

Taken together, however, some of these genes hold the promise of helping rice farmers in developing countries -- who feed more than 2 billion people -- keep the harvests coming under increasing pressure from rising populations and extreme climate events expected from global warming.

This week, two groups of Japanese scientists are reporting progress on two important fronts: boosting disease resistance in rice; and giving rice the ability to withstand prolonged, deep-water flooding. In the case of flooding, they do this not by temporarily shutting down rice growth, as other researchers have, but by triggering a growth spurt when the rice finds itself in over its head.

The good news is that these look like they can be bred into current strains without resorting to the kind of high-tech genetic engineering that sets so many people's teeth on edge, explains Susan McCouch, a Cornell University plant geneticist who specializes in rice research.

"There's been a lot of hype around moving genes around from once species to another with genetic engineering" to develop more stress-resistant crops, Dr. McCouch said during a phone chat.  "But both of these studies are based on the utilization of natural variations" enhanced through traditional crossing-breeding.

This sidesteps the need for regulations imposed on growers who want to use crops that get their hardiness from genes introduced from other plant species, she adds.

Who cares? More than 2 billion people, who rely on rice as a staple. And the developing-country farmers that have to grow the grain under increasingly marginal conditions.

One team of Japanese scientists report in tomorrow's issue of the journal Science that they've isolated a naturally occurring, but odd form of a rice gene dubbed pi21. Pi21 is present in all rice varieties. But this version -- which, ironically, is missing some pieces compared with the "normal" gene --  increases the plant's ability to win out over rice-blast infections. Rice blast is one of the most prevalent diseases rice faces worldwide.

And the team identified the gene's location on the rice plant's chromosome. This solves a decades-old puzzle that allows the mutant gene to be bred into many rice varieties without sacrificing flavor -- a goal that has been elusive in the past.

Rice defense strategies

Most approaches to conferring disease resistance in rice involve coaxing an existing gene into overdrive to generate the compounds that will knock the fungus flat as soon as it tries to infect the plant, say the researchers, led by Shuichi Fukuoka, with the QTL Genomics Research Center in Japan's Tsukuba City.

Two problems make this a less-than-ideal approach, they argue.  The rice blast fungus evolves resistance to the plant's intense burst of fungus-fighting agents. And each variety of rice has its own unique variation on the genetic blueprint for the agents, making it difficult to come up with a more-universal weapon.

Breeders had noticed that some varieties of rice have defense mechanisms that allow the fungus to gain a foothold. But then the rice plant builds its counterattack over time. The Japanese team identified the oddities in the mutant pi21 gene that made this possible.

Breeders had noticed this slo-mo defense. So they tried to breed the trait in different rice varieties. But the rice ended up with other traits that breeders -- and customers --  didn't like, such as bad-tasting rice.

By identifying a gene near Pi21 associated with the yuck factor, the team has made it easier to use precision breeding techniques to get disease-resistance without triggering upturned noses.

We like water, but not that much water

A second group has tackled another problem -- ensuring rice can survive prolonged flooding.  Rice germinates in flooded fields. But not all rice can endure prolonged flooding.

Three years ago, scientists reported that by throwing a naturally occurring rice gene into overdrive, they could induce a rice plant to in effect suspend its growth for far longer than usual. The gene in question was one of three variations of the plant' native "submergence" gene. The variety in question typically could endure up to a couple of weeks under water, but not much longer.

Once the new rice variety resumed its normal growth, the rice yields and quality matched those of rice unaffected by excessive flooding.

This time around, a team of Japanese scientists identified genes from so-called deep-water varieties that allow them to survive prolonged inundation.  Then they bred these with non-deep-water varieties in ways that passed along the water wings. Their results appear in this week's issue of the journal Nature.

The genes involved in this work (cleverly named SNORKEL1 and SNORKEL2) in effect accelerate growth when the rice plant becomes inundated, allowing it to rise above the surface of the water. Plants could survive this way in up to 4 meters (a shade more than 13 feet) of water.

The yin and yang of rice survival

These discoveries represent a kind of yin and yang for conferring greater stress tolerance to rice as climate changes, McCouch suggests.

With global warming come projections of increases in severe weather, including an increased frequency of drought, and more frequent flooding -- either in brief, flash-flood form, or as larger floods, depending on location ans season.

The ability to ward off rice blast is important when rice is stressed by drought and high temperatures. And you've gotta love SUBMERGENCE and SNORKEL when the water runs high for a long period of time.