Each year an estimated 15 million hectares of rice lands (a region half the size of Italy) in South and Southeast Asia are inundated by flash floods. In Bangladesh, during the monsoon, roads are so wet that they become waterways for homemade sailboats rigged with cloth, jute, and bamboo. Such lands are home to an estimated 140 million people of whom 70 million are living on less than $1 a day, the highest concentration of poor people in the world.

Here, losses of rice production can be over $1 billion per year. This number, however does not capture the human suffering caused by the catastrophic crop losses where people get about two-thirds of their total calories from rice.

Although rice is the only cereal that can withstand some flooding, most rice varieties will die if submerged for too long. There are a few rare exception and these are of great interest to rice breeders. One of these is the traditional Indian rice variety, FR13A.

This rice plant has an unusual and agronomically important trait- the seedlings are able to withstand fourteen days of submergence. It is, however, low yielding and no longer widely grown. FR13A originated in the state of Orissa, in eastern India, bordered on the east by the Bay of Bengal. Hindu temples dating to the thirteenth century are scattered through the area. Today most of the people there still speak the ancient dialect of Oriya, and the majority are still rice farmers. For over fifty years, breeders tried to use FR13A as a parent plant to introduce the submergence tolerance trait into high yielding, tastier varieties favored by rice farmers in other parts of Asia.

Frustratingly, the resulting new varieties were of poor quality. The main reason for this breeding failure was that, because they were not really sure which genes were needed or where in the genome they were located, the breeders accidentally introduced other genes that reduced the overall quality of the rice.

In 1996, Dave Mackill, a scientist at the International Rice Research Institute who had been studying this problem for 10 years, asked if I would use my expertise in rice genetics to help him identify the submergence tolerance gene from FR13A. Within a couple of years after joining my lab, the husband and wife team of Kenong and Xia Xu were able to locate the submergence tolerance trait to a very small region of one of the rice chromosomes. Computer programs allowed us to predict the function of the genes in this region, one of them, an ethylene responsive transcription factors, was of particular interest. Based on what we knew about this gene, we hypothesized that it might act as a master switch to regulate complex functions of the plant. It was as if Kenong and Xia had been able to unravel a ball, woven from 42,000 silken threads all of a slightly different hue, and to pull out one thread, interlaced but distinct from the others.

Unlike weavers, geneticists cannot determine if the thread they hold is the one they want simply by looking at it; instead they need to test it by weaving it into another pattern—in this case another rice plant that normally cannot survive floods. So that is what we did. We genetically engineered (GE) this single thread, carrying the submergence tolerance trait, into a rice variety that normally would die in a flood. We wanted to know if incorporation of this one gene would allow the plant to survive.

To test this hypothesis, we transplanted the young GE seedlings and then submerged them for over two weeks. After 10 days, we could see that only a few of the control rice plants lacking the gene survived the flood and these were weak, spindly and very pale. The flaccid appearance is typical of plants that have drowned, lacking the air and sunlight needed to function. It was unlikely that this group of plants would survive much
longer.

We then looked at the row of GE plants that carried the genetic information from the submergence tolerant Indian variety. If we had identified and introduced the correct gene, the plants would have survived the extended time underwater and recovered. I hurried over and gently touched the bright green leaves of the first plant. My eyes quickly traveled down the row. They were alive. It was as though the rice plants had been able to hold their breath until the water was gone.

Our work represents the latest genetic change in the rice plant, which was first cultivated along the Yangtze River 6000 years ago. Since that time, hundreds of thousands of rice
varieties have been developed. It is likely that FR13A was selected by Orissan farmers because it could survive the floods particular to that area. It was then handed down from one generation to the next,prized then, as now, for its submergence tolerance. Our latest work tells us that the submergence tolerance trait is found not only in the Orissan variety, but also in two traditional varieties from Sri Lanka. It appears that ancestors of the Sinhalese, who originated from Orissa and migrated to the island twenty-five hundred years ago, transported these precious rice grains over thousands of kilometers.

Perhaps as geneticists, we are acting as humans have always done: learning the secrets of the sacred and ancient and passing that knowledge to others, who will then use that information in a new and unexpected way.

The submergence tolerance gene has now returned to southern Asia in another new form. With the use of marker-assisted breeding (a kind of hybrid between conventional breeding and genetic engineering) Dave and coworkers have introduced this gene into rice varieties that are adapted to habitats in South and Southeast Asia. These genetically modified plants can withstand fourteen days of submergence, and they yield and taste the same as their parent variety that is popular with local growers.

Last fall Dave assessed the productivity of these varieties on farm trials in Bangladesh. The weather in Asia last year was ferocious. Monsoon rains inundated countries from the Philippines to Nepal. Super typhoons slammed into China and Japan. All of this was bad for rice. And what’s bad for rice is especially bad for Bangladesh.

Jon Hamilton, a National Public Radio correspondent interviewed farmers who had planted sub1 rice. This is his report

“Gobindra Chandra Rai is a farmer whose field had been under water just a few weeks earlier. He says that when the floods came, the whole area was submerged up to about waist high.

The government gave farmers in Gobindra’s village seedlings with the flood-resistance gene, but most hadn’t planted them in time. When the monsoon floods came early, Gobindra was the only one that had. So he and his neighbors watched Gobindra’s field anxiously.

The field was under water for eight days. Gobindra says that usually after eight days, the crop would be damaged. But the sub-1 rice is still thriving. He tends to it carefully. If a stalk is leaning, he straightens it. If a leaf is muddy, he squeezes it clean between two wet fingers.

Gobindra says his neighbors are amazed by what they’ve seen in his paddy. Standing in a semi-circle in front of a shed made of bamboo and corrugated sheet metal, they line up to talk about Gobindra’s rice. Men stand up front. Women farther back. And little boys climb on anything tall enough to give them a better look.

Many of the farmers can’t read or write. But when it comes to rice science, they’re at the cutting edge. And every single one in Gobindra’s village now plans on planting the sub-1 variety.”