Rice—one of the world’s most important crops—was domesticated more than once, according to a new study. The work could lead to a better understanding of how civilizations arose throughout Asia and whether they developed independently, or whether agricultural and cultural advances in one region were copied in others. It could also guide programs to improve the grain crop that more than half of the world’s population depends on.

There are four main varieties of rice: japonica, a short-grained rice grown in Japan, Korea, and eastern China; indica, a long-grained variety common in India, Pakistan, and most of Southeast Asia; aus, grown primarily in Bangladesh; and aromatic rice, which includes more exotic varieties such as India's basmati and Thailand's jasmine.

Scientists have primarily focused on indica and japonica because archaeological findings suggest both have a long history of cultivation. Researchers generally agree that humans living in what is now southern China domesticated japonica between 8200 and 13,500 years ago. The precise locale within southern China is still debated. But the spread of agriculture resulted in a more stable food supply that allowed hunter-gatherers to settle in villages with increasing populations and the more complex societies and cultures that led to the rise of Eastern civilizations.

Those claiming one domestication event believe indica emerged from crosses between japonica and wild species as rice cultivation spread through Asia. This hypothesis is strongly supported by Bin Han, a geneticist at the Chinese Academy of Sciences' Institute of Plant Physiology and Ecology in Shanghai, and colleagues in an October 2012 paper in Nature. In this scenario, aus and aromatic varieties emerged from later crosses.

Those arguing for two separate domestication events generally agree that japonica emerged in southern China, but they contend that indica was independently domesticated in a region straddling India and western Indochina.

The new analysis, from a group led by Terence Brown of the University of Manchester in the United Kingdom, adds a third and separate domestication locale, for aus, in a region stretching from central India to Bangladesh.

Interestingly, both the Han and Brown teams rely on the same genetic data: sequences from 446 samples of wild rice and over 1000 cultivated varieties. But just as two detectives examining a crime scene might think the clues point to different culprits, the two teams reach differing conclusions. Both analyses center on what are called domestication sweeps, regions of the genomes of cultivated rice varieties that differ from wild populations and that researchers believe were selected for by early farmers seeking to enhance desirable plant traits. These include regions that allow plants to grow vertically and thus more densely, as opposed to spreading over the ground, and to keep ripe grain on the stalk, instead of shedding it as most wild varieties do, a characteristic called shattering.

Han and his colleagues contend that that the domestication sweeps found in all cultivated Asian rice varieties are very similar and can be traced back to a single group of wild ancestors in southern China. But the Brown team says the genetic evidence indicates that the genes that proved advantageous for farming were present in many wild rice varieties widely distributed across the southern Asian continent. Early farmers in three separate geographic locations were all striving to select rice plants showing the same desirable traits. And that resulted in similar domestication sweeps appearing in three different varieties of cultivated rice. "Rice domestication was a multiregional process separately producing the indica, japonica, and aus types of rice," the group writes online today in Nature Plants.

The methods are "rigorous and well substantiated," says Susan McCouch, a rice geneticist at Cornell University. Brown and his colleagues "clearly demonstrate that the most parsimonious and coherent interpretation for the data is that there were at least three independent domestications of [rice] from well differentiated ancestral populations in Asia," she says.

Han is sticking to his conclusions. The new paper is "definitely wrong with the data analysis," he wrote in an email. He says his team will publish a detailed rebuttal shortly.

There are some sticky questions. Briana Gross, a plant geneticist at the University of Minnesota, Duluth, says there is convincing evidence that at least one of the major domestication sweeps—causing white grains—arose in japonica, and spread to other variety groups. If the three varieties were domesticated separately, she asks how did this trait get into all three?

Even McCouch acknowledges this latest finding is unlikely to be the last word. "I look forward to the many discussions this paper is likely to provide.”