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Rice: 10,000 varieties from 1 source

NYU/WASHINGTON U.-ST. LOUIS (US) — A study of the genome of domesticated rice shows the crop had its beginnings from a single origin about 9,000 years ago in the Yangtze Valley of China.

Asian rice, Oryza sativa, one of world’s oldest crop species, is also highly diverse, with tens of thousands of varieties known throughout the world. Two major subspecies of rice—japonica and indica—represent most of the world’s varieties.

Because rice is so diverse, its origins have been the subject of scientific debate. One theory—a single-origin model—suggests that indica and japonica were domesticated once from the wild rice O. rufipogon. Another—a multiple-origin model—proposes that these two major rice types were domesticated separately and in different parts of Asia.

The multiple-origin model has gained currency in recent years as biologists have observed significant genetic differences between indica and japonica, and several studies examining the evolutionary relationships among rice varieties supported more than domestication in both India and China.

A re-assessment of the evolutionary history of domesticated rice, published in the Proceedings of the National Academy of Sciences, concludes that because they have a closer genetic relationship to each other than to any wild rice species found in either India or China, the two species have the same origin.

“As rice was brought in from China to India by traders and migrant farmers, it likely hybridized extensively with local wild rice,” explains Michael Purugganan, professor of genomics and biology at New York University and one of the study’s co-authors. “So domesticated rice that we may have once thought originated in India actually has its beginnings in China.”

Researchers also examined the phylogeny of domesticated rice by re-sequencing 630 gene fragments on selected chromosomes from a diverse set of wild and domesticated rice varieties. Using new modeling techniques, which had previously been used to look at genomic data in human evolution, those results also show that the gene sequence data is more consistent with a single origin of rice.

Using a molecular clock to see when rice evolved, the researchers pinpointed the origin of rice at possibly 8,200 years ago, while japonica and indica split apart from each other about 3,900 years ago, dates consistent with archaeological studies.

Archaeologists have uncovered evidence in the last decade for rice domestication in the Yangtze Valley beginning approximately 8,000 to 9,000 years ago while domestication of rice in the India’s Ganges region was around about 4,000 years ago.

“This study is a good example of the new insights that can be gained from combining genomics, informatics, and modeling,” says Barbara Schaal, professor of biology at Washington University in St. Louis, who is also a co-author.
“Rice has a complicated evolutionary history with humans and has accompanied them as they moved throughout Asia. This work begins to reveal the genetic consequences of that movement.”

Researchers from Stanford University and Purdue University contributed to the study, funded by the National Science Foundation Plant Genome Research Program.

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