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Rice so nice it was domesticated thrice

Rice is unique among wild plants for having been domesticated independently on three continents: Asia, Africa, and now South America, researchers have discovered. The New World variety, tamed about 4000 years ago, apparently was abandoned after Europeans arrived. But its genetic legacy could potentially help improve Oryza sativa, the Asian rice species that is now a dietary staple for half the world’s population.

Despite widespread consumption of wild rice by indigenous peoples, scant evidence supported the grain’s domestication in the New World. But botanists have become increasingly adept at analyzing phytoliths, microscopic bits of silica drawn from the soil that accumulate in the tissues of plants as they grow. Phytoliths persist after the vegetation decays and scientists can decipher, from their shapes, the genus and sometimes the species of plant in which they formed and whether they came from the stalk, leaves, or seeds.

A group led by archaeobotanist José Iriarte of the University of Exeter in the United Kingdom examined 320 rice phytoliths recovered from a trench at Monte Castelo, an archaeological site in the southwestern Amazon basin in Brazil that was occupied for millennia: from more than 9000 years ago into the 14th century. The phytoliths increased in size and number from the oldest layers of the dig to the youngest, indicating that “wild rice was modified by human intervention to produce larger grains,” the authors conclude in a paper published online this week in Nature Ecology & Evolution. It’s “another proof of the ingenuity of Native American plant breeders,” Iriarte says.

“The paper is convincing,” says Charles Clement, a plant geneticist at the National Institute of Amazonian Research in Manaus, Brazil, who was not involved in the study. Previous investigators missed rice domestication in the region, he says, because phytolith analysis “has only started to be used to search for signs of domestication (in Amazonia) in the last decade.” “Whether in Asia, Africa, or South America, local populations recognized the great potential of the Oryza plants and made use of them, which finally led to the advent of domesticated rice,” adds Zhao Zhijun, an archaeobotanist at the Chinese Academy of Social Sciences’s Institute of Archaeology in Beijing, who was not involved in the study.

Researchers collecting soil samples bearing rice phytoliths at the Monte Castelo archaeological site in Brazil.

Arqueotrop_University of São Paulo

The discovery “was a wonderful surprise,” Iriarte says. His team was looking for hints of cassava domestication and for clues to when maize farming spread to the Amazon. But in sifting the soil samples, Ph.D. student Lautaro Hilbert noticed the unusual abundance of rice phytoliths. Another remarkable aspect is that the Monte Castelo residents were farming maize and rice simultaneously, says Briana Gross, a plant evolutionary geneticist at the University of Minnesota in Duluth, who was not a member of the team.

Iriarte’s group suggests that New World rice cultivation was a response to increasing rainfall at Monte Castelo from 6000 to 4000 years ago that could have expanded wetlands and caused seasonal flooding. Such conditions would be unfavorable for other food resources but suited for the wild Oryza species, prompting farmers to manipulate and ultimately domesticate rice even while they grew maize and other crops, such as squash.

The authors suggest that the indigenous population decline and cultural disruption during European colonization was a death knell for domesticated rice in the Americas. Gross suggests that researchers can now look in wild rice populations for genetic traits that early Amazonian farmers bred for; if these persist, they might be exploited for improving modern cultivated varieties.