The 1960s marked a turning point for agriculture in Asia: that's when plant breeders launched a "green revolution" in rice production, selecting variants of a single gene that boosted yields across the continent. A new study finds that prehistoric farmers were revolutionaries, too. They apparently harnessed that same gene when they first domesticated rice as early as 10,000 years ago.
The history of rice farming is very complex, but the basic facts are well established. All of today's domesticated rice belongs to the species Oryza sativa, which descends from the wild ancestor Oryza rufipogon. O. sativa has two major subspecies, japonica (short-grain rice grown mostly in Japan) and indica (long-grain rice grown mostly in India, Southeast Asia, and southern China).
During the 1960s, plant breeders working in Asia greatly increased rice yields by selecting for mutations in a gene called semi-dwarf1 (SD1), which shrinks the length of the plant's stem. Dwarf plants require less energy and nutrients, raising the number of rice grains that can be harvested, and they are also less vulnerable to being knocked over by storms, which can decimate rice fields.
To see what role SD1 might have played during the early domestication of rice , a team led by plant geneticist Makoto Matsuoka of Nagoya University in Japan examined the evolutionary history of mutations in this gene that could be associated with shorter stem length. The enzyme produced by SD1 is known to control a biochemical pathway that promotes growth in the stems and leaves of the rice plant, so the team measured the effects of different SD1 mutations by introducing genes with those mutations into bacteria and seeing how much enzyme was produced.
Matsuoka and his colleagues identified an ancient mutation called SD1-EQ that was closely associated with shorter stem length. And while this mutation was found in japonica and to a lesser extent in indica varieties, it did not appear in the wild ancestor O. rufipogon. This suggested that SD1-EQ might have been selected for during the domestication of rice.
For further evidence, the team looked at the variability of genes that lie adjacent to SD1 in the genome, in 16 varieties of japonica, 15 varieties of indica, and 16 varieties of O. rufipogon. Usually, when genes have been favored by selection, neighboring genes show much less variation among different individuals . The team found that genetic diversity around the SD1 gene in japonica was only 2% of that in O. rufipogon—suggesting that a variant of SD1 in fact had been selected in ancient times. The SD1 region in indica, however, still had 75% of the diversity of the wild ancestor.
In its report online this week in the Proceedings of the National Academy of Sciences, Matsuoka and his colleagues conclude that the stem-shortening mutation SD1-EQ arose during prehistoric times  in japonica, when the plant was first being domesticated. They suggest that japonica and indica each evolved from O. rufipogon long before rice domestication began and then were independently domesticated in different regions. Later, the SD1-EQ mutation found its way into indica plants, perhaps through crossbreeding of the two subspecies.
The findings fit well with the archaeological record of early rice production, particularly in northern China, says archaeobotanist Dorian Fuller of University College London. Wild rice, Fuller points out, is a plant that prefers large bodies of standing water. "It produces extremely tall, long [stems] in order to grow in deeper water." But the earliest rice farmers cultivated the plants at the margins of wetlands, where the water was not as deep. In doing so, they might have unconsciously selected for shorter plants, Fuller says.
Early farmers might have also consciously cultivated shorter plants, given their greater yield and ability to survive storms, adds Susan McCouch, a plant geneticist at Cornell University. This deliberate selection of dwarf plants, McCouch says, in effect led to genetic selection for the SD1-EQ gene by farmers who had no knowledge of modern genetics.