June 2011, Week 4


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Fri, 24 Jun 2011 23:20:19 -0400
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Ancient Farmers Started the First 'Green Revolution'

by Michael Balter
June 7, 2011

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

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

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

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.


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