By Krishna Ramanujan
Some 10,000 years ago white rice evolved from wild red rice and began
spreading around the globe. But how did this happen?
Researchers at Cornell and elsewhere have determined that 97.9 percent
of all white rice is derived from a mutation (a deletion of DNA) in a single
gene originating in the Japonica subspecies of rice. Their report, published
online in the journal PloS (Public Library of Science) Genetics, suggests
that early farmers favored, bred and spread white rice around the world.

The researchers report that this predominant mutation is also found in
the Indica subspecies of white rice. They have found a second independent
mutation (a single DNA substitution) in the same gene in several Aus
varieties of rice in Bangladesh, accounting for the remaining 2.1 percent of
white rice varieties. Neither of these two mutations is found in any wild
red rice species.

Both mutations produce shortened versions of the same protein in which
the missing part is responsible for activating the molecular pathway leading
to grain color in rice.

"We think that other domains of this protein are critical for other
functions in the plant, because we never see the protein entirely deleted,
just the part of the molecule that affects the pathway for grain color,"
said Susan McCouch, Cornell professor of plant breeding and genetics and the
paper's senior author. Megan Sweeney, Cornell Ph.D. '06 and postdoctoral
associate, was the paper's lead author.

The researchers speculate that ancient farmers actively bred and
spread white rice varieties first throughout the Himalayan region and then
the rest of the world because the varieties cooked faster (requiring less
fuel), their hulls were easier to remove compared with red rice, and disease
and insects were easier to see amid the white grains. The farmers also may
have favored one mutation over the other because it may have produced
favorable grains more consistently, the researchers say.

In 2006 the researchers first identified the gene that makes the rice
seed's bran layer, or pericarp, white. This gave rice breeders and engineers
a genetic marker to help develop new breeds. The Cornell researchers
regularly introduce favorable genes from wild red rices into elite white
cultivars to improve yields and provide better responses to stress, but they
generally select against the gene for red pericarp because it is associated
with such unfavorable "weedy" linked traits as seed dormancy and
"shattering" (where seeds fall easily from the stalk).

"Breeders can now begin to screen for the red pericarp gene while
selecting against closely linked traits like shattering and dormancy," said
McCouch. The new tools may lead to more diverse domestic rice varieties.

Also, breeders are interested in using the marker to predict whether
new generations will contain white or red grains, using DNA from young
seedlings, long before the plants set seed.

McCouch noted that due to the genetics of pericarp color in rice
(white grain is recessive and maternally inherited), when white grains
appear in the panicle (the grain clusters on the stems), it is an indication
that all seeds in the clusters will be white -- and offspring from these
seeds will continue to produce white-grain plants. The researchers theorize
that women who shucked rice for cooking thousands of years ago would have
recognized the value of the white seeds and may have set aside selected
panicles for breeding and planting.

Scott Williamson and Carlos Bustamante, both researchers in Cornell's
Department of Biological Statistics and Computational Biology, were also
co-authors on this paper. The research was supported by the Plant Genome
Program of the National Science Foundation, the Generation Challenge
Program, Chengbuk National University and Korea's National Institute of
Agricultural Biotechnology.


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