Rice gene identification should lead to other grain gains

Scientists in China, Seattle, Wash., and San Diego, Calif., have successfully identified as many as 55,000 genes in the two major strains of rice, a breakthrough that should lead to more rapid agronomic improvement in not only rice, but the other major grains as well.

Genetic sequencing of rice does not come without controversy. The announcement in the April 5 edition of Science, the Journal of the American Association of Advancement of Science, once again ignites the controversy over biotech food crops.

However, Kent Bradford, director of the Seed Biotechnology Center, University of California, Davis, said the first even genomic sequencing of a crop plant would probably have a greater impact on traditional rice breeding than in biotechnology. It will affect both.

“It will speed up the processing of taking beneficial characteristics from one rice variety and putting into another,” he said. “It will reduce the time and therefore the expense of traditional breeding.”

Although the 50,000-gene sequence of rice is larger than that of humans, who have only 30,000 to 40,000 genes, rice has the smallest amount of DNA compared to other crop grains, according to Bradford.

Gene similarities

Bradford said there is a certain “synteny” or similarity between rice genes and wheat, barley and corn genes.

“Wheat has six chromosomes while rice has three. Wheat has a huge genome that is very difficult to sequence. Based on what these scientists have learned from rice, we will now have a lot of clues about what specific genes do what in wheat and other grains,” said Bradford.

Dr. Steve Briggs, president of the Syngenta Torrey Mesa Research Institute where part of the gene sequencing was done, said researchers found that 98 percent of the known corn, wheat and barley genes are present in rice.

Together, wheat, barley, corn and rice represented two-thirds of all calories consumed by people in developing countries, according to the U.N. Food and Agriculture Organization.

With this genomic sequencing, plant breeders can now more quickly identify desirable traits like cold tolerance and disease resistance to enhance rice yields. For the consumer, it means the nutritional content can be improved quicker.

University of California, Davis molecular biologist Pamela Ronald, who isolated the first disease-resistant gene in rice, said global cereal yield must increase 80 percent over the 1990 average in the next 20 years just to keep pace with increases in global population.

Better understanding

With this study, plant researchers will now be better able to understand how genes functions in crop plants and develop hardier and more productive varieties by introducing genes with desirable traits using traditional breeding or genetic engineering, she says.

There are more than 100,000 specimens of traditional rice varieties and wild rice species maintained at the International Rice Research Institute Genebank. The genome sequencing data will enable researchers to identify genes from those seed specimens that have agricultural importance.

“This work has potentially huge benefits for California rice growers,” said longtime Northern California UC farm advisor Jack Williams.

The scientific breakthrough elicits mixed emotions for rice growers who obviously want to see improvements made in the rice varieties they produce, but do not want the genomics sequencing announcement to raise fears of genetically modified foods (GMO) rice reaching customers who do not want it.

Tim Johnson, CEO of the California Rice Commission, said the negative perception of GMO has subsided in the past year domestically, but Japan and Turkey, both good California rice customers, do not want GMO rice.

California's rice industry does not want to repeat the mistakes of the corn and soybean industries which mistakenly put GMO products on the market, creating a market backlash.

Zeneca earlier announced it had decoded rice genes. Zeneca is now part of Syngenta, one of the two entities announcing the gene sequencing.

Certification law

In the wake of the Zeneca announcement and the possibility of biotech rice being developed, the state's rice industry pushed through the state legislature in 2000 a rice certification law to keep rice varieties separated to protect the state's $500 million per year rice industry from a GMO fallout like corn experienced when taco shells were inadvertently made with GMO corn not approved for human consumption.

Johnson said the industry is equipped to segregate and certify rice varieties from harvest through processing and shipping.

Some viewed the certification law as anti-genetic modification. Johnson said that is not true and he expects biotech rice varieties will be in California within the next three to five years.

He said the gene sequencing announcement “portends great things to come” in rice breeding, hopefully to overcome problems the watergrass herbicide resistance producers are now battling.

Keep rice separate

“We are confident we can keep separate biotech rice for customers who want that and non biotech rice for customers who prefer that. The California rice industry is in a position to take advantage of this new technology and at the same time meet our customers' demands.”

The gene sequences were developed by competing private and public research groups, a Syngenta biotechnology laboratory in San Diego and a team of Chinese scientists working in Bejing and the University of Washington in Seattle.

The Chinese mapped the genes for indica rice, the most common rice type grown in China and other Asian Pacific regions. Work done at Syngenta's Torrey Mesa Research Institute in San Diego was on japonica rice varieties, the most common rice grown in California and in more arid regions. The japonica genome is expected to reveal the gene responsible for vitamin A production.

Science magazine editor Donald Kennedy said the joint public-private represented a spirit of cooperation, it also spawned another controversy.

While the Chinese work will be deposited in a fully accessible online forum called GenBank, the Syngenta work will not be posted there and will be in a proprietary databank controlled by Syngenta. Normally, making such genetic data freely available is a prerequisite for publication in a peer review scientific journal.

Access disappointing

Syngenta pledges to make the information available to academia who pledge not to use it commercially.

UC Davis biologist Ronald and others were disappointed that the access to the Syngenta information will be limited. She said private company collaborations can become stalled in legalese.

Kennedy acknowledged validity of the criticism of the magazine's decision to compromise “accepted community standards” by allowing Syngenta to withhold its information from the GenBank at the time of publication. Syngenta has said it will work with public research institutions to produce a finished version of the rice genome that is 99.99 percent accurate. The finished version will be deposited in the GenBank, according to the company.

Kennedy defended the National Academy of Sciences decision to allow Sygenta propriety rights to the initial sequencing information, saying it was too valuable to squabble over proprietary rights.

The academy made a similar concession with the historic publication of the human genome sequence by a private company.

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