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Scientists Sequence Rice Genome

ricepaddies
Image: MA LIWEN/Courtesy of Qiu BaoXing

In a move that may lead to hardier versions of one of the world's most important foods, scientists have unveiled two maps of the rice genome. These draft DNA sequences of the plant, published today in the journal Science, could help speed improvements in the nutritional quality and yields of a crop that is a staple for more than half the world's population.

Jun Yu of the Beijing Genomics Institute and the University of Washington Genome Center, together with colleagues from 11 Chinese institutions, sequenced the rice strain known as indica, which is the most commonly grown type of rice in China and many other Asian-Pacific areas. A second team, led by Stephen Goff and his colleagues at the company Syngenta in Basel, Switzerland, uncovered the code of the japonica strain. Both groups utilized the so-called whole-genome shotgun technique--the process used by Celera in Rockville, Md., to decode the human genome--to assemble their maps.

The two blueprints reveal that a rice plant probably contains more genes than a person does. Whereas estimates of the number of genes in the human genome lie between 30,000 and 40,000, indica rice contains between 45,000 and 56,000 genes, and japonica rice could have as many as 63,000 genes. The reason for the multitude, scientists suggest, is because plants rely on gene duplication for protein diversity. Protein diversity in humans, in contrast, exploits a process known as alternative splicing. "Think of alternative splicing as a Swiss Army knife," explains Gane Ka-Shu Wong of the University of Washington Genome Center. "It lets you do different things with the same gene. Rice doesn't like Swiss Army knives, so it has more genes, even if it may not do as many things with these genes as humans do with theirs."

The indica sequence--available publicly through the GenBank database--covers 92 percent of the rice genome. The japonica map, though 99 percent complete, is currently available only through Syngenta and Science, a limitation that has drawn criticism for potentially slowing the pace of new research. According to Steven Briggs, head of genomics for Syngenta and co-author of the Science paper, the company plans to work with the Beijing Genomics Institute and the International Rice Genome Sequencing Project, a consortium of public laboratories, to produce a 99.99 percent accurate map. This improved map, which will most likely take between 12 and 18 months to complete, will then be released through GenBank, Briggs says.

Knowing the genetic code of the plant should help breeders develop strains of the crop with specific properties, such as pest-resistance or high yield, more quickly than current methods, which may require years of crossing plants to achieve a desired trait. The map may also prove useful in understanding the characteristics of related crops, including maize, wheat and barley. In an accompanying commentary, Pamela C. Ronald of the University of California at Davis and Hei Leung of the International Rice Research Institute in Manila, Philippines, write that the publication of the draft sequences "provides a rich resource for understanding the biological processes of plants and promises to positively impact cereal crop production."

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