By latest official estimate, the world’s human population numbered 6,157,000,000 in the year 2001. Over half of this Homo sapiens body count subsists mainly on rice.
In 2001, sequencing of the human genome was announced by two gene-mapping labs. One, the International Genome Sequencing Consortium, was public; the other, Celera Genomics Group in Rockville, Md., private. Also, last year, two species of rice were mapped again, by one not-for-profit agency, the Chinese Beijing Genomics Institute (BGI), and by one for-profit agency, Torrey Mesa Research Institute, (TMRI) in San Diego. The institute is a branch of Geneva-based Syngenta AG, of which Novartis AG is a part.
Today’s issue of Science, dated April 5, 2002, devotes its cover, plus some 43 pages, to its rice genome story. This coverage features the two research papers, which report sequencing of two rice strains. In addition, the journal carries “Perspectives,” news features and editorials highlighting the significance of the rice genome to the world’s population.
Fully 96 co-authors from 12 research centers (11 Chinese and one Americ an) contribute to the BGI report, titled: “A draft sequence of the rice genome (Oryza sativa L. ssp. indica).” That strain of the grain is the most widely cultivated subspecies of rice in China and most of the rest of Asia. BGI expressed its “feeling that China should sequence its own rice.” The Beijing team counted 46,022 to 55,615 genes in the genome’s 466 megabases. The Chinese co-authors noted that the indica they sequenced “is the paternal cultivar of a super-hybrid rice, LYP9, which has 20 [percent] to 30 percent more yield per hectare than the other rice crops in cultivation.”
It took only 57 co-authors at TMRI to present: “A draft sequence of the rice genome (Oryza sativa L. ssp. japonica).” This rice is much favored in Japan and other countries with temperate climates. Both sequences are works in progress, and admittedly contain numerous gaps and errors. Warts and all, BGI deposited its draft rice sequence numbering 32,000 to 50,000 genes in GenBank (http://btn.genomics.org.cn/rice). It concludes that each rice gene codes for just a single protein, whereas human genes often express multiple proteins.
Syngenta, But Not Chinese, Shuns GenBank
Unlike the disputes that still mark the contentious human genome projects, the rival rice contenders are observing a plateau of cooperation. But to reach that lofty height, Syngenta and Science had to duke it out over the company’s refusal to deposit its proprietary nucleotide sequence data in GenBank as always required by the journal. This led its editor-in-chief, David Kennedy, to preface Science’s voluminous coverage with a one-page statement headed succinctly, “The Rice Genome.”
“The value of having this information in the public domain,” Kennedy said, “rests on the hundreds of millions of people around the world who depend on rice, and whose nutritional status and health may be improved as a result. Not only are more calories obtained from rice than from any other single food [but also] the rice sequence affords entry into the similar, but larger, genomes of the other cereal grains on which the world depends.”
Kennedy acknowledged that granting a GenBank waiver to Syngenta “attracted some controversy.” And he recalled that Science once and only once before had given Celera a similar license over the human genome project. Syngenta is making its data publicly available via its own website (tmri.org) or on a CD-ROM.
At a press briefing last week, he said, “It would be ideal to have one-stop shopping for all genomic data at GenBank.” He added, “We think that the public benefit of bringing this important science out of trade-secret status greatly outweighs the cost of granting an exception.”
Steven Briggs, senior author of the TMRI paper, who heads that institute, told the press that Syngenta believes it has “a significant commercial advantage,” and isn’t ready to permit unrestricted use of its data by its competitors. But he foresees that much of the Syngenta sequence is likely to end up in GenBank over the next “12 to 18 months.”
Both groups did their sequencing by the bold approach of whole-genome shotgunning. This technique, which Celera also resorted to in sequencing the human genome, chops up the entire genome into fragments, sequences each one several times, and sorts the data in proper order, using high-power computers. Syngenta did enough sequencing to cover the japonica genome six times, attaining 99 percent coverage and accuracy, but leaving thousands of data gaps.
From Low-Profile Rice To Higher Grains
“In stage two of the project,” the Chinese co-authors observed, “our objective will be to obtain a high-quality sequence, fully integrated with the physical genetic maps, and with complete gene annotations. We will then apply the experiences gained from the rice genome project to other agriculturally important crops, including Zea mays (maize) and Triticum aestivum (wheat).”
TMRI’s co-authors noted, “Homologues of 98 percent of the known maize, wheat and barley proteins are found in rice. Their genomes are estimated at 3,000, 5,000 and 16,000 megabase pairs, respectively. More than 500 million tons of each of these three cereals are produced annually worldwide. The rice genome sequence provides a foundation for the improvement of cereals, our most important crops.”
Stanford University molecular biologist Chris Somerville pointed out that, “nobody makes money on rice seeds. Companies are interested in rice because of the potential payoff in the sizeable markets for maize, barley, sorghum and wheat seeds.” Plant pathologist Pamela Ronald, at the University of California, Davis, said, “The extensive DNA similarity between rice and other cereals will provide a short cut to the isolation of genes of agronomic importance in cereals, as well as other crop species.”
A Japanese rice geneticist, Masahiro Yano, seeks to link important agronomic traits, such as pest resistance, to particular regions of rice’s 12 chromosomes. He has used computer programs to find several genes that control flowering time. Eventually, Yano hopes to have a whole collection of such genes, so breeders could take varieties with desirable flowering traits and move them from northern to southern latitudes or vice versa.