Two UW researchers — Dr. Jun Yu, an American, and Dr. Gane Ka-Shu Wong, a Canadian — and a major new genome sequencing center in China have sequenced the genetic code for rice, one of the most important food staples in the world.
The Chinese center is making the complete genome sequence of rice available to the public. An analysis of the sequence appears in the April 5 issue of Science, published by the American Association for the Advancement of Science. Among the findings: rice may have more genes than humans.
The rice paper is only a start. Created just a few years ago, the Chinese center is now engaged in sequencing two other varieties of rice, as well as the genomes of corn, the pig and the chicken. All are staples of the Chinese diet.
“If you think about why the Chinese want to sequence rice, it’s the No. 1 food on the table. There is nothing in the Chinese diet that compares with rice,” says Dr. Jun Yu, the American scientist who is one of the four lead authors on the paper, and the principal investigator for the rice project. He is a research scientist at the UW Genome Center, an associate director of the Chinese center, and a professor with the Chinese Academy of Sciences.
A collaborator says that the world can expect other significant genomic news from the Chinese center in the future.
“I am very impressed with the contributions the Chinese genome center has made to large-scale sequencing. Their institute joined the Human Genome Project at quite a late stage, but managed to make a substantial contribution. This demonstrates that they have rapidly gotten up to speed with comparable sequencing laboratories around the world,” says Dr. Merete Fredholm, professor in the Division of Animal Genetics and Breeding of the Royal Veterinary and Agricultural University in Denmark. “Their latest achievement, the sequencing of the rice genome, shows that they are still making rapid progress. No doubt they will play a very important role in science in the future.”
Rice is a staple for more than half of the world’s population. According to a national survey, cereal grains account for 67 percent of the energy intake in the Chinese diet. Yu says that rice accounts for 40 percent of the grains grown in China.
There is a reason that researchers began with the variety of rice that they did. The sequence is of the form of rice, Oryza sativa L. ssp. indica, that is the most commonly grown in China and many Asian-Pacific areas. It is the paternal cultivar of a super-hybrid rice, LYP9, which has 20 to 30 percent more yield than other rice varieties. The sequencing center is also working on the maternal cultivar of LYP9, to better understand why hybrid varieties of rice grow so much more vigorously.
Rice has the smallest genome among the major cereal crops, and is expected to be a model for other commonly cultivated cereal crops, including corn and wheat, whose genomes are six and 40 times larger than rice. The researchers say that they have learned quite a lot about rice, but it is still too early to translate their findings into better crops.
There have been other efforts to sequence rice involving japonica varieties. However, the Chinese center is the first to release the full sequence to the public databases. “We want to encourage the scientific field to conduct more research on rice. The way you push the field forward is by providing information,” Yu says.
Among the more surprising lessons: rice has 46,000 to 55,600 genes, while the human genome has only 30,000 to 40,000 genes.
“We all like to believe we as humans are better than anything else, and that we have more of everything. But if we pride ourselves on the number of genes in our genome, then we lose to a lowly rice plant,” says Dr. Gane Ka-Shu Wong, a Canadian scientist who is another of the four lead authors. He is a research scientist at the UW Genome Center, a professor of genome biology at the Chinese center, and a visiting professor at the Chinese Academy of Sciences. He oversaw the assembly and annotation of the rice genome sequence, and wrote the manuscript that will appear in Science.
The researchers theorize that rice has more genes than humans do because in plants, protein diversity depends on gene duplication. In humans, protein diversity depends not only on gene duplication, but also, on alternative splicing.
“Think of alternative splicing as a Swiss army knife. 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,” Wong says.
The Chinese center has its roots in the University of the Washington in the early 1990s and recruiting by UW Genome Center Director Maynard Olson, one of the co-founders of the Human Genome Project. When he was helping to establish a molecular biotechnology program at UW, he recruited both Yu and Wong, who have been working together ever since. The Chinese center opened in 1998 and has grown to include 600 employees and 80 sequencing machines at two locations, in Beijing and Hangzhou.
Wong was brought up in Western Canada. He graduated from the University of British Columbia, in Vancouver, before moving to the United States for Ph.D. studies in experimental low temperature physics at Cornell University.
Yu was born in a small village in Northern China. He was sent to Mongolia during the Cultural Revolution. He later graduated with a degree from a Chinese university (Jilin) before coming to the United States for Ph.D. studies at New York University, under the CUSBEA (China-United States Biochemistry and Molecular Biology Examination and Administration) program organized by Ray Wu.
The center’s executive director, Jian Wang, had previously studied at UW. Several other people prominent in the Chinese center have spent time at UW.
The Chinese have shown great pride in the center’s accomplishments. A display of their contribution to the Human Genome Project, complete with a MegaBACE 1000 sequencing machine, is featured prominently in The National Museum of History, in Beijing. Wong says that when he accompanied the genome center’s director, Huanming Yang, on a walk in old-town Beijing, people on the street recognized the man and walked up to him to shake his hand.
“It has been very satisfying for the UW Genome Center to be able to play a supporting role,” Olson says. “More U.S. scientists should take an interest in international science, particularly in developing countries. Science is one of the strongest common denominators we have that crosses national and cultural boundaries. Vigorous, mutually beneficial interactions between U.S. scientists and their international peers can establish relationships and set examples that will spill over into other areas of international cooperation.”