Twice as Many Predicted Genes in "Finished" Rice Chromosome

The smallest rice chromosome has nearly twice as many predicted genes as the draft DNA sequence had indicated, according to a new study by researchers at TIGR and collaborators. The "finished" sequence and analysis of rice Chromosome 10 confirms that the rice genome is closely similar to that of other grains particularly sorghum and maize. The study also offers a close look at the compacted short arm of the chromosome.

June 5, 2003

The smallest rice chromosome has nearly twice as many predicted genes as the draft DNA sequence had indicated, according to a new study.

The "finished" sequence and analysis of rice Chromosome 10, published in the June 6 issue of Science, confirms that the rice genome is closely similar to that of other grains, particularly sorghum and maize. The study also offers a close look at the compacted short arm of the chromosome, which is a gene-poor heterochromatic region of the rice genome.

Robin Buell, who leads the rice genome sequencing team at The Institute for Genomic Research (TIGR), says the "finished" sequence - which helped researchers identify about 1,700 additional rice genes -shows the importance of completing a draft DNA sequence. "This work clearly demonstrates the importance of finished sequence," says Buell. "The finished Chromosome 10 sequence of rice will be a major component for future comparative studies of other cereals, such as corn and wheat."

Chromosome 10 was sequenced by a U.S. group - led by Buell at TIGR and by Rod A. Wing at the University of Arizona - with funding from the U.S. Department of Agriculture, the National Science Foundation (NSF) and the Department of Energy. That effort was part of the International Rice Genome Sequencing Project (IRGSP), a public effort that is completing the sequences of all 12 rice chromosomes, which have a total of 430 million DNA base pairs.

Rice is one of the world's most important foods, providing more than half of the daily calories for about a third of the world's population. The IRGSP sequenced the genome of the japonica subspecies of rice (Oryza sativa) that is cultivated in Japan, Korea and the United States. Another rice subspecies, indica, has been sequenced by a Chinese institute.

The IGRSP public consortium announced in December 2002 that it had completed an advanced, high-quality draft genome sequence of rice. The data - freely available on the internet to all scientists worldwide - are expected to help plant scientists develop improved rice strains that are hardier and more productive. The draft sequence also provides an important tool for scientists who focus their research on other cereal crops (including maize, wheat and barley) with genomes that are colinear with rice.

Buell said that the new study predicts a total of about 3,500 genes on Chromosome 10, which encompasses about 22 million DNA base pairs. The previous estimate, based on the draft genome blueprint, had predicted about half that number of genes.

The analysis of the "completed" genome - which still has seven gaps, representing about 4 percent of the total chromosome sequence - also found that the chromosome is "modular," with a long arm that is rich with genes and a short arm that has relatively few genes. That short arm has an abundance of heterochromatin, a stretch of highly compacted DNA with few genes in it. Buell says this is the first large stretch of heterochromatin in plants that has been studied in depth.

In an effort to determine the functions of many of the genes, Buell, Wing and colleagues also compared the proteins encoded by the chromosome with those encoded by the model plant Arabidopsis thaliana. They found matches for about two-thirds of the proteins, indicating that some of the genes were responsible for functions - such as producing enzymes and binding nucleic acids - that are carried out by many plants.

Rice, setting a record for a single species, has been the focus of four separate genome-sequencing initiatives, including the IRGSP and private initiatives by agribusinesses Syngenta and Monsanto Co., both of which have shared their rice sequence data with the public project. In addition, a separate research project at the Beijing Genomics Institute (BGI) has developed a draft sequence of subspecies indica 93-11, which is the main subspecies grown in China and Southeast Asia.

Scientific papers by Japanese and Chinese IRGSP research groups detailing the complete draft sequences of rice chromosomes 1 and 4 were published last fall in the journal Nature, and IRGSP papers on the "complete" sequences of the remaining rice chromosomes are planned. The final, "finished" rice genome sequence is expected by 2004.

The rice project is an important part of TIGR's plant genomics program, which includes other major research projects involving, maize (corn), potato, and the model plant Arabadopsis thaliana and some of its close relatives. TIGR had sequenced about one-third of the Arabadopsis genome as part of an international consortium that published its results in Nature in December 2000. TIGR is also conducting research involving pine, barley, banana, and plant pathogens.

TIGR's president, Claire M. Fraser, Ph.D., said the rice genome sequence is an important step towards better understanding one of the world's most important crops and in gaining insight into related crops - such as maize, wheat and barley - which have much larger genomes. "The rice genome sequence will benefit a large number of plant genomics projects and offers the potential to help millions of people across the globe," Fraser said.