The Hindu : Rice chromosome sequence to be published

Online edition of India's National Newspaper
Thursday, Nov 21, 2002

Science & Tech

Science & Tech

Rice chromosome sequence to be published

By N. Gopal Raj

THIRUVANANTHAPURAM Nov. 20. The first ``essentially complete'' sequences of two rice chromosomes from the International Rice Genome Sequencing Project are being published in the latest issue of Nature.

In April this year, two groups, one from the Switzerland-based agrobiotech company, Syngenta, and the other involving a consortium of Chinese research institutions had published draft genome sequences of the japonica and indica rice varieties respectively. Both groups used the whole genome shotgun sequencing method.

The publication of the draft sequences had raised questions about the relevance of the international project, which began in 1998. The international effort, involving 10 countries (including India), was using a slower sequencing method but one, which would provide a more accurate and complete genome sequence of the japonica variety.

Scientists involved in the international programme argued at the time that there were important reasons for achieving a publicly available finished rice genome sequence. Now, the publication of the almost complete sequences of Chromosomes 1 and 4 seems likely to vindicate that stand.

The finished sequence for Chromosome 1 published by Japanese scientists has just eight gaps, together comprising only about five per cent of the chromosome. The draft sequence is estimated to have 2,800 to 4,200 gaps. The complete sequence shows the chromosome could be carrying 6,756 genes, of which 69 per cent coded for proteins with no known function. The draft sequence had estimated 4,467 genes on this chromosome. Because of the gaps, only half the genes predicted in the draft sequence contained the complete coding region.

There were at least three compelling reason for obtaining finished high-quality sequence for the complete rice genome, observed the Japanese scientists. First, the ability to determine gene function was highly dependent on having accurate sequences. Second, as a model plant for cereals, the complete rice sequence would directly affect what could be accomplished with other cereals. Finally, identification of genes responsible for agronomic traits of economic importance required a precise genomic sequence mapped accurately onto the chromosomes. In addition, a high-quality finished sequence provided the only real opportunity to study gene regulation, they remarked. The Chinese scientists who handled the sequencing of Chromosome 4 say they were able to achieve an accuracy exceeding 99.99 per cent. Their sequence has just seven gaps. They estimate that there are 4,658 genes on this chromosome, of which 65 per cent have unknown function. Some 161 genes on this chromosome appeared to be devoted to disease resistance and plant defence, including a cluster of the Xa1 gene associated with blight resistance.

The Chinese scientists also compared Chromosome 4 of the japonica and indica varieties. Although the chromosome sequences were similar, deviations were also quite frequent. Chromosome 4 in japonica was probably larger than its counterpart in indica. If this held true for other chromosomes, then the indica genome would be smaller than that of japonica, they say.

The international project is scheduled to complete phase-2 sequencing of rice's 12 chromosomes by the year-end. Now, about 65 per cent of the rice genome is at this stage when most of the sequencing works as well as aligning the sequences on the chromosomes are completed. But the final phase where any gaps which remain are closed and the finishing quality improvements done would continue.

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Rice chromosome sequence to be published