Monday, Apr 29, 2002
Sequencing the rice genome
By N. Gopal Raj
Such insights will, hopefully, point the way to novel solutions for the intractable problems which currently limit yield increases in rice and other cereals.
WHEN THE journal Science recently published the genome sequence of two rice varieties, it created a considerable stir. It was "the first of the sequencing projects to yield tangible results for humankind from the standpoints of food security and combating malnutrition", remarked the Directors-General of two leading international crop research centres, the International Rice Research Institute (IRRI) in the Philippines and the International Maize and Wheat Improvement Centre (better known by the acronym CIMMYT) in Mexico.
Rice is the first crop plant to have its genetic code laid bare. Sequencing deciphers the ordering of four chemicals termed `bases' which make up the genetic code. With the full genome sequence in hand, scientists can discover all the genes in rice and, more importantly, how those genes function. Such insights will, hopefully, point the way to novel solutions for the intractable problems which currently limit yield increases in rice and other cereals.
In order to feed a growing global population such yield increases are badly needed in all cereals, including rice. It is estimated that the world's cereal yield has to increase by 80 per cent during the next 20 years. In Asia, where rice is a staple for most people, rice yields have to rise by 60 per cent by the end of the decade.
Rice has the advantage that it has the smallest genome of all cereals. Its genome is about 430 million bases in size, compared to three billion for maize and 16 billion for wheat. So it would be quicker and cheaper to sequence the rice genome. "Having a completely sequenced genome is like having a dictionary with all the necessary words, but without meanings assigned to those words," says Hei Leung of the IRRI. Scientists had to find out the meaning of those words (the genes) and then compose essays by developing new rice varieties. The race now is not just to locate genes, but also to identify their function.
One approach for discovering the function of genes is to create "deletion mutants", rice plants which have specific genes deleted, and see how they differ from the normal rice types. The IRRI is expected to have about 40,000 deletion mutants by the middle of this year. Institutions in the U.S., Japan, Korea, Australia and Europe too are working with rice mutants. One of the IRRI's principal goals was to bring different institutions together to share the mutant stocks as a foundation for large-scale discovery of gene function, Dr. Leung told The Hindu.
With the genome sequence in hand, scientists are now better placed to study the genetic variations in rice and find out why some varieties perform better under adverse conditions. The IRRI's rice germplasm collection has more than one lakh accessions. India is blessed with an enormous genetic diversity in rice. The Central Rice Research Institute at Cuttack counts some 42,000 varieties in its germplasm collection.
For the gene hunters, such genetic diversity is an invaluable resource. Some Indian research groups are already studying Indian rice types to find agronomically useful genes which could be suitably manipulated. The Bangalore-based biotechnology company, Avestha Gengraine Technologies, is, for instance, looking at the chemical pathway and the genes involved in giving Basmati rice its unique aroma.
An important aim of such genomics research is making plants hardier. Raising rice and cereal production will require varieties, which can give high yields even in sub-optimal conditions. They'll need to cope with drought, flood, salinity and nutrient-poor soils. Such abiotic stresses could be decreasing rice yields by about 15 per cent in Asia, twice the effect created by biotic stresses such as disease and pest attacks. Scientists also want to understand the plant's natural resistance mechanisms to biotic stresses.
Mechanisms which make plants naturally resistant to biotic and abiotic stresses may not be simple phenomena. On the contrary, different chemical pathways with a large number of genes, some of which work by regulating other genes, are likely to be involved. If just one gene governed drought tolerance, "we'd have done it by now", points out Dr. Leung.
Drought tolerance is really an assembly of traits, involving many genes working in half-a-dozen chemical pathways, remarks Arjula Reddy of the Department of Life Sciences, University of Hyderabad. His group has isolated several genes regulating these pathways. Again, some 2,000 genes could be involved in rice's defence mechanisms against disease.
When individual genes increased a plant's resistance to a stress factor by only a small amount, a block of genes would have to be moved in order to provide sufficient resistance to a new variety, argues Prof. Reddy. Under such circumstances, the genetic sequence information could be used to create molecular markers for use in a conventional breeding programme. The markers allowed breeders to identify early on whether the progeny had received the desired genes.
Moving a block of genes by crossing two parental strains carried the risk of the progeny inheriting undesirable traits too, points out Anil Grover of the University of Delhi, South Campus. If suitable genes could be identified, the transgenic approach allowed just those traits to be introduced into another rice variety.
Besides, there were many reports in the scientific literature of plant resistance having been improved even with the introduction of a single gene, adds Dr. Grover. His own group had separately introduced two genes for flood tolerance into rice plants. `Pyramiding' both genes in the same plant might further increase their capacity to withstand flooding.
Internationally, an important thrust area will be raising the efficiency of rice's photosynthesis, the process by which plants capture the sun's energy, using sunlight to convert carbon dioxide and water into food material. Rice uses the slower and more inefficient C3 photosynthetic route. If the process can be changed to the more efficient C4 process found in maize and sorghum, rice yields could rise dramatically. But as the C4 process bifurcates photosynthesis into two separate pathways operating in different types of cells, introducing the process into rice is not likely to be easy.
With the publication of the rice genome sequence, all these activities in the functional genomics of rice are likely to receive a considerable boost. The IRRI, in collaboration with its partners in the national agricultural systems, is preparing to take advantage of this "treasure trove", according to its Director-General, Ronald Cantrell. It has already started an international functional genomics working group, bringing together various research institutions. In India, the Union Government's Department of Biotechnology is understood to have called a meeting in May to discuss the opportunities which have opened up with the sequencing of the rice genome. However, as a perspective article published in the rice genome issue of Science pointed out, while the new knowledge derived from genomics research would make an important contribution, achieving food security would also require solutions to a multitude of social and economic issues.
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