Sequencing the rice genome

Wed May 1 05:52:03 PDT 2002

The Hindu

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.