MAPPING OF THE RICE GENOME

Triumph Of Public Funded Research

Amit Sen Gupta

IT has been argued that if cereals – rice, wheat, corn, maize, etc --- had not been cultivated by man, human civilisation may not have existed in the form we know today. Settled agriculture was crucially dependant on the cultivation of cereals, all of which are believed to have descended from a wild grass that existed over 50 million years ago. Over millions of years, the earth has seen the evolution of crops like rice, wheat and corn that we are familiar with.

Rice has been cultivated by humans since the Neolithic era or late stone age, which started some 10,000 years ago. Human intervention has refined the many varieties of cereals through selective breeding. Now we have the tools to immensely increase our knowledge about the commonest cereal on earth – rice.

RICE GENOME MAPPING UNDER THE AEGIS OF IRGSP

The science journal Nature, recently announced the successful mapping of the rice genome by an international team working in tandem under the aegis of the International Rice Genome Sequencing Project (IRGSP). The IRGSP is a consortium of publicly funded laboratories, established in 1997 to obtain a high genetic mapping of the rice genome using the variety called Nipponbare – a rice variety of the sub-species japonica that is grown in Japan and temperate regions of Europe. The consortium is currently comprised of ten members: Japan, the United States of America, China, Taiwan, Korea, India, Thailand, France, Brazil, and the United Kingdom. The team was led by Japan, where some of the preliminary work had already been done before commencement of the Project in 1997.

Mapping of a genome means knowing the sequence and number of genes that contain all the genetic information of a particular organism. This genetic information is present in all cells of a living organism in the form of codes that are made by the arrangement of 4 basic building blocks – in plants these building blocks are four complex sugars called adenine, thymine, cytosine and guanine. These building blocks are arranged in particular sequences in the DNA of each cell of a living organism. A number of pairs of these blocks form a single gene – which is responsible for regulating a particular characteristic of the organism by regulating the production of specific proteins. All the genes in an organism put together are called the genome. The mapping of the rice genome is the largest exercise of genome mapping undertaken, larger even than the mapping of the human genome that was accomplished a few years back – again by a consortium of public funded laboratories. In fact the accuracy and coverage of the mapping in the case of the rice genome is believed to be of higher quality than the human genome mapping.

THE IMPORTANCE OF RICE GENOME

There are several reasons why the mapping of the rice genome is being seen as something of a landmark. The first reason has to do with the importance of rice as a source of food in the world. Rice provides 20 per cent of the world's dietary energy supply, while wheat supplies 19 per cent and maize 5 per cent. Rice represents 30 per cent of global cereal production today, and production levels have doubled over the past 30 years. 3.2 billion people, i.e. about half of the present population of the world consume rice as the principal source of calories that provide them with energy. While 89 countries in the world grow rice, 90 per cent of rice is consumed in Asia. In Africa there is a major move to switch to rice from other traditional cereals – thus rice is the staple food for a majority of poor people in the world. Current consumption trends suggest that about 4.6 billion people will be reliant on rice by the 2025.

Another reason for choosing rice for genome mapping was that the rice genome is by far the simplest among all major cereals -- six times smaller than that of corn and 37 times smaller than that of wheat. Rice plants have 12 chromosomes containing about 37,544 different genes, which are in turn made up of about 389 million base pairs (i.e. pairs of the basic 4 building blocks) of DNA. By comparison, corn has 3 billion base pairs. It still is a more complex genome than the human genome which has about 20,000 known genes arranged in 24 chromosomes.

Not only is the rice genome the simplest, it is also in many ways the basic framework for the genomes of other cereals. Thus mapping of the rice genome will also help in understanding and subsequent mapping of the genomes of other cereals.

BENEFITS OF THE GENOME MAPPING

The key issue however is, what benefits are expected from the mapping of the rice genome. To understand this we need to understand something about the rice plant. The plant is abundant in nature – and there are an estimated 120,000 varieties in nature – most of which are non-cultivated wild varieties. In spite of its abundance and large diversity of species, the plant has a number of problems. Typically the rice plant is extremely dependant on water – over 5,000 litres of water are required on an average to produce 1 kg of rice. It is also incapable of withstanding low temperatures. Thus the cultivation of rice is difficult in water scarcity areas and in colder climates. With global warming projected to increase the incidence of drought years in the future, this problem could accentuate over the years. Hybrid varieties of rice which can withstand more difficult conditions are more difficult to develop than say wheat. As a consequence the growth in rice production that averaged about 4 per cent till the 1960s has now dipped to 1 per cent --- that is much below the rate of growth of population of those who consume rice. Further, despite the widely prevalent use of rice as a staple, rice is also a deficient food in some ways. It is deficient in Vitamin A and iron. Rice actually produces a chelating compound, phytic acid that takes iron out of the diet.

Mapping of the rice genome provides the tools to create varieties that address many of these problems – high yielding, less water dependant, disease resistant, and more nutritious. New varieties that are created using the knowledge now available through the mapping of the genome do not necessarily have to be varieties that are transgenic – i.e. varieties that are created by introducing genes of other plants into the rice plant. This is important to understand as the development of transgenic varieties have been mired in controversy. Some years back the introduction of “golden rice” which contained genes from the daffodil plant to induce Vitamin production in the rice plant, was opposed by many quarters. While techniques for genetic manipulation make progress many of the technological problems and dangers of creating transgenic varieties are likely to reduce appreciably. But the mapping of the genome allows manipulation of the rice plant even without going the transgenic route.

The genome map provides vital information about the rice plant which can be used to improve rice varieties by techniques that do not involve introduction of “foreign” genes. For example, rice already produces provitamin A, but as it is present in the husk, it is removed when rice is processed (traditional method of parboiling in India is in fact designed to retain the Vitamin A from the husk). With knowledge of the genome, it should be possible to coax this gene to produce provitamin A in the seed without using transgenic technologies. Already, researchers in Japan, using the new map, are hot on the trail of genetic variations that might allow rice to grow in colder climates, while research in the Philippines is progressing on strains that could yield enough even in drought years to keep a farm family from starving.

The mapping of the rice genome could also have another useful fallout. Knowledge of the rice genome will help greatly in the search for useful traits carried by in the collection of a huge number (almost a 100,000) of traditional varieties and wild species of rice managed by the International Rice Research Institute. It could result in increased interest in the genetic diversity of rice and could help raise public awareness about the loss of genetic diversity caused by abandoning traditional varieties in favour hybrids. The development of rice genomics can make it easier the transfer of advantageous traits to locally adapted varieties.

In addition of course, knowledge of the rice genome helps unravel the genomes of other cereals. All cereals are close genetic relatives, and rice, with the smallest genome, proved to be the easiest to analyze. It is a crucial model for understanding the biology of all cereals.

MONSANTO AND SYNGENTA JOIN THE BANDWAGON

The story of the mapping of the rice genome would be incomplete without a mention of a parallel exercise to the Project that was carried out by two giant biotech companies. In 2000/2001 two of the largest Biotech companies in the world – Monsanto and Syngenta – separately and in quick succession announced that they had mapped the rice genome. They also announced that they were willing to co-operate with the International Rice Genome Sequencing Project and share some of their findings. The first question that arises is that if these two had already mapped the rice genome, why was it necessary for the international project to continue. And second, why did they agree to co-operate with the public funded Project.

The answer lies in the fact that the Monsanto and Syngenta “maps” were actually rough “drafts” - much poorer in accuracy than what the international project produced. For example, international Project demarcated 6756 genes on chromosome 1, whereas Syngenta only reported 4467, of which half of those predicted did not have a complete coding sequence. If the two companies had on their own produced accurate mappings, it would have been a disaster for research on rice varieties. The two would then have ensured that none of the information would be available in public domain – the international Project is committed to putting all its information in public databases. But because they realised that their maps were not good enough, they offered to cooperate so that they could also use the final product for their own needs.

Further, it must also be understood that Monsanto and Syngenta are not really interested so much in rice – the poor man’s staple. But their crude draft is sufficient for them to characterise the genes which are of economic interest in other cereals, using rice as a basis. Their interest lies in crops like corn and wheat – the rich man’s staple consumed in North America and Europe.

In the final analysis the mapping of the rice genome marks another triumph of public funded research. However tangible benefits will take time to accrue – in some cases over a decade. It is hoped that these benefits too will be available in the public domain just as the genome map is now available in public domain. It would be a great pity if the likes of Monsanto and Syngenta were to appropriate the public domain knowledge for their private gains.