Mapping high-density expression genes in rice It is necessary to investigate the function of the approximately 40,000 rice genes in order to breed new varieties of rice to cope with the population explosion, to solve food problems caused by the global environmental changes expected in this century, and to produce high quality rice that meets the needs of domestic consumers. It is also essential to know where the expression genes that actually function in rice are located in the genome. Once this is achieved, DNA markers can be used as guidelines to accelerate the rice genome sequencing efforts by the Japan-led international consortium for selecting systems with traits such as good eating quality, and to isolate useful genes.
In the first phase of the rice genome project, implemented from fiscal 1991 to 1997, the National Institute of Agrobiological Sciences (NIAS) and the Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF) determined the expressed sequence tags (ESTs) covering about 40,000 genes and catalogued these rice genes. In fiscal 1998, a project was also launched to identify the location of each expression gene on an experimental basis by grouping these genes into 8,500 classes. In the previous rice genome project, physical maps that cover 81 percent of the genome were produced by incorporating fragments of the rice genome into yeast artificial chromosomes (YACs) for cloning and then fixing each YAC clone onto the genome. These YACs have now been used for mapping individual expression genes. Some of these expression genes were checked to see if they are sequenced on a specific YAC by using PCR to amplify a specific sequence. As a result, it was possible to identify on which YAC each of the sequences, corresponding to a total of 6,591 expression genes, are located, and to map each expression gene on the genome based on the information. This means that one expression gene per 65 kb on average was mapped, marking the first time that expression genes in plants have ever been mapped at such a high density. Showing the distribution of expression genes on a genomic level has led to many new findings. The distribution of the 12 chromosomes in rice is not uniform, with their density being high at both ends of each chromosome and low at the center; there also exist chromosomes with high and low genetic densities. The location of expression genes is important, since they assist with isolating useful genes. Dwarf rice genes have already been isolated using this clue. Meanwhile, in the rice genome sequencing project now under way, the international consortium has decided to map PAC/BAC clones accurately on the genome. To do this, markers are essential to map the PAC/BACs with good accuracy. A total of 6,591 expression genes mapped on the genome are currently being utilized by the member agencies of the consortium to accurately sequence the rice genome. The results of these efforts were published in the March 2002 issue of the Plant Cell International Journal. They are also posted on the homepage of the rice genome project (RGP) teamfs Web site along with detailed information on individual expression genes. A high quality draft sequence of the whole rice genome is scheduled to be complete by the end of 2002. A more detailed map of expression genes will be completed on the basis of the genome sequences when they become clear. The functions of many rice genes can be identified by utilizing this map for genetic study and research into genetic functions, raising expectations for its application to the production of useful varieties of rice and the genomic analysis of other crops.
Glossary
Rice genome: The genome is a complete set of all the hereditary information about one type of living thing, written in sequential form as DNA in the chromosomes. Information on the rice genome is divided into 12 chromosomes and represented by a total of 430 million codons.
YAC, BAC, PAC: Abbreviated names for DNA that becomes a vector (carrier) with the function of amplifying a long fragment of DNA in the genome within test organisms (hosts) such as E. coli and yeast and to preserve them in a stable condition. YAC has yeast as its host, while BAC and PAC have E. coli as their hosts.
International consortium: A team of international collaborators established to sequence the rice genome. The members of the group consist of 10 countries around the world plus regional public organizations that are supported financially by their governments. The consortium is working to make materials for analysis and methodology common to all members and to promote their mutual exchanges. The results of such efforts are released to public databases for utilization by researchers all over the world.
A word from the author
A map showing the location of functional rice genes in the genome will become a useful landmark for rice researchers around the world. (Takashi MAYSUMOTO, NIAS)