Elucidating the sequence of rice chromosome 1 and its significance The rice genome consists of 12 pairs of chromosomes with a total of 430 million bases. Hidden in the genome are all the botanical secrets, which made rice a staple crop in many countries worldwide. Certain characteristics of rice such as nutritional quality, yield stability and disease resistance, are the result of the blending of information hidden in what are called "genes," present in the rice genome. Over its long history of cultivation, many desirable traits of rice have been selected and maintained. However, many specific genes which carry the information that makes rice attractive to the human palate are still unknown. The rice genome analysis is intended to clarify all the genetic information contained in the rice genome and to obtain the basic data to develop new improved rice varieties that will provide higher yield to producers and will be more palatable to consumers. These information will be derived mainly from the nucleotide sequence or the genetic information hidden in DNA's four base sequences of A, G, C, and T. If it is possible to obtain this information, to find out where genes are located, and discover their function, the knowledge may be used to produce rice of more desirable quality. In rice chromosome 1 alone, about 50 million sequences have been identified. These base sequences are analyzed in the following three stages: 1) DNA fragments are selected from rice genome libraries and correctly aligned using molecular markers. 2) The fragments are cut into smaller pieces, sequenced using an automatic sequence analyzer, and reassembled to obtain the sequences of the original fragments. 3) The genes coded in the nucleotide sequences are predicted using a gene prediction programs. Using this approach, a total of 370 fragments of chromosome 1 were selected and analyzed, and 84 percent of the total were reproduced. The base sequences of these fragments were read with 99.9 percent accuracy. A computer-based prediction indicated that there exists a total of as many as 7,000 genes in the sequences of chromosome 1. This number was far greater than expected. The evaluation of this result must await the completion of the sequencing of the whole rice genome and improvements in prediction programs. This chromosome has been known to have a gene that controls plant length and a gene that controls the shedding habit, but its function remains to be clarified. In addition to these genes, there may exist many other unknown genes. It is expected that the elucidation of the genetic function of chromosome 1, for which a basic tool called a base sequence is now available, will make rapid progress, resulting in the production of high quality rice. (This research has been conducted in cooperation with the Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries.)
Glossary Genome: The total DNA or complete collection of genetic information including the genes in every living things.
Gene: A segment of DNA base sequence carrying the information that determines the acid amino sequence of a protein
Rice genome library: A collection of DNA fragments derived from the nuclei of rice cells, where DNA present is extracted and cut to lengths of 150,000 bases on average using a 'pair of scissors' called a restriction enzyme, so that each fraction of DNA can be freely increased or taken out by connecting it to frames (vectors) called PAC and BAC
Shedding habit: This refers to the ease with which the seeds separate from the rice panicle. If the seeds of grasses do not naturally separate from the panicle and fall to the ground, the next generation of grasses will not grow. In agriculture, however, yields will decline if the seeds fall too easily. Therefore, a habit of not shedding except as a result of threshing is preferred. Varieties with this habit of retaining the grain have been selected over the history of rice breeding.
A word from the author Sequencing the rice genome will provide the basic data that will determine the direction of rice research in the future. It is an important task for us to determine the accurate sequence of the rice genome and release them immediately to the public domain. In the process, we hope that the sequence data will be used to further improve rice and other cereal crops. We also hope that this effort will raise the scientific reputation of Japan in the international community.(Takuji SASAKI, NIAS)