Rice genomics to understand rice plant as an assembly of genetic codes

Abstract

Rice genome research is a topic and an attractive theme in plant genomics. Because of its practical importance to feed about half of the world’s population, and because of predicted unbalance of food supply and population increase in the near future, breeders, geneticists and molecular biologists in plant fields have strong concern in the results of rice genome research. In this review, recent research results of the rice genome are presented to offer information to develop ideas for understanding and improvement of rice plants. RICE is one of the most important crops in the world that provides food for about half of the world population. In areas such as Asia, Africa and Latin America where the demand for rice is a top priority, the population is expec ted to increase 1.5-fold by 2025. However, the capability of land to sustain rice yield is almost saturated as a result of insufficient irrigation or limited adaptation of cultiva ted rice to prevailing environmental conditions. To over come this situation, we must introduce new innovation s or novel strategies for breeding new rice varieties. One approach is to select favourable progenies using reliable DNA markers or introduce favourable genes by trans formation. These strategies can be realized only by under standing the concept of inher itance in rice plants based on indispensable information encoded in the DNA. There exists a large number of local cultivars of Oryza sativa in which two major subspecies, japonica and indica varieties are known. Unlike in the case of humans, the long history of evolution of Oryza species generates much more divergence in nucleotide sequences. Hence, one specific rice variety must be chosen as a standard for a complete analysis of its entire genome. If not, the utilization of genetic information in unders tanding the rice plant would be limited because of the existence of polymorphism among alleles of many rice varieties. Therefore, the Japanese Rice Genome Research Programme (RGP) uses the japonica variety, Nipponbare as a resource for genetic and molecular analysis of the rice genome. Alternatively, for genetic dissection of the rice genome, a high frequency in polymorphism within the DNA sequences is favourable to generate many molecular genetic markers. For this purpose, the indica and japonica varieties are preferred as parents to produce progenies for linkage analysis. Once genetic markers that can unambiguously define the chromosomal regions are established, molecular dissection should be promptly per formed. The ultimate goal beyond dissecting the genome by genetic analysis is to decode all of the information for inheritance written in the DNA. The advancement of genome analysis supported by automated equipments was unexpected a decade ago. At present however, an automated capillary DNA sequencer can sequence daily a total of about 380 kb of template DNA with the aid of robotic machines for sample preparation. In addition, huge amounts of sequences are expediently accelerated through the development of innova tive computer software and hardware systems. While whole genome sequencing programmes are costly endeavours, the information encoded in the sequences remains extremely valuable. In this article, the processes involved in genome analy sis and the results obtained from each step, and examples of their application are described.