Rice Genetics IV - IRRI books - International Rice Research Institute

Bioinformatics and the rice genomeB.A. Antonio, K. Sakata, and T. SasakiAs rice genomics data continue to accumulate at a rapid rate, databases arebecoming more valuable for storing and providing access to large and rigorousdata sets. This chapter gives an overview of available resources on ricebioinformatics and their role in elucidating and propagating biological andgenomic information on rice. Of particular focus here is the informatics infrastructuredeveloped at the Rice Genome Research Program (RGP) followingan extensive rice genome analysis. The database named INE (INtegratedRice Genome Explorer) integrates genetic and physical mapping informationwith the genome sequence being generated in collaboration with the InternationalRice Genome Sequencing Project (IRGSP). Database links are initiallyevaluated using a query tool to explore and compare data across the riceand maize genome databases and for potential application to multiple-cropdatabase querying. A proposed logistics for interlinking these resources ispresented to integrate, manipulate, and analyze information on the rice genome.One of the biggest challenges of rice bioinformatics lies in the emergingrole of rice as a model system among grass crop species. In view of theimportance of comparative genomics in the formulation of new knowledge onplant genome structure and function, bioinformatics remains an essentialstrategy for gaining new insights into the needs and expectations of ricegenomics.Bioinformatics is a new field that emerged in parallel with the advances achieved ingenomic analysis. Improved techniques in molecular biology played a key role incatalyzing large-scale sequencing of expressed sequence tags (ESTs), construction ofwhole genetic maps with specified markers, physical mapping with large insert-sizelibraries, whole genome sequencing, and transcriptional profiling (Benton 1996). Thisscenario of rapid technology development combined with mass production of genomicdata led to a vital need to transform massive information into more manageableforms by way of bioinformatics. Advances in computer technology including theemergence of the World Wide Web and the Internet, now dominating every aspect ofBioinformatics and the rice genome 293