Rice Genetics IV - IRRI books - International Rice Research Institute

Database structureA characteristic feature of INE is the integrated genetic and physical map of rice. Thehigh-density linkage map currently contains 2,275 DNA markers (Harushima et al1998) and an updated version with about 3,000 markers will be released soon. Informationon the markers includes the probe size, the RFLP pattern as a result of parentalscreening, the sequence data, as well as the results of similarity searches. The markerson the genetic map are traceable to the ordered YAC (yeast artificial chromosome)clones covering 70% of the whole genome (Saji et al 2001). Information on the insertsize of the clones is also provided. At present, approximately 4,500 ESTs are beingassembled in the database. These ESTs were mapped by polymerase chain reaction(PCR) screening of our YAC library and positioned using the YAC physical map as abase (Wu et al 2000). Together with the genetic markers, these ESTs are subsequentlyused for ordering the PAC clone contigs to construct a sequence-ready physical mapthat serves as the template for genome sequencing. Integrating the structural informationof the rice genome allows efficient use of available data particularly in the functionaland applied aspects of genomics.As part of the sequencing effort of RGP, the sequence data for chromosomes 1and 6 are incorporated in INE. The ordered PAC clones in these chromosomes aredisplayed and linked to the sequence of the clone and the annotation of the sequenceusing various similarity searches and gene prediction programs. The annotation pageconsists of the annotation map for each clone and tables summarizing the predictedgenes, including the results of the similarity searches and gene prediction programs.Furthermore, a list of low-quality sequence data is provided in a separate link as arequirement of the IRGSP to maintain an accuracy of less than one error in 10,000base pairs (greater than 99.99%).Navigation and visualizationThe integrated maps for each chromosome facilitate a general overview of the genomicinformation in a particular chromosome. The maps can be manipulated byzoom in/out, which enables browsing at detail-oriented levels. Another distinct featureof INE is the rapid display of integrated maps. This has been achieved by programmingthe viewer in Java language using an application GIOT (Genome Informationdisplay Orderly Tool) developed by Mitsubishi Space Software Co. Ltd. Thisattribute contributes to smooth navigation of specific information associated with eachdata set. Clicking on a particular marker opens a Java applet window containing detailssuch as screening data, image sets, sequences, etc., as well as detailed contigmaps in the case of sequenced regions of the chromosome. These features allow gettingall specific information together with an overall view of the distribution of themarkers and clones in a short time. In addition, different chromosomes can be displayedsimultaneously for direct comparisons between or among chromosomes.The integrated map allows users to correlate various genomic information such asDNA markers, large insert clones, and associated ESTs. The genome sequence canalso be directly traced to the physical and genetic maps. This will undoubtedly providevaluable information for positional cloning of target genes and for analysis of300 Antonio et al