Rice TOGO Browser: A platform to retrieve integrated information on rice functional and applied genomics

Abstract

The Rice TOGO Browser is an online public resource designed to facilitate integration and visualization of mapping data of bacterial artificial chromosome (BAC)/P1-derived artificial chromosome (PAC) clones, genes, restriction fragment length polymorphism (RFLP)/simple sequence repeat (SSR) markers and phenotype data represented as quantitative trait loci (QTLs) onto the genome sequence, and to provide a platform for more efficient utilization of genome information from the point of view of applied genomics as well as functional genomics. Three search options, namely keyword search, region search and trait search, generate various types of data in a user-friendly interface with three distinct viewers, a chromosome viewer, an integrated map viewer and a sequence viewer, thereby providing the opportunity to view the position of genes and/or QTLs at the chromosomal level and to retrieve any sequence information in a user-defined genome region. Furthermore, the gene list, marker list and genome sequence in a specified region delineated by RFLP/SSR markers and any sequences designed as primers can be viewed and downloaded to support forward genetics approaches. An additional feature of this database is the graphical viewer for BLAST search to reveal information not only for regions with significant sequence similarity but also for regions adjacent to those with similarity but with no hits between sequences. An easy to use and intuitive user interface can help a wide range of users in retrieving integrated mapping information including agronomically important traits on the rice genome sequence. The database can be accessed at http://agri-trait.dna.affrc.go.jp/.

Fig. 1

The Rice TOGO Browser consists of three viewers: (A) a chromosome viewer that provides an overview of the relative chromosome position of selected genes and traits in the entire genome of rice; (B) an integrated map viewer for the genetic and physical mapping information; and (C) a sequence viewer for a detailed characterization of structural features of the genomic sequence of a gene or chromosomal region.

Fig. 2

Search for a specified region or trait. (A) The result display generated by a search for a genomic region flanked by markers (RM10010 and RM10026) can be viewed as a tabular list and downloaded as a text file. The integrated map viewer with links to ‘RFLP/SSR marker’ and the sequence viewer allow a user to obtain additional information on markers and genome sequence in the selected region. (B) The search for a trait is initiated by selecting a trait category. The chromosome viewer displays the position of the QTLs associated with a phenotypic trait.

Fig. 3

Graphical display of a BLAST NAVi search using the sequence OsNAC2 (AB028181) as a query and the ‘Rice full-length cDNA clones (KOME)’ as the subject. (A) The search result is provided in a graphical view with a designated color for each range of similarity score and a tabular list of the details of subject sequences with similarity to the query sequence. Both AK061745 and AK104626 are derived from the same gene and included no-hit regions in the 3′ end shown in gray. For AK071020, the highest scoring segment pair was obtained only in the 3′ half of the sequence. The ‘View Alignment’ link provides a detailed graphical representation of the alignment for each subject sequence. (B) A detailed graphical view of the high scoring segment pair between the query sequence (AB028181) and AK071020. The similarity of entire regions between the sequences can be examined in detail via two graphical viewers showing the high-scoring regions of the subject sequence mapped to the query sequence (B-1) or the high-scoring regions of the query sequence mapped to the subject sequence (B-2). Clicking the ‘Mapping Hit to Subject’ or ‘Mapping Hit to Query’ button respectively, located at the bottom right corner of the graphical viewer, facilitates this function. (C) Viewer for the no-hit region and a link for downloading the sequence.