PlantGM: a database for genetic markers in rice (Oryza sativa) and Chinese cabbage (Brassica rapa).

UNLABELLED: The Plant Genetic Map Database (PlantGM) has been developed as a web-based system which provides information about genetic markers in rice (Oryza sativa) and Chinese cabbage (Brassica rapa). The database has three major parts and functions; (1) Map Search, (2) Marker Search, and (3) QTL Search. At present, the database provides characterization information for about 3258 genetic markers. It has 2800 RFLP and 112 QTL markers related to rice in addition to 321 RFLP and 25 PCR-based markers for Chinese cabbage. In addition, a genetic linkage map was also constructed by using 1,054 markers from 2,912 markers in rice. AVAILABILITY: The database is available for free at http://www.niab.go.kr/nabic/PlantGM.

Background

Rice (Oryza sativa) and Chinese cabbage (Brassica rapa)are two of the most important crops in Korea and northeast Asia. Several databases have been constructed: rice [1], Chinese cabbage [2], and rice QTL markers [3] to increase the importance of genetic marker. In rice, several linkage maps based on various genetic markers have been constructed for the purpose of displaying positional relationships among mapped markers in each chromosome [4], identifying a candidate gene by QTL information [5], and matching a gene by combining mapping information [6]. In Chinese cabbage, the maps have been constructed in order to display the 139 RFLP loci organized into ten linkage groups [7] and, to contain the 545 sequence-tagged loci covering 1287 cM [8]. The National Institute of Agricultural Biotechnology (NIAB) has developed a webbased database system to provide information about genetic markers in rice and Chinese cabbage. A subscriber is assisted in tracing new structures of the chromosome and gene positional functions through comparisons using specific genetic markers.

Methodology

Dataset

The information on markers was collected from Brassica rapa genome project [2], rice genome project (Oryza sativa, Tongil: Indica/Japonica) of NIAB [9] in Korea. At present, the markers’ information consist 3,258 markers for rice and Chinese cabbage. It has the 2,800 RFLP and 112 QTL markers related to rice and, added 321 RFLP and 25 PCR-based markers related to Chinese cabbage (Brassica rapa). In order to compare in which get the genetic marker by genome project, additional information of genetic markers were collected from GRAMENE database [10].

Development

The platform was developed by MYSQL and JAVA language, and data was stored in Oracle relational database management system (RDBMS). Using the collected markers, we have developed a genetic linkage map by two stages:(i) polymorphic markers (ii) QTL markers. To construct a genetic map for polymorphic markers, we have analyzed data from 942 polymorphic markers by Kosambi function [11]. The map has been developed by INE (INtegrated rice genome Explorer) method which displays positional relationships among mapped markers in each chromosome [4]. To construct a genetic map for QTL markers, we have analyzed data from 112 QTL markers by Haldane mapping function [12]. The final integrated map was constructed by using 1,054 markers in each 12 chromosomes among 2,912 markers of rice.

Implementation and features

The PlantGM database is a web-based system that will provide information about genetic markers in rice and Chinese cabbage. The database has three major parts and functions namely, map search, marker search and QTL search. The individual data tables are linked to each other through their respective hypertext as shown in Figure 1. A user can access the individual characterization table by clicking a specific marker name on the linked hypertext in search result table (Figure 1). The ’name‘ field provides a detailed table (Figure 1a), which has a records about organism name, genus, species, subspecies, description, reference and image. The double click based hypertext views the characterization information with RFLP-PCR image of Chinese cabbage where applicable (Figure 1b).

Figure 1

A snap shot of the database. The individual view table shows samples of searching result; (a) Marker trait information table (ex: 8_shr-2, seed of rice) by clicking a specific marker name in the upper area (b) Marker trait view table (ex: 97AS1872, RFLP-PCR image of Chinese cabbage)

Discussion

The PlantGM database provides the marker characterization information with phenotype image for rice and Chinese cabbage. The database is constantly updated and hence gives an up-to-date collection. There are 3,258 specific markers which are readily available in the database for rice and Chinese cabbage. A genetic linkage map database system in rice was constructed using the collected 1,054 markers. The genetic map provides locus of marker with linked information for polymorphic markers and QTL marker. It is possible to detect specific markers on each of the 12 chromosomes and the information present with associated trait and a mapped locus on a genetic map in rice using the system.