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About This Database

High-density linkage map information

Data description
Data name
High-density linkage map information
DOI
10.18908/lsdba.nbdc00318-03-001
Description of data contents
Information of High-density linkage maps of rice RFLP (Restriction Fragment Length Polymorphism).
Data file
File name :
rgp_gmap2000_main.zip
File URL :
File size :
30.0 KB
Simple search URL
http://togodb.biosciencedbc.jp/togodb/view/rgp_gmap2000_main#en
Data acquisition method

The rice RFLP linkage map was composed of a combination of nearly 1000 new RFLP marker and markers described in "A High-Density Rice Genetic Map 1998", which contains total 3267 DNA markers.
For the RFLP analysis of additional markers, we often used the 3' untranslated region (UTR) of a cDNA fragment as a probe rather than the whole insert. In such a case, the marker name ends with the letter S. To amplify the 3'UTR as well as the desired portion of the insert, use the universal primer M13RV and the appropriate specific primer that can be designed using sequence data of the 3' ends.
The marker designation and other miscellaneous details follow the data at "A High-Density Rice Genetic Map 1998".
Data analysis method

This table includes the map position of each marker from the telomeric end of the short arm of each chromosome (genetic distance in cM), the chromosome number, the marker name, and (where available) DDBJ accession numbers of the sequences of both the 5' and 3' ends of insert fragments of the probes used in the RFLP analysis.
Further analysis was performed with MAPMAKER/EXP 3.0.
Number of data entries

3,267 entries
Data detail
Data item Description
Chrom. No.

Chromosome number
Floating marker

Floating marker."F" in this column indicates that the segregation data of the locus did not show any recombination to the loci with the different positions.If "F" is indicated in the column, the minimum position is shown in column "position" and the maximum position is shown in column "max".
Position

The genetic distance of the locus from the short arm end.If "F" is indicated in "Floating marker" column, the minimum position is shown in this column.
Max

If "F" is indicated in "Floating marker" column, the maximum position is shown in this column.
Marker name

Marker name: The "Marker name" corresponds to the "Real name" in "Detailed information of DNA markers".
Accession 5'_1

The DDBJ sequence accession number for 5' end of insert fragment that was used as a probe.
Accession 5'_2

If there are two accession numbers for 5' end, another number is shown in this column.
Accession 3'

The DDBJ sequence accession number for 3' end