About This Database

Detailed information of DNA markers

Data description

Data name

DOI

10.18908/lsdba.nbdc00318-03-002

Description of data contents

Detailed information of DNA markers that were used to create the rice genetic map.

Data file

File name :

rgp_gmap2000_marker.zip

File URL :

https://dbarchive.biosciencedbc.jp/data/rgp-gmap2000/LATEST/rgp_gmap2000_marker.zip

File size :

46.7 KB

Simple search URL

http://togodb.biosciencedbc.jp/togodb/view/rgp_gmap2000_marker#en

Data acquisition method

As the source of polymorphic DNA markers for map construction, we used two types of cDNA clones (callus and roots), three types of genomic clones (randomly selected clone, NotI-linking clone, YAC end-clone) and RAPD (Randomly amplified polymorphic DNA) markers, all of which were derived from the japonica rice cultivar, Niponbare. Other DNA clones derived from wheat and other rice varieties were also utilized.

Data analysis method

The probe sizes of the W-markers are the original insert sizes communicated by Dr. Michael Gale, John Innes Centre, Norwich, UK.
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
Locus name	Locus name
Real name	If the polymorphism is detected at multiple locations, the locus name of marker that match the original sequence information is referred to as "Real name". The "Real name" corresponds to the "Marker name" in ""High-density linkage map information".
Restriction enzyme	Names of restriction enzymes to detect the polymorphism between Nipponbare and Kasalath
Nipponbare band size (kb)	Southern band size of Nipponbare (kb)
Kasalath band size (kb)	Southern band size of Kasalath (kb)
Probe size (kb)	Probe size
Vector	Cloning vector
Cloning site	Cloning site
Special primers or restriction enzymes for NotI-linking clone	Special primer set or restriction enzyme set for the preparation of NotI-linking marker
Primer sequence 1	Primer sequence 1 of marker
Primer sequence 2	Primer sequence 2 of marker
PCR protocol	PCR protocol for markers
Image file name	Parental Southern image file name