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Life Science Database Archive
RGP gmap2000

Detailed information of DNA markers

Data detail

info Data name Detailed information of DNA markers
info DOI 
info Description of data contents 

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

info 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
info Simple search URL 
info 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.

info 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.

info Number of data entries 

3,267 entries

Data itemDescription
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