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Data name ⇅	Database name ⇅	DOI ⇅	Description of data contents ⇅	Data acquisition method ⇅	Data analysis method ⇅	Data detail
Detailed information of DNA markers	RGP gmap2000	10.18908/lsdba.nbdc00318-03-002	Detailed information of DNA markers that were used to create the rice genetic map.	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.	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.	Data detail open_in_full
High-density linkage map information	RGP gmap2000	10.18908/lsdba.nbdc00318-03-001	Information of High-density linkage maps of rice RFLP (Restriction Fragment Length Polymorphism).	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".	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.	Data detail open_in_full
Genotype data	RGP gmap98	10.18908/lsdba.nbdc00318-02-004	Genotype data for all segregants (186 individuals) of each chromosome.	These data are the results of linkage analysis that used 186 F2 plants from a single cross between Nipponbare and Kasalath.	Linkage analysis was performed using MAPMAKER/EXP 3.0.	Data detail open_in_full
High-density linkage map information	RGP gmap98	10.18908/lsdba.nbdc00318-02-002	Information of High-density RFLP (Restriction Fragment Length Polymorphism) linkage map of rice.	We used a marker derived from a cDNA clone of Nipponbare. The position of the locus has been identified by examining a recombination value between Nipponbare and Kasalath experimentally. An annotation for the sequence of the marker was estimated using a protein database. 1174 points are discrete positions on the map; each chromosome, 159, 129, 148, 95, 107, 104, 88, 83, 54, 68, 79, 60.	The 186 F2 plant mapping population used was derived from rice cultivars Nipponbare and Kasalath. The main sources of the markers in this map derives from various cDNA libraries of Nipponbare, and markers are indicated by clone names denoted with C, R, G, Y, L, P, T, W, B, M, V or TEL numbers. The first letter of the marker name indicates the category of mapped clones as follows: C, cDNA clones derived from callus library; R, cDNAs from root library; G, random genomic clones; Y, YAC-end clones; L, NotI-linking clones; P, randomly amplified polymorphic DNAs; T, STS markers; W, wheat clones; B, barley clones; M, maize clones; TEL, telomere-associated sequences; S, cDNAs from etiolated shoot (S with numbers < 10,000) and green shoot (S with numbers > 10,000); F, cDNAs from shoot of a near-isogenic line; and V and other symbols (Ky4, Kyu08, Kyy03, SINE1_r6), clones derived from other rice varieties. W numbers correspond to the PSR numbers of clones developed by M. D. Gale (John Innes Centre, UK). Markers denoted with a V contain both genomic and cDNA clones including SINE1r6 isolated in other works. Letters A, B, C and D following the clone number indicate that those loci were assigned by mapping with one of the polymorphic DNA fragments of the multiple copy sequences. L and R following the Y number marker indicate left and right end clones, respectively, of YAC clones. Name etc of protein coded by determination of location of RFLP markers were estimated by a similarity search in both the PIR (Rel.48.0) and SWISS-PROT (Rel.33) protein databases.	Data detail open_in_full
Linkage order information	RGP gmap98	10.18908/lsdba.nbdc00318-02-005	About the 1174 frame markers of the linkage map, following informations were listed by each chromosome; marker names, genetic distance to the next marker, number of genotyped plants, and genetic types of marker.		Preferred orders of markers with different positions on entire chromosomes were checked by the "ripple" command with window size 5 and an LOD threshold of 2.0.	Data detail open_in_full
Data name	Database name	DOI	Description of data contents	Data acquisition method	Data analysis method	Data detail