RGP gmap98
2015/02/12Web Site: http://rgp.dna.affrc.go.jp/E/publicdata/geneticmap98/geneticmap98.html
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/rgp-gmap98/
The database of DNA markers that were used to create the rice genetic map.
README Content
1. Database Component
- README
- The linked list of data
- High-density linkage map information
- List of isozyme loci
- Genotype data
- Linkage order information
- Southern images
2. Data Description
2.1 README
| Data name | README |
| Description of data contents | HTML file to describe "RGP gmap98" data. |
| File | README_e.html(English) |
2.2 The linked list of data
| Data name | The linked list of data |
| Description of data contents | List of link information to related data on each chromosome of rice high-density linkage maps. |
| File | rgp_gmap98_main.zip (355 B) |
Data items are the following:
| Data item | Description |
|---|---|
| Chrom. No. | Chromosome number |
| Genotype data | The link to genotypical data for all segregants (186 individuals) on a simple search site |
| Linkage order | The link to marker information in order of the linkage map on a simple search site |
| Map image file | The link to rice high-density linkage maps on a simple search site |
2.3 High-density linkage map information
| Data name | High-density linkage map information |
| Description of data contents | Information of High-density RFLP (Restriction Fragment Length Polymorphism) linkage map of rice. |
| File | rgp_gmap98_detail.zip (37.2 KB) |
Data items are the following:
| 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 recombinations to those of the loci with the different positions. If "F" is indicated in this column, the minimum position is shown in "Position" column, and the maximum position is shown in "Max" column. |
| Position | The position of the locus from the short arm end. If "F" is indicated in "Floating marker" column, this column is shown the minimum position. |
| Max | If "F" is indicated in "Floating marker" column, this column is shown the maximum position |
| Arm | Chromosome arm was confirmed in strains of telo-torisomy, by markers used to determine the position of the centromere on linkage map |
| Locus name | Locus name |
| Image file name | Parental Southern image file name |
| Accession | DDBJ accession number of the marker |
| Accession 2 | If marker has two accession numbers, another number is shown in this column |
| Orignal clone name | The original name of the clone |
| Protein | Name of the most similar protein appearing in PIR database R48.0 and SWISS-PROT R33 |
| Organism | Organism of the most similar protein appearing in PIR database R48.0 and SWISS-PROT R33 |
| Score | Bits score of the most similar protein appering in PIR database R48.0 and SWISS-PROT R33 |
2.4 List of isozyme loci
| Data name | List of isozyme loci |
| Description of data contents | List of information about a cDNA clone that were mapped in the present high-density linkage map, and that were putatively identified as isozyme genes. |
| File | rgp_gmap98_isozyme_loci.zip (611 B) |
Data items are the following:
| Data item | Description |
|---|---|
| Chrom. No. | Chromosome number |
| Isozyme locus | Isozyme locus |
| Enzyme name | Enzyme name |
| cDNA locus 1 | cDNA locus 1 |
| Position 1 | Position 1 |
| cDNA locus 2 | cDNA locus 2 |
| Position 2 | Position 2 |
| cDNA locus 3 | cDNA locus 3 |
| Position 3 | Position 3 |
| cDNA locus 4 | cDNA locus 4 |
| Position 4 | Position 4 |
2.5 Genotype data
| Data name | Genotype data |
| Description of data contents | Genotype data for all segregants (186 individuals) of each chromosome. |
| File | rgp_gmap98_genotype_data.zip (48.4 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Chrom. No. | Chromosome number |
| Locus | Locus name |
| Genetic code | Genetic code by MAPMAKER |
2.6 Linkage order information
| Data name | Linkage order information |
| Description of data contents | 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. |
| File | rgp_gmap98_linkage_order.zip (8.7 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Chrom. No. | Chromosome number |
| Markers | Marker name |
| Distance | The genetic distance to the next marker (cM) |
| Genotypes | The genotypical number that was observed per each marker in mapping population. codom : Codominant marker +/- : Dominant marker |
2.7 Southern images
| Data name | Southern images |
| Description of data contents | Parental Southern hybridization image files. |
| File | rgp_gmap98_southern_image.zip (69.2 MB) |
3. License
Last updated : 2015/02/12
You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.
The license for this database is specified in the Creative Commons Attribution-Share Alike 2.1 Japan.
If you use data from this database, please be sure attribute this database as follows: "RGP: A HIGH-DENSITY RICE GENETIC MAP © National Institute of Agrobiological Sciences licensed under CC Attribution-Share Alike 2.1 Japan".
The summary of the Creative Commons Attribution-Share Alike 2.1 Japan is found here.
With regard to this database, you are licensed to:
- freely access part or whole of this database, and acquire data;
- freely redistribute part or whole of the data from this database; and
- freely create and distribute database and other derivative works based on part or whole of the data from this database,
under the license, as long as you comply with the following conditions:
- You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any derivative work.
- You must distribute any derivative work based on part or whole of the data from this database under the license.
- You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
National Institute of Agrobiological Sciences
Takashi Matsumoto
E-mail: mat[at]affrc[dot]go[dot]jp
Yuichi Katayose
E-mail: katayose[at]affrc[dot]go[dot]jp
4. Update History
| Date | Update contents |
|---|---|
| 2015/02/12 | RGP gmap98 English archive site is opened. |
| 2013/04/01 | The URL of RGP gmap98 is changed to "http://rgp.dna.affrc.go.jp/E/publicdata/geneticmap98/geneticmap98.html." |
| 1998/01/17 | RGP gmap98 (http://rgp.dna.affrc.go.jp/publicdata/geneticmap98/geneticmap98.html) is opened. |
5. Literature
Y Harushima, M Yano, A Shomura, M Sato, T Shimano, Y Kuboki, T Yamamoto, S Y Lin, B A Antonio, A Parco, H Kajiya, N Huang, K Yamamoto, Y Nagamura, N Kurata, G S Khush, and T SasakiA High-Density Rice Genetic Linkage Map with 2275 Markers Using a Single F2 Population
Genetics January 1, 1998 vol.148 no.1 479-494
PMID: 9475757
6. Contact address
When you have any question about "RGP gmap98", contact the following:2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
National Institute of Agrobiological Sciences
Takashi Matsumoto
E-mail: mat[at]affrc[dot]go[dot]jp
Yuichi Katayose
E-mail: katayose[at]affrc[dot]go[dot]jp