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Physical and Genetic Mapping Information for Rice Genetic Markers
 


To integrate the genetic and physical map positions of rice genetic markers, we collected 13,895 marker sequences from Gramene (649 Cornell markers) and the Japanese Rice Genome Program (13,246 RGP markers). Terminal polyA/polyT and Ns at the ends of marker sequences were then trimmed. The resulting marker sequences were aligned to the MSU Rice Genome Annotation Project pseudomolecules (Version 6.1) if they met a threshhold of greater than 95% identity over a minimum of 90% of the marker sequence length. Alignments for the RGP and Cornell markers were performed independently using the GMAP program. The marker name, marker accession number, chromosome number, cM position, physical position are provided.

Genetic and physical mapping information can be obtained from the following search criteria:
- Using the genetic position on rice chromosome(s)
- Genetic Marker name.
- GenBank Marker accession.

Note: Since the analyses for RGP and Cornell markers were performed separately, the RGP marker data will appear first followed by the Cornell marker data.

Choose chromosome, marker type and genetic map interval:

Chromosome:
Marker Source: RGP Cornell All
Start cM: End cM:
Output:

 HTML(500 rows/page) Tab-delimited Text


To obtain physical and genetic mapping data for a genetic marker:
(e.g., RGP: E4355 or S1176; Cornell: RZ421 or RG2)

Enter the name of the genetic marker:


To obtain physical and genetic mapping information for a particular GenBank accession:
(e.g. D40097 or AU057384)

Enter the GenBank accession here:


 
   
 
For Rice Comments/Questions send mail to the MSU Rice Genome Annotation Project team.
 
Photographs courtesy of Robin Buell (MSU), Jiming Jiang (University of Wisconsin), and the USDA Agricultural Research Service