Establishing Marker-Marker Correspondences for JRGP and Cornell Rice
Genetic Markers

The markers consist of JRGP2000 map study markers
from(http://rgp.dna.affrc.go.jp/publicdata/geneticmap2000/index.html)
and the RG/RZ markers from the Gramen Cornell Rice Consensus
(http://www.gramene.org/gramene/map/table?class=Map).

Out of 3,267 JRGP and 378 Cornell markers, 2,845 have sequences in
GenBank. Many of the markers have a 3' and a 5' accession or an older
version of the sequence.  And 318 markers are multi-hybridizing markers
that are known to hybridize to multiple locations.  They are deposited in
GenBank under the same accession and usually have A/B/C... suffix after
the marker name.  So in all, 4,205 sequences representing the  markers
were downloaded.

The JRGP markers contain 800 markers without a listed accession marker.
A total of 1,374 genomic and 1,893 cDNA markers are in the JRGP map study.
In the Cornell Rice Consensus, 164 markers are genomic and 214 are cDNAs.

Blatting the file containing the sequences against itself results in
5,316 matches with minScore=120.  Most of these are self-alignments for
each of the sequences.  Deleting these leaves 689 entries.

If accessions A and B align, there will be most of the time two entries
in the blat results: A->B and B->A.  Removing the second of the two
matches leaves 362 matches that contain a total of 352 markers.

Of the 362 matches, 113 are Cornell-JRGP hits; 31 are Cornell-Cornell,
and 218 are JRGP-JRGP matches.  The 362 matches represent 279 unique
marker-to-marker correspondences.

Of the 352 markers, 49 are the multi-hybridizing ones.  Exluding these,
marker correspondencess that from different chromosomes or are more than
30cM apart are flagged as discordant.  A total of 153  correspondences
fall into the discordant category.

The 126 concordant correspondences went into the Map Viewer.

September 10, 2001
