Rice Integration Map

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Rice Integration Map

The Rice Integration Map is described in: Chen, M., G. Presting, W. Barbazuk, J. Goicoechea, B. Blackmon, H. Kim, G. Fang, D. Frisch, Y. Yu, S. Higingbottom, J. Phimphilai, D. Phimphilai, S. Thurmond, B. Gaudette, P. Li, J. Liu, J. Hatfield, S. Sun, K. Farrar, C. Henderson, L. Barnett, R. Costa, B. Williams, J. Gilbert, S. Walser, M. Atkins, C. Hall, I. Bancroft, J. Salse, F. Regad, T. Mohapatra, N. Singh, A. Tyagi, C. Soderlund, R. Dean, R. Wing (2002). An Integrated physical and genetic map of the rice genome. Accepted in Plant Cell - March Issue.

CUGI was funded by Novartis to fingerprint the Rice nipponbare library. The clones were digested with HindIII, run on agarose gels, band-called using Image, and automatically assembled using FPC. The average band size is 28, and the contigs were assembled at a 1e-12. The contigs were manually edited to join contigs, no manual editing was performed on the order of the clones (see Band Quality below). 79% of the genome is covered by anchored contigs.

Monsanto has a 5x draft sequence of a minimal tiling path of clones. In collaboration with Monsanto, this sequence was used to join contigs. This was done by BLAST'ing the sequence against the BAC ends, creating markers of the sequenced clones, and attaching the BAC markers to clones in which they have a high hit to one of the BESs. These can be viewed in WebFPC as the OJ markers.

This rice integraion map was frozen in the fall of 2001.

Contig Sizes
Clone Cov Marker Anchor Contig Single >200 200:101 100:51 50:26 25:10 9:3 =2 >5Q
66384 20x 3348 1749 457 2778 107 99 58 37 41 47 68 -

Select large WebFPC or small WebFPC See the documentation for platforms its been tested on and how to use.

The current FPC rice map is continually being updated. The sequenced contigs between the two maps are linked by the rice status page.


  • Clones starting with 'a' are from our HindIII library (AGI name OSJNBa).
  • Clones starting with 'b' are from our EcoRI library (AGI name OSJNBb).
  • Clones starting with 'OJ' are from Monsanto.
  • Clones starting with 'PAC' are from the RGP.
  • Clones with a 'sd1' are sequenced clones that have been digested using the Fsd program and entered into FPC. If a clone is larger than 150kb, its will be broken up into 80% overlapping clones numbered sd2, etc.

Sequenced Clones:

  • Yellow: SD clones (end with "sd1"), sequenced clones from genbank that have been digested. These clones have been placed in contigs by finding the highest hit based on a 1e-10 cutoff, and adding the clone in that position.
  • Gray: The corresponding AGI clone, if one exists.
  • Orange: Clones that have been selected from sequencing, but are not submitted to Genbank.
  • Note: In WebFPC, the number of sequence clones is often twice as many as there really is since its counting both the Yellow and gray clones. I need to fix this.


  • The anchored markers (shown along the bottom of each contig) are from the Japanese high density linkage map.
  • A remark is associated with each clone that has marker results from an external laboratory.
  • The markers starting with an "OJ" are BAC markers, as desribed in the manuscript.

Band Statistics:

Diff Number Percent
0 14271 75.2
1 1347 7.1
2 1038 5.5
3 812 4.3
4 625 3.3
5 400 2.1
6 286 1.5
7 186 0.9
Bands are selected interactively using Image. Our highly trained band callers have produced high quality bands. Comparing duplicate gels from 678 clones, the table shows the number of bands the have the same value (Diff=0), a value difference of 1 (Diff=1), etc. The remaining 5.8% of the bands did not a have a mate, indicating a F+, F- or a difference greater than 7. As shown in Soderlund et al. (Genome Research 10:1772), the higher the quality of data, the higher precision of the clone coordinates, hence, the order of the close is close to correct, though there will be some slipage of coordinates.

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