Flow diagram of the AFLP marker anchoring procedure of the potato AFLP physical map. The anchoring procedure is illustrated for genetic marker EAAGMCGA_326.6. (A) The marker from parent RH is traced back in the original radioactive gel of the genetic map. (B) As an intermediate step, a new radioactive gel is made with primer combination EAAGMCGA of the parental DNAs and 21 of the BAC superpools, and the position of the marker is identified. (C) The full set of BAC pools is examined with primer combination EAAGMCGA using capillary electrophoresis. The position of the marker is identified in these capillary fingerprints by comparison of the patterns of the first 21 lanes to those in (B). The band scoring interval of marker EAAGMCGA_326.6 was set to 324.0-324.3 bp and the average size was measured to be 324.1 bp. (D) Fingerprint bands are scored within this size interval and from the 31 positive superpool lanes (A02....H12) a list of quarter plate pool IDs is generated (001Q1... 192Q3) that are candidates for having the marker. (E) Seven of the QPP's identify the contig with the marker in the physical map, on the basis of matching BACs that have the marker band (e.g. BAC RH042F12 is from well F12 of library plate number 042, which is present in quarter plate pool 042Q4).