Performance of the BAC superpool design in AFLP marker anchoring. (A) Numbers of placed (blue) versus unplaced (light blue) QPPs for markers with an increasing BAC copy number in the physical map. The resolved positive QPP counts show the innate capacity of the pooling design to accurately locate markers in the QPPs, which declines at high marker copy numbers. With the AFLP marker anchoring procedure, this decline in pooling design performance was compensated, and markers with relatively high copy numbers were identified on BAC clones without losses. (B) Distribution of the number of anchored BACs per AFLP marker. This figure closely represents the marker copy number distribution in the BAC pools.