The long-range restriction map surrounding the mouse agouti locus reveals a disparity between physical and genetic distances.

Isolation of a gene based on its location, which depends on aligning physical landmarks with the genetic map, can yield basic information about genome structure and organization. As a first step toward isolating the mouse agouti (A) locus, we have begun to define the physical position of this gene relative to genetically linked DNA probes from the Psp, Emv-15, and Src loci. Using a combination of pulsed-field gel techniques that include partial digestion with rare-cutting restriction enzymes and analysis of polymorphic sites present in certain inbred strains, we have constructed long-range restriction maps for each of the probes that span a total of more than 3000 kb. The Src and Emv-15 probes are less than 600 kb apart, but are separated from the Psp probe by at least 1500 kb. By determining the position of a 75-kb deletion that inactivates agouti function, we have localized the A locus to within 500 kb of the Psp probe, but more than 600 kb away from the Emv-15 probe. These physical distances contrast with the known recombination frequencies, 3 +/- 3 cM for A-Psp and less than 0.3 cM for A-Emv-15, and suggest that recombination between A and Emv-15 may be suppressed.