Patent ID: 7300751

Claim:
A method for identifying genetic markers comprising: (a) obtaining genomic DNA from a first source having a first phenotype or trait of interest; (b) digesting said DNA with at least one restriction endonuclease having a degenerate recognition or cleavage sequence comprising at least one degenerate base, wherein: (i) said degenerate sequence is represented by the formula N m , where N is the extent of degeneracy, and m is the number of degenerate bases; and (ii) said at least one restriction endonuclease having a degenerate recognition or cleavage sequence comprising at least one degenerate base is selected from the group consisting of three base cutters, four base cutters, five base cutters, and six base cutters, not including degeneracy, (iii) to produce restriction fragments having N m different single-stranded overhangs for each restriction endonuclease; (c) ligating restriction fragments having identical overhangs with a series of adapters whose sequences are complementary to said overhangs; (d) amplifying said restriction fragments; (e) separating said amplified restriction fragments to produce a restriction fragment pattern; (f) obtaining genomic DNA from at least one additional source having a second phenotype or trait of interest; (g) repeating b) through e) for said DNA from said at least one additional source; (h) comparing the restriction fragment patterns from each source; (i) selecting restriction fragments associated with a phenotype or trait of interest; and (j) using said selected restriction fragments as markers for said phenotype or trait of interest.