Method for identification of genetic markers

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 said degenerate sequence represented by the formula Nm, where N is the extent of degeneracy, and m is the number of degenerate bases, to produce restriction fragments having Nm 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.