Effective pairwise combination of long primers for RAPD analyses in roses

Twenty-four primers of different lengths (eight each of 10, 15 and 20 bp) were tested each in RAPD reactions with DNA of Rosa multiflora and Rosa canina. The reactions with single primers of a particular length were compared with all 28 pairwise combinations within each length class in both single primer reactions and in primer combination reactions. All primer classes produced fragment patterns of comparable complexity. However, the number of new fragment patterns and the number of fragments containing repetitive DNA was dependent on the primer length. Combinations of long 15- and 20-mer primers produced more new fragments and a lower amount of repetitive DNA than shorter 10-mer primers. Implications for the use of long primer combinations in projects which require large marker numbers are discussed in comparison with other marker systems.