Comparison of RAPD, STS, ISSR and AFLP molecular methods used for assessment of genetic diversity in hop (Humulus lupulus L.)

The cluster analysis of ten hop (Humulus lupulus L.) varieties and the comparison of amplified DNA polymorphism were assessed using RAPD, STS, ISSR and AFLP molecular methods. Thirty-five RAPD primers generated an average of 13.4 products with 5.7 polymorphic products (42.3% of polymorphism). Ten STS primer combinations generated an average of 9.3 products with 6.6 polymorphic products (71% of polymorphism). Seven ISSR microsatellite polymorphic primers and seven primer combinations generated an average of 12.9 products with 4.2 polymorphic products (32.6% of polymorphism) in agarose gels and 86.2 products with 24.3 polymorphic products (28.3% of polymorphism) in polyacrylamide gels. A total of 56 AFLP primer combinations generated an average of 91 products with 52.5 polymorphic products (57.6% of polymorphism). All molecular methods accurately distinguished all tested varieties, except for Osvald's clones (31, 72 and 114), which were only distinguished by AFLP. The similarities between varieties were revealed by cluster analyses. These analyses were very similar for all molecular methods. Pairwise values of JCS (Jaccard's similarity coefficient) ranged from 0.02 to 1.0 and the mean JCS values ranged from 0.395 (AFLP) to 0.462 (ISSR). The highest correlation coefficient was between ISSR and RAPD (0.966) and the lowest was between AFLP and STS (0.867). STS had the highest correlation of chemical data with molecular methods (0.592) and ISSR had the lowest (0.435).