Efficiency of different PCR-based marker systems in assessing genetic diversity among winter rye (Secale cereale L.) inbred lines

Summary The aim of this study was to investigate the efficiency of ISSR, SSR, and SAMPL marker systems in detecting genetic polymorphism among 30 winter rye inbred lines and to compare the results of cluster analysis performed on data from these marker systems using different statistical methods and coefficients. Each marker system was able to discriminate among the materials analyzed with the lowest value of average genetic similarity (GS) obtained with ISSR markers (0.2888) and the highest with SAMPLs (0.5381). EST-derived SSRs turned out to be less efficient in detecting genetic diversity than those from genomic libraries (average GS values 0.3814 and 0.3221, respectively). The average GS value for combined SSR data was 0.3569. The lack of correlations between similarity and cophenetic matrices obtained with various methods systems suggests that different marker systems should be used simultaneously for a genetic diversity study to exploit as many sources of polymorphisms as possible.