Genetic relationship of 36 strawberry cultivars was analyzed using three molecular marker systems; inter simple sequence repeats (ISSR), inter-retrotransposon amplified polymorphism (IRAP) and start codon targeted (SCoT) polymorphism. SCoT, IRAP and ISSR primers generated 238, 113 and 122 bands, respectively, of which 85.2, 91.5 and 89.35% were polymorphic. IRAPs with the highest values of expected heterozygosity (He), Shanonn index (I) and resolution power (Rp) were more powerful compared with SCoT and ISSR. However, the highest value of marker index was calculated for ISSRs. The genetic relationships were estimated using Dice similarity coefficient between different pairs of cultivars which varied from 0.577 to 0.901 for SCoT, 0.547 to 0.918 for IRAP, and 0.531 to 0.983 for ISSR. The UPGMA dendrograms using the SCoT and ISSR data classified cultivars into four major clusters; whereas based on the IRAP and combined data, the cultivars were divided into three major clusters. Approximately 50% of the cultivars with affiliation to pedigree and geographic origins were assigned to their major clusters. The results demonstrated that SCoT, ISSR and IRAP marker systems are useful for identification and genetic diversity analysis of strawberry cultivars.
