Canola (rapeseed) is one of the oilseed plants which is superior to other cultivated oilseeds in Iran due to appropriate and positive agronomical traits. Canola is cold tolerant, relatively tolerant to water-limited situations, better tolerant of saline conditions, and has high rotation value. It also has both spring and winter genotypes and eventually higher oil yield in unit area. Information on genetic diversity of crops has a great deal of importance in order to conserve genetic resources and germplasm, to develop genetic background and also its application in breeding programs. Hence, Brassica wild relatives have desirable and suitable agronomical traits such as cytoplasm and nuclear male sterility, resistance against diseases, insects and nematodes, tolerance to cold, salinity and drought stresses they can be exploited in breeding programs. To investigate the intra and inter- species genetic diversity of Brassica based on morphological characteristic and ISSR markers two experiments were conducted during 2012-2013. In the first study, genetic diversity between 36 accessions of six Brassica species was evaluated for morphological traits using multivariate statistical analysis. The results indicated considerable variation in the studied germplasm for all traits. Cluster analysis based on morphological traits could separate genotypes of different species from each other. In the second study, genetic diversity between 56 accessions belonging to ten species was evaluated using ISSR technique. From the 23 primers used, 186 polymorphic markers were scored to differentiate between accessions. Accordingly ISSR analysis revealed that cultivated B. napus accessions were less diverse than other species. Applying UPGMA method of cluster analysis could separate species appropriately from each other. Principal coordinate analysis (PCoA) confirmed the result of cluster analysis. Results of molecular variance analysis (AMOVA) based on species, showed that 35.46% of diversity was related to between species and the remnant was attributed to diversity within species. Results obtained from present study pointed out a low correlation (0.05%) between clustered diagrams created from morphological data and using ISSR markers data. Nevertheless, using ISSR marker in comparison with morphological data, genetic similarity between studied accessions was much better determined implying the ISSR marker efficiency in distinguishing species of Brassica genus. Keywords: Brassica , morphology, ISSR, molecular, cluster analysis, phylogeny, genetic similarity
