Genus Allium includes some economically important species like common onion, garlic, chives, and leek under worldwide cultivation. In this study, genetic diversity of some cultivars belonging to three species (Allium sativum L., Allium cepa L. and Allium currat L.) of this genus was investigated using sixteen SSR and three ISSR primers. All primers generated a total of 100 fragments, distributed as, 39% monomorphic, 33% polymorphic and 28% unique. The percentage of polymorphism identified by SSR and ISSR primers varied between 25 and 92.9%. With the highest variability detected for SSR and ISSR regions, the results of similarity demonstrated the presence of a concealable relationship amongst Allium species with a significant degree of similarity among clones belonging to the same species of this genus. DNA sequence of the monomorphic band generated from the five clones and cultivars used in the present work by one of the SSR primers (Asa20) were aligned together and with the earlier obtained sequences belonging to different genera and species. Although all of these sequences were obtained from one monomorphic band using the same primer, the pairwise alignment of the two onion clones showed only 75.49% of homology and nearly the same percentage of homology (73.76%) was obtained between the sequences generated from the two garlic clones. The dendrogram based on genetic similarities between cultivars showed three major clusters. Cluster 1 included only the Egyptian Leek cultivar; cluster 2 comprised the two garlic clones and cluster 3 composed of the two onion cultivars. Generally, the present results corroborate the idea that SSR and ISSR techniques seems to be a convenient tool for genetic diversity of the genus Allium.

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