Genetic relations among some closely related Iranian pomegranate genotypes were investigated. Ten primer combinations and one E+AGA-M+CGA combination were used for detecting alliance among Iranian pomegranate individuals and genotypes with similar names, from Yazd and Isfahan areas. Maximum similarity (79.1%) existed between two local cultivars Dabbei Bam and Dokhtar Hamoomi while a minimum occuring (20.3) in Poost Siah and Ameneh Khatooni cultivars. The two latter cultivars from two distinct geographical regions of Yazd & Isfahan were used for comparison. At the similarity level of 64%, seven cultivars were categorized in two distinct groups while the remaining four, each in a separate group. Despite the low level of detected polymorphism by AFLP, differences were observed among genotypes in one cultivar as well as between the two geographical regions.
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