ORIGINAL PAPER Analysis of the molecular variation between and within cultivated and wild Pistacia species using AFLPs Parvin Salehi Shanjani & Mohsen Mardi & Leila Pazouki & Marianna Hagidimitriou & Damiano Avanzato & S. Mostafa Pirseyedi & Mohammad Reza Ghaffari & S. Mojtaba Khayam Nekoui Received: 9 August 2008 / Revised: 5 November 2008 / Accepted: 4 December 2008 / Published online: 21 February 2009 # Springer-Verlag 2009 Abstract Knowledge of pistachio genetic diversity is necessary for the formulation of appropriate management strategies for the conservation of these species. We analysed amplified fragment length polymorphisms in a total of 216 pistachio accessions, which included seven populations from three wild species (Pistacia vera, Pistacia khinjuk and Pistacia atlantica subsp. kurdica) and most of the important cultivars from Iran, together with some foreign cultivars. High levels of genetic diversity were detected within the Iranian cultivars, and they showed a clear separation from foreign cultivars, as revealed by unweighted pair group method with arithmetic averaging and supported by analysis of molecular variance. The lowest amount of polymorphism was observed in P. atlantica subsp. kurdica, which showed the lowest number of total bands as compared to the other species. This revealed strong genetic erosion of P. atlantica subsp. kurdica, which reflected a severe decline in habitat and over-exploitation. Based on these findings, strategies are proposed for the genetic conservation and management of pistachio species and cultivars. Keywords AFLP . Pistacia . Pistachio . Genetic diversity . Population genetics Introduction Iran is considered to be one of the main centres of genetic diversity for pistachio due to the fact that a large number of cultivated pistachio accessions, in addition to wild species, are found in this region. In total, these species form the major part of Iranian forests. The deciduous, dioecious and wind-pollinated tree species Pistacia vera L. is a member of the Anacardiaceae family. P. vera is the only cultivated and commercially grown species in the genus (Zohary 1996). Pistachio cultivation dates back to ancient times and probably started in an area that is close to the wild stands of pistachio, in the low mountains and foothills of the semi-desert region of south-central Asia. This range extends from northeastern Iran and northern Afghanistan to western Tien-Shan and the Karatau mountains, through Turkmenistan, Uzbekistan, Taji- kistan, Kazakhstan and Kyrgyzstan (Kayimov et al. 2001). From its presumed centre of origin, pistachio cultivation spread first within the ancient Persian Empire and then moved gradually westward. In fact, according to Joret (1976), the name pistachio appears to originate from the Tree Genetics & Genomes (2009) 5:447–458 DOI 10.1007/s11295-008-0198-1 P. S. Shanjani : M. Mardi (*) : L. Pazouki : S. M. Pirseyedi : M. R. Ghaffari : S. M. Khayam Nekoui Department of Genomics, Agricultural Biotechnology Research Institute of Iran, Mahdasht Road, Karaj, Iran e-mail: mardi@abrii.ac.ir P. S. Shanjani Natural Resources Gene Bank, Research Institute of Forests and Rangelands, P.O. Box 13185-116, Tehran, Iran M. Hagidimitriou Pomology Laboratory, Department of Crop Science, Agricultural University of Athens, Athens, Greece D. Avanzato CRA–Istituto Sperimentale per la Frutticoltura di Roma, via di Fioranello 52, 00134 Rome, Italy