Biton, I., Institute of Plant Science, Volcani Center, Agricultural Research Organization (ARO), P.O. Box 6, Bet-Dagan, Israel
Doron-Faigenboim, A., Institute of Plant Science, Volcani Center, Agricultural Research Organization (ARO), P.O. Box 6, Bet-Dagan, Israel
Jamwal, M., Institute of Plant Science, Volcani Center, Agricultural Research Organization (ARO), P.O. Box 6, Bet-Dagan, Israel
Mani, Y., Institute of Plant Science, Volcani Center, Agricultural Research Organization (ARO), P.O. Box 6, Bet-Dagan, Israel
Eshed, R., Institute of Plant Science, Volcani Center, Agricultural Research Organization (ARO), P.O. Box 6, Bet-Dagan, Israel
Rosen, A., Institute of Plant Science, Volcani Center, Agricultural Research Organization (ARO), P.O. Box 6, Bet-Dagan, Israel
Sherman, A., Institute of Plant Science, Volcani Center, Agricultural Research Organization (ARO), P.O. Box 6, Bet-Dagan, Israel
Ophir, R., Institute of Plant Science, Volcani Center, Agricultural Research Organization (ARO), P.O. Box 6, Bet-Dagan, Israel
Lavee, S., Institute of Plant Science, Volcani Center, Agricultural Research Organization (ARO), P.O. Box 6, Bet-Dagan, Israel, Institute of Plant Science, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel
Avidan, B., Institute of Plant Science, Volcani Center, Agricultural Research Organization (ARO), P.O. Box 6, Bet-Dagan, Israel
Ben-Ari, G., Institute of Plant Science, Volcani Center, Agricultural Research Organization (ARO), P.O. Box 6, Bet-Dagan, Israel

The olive (Olea europaea L.) was domesticated in the Mediterranean area over 6000 years ago and is currently one of the area’s most important oleaginous crops. Due to its economic, cultural and ecological importance, breeding programs aimed at obtaining new olive cultivars have been developed in most olive-producing countries. An efficient breeding program requires a large and genetically variable germplasm collection. In this study, we used next-generation sequencing technology for the identification of 145,974 single nucleotide polymorphism (SNPs) loci. A subset of 138 SNPs was then used to analyze the genetic relationships between 119 cultivars making up most of the Israeli germplasm collection. The various cultivars did not cluster according to their geographic origin but rather showed a high correlation with their function (oil, table or dual purpose). Comparison of genetic diversity between 15 cultivars using SSRs and SNPs revealed that for the purposes of analyzing genetic variation between olive cultivars, the SSR marker seems more suitable. However, based on the analysis of several trees of the same cultivar sampled from different nurseries, the SNP marker proved to be a more reliable criterion for cultivar identification. This study presents the most comprehensive SNP analysis of olive phylogeny to date. Based on the rapid development of SNP genotyping methods over the last few years, we believe that in the near future, we will be able to genotype many sample genomes using the appropriate SNPs at a reasonably low cost. Therefore, we can expect that in the future, SNPs will definitely be the marker of choice for biodiversity analysis as well as for gene cloning and QTL identification in olives. © 2015, Springer Science+Business Media Dordrecht.