Hübner, S., Department of Evolutionary Biology, Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 31905, Israel
Günther, T., Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, D-70593 Stuttgart, Germany
Flavell, A., Division of Plant Sciences, University of Dundee at SCRI, Invergowrie, Dundee 5DA, United Kingdom
Fridman, E., R.H Smith Institute of Plant Science and Genetics in Agriculture, R.H Smith Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel
Graner, A., Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
Korol, A., Department of Evolutionary Biology, Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 31905, Israel
Schmid, K.J., Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, D-70593 Stuttgart, Germany

The domestication of plants frequently results in a high level of genetic differentiation between domesticated plants and their wild progenitors. This process is counteracted by gene flow between wild and domesticated plants because they are usually able to inter-mate and to exchange genes. We investigated the extent of gene flow between wild barley Hordeum spontaneum and cultivated barley Hordeum vulgare, and its effect on population structure in wild barley by analysing a collection of 896 wild barley accessions (Barley1K) from Israel and all available Israeli H. vulgare accessions from the Israeli gene bank. We compared the performance of simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) marker data genotyped over a core collection in estimating population parameters. Estimates of gene flow rates with SSR markers indicated a high level of introgression from cultivated barley into wild barley. After removing accessions from the wild barley sample that were recently admixed with cultivated barley, the inference of population structure improved significantly. Both SSR and SNP markers showed that the genetic population structure of wild barley in Israel corresponds to the three major ecogeographic regions: the coast, the Mediterranean north and the deserts in the Jordan valley and the South. Gene flow rates were estimated to be higher from north to south than in the opposite direction. As has been observed in other crop species, there is a significant exchange of alleles between the wild species and domesticated varieties that needs to be accounted for in the population genetic analysis of domestication. © 2012 Blackwell Publishing Ltd.