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Background   Hordeum chilense , a native South American diploid wild barley, is a potential source of useful genes for cereal breeding. The use of this wild species to increase genetic variation in cereals will be greatly facilitated by marker-assisted selection. Different economically feasible approaches have been undertaken for this wild species with limited direct agricultural use in a search for suitable and cost-effective markers. The availability of Expressed Sequence Tags (EST) derived microsatellites or simple sequence repeat (SSR) markers, commonly called as EST-SSRs, for barley ( Hordeum vulgare ) represents a promising source to increase the number of genetic markers available for the  H. chilense  genome.    Results  All of the 82 barley EST-derived SSR primer pairs tested for transferability to  H. chilense  amplified products of correct size from this species. Of these 82 barley EST-SSRs, 21 (26%) showed polymorphism among  H. chilense  lines. Identified polymorphic markers were used to test the transferability and polymorphism in other Poaceae family species with the aim of establishing  H. chilense  phylogenetic relationships.  Triticum aestivum - H. chilense  addition lines allowed us to determine the chromosomal localizations of EST-SSR markers and confirm conservation of the linkage group.    Conclusion  From the present study a set of 21 polymorphic EST-SSR markers have been identified to be useful for diversity analysis of  H. chilense , related wild barleys like  H. murinum , and for wheat marker-assisted introgression breeding. Across-genera transferability of the barley EST-SSR markers has allowed phylogenetic inference within the Triticeae complex.

Transferability and polymorphism of barley EST-SSR markers used for phylogenetic analysis in Hordeum chilense