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

Almudena Castillo1, Hikmet Budak2, Rajeev K Varshney35, Gabriel Dorado4, Andreas Graner5 and Pilar Hernandez1*

Author Affiliations

1 Institute for Sustainable Agriculture (IAS-CSIC), Alameda del Obispo s/n, 14080 Córdoba, Spain

2 Sabanci University, Engineering and Natural Sciences, Biological Science and Bioengineering Program, Orhanli 34956 Tuzla-Istanbul, Turkey

3 International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru – 502 324, Andhra Pradesh, India

4 Dep. Bioquímica y Biología Molecular, Campus Rabanales, C6-1-E17, Universidad de Córdoba, 14071 Córdoba, Spain

5 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany

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BMC Plant Biology 2008, 8:97  doi:10.1186/1471-2229-8-97

Published: 28 September 2008



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.


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.


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.