Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice Rajeev K. Varshney a , Ralf Sigmund a , Andreas Bo ¨rner a , Viktor Korzun b , Nils Stein a , Mark E. Sorrells c , Peter Langridge d , Andreas Graner a, * a Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany b Lochow-Petkus GmbH, PF 1197, D-29296 Bergen, Germany c Cornell University, Ithaca, NY14850, USA d Australian Centre for plant Functional Genomics, University of Adelaide Waite Campus, PMB1 Glen Osmond, 5064 South Australia Received 10 June 2004; received in revised form 23 July 2004; accepted 3 August 2004 Available online 26 August 2004 Abstract Recent increase in the availability of expressed sequence tag (EST) data has facilitated the development of microsatellite or simple sequence repeat (SSR) markers in a number of plant species groups, including cereals. As these SSRs are derived from ESTs/genes (EST- SSRs), they exhibit a higher potential for transfer through cross-amplification in related species than SSR markers generated from genomic DNA libraries. In this study, a sub-set of 165 EST-SSR markers from a total of 185 assigned to the genetic map of barley was examined for transferability to wheat, rye and rice. A higher proportion, i.e., 78.2% of barley markers showed amplification in wheat followed by 75.2% in rye and 42.4% in rice. Furthermore, in silico comparison of SSR-ESTs (ESTs containing SSRs) corresponding to 185 mapped barley EST- SSR loci against 1,369,182 publicly available cereal ESTs showed significant homology with ESTs of wheat (93.5%), rye (37.3%), rice (57.3%), sorghum (51.9%) and maize (51.9%). Sequence similarity of the barley ESTs with 379,944 ESTs of the two model dicot species, Arabidopsis and Medicago suggested theoretical transferability of barley markers into dicot species although at low frequency (9.7% in Arabidopsis and 8.6% in Medicago). In silico comparative mapping (sequence comparison) of mapped barley SSR-ESTs against the mapping data of rye, wheat and rice indicated the presence of orthologues of the barley SSR-ESTs in the respective species. Furthermore, nine barley EST-SSRs were experimentally mapped to a rye genetic linkage map and all could be located in the expected orthologous region compared to their position in barley. # 2004 Elsevier Ireland Ltd. All rights reserved. Keywords: EST-SSRs; SSR-ESTs; Microsatellites; Transferability; Comparative mapping; Barley 1. Introduction The advent of DNA marker technology has facilitated the rapid generation of many high-density genetic and physical maps and has permitted genetic map comparisons through the use of common markers between both closely and, less commonly, distantly related species. Despite the fact that the genome size of cereals varies up to 40-fold, comparative genetic mapping among several species of Poaceae has revealed extensive genome colinearity [1,2]. In this context, it has proved possible to demonstrate that 30 linkage blocks from the rice genetic map are sufficient to reconstitute the seven Triticeae (e.g., wheat (Triticum aestivum L.), rye (Secale cereale L.) and barley (Hordeum vulgare L.)), 12 rice and the 10 maize chromosomes [1]. Among the different kinds of molecular markers that are available, restriction fragment length polymorphisms (RFLPs) provided the major means for resolution of genomic conserved synteny and colinearity. Because of their hybridization-based ability to identify orthologous DNA fragments, even if sequence conservation is as low as 70%, comparative mapping could be performed in a number of plant species including cereals (e.g., [3–5]). Due to their simple and cost-effective www.elsevier.com/locate/plantsci Plant Science 168 (2005) 195–202 * Corresponding author. Tel.: +49 39482 5521; fax: +49 39482 5155. E-mail address: graner@ipk-gatersleben.de (A. Graner). 0168-9452/$ – see front matter # 2004 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.plantsci.2004.08.001