BMC Genomics Research article A novel resource for genomics of Triticeae: BAC library specific for the short arm of rye (Secale cereale L.) chromosome 1R (1RS) Hana Šimková1,2, Jan Šafář1, Pavla Suchánková1, Pavlína Kovářová1, Jan Bartoš1, Marie Kubaláková1,2, Jaroslav Janda1, Jarmila Жíhalíková1,2, Rohit Mago3, Tamas Lelley4 and Jaroslav Doležel*1,2 BioMed Central Open Access Address: 1Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Sokolovská 6, CZ-77200 Olomouc, Czech Republic, 2Department of Cell Biology and Genetics, Palacký University, Šlechtitelů 11, CZ-78371 Olomouc, Czech Republic, 3CSIRO Plant Industry, GPO box 1600, Canberra, ACT 2601, Australia and 4Department of Agrobiotechnology, IFA-Tulln, Konrad Lorenz Str. 20, A-3400 Tulln, University of Natural Resources and Life Sciences, Vienna, Austria Email: Hana Šimková - simkovah@ueb.cas.cz; Jan Šafář - safar@ueb.cas.cz; Pavla Suchánková - suchankova@ueb.cas.cz; Pavlína Kovářová - p.kovarova@centrum.cz; Jan Bartoš - bartos@ueb.cas.cz; Marie Kubaláková - mariek@ueb.cas.cz; Jaroslav Janda - janda@Ag.arizona.edu; Jarmila Жíhalíková - cihal@ueb.cas.cz; Rohit Mago - rohit.mago@csiro.au; Tamas Lelley - tamas.lelley@boku.ac.at; Jaroslav Doležel* - dolezel@ueb.cas.cz * Corresponding author Published: 21 May 2008 BMC Genomics 2008, 9:237 doi:10.1186/1471-2164-9-237 This article is available from: http://www.biomedcentral.com/1471-2164/9/237 Received: 8 December 2007 Accepted: 21 May 2008 © 2008 Šimková et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Genomics of rye (Secale cereale L.) is impeded by its large nuclear genome (1C~7,900 Mbp) with prevalence of DNA repeats (> 90%). An attractive possibility is to dissect the genome to small parts after flow sorting particular chromosomes and chromosome arms. To test this approach, we have chosen 1RS chromosome arm, which represents only 5.6% of the total rye genome. The 1RS arm is an attractive target as it carries many important genes and because it became part of the wheat gene pool as the 1BL.1RS translocation. Results: We demonstrate that it is possible to sort 1RS arm from wheat-rye ditelosomic addition line. Using this approach, we isolated over 10 million of 1RS arms using flow sorting and used their DNA to construct a 1RS-specific BAC library, which comprises 103,680 clones with average insert size of 73 kb. The library comprises two sublibraries constructed using HindIII and EcoRI and provides a deep coverage of about 14-fold of the 1RS arm (442 Mbp). We present preliminary results obtained during positional cloning of the stem rust resistance gene SrR, which confirm a potential of the library to speed up isolation of agronomically important genes by map-based cloning. Conclusion: We present a strategy that enables sorting short arms of several chromosomes of rye. Using flow-sorted chromosomes, we have constructed a deep coverage BAC library specific for the short arm of chromosome 1R (1RS). This is the first subgenomic BAC library available for rye and we demonstrate its potential for positional gene cloning. We expect that the library will facilitate development of a physical contig map of 1RS and comparative genomics of the homoeologous chromosome group 1 of wheat, barley and rye. Page 1 of 9 (page number not for citation purposes)