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Open Access 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 Šimková12, Jan Šafář1, Pavla Suchánková1, Pavlína Kovářová1, Jan Bartoš1, Marie Kubaláková12, Jaroslav Janda1, Jarmila Číhalíková12, Rohit Mago3, Tamas Lelley4 and Jaroslav Doležel12*

Author Affiliations

1 Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Sokolovská 6, CZ-77200 Olomouc, Czech Republic

2 Department of Cell Biology and Genetics, Palacký University, Šlechtitelů 11, CZ-78371 Olomouc, Czech Republic

3 CSIRO Plant Industry, GPO box 1600, Canberra, ACT 2601, Australia

4 Department of Agrobiotechnology, IFA-Tulln, Konrad Lorenz Str. 20, A-3400 Tulln, University of Natural Resources and Life Sciences, Vienna, Austria

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BMC Genomics 2008, 9:237  doi:10.1186/1471-2164-9-237

Published: 21 May 2008

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.