Open Access Research article

A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R

Jan Bartoš1*, Etienne Paux2, Robert Kofler3, Miroslava Havránková1, David Kopecký1, Pavla Suchánková1, Jan Šafář1, Hana Šimková1, Christopher D Town4, Tamas Lelley3, Catherine Feuillet2 and Jaroslav Doležel15

Author Affiliations

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

2 INRA- Université Blaise Pascal, UMR GDEC 1095, 234 Avenue du Brezet, F-63100 Clermont-Ferrand, France

3 University of Natural Resources and Applied Life Sciences, Department for Agrobiotechnology, Institute for Plant Production Biotechnology, Konrad Lorenz Str. 20, A-3430 Tulln, Austria

4 The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville MD 20850, USA

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

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BMC Plant Biology 2008, 8:95  doi:10.1186/1471-2229-8-95

Published: 19 September 2008



Rye (Secale cereale L.) belongs to tribe Triticeae and is an important temperate cereal. It is one of the parents of man-made species Triticale and has been used as a source of agronomically important genes for wheat improvement. The short arm of rye chromosome 1 (1RS), in particular is rich in useful genes, and as it may increase yield, protein content and resistance to biotic and abiotic stress, it has been introgressed into wheat as the 1BL.1RS translocation. A better knowledge of the rye genome could facilitate rye improvement and increase the efficiency of utilizing rye genes in wheat breeding.


Here, we report on BAC end sequencing of 1,536 clones from two 1RS-specific BAC libraries. We obtained 2,778 (90.4%) useful sequences with a cumulative length of 2,032,538 bp and an average read length of 732 bp. These sequences represent 0.5% of 1RS arm. The GC content of the sequenced fraction of 1RS is 45.9%, and at least 84% of the 1RS arm consists of repetitive DNA. We identified transposable element junctions in BESs and developed insertion site based polymorphism markers (ISBP). Out of the 64 primer pairs tested, 17 (26.6%) were specific for 1RS. We also identified BESs carrying microsatellites suitable for development of 1RS-specific SSR markers.


This work demonstrates the utility of chromosome arm-specific BAC libraries for targeted analysis of large Triticeae genomes and provides new sequence data from the rye genome and molecular markers for the short arm of rye chromosome 1.