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Comparative mapping of DNA sequences in rye (Secale cereale L.) in relation to the rice genome

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Abstract

The rice genome has proven a valuable resource for comparative approaches to address individual genomic regions in Triticeae species at the molecular level. To exploit this resource for rye genetics and breeding, an inventory was made of EST-derived markers with known genomic positions in rye, which were related with those in rice. As a first inventory set, 92 EST-SSR markers were mapped which had been drawn from a non-redundant rye EST collection representing 5,423 unigenes and 2.2 Mb of DNA. Using a BC1 mapping population which involved an exotic rye accession as donor parent, these EST-SSR markers were arranged in a linkage map together with 25 genomic SSR markers as well as 131 AFLP and four STS markers. This map comprises seven linkage groups corresponding to the seven rye chromosomes and covers 724 cM of the rye genome. For comparative studies, additional inventory sets of EST-based markers were included which originated from the rye-mapping data published by other authors. Altogether, 502 EST-based markers with known chromosomal localizations in rye were used for BlastN search and 334 of them could be in silico mapped in the rice genome. Additionally, 14 markers were included which lacked sequence information but had been genetically mapped in rice. Based on the 348 markers, each of the seven rye chromosomes could be aligned with distinct portions of the rice genome, providing improved insight into the status of the rye–rice genome relationships. Furthermore, the aligned markers provide genomic anchor points between rye and rice, enabling the identification of conserved ortholog set markers for rye. Perspectives of rice as a model for genome analysis in rye are discussed.

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Acknowledgments

This work was funded in part by the German Federal Ministry of Education and Research (BMBF) in conjunction with the GABI programme (BMBF Grant #0312289B). Helpful discussion by Dr. B. Truberg on the design of the local relational database is gratefully acknowledged. We are grateful to two anonymous reviewers for their valuable comments on the manuscript.

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  1. J. R. van der Voort

    Present address: Enza Zaden Research and Development B.V., P.O. Box 7, 1600 AA, Enkhuizen, The Netherlands

Authors and Affiliations

  1. Julius Kühn Institute, Federal Research Institute for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany

    B. Hackauf & P. Wehling

  2. Centre for Biotechnology, Tykistökatu 6, 20521, Turku, Finland

    S. Rudd

  3. KEYGENE N.V., P.O. Box 216, 6700 AE, Wageningen, The Netherlands

    J. R. van der Voort

  4. State Plant Breeding Institute, University of Hohenheim (720), Fruwirthstraße 21, 70599, Stuttgart, Germany

    T. Miedaner

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Communicated by M. Xu.

Dedicated to Prof. em. Dr. Dr. h.c. Günter Wricke on occasion of his 80th birthday.

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Hackauf, B., Rudd, S., van der Voort, J.R. et al. Comparative mapping of DNA sequences in rye (Secale cereale L.) in relation to the rice genome. Theor Appl Genet 118, 371–384 (2009). https://doi.org/10.1007/s00122-008-0906-0

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