Open Access Highly Accessed Research article

From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.)

Grit Haseneyer1, Thomas Schmutzer2, Michael Seidel3, Ruonan Zhou4, Martin Mascher2, Chris-Carolin Schön1, Stefan Taudien5, Uwe Scholz2, Nils Stein4, Klaus FX Mayer3 and Eva Bauer1*

Author Affiliations

1 Plant Breeding, Technische Universität München, Centre of Life and Food Sciences Weihenstephan, 85354 Freising, Germany

2 Bioinformatics and Information Technology, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany

3 MIPS/IBIS, Institute for Bioinformatics and Systems Biology, Helmholtz Centre Munich, German Research Centre for Environmental Health (GmbH), 85764 Neuherberg, Germany

4 Genome Diversity, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany

5 Genome Analysis, Leibniz Institute for Age Research, Fritz-Lipmann-Institute (FLI), 07745 Jena, Germany

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BMC Plant Biology 2011, 11:131  doi:10.1186/1471-2229-11-131

Published: 28 September 2011



The improvement of agricultural crops with regard to yield, resistance and environmental adaptation is a perpetual challenge for both breeding and research. Exploration of the genetic potential and implementation of genome-based breeding strategies for efficient rye (Secale cereale L.) cultivar improvement have been hampered by the lack of genome sequence information. To overcome this limitation we sequenced the transcriptomes of five winter rye inbred lines using Roche/454 GS FLX technology.


More than 2.5 million reads were assembled into 115,400 contigs representing a comprehensive rye expressed sequence tag (EST) resource. From sequence comparisons 5,234 single nucleotide polymorphisms (SNPs) were identified to develop the Rye5K high-throughput SNP genotyping array. Performance of the Rye5K SNP array was investigated by genotyping 59 rye inbred lines including the five lines used for sequencing, and five barley, three wheat, and two triticale accessions. A balanced distribution of allele frequencies ranging from 0.1 to 0.9 was observed. Residual heterozygosity of the rye inbred lines varied from 4.0 to 20.4% with higher average heterozygosity in the pollen compared to the seed parent pool.


The established sequence and molecular marker resources will improve and promote genetic and genomic research as well as genome-based breeding in rye.

EST resource; next generation sequencing; Secale cereale L.; Rye5K SNP array; single nucleotide polymorphisms