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

For all author emails, please log on.

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

Published: 28 September 2011

Additional files

Additional file 1:

Set of plant tissues for RNA extraction. RNA of each rye inbred line was extracted from plant tissues exposed to various stress treatments and harvested at different developmental stages.

Format: XLS Size: 33KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

Establishment and description of the Sce_Assembly02 generated for in silico SNP mining. The Sce_Assembly02 was performed in three steps using the MIRA assembler V2.9 on integrated standard settings: Firstly, raw sequence reads surpassed a quality filtering process where 454 sequencing adapter and cDNA synthesis primer sequences as well as low quality reads were removed. Secondly, the cleaned and trimmed sequence reads were subjected to a line-specific assembly where reads of each inbred line were aligned in a separate assembly run. Non-aligned reads in the line-specific assemblies, i.e. singletons, were rejected. Thirdly, those reads that merged into contigs in the line-specific assemblies were moved further to the Sce_Assembly02 starting again with the cleaned and trimmed reads, but now from all five inbred lines. This strategy resulted in contig sequences that were used for SNP detection and subsequently for the design of the high-throughput genotyping SNP array. With regard to SNP discovery this assembly allowed the deduction of critical information about the SNP position like allele coverage.

Format: XLS Size: 36KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

GigaBayes parameters. Only parameters different from GigaBayes program default settings are listed.

Format: XLS Size: 25KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

Association of multi-line and single-line contigs of the Sce_Assembly03 to the Brachypodium chromosomes Bd1 to Bd5. The four heatmaps per chromosome are depicting the density of Brachypodium genes, homologous rye sequences, contigs represented on the Rye5k SNP array, and SNPs that were heterozygous among 59 rye inbred lines (from top to bottom) by going along the Brachypodium chromosomes in a sliding window with 0.5 Mb window size and a 0.1 Mb shift and determining for each window the number and percent bp coverage of the respective tagged genes. The density values were corrected for the number of Ns per window, if the N content exceeded 60% the value was set to zero and drawn in white color. The number was extrapolated to number per Mb to facilitate comparisons. The heatmaps were created from density values using the Python pylab module in combination with the jet colormap (low to high values from blue to red). Minimum, maximum, and mean number of genes/Mb in Brachypodium and hits/Mb in rye, respectively, were given on the left of each map. The ruler on top gives the chromosome length in Mb.

Format: PNG Size: 306KB Download file

Open Data

Additional file 5:

GO categories found in the Sce_Assembly03 multi-line and single-line contig sequences on Blast2GO level 2. Categories with an occurrence less than 0.05% were summarized in "others".

Format: PNG Size: 312KB Download file

Open Data

Additional file 6:

SSR motifs detected in 338,536 contigs of the five line-specific assemblies. Mononucleotide repeat motifs were discarded. Mixed motifs describe two close SSR motifs which are separated by less than 100 bp.

Format: XLS Size: 18KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 7:

Description of the Rye5K SNP array. SNP containing contigs represented on the Rye5K SNP array were listed including candidate SNP position, probe design sequences provided to Illumina Inc. (San Diego, USA), and GO annotations.

Format: XLS Size: 1.6MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 8:

Observed residual heterozygosity of 54 rye inbred lines representing the two heterotic pools. Heterozygosity was calculated based on genotyping data obtained with the Rye5K SNP array. Lines from the pollen parent pool were in generations F3 to F4, lines from the seed parent pool were in generation F6.

Format: XLS Size: 25KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data