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A transcriptome map of perennial ryegrass (Lolium perenne L.)

Bruno Studer1*, Stephen Byrne1, Rasmus O Nielsen2, Frank Panitz2, Christian Bendixen2, Md Shofiqul Islam1, Matthias Pfeifer3, Thomas Lübberstedt4 and Torben Asp1

Author Affiliations

1 Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Centre Flakkebjerg, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark

2 Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Centre Foulum, Aarhus University, Blichers Allé 20, 8830, Tjele, Denmark

3 Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany

4 Department of Agronomy, Iowa State University, 1204 Agronomy Hall, 50011, Ames, IA, USA

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BMC Genomics 2012, 13:140  doi:10.1186/1471-2164-13-140

Published: 18 April 2012

Additional files

Additional file 1:

Figure S1. SNP validation by high resolution melting (HRM) curve analysis (A) and direct sequencing of PCR fragments (B). (A) shows the normalized melting curves of a target SNP for twelve mapping individuals along with the parental genotypes that were used for short amplicon melting as described by Studer et al. [77]. The melting curves given in grey represent individuals being homozygous for the target SNP, while red melting curves indicated heterozygous individuals. The sequencing trace file given in (B) illustrates the results from direct sequencing of PCR products amplified from the parental genotype being heterozygous for the target SNP. Sequencing of PCR fragments was performed at Eurofins MWG Operon, Ebersberg, Germany.

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Additional file 2:

Detailed description of SNP markers. This table contains the unigene names and GenBank accession numbers along with detailed mapping information (the linkage group and map position) and the SNP polymorphism used for GoldenGate genotyping.

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Additional file 3:

Figure S2.Heat map of DNA markers on the perennial ryegrass transcriptome map. Marker density on each linkage group (LG) was visualized as heat maps by counting the number of markers in a window of 3 centi Morgan (cM) size shifted in 0.3 cM steps along a LG using an in-house python script. Color scale was adapted to the minimum (dark blue = 0 marker/2 cM) and maximum (red = 17 to 52 marker/3 cM) window counts, adjusted for each LG separately.

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Additional file 4:

Figure S3.Summary of unigene annotation. The 732 non redundant Lolium unigenes were subjected to a BLASTN search against the non-redundant (nr) nucleotide database of Genbank, mapped and functionally annotated based on Gene Ontology (GO) using the Blast2GO search tool [56].

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Additional file 5:

Figure S4. Description of biological processes affected by mapped Lolium unigenes. Biological processes were determined based on Gene Ontology (GO) using the Blast2GO search tool [56]. The number of mapped unigenes involved in a specific process is given in parenthesis.

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Additional file 6:

Figure S5.Description of cellular components involved in molecular functions of mapped Lolium unigenes. Mapped unigenes were allocated to cellular components based on Gene Ontology (GO) using the Blast2GO search tool [56]. The number of unigenes for each cellular component is given in parenthesis.

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