Open Access Research article

Effect of the down-regulation of the high Grain Protein Content (GPC) genes on the wheat transcriptome during monocarpic senescence

Dario Cantu1, Stephen P Pearce1, Assaf Distelfeld12, Michael W Christiansen13, Cristobal Uauy4, Eduard Akhunov5, Tzion Fahima6 and Jorge Dubcovsky1*

Author Affiliations

1 Department of Plant Sciences, University of California Davis, USA

2 Faculty of Life Sciences, Plant Sciences, Tel Aviv University, Israel

3 Aarhus University, Faculty of Agricultural Sciences, Department of Genetics and Biotechnology, Slagelse, Denmark

4 Department of Crop Genetics, John Innes Centre, Norwich, UK

5 Department of Plant Pathology, Kansas State University, USA

6 Department of Evolutionary and Environmental Biology, University of Haifa, Israel

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BMC Genomics 2011, 12:492  doi:10.1186/1471-2164-12-492

Published: 7 October 2011

Additional files

Additional file 1:

Figure S1 - WT and GPC-RNAi plants 22 days after anthesis. Figure S2 - Frequency distribution of lengths of 454 reads (A) and assembled transcripts (B). Figure S3 - Relative distribution of counts coverage of 454 and Illumina data (contigs and singletons). Figure S4 - Boxplots showing the distributions of raw (left) and normalized (right) Illumina counts. Figure S5 - Sample clustering based on counts of Illumina reads mapped on singletons (left) and unigenes (right). Figure S6 - Principal component analysis of the Illumina data. Figure S7 - Transcript levels of isogroups validated by qRT-PCR (Table 1P≤0.05) and not included in Figure 5 across a senescing time course. Table S1 - Summary of 454 sequencing results. Table S2 - Summary of Illumina sequencing results. Table S3 - Summary of Illumina reads counts. Table S4 - Isogroups analysed by qRT-PCR, homeologues, primer sequences and primer efficiencies. Table S5 - Percent distribution of the functional grouping of the singletons based on GO-slim annotation. Table S6 - Abundance of transposable elements in the assembled transcriptome and in the singletons and their differential expression in WT and GPC-RNAi flag leaves.

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Open Data

Additional file 2:

Multi-fasta file with the sequences of 146,671 singletons.

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Open Data

Additional file 3:

Normalized Illumina counts of reads mapped onto 454 contigs with calculated P-values for MWW, edgeR and DESeq statistical analyses. The table includes also isotigs and contigs IDs with the corresponding GenBank accession number and the associated GOSlim terms. Cell color-coding: red color corresponds to ≥2 fold up-regulation, green color corresponds to ≥ 2 fold down-regulation, yellow color corresponds to P≤0.01, and orange color corresponds to P≤0.05.

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Open Data

Additional file 4:

Normalized Illumina counts of reads mapped onto 454 singletons with calculated P-values for MWW, edgeR and DESeq statistical analyses. Cell color-coding: red color corresponds to ≥2 fold up-regulation, green color corresponds to ≥ 2 fold down-regulation, yellow color corresponds to P≤0.01, and orange color corresponds to P≤0.05.

Format: XLSX Size: 2.5MB Download file

Open Data

Additional file 5:

Normalized Illumina counts of reads mapped onto wheat unigenes with the calculated P-values for MWW, edgeR and DESeq. Cell color-coding: red color corresponds to ≥2 fold up-regulation, green color corresponds to ≥ 2 fold down-regulation, yellow color corresponds to P≤0.01, and orange color corresponds to P≤0.05.

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Open Data

Additional file 6:

Set of 815 isogroups differentially regulated at both edgeR and DESeq tests (P≤0.01). Cell color-coding: red color corresponds to ≥2 fold up-regulation, green color corresponds to ≥ 2 fold down-regulation, yellow color corresponds to P≤0.01, and orange color corresponds to P≤0.05. Data are sorted by fold-change.

Format: XLSX Size: 139KB Download file

Open Data

Additional file 7:

Set of 691 isogroups differentially regulated at edgeR (P≤0.01) DESeq tests (P≤0.01) and MWW (P≤0.05) tests. Cell color-coding: red color corresponds to ≥2 fold up-regulation, green color corresponds to ≥ 2 fold down-regulation, yellow color corresponds to P≤0.01, and orange color corresponds to P≤0.05. Data are sorted by fold-change.

Format: XLSX Size: 120KB Download file

Open Data

Additional file 8:

Set of 748 isogroups similar to transposable elements. Cell color-coding: red color corresponds to ≥2 fold up-regulation, green color corresponds to ≥ 2 fold down-regulation, yellow color corresponds to P≤0.01, and orange color corresponds to P≤0.05.

Format: XLSX Size: 164KB Download file

Open Data