Identification of genes and pathways associated with aluminum stress and tolerance using transcriptome profiling of wheat near-isogenic lines

Additional file 1:

Microarray data of candidate stress-associated genes. The differential expression between Al-treated and control (non-treated) samples was analyzed to identify genes that are significantly over-expressed two-fold or more. A first round of selection retained 70 genes for which there is at least two wheat lines with p values > 0.001 AND p values > 0.01 in the other two lines. A second round of selection for which there was at least three lines with p values > 0.001 retained an additional 13 genes (in yellow) for a total of 83 candidate genes. A = Atlas66; B = Bounty; C-T = Century-T; C-S = Century-S. Numbers associated with the line's abbreviation (0, 5 or 50) represents the Al concentration in μM while the following letter indicates the biological replicate sample number (S1 to S3).

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Additional file 2:

Microarray data of candidate tolerance-associated genes. The differential expression between Al-treated tolerant and sensitive lines (A 50 – B 5 and C-T 50 – C-S 5) was analyzed to identify genes that are significantly over-expressed two-fold or more in tolerant compared to sensitive lines (ANOVA p values > 0.001 in one pair AND p values > 0.01 in the other pair of wheat lines). Genes on this list that were not differentially expressed between Al-treated and the controls (non-treated) are classified as constitutively expressed. A = Atlas66; B = Bounty; C-T = Century-T; C-S = Century-S. Numbers associated with the cultivar's abbreviation (0, 5 or 50) represents the Al concentration in μM while the following letter indicates the biological replicate sample number (S1 to S3). A: Constitutively expressed candidate genes associated with Al tolerance. B: Up-regulated candidate genes associated with Al tolerance.

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Additional file 3:

Primers used for amplification of different transcripts. The transcripts representing the different probesetIDs boxed in Table 1 and Table 2 were used to design unique primers for qRT-PCR.

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