For TFG, the nutrient, light, and accession effects were all significant, but no G×E effects were significant.
Year and accession effects were assessed by two-factor analysis of variance with [R] software (R Development Core Team 2005).
For each accession, the effect of virus infection on the production of viable seeds was estimated as the ratio of seed number in infected vs. mock-inoculate plants multiplied by the percentage seed germination, and CMV virulence as V = 1 SNixSGi)/ SNmxSGm).
In addition to this accession-specific effect, the cold acclimation process most significantly affected proteins related to processes involved in photosynthetic light reactions and the Calvin cycle (Additional file 4: Table S2).
For group 1, most infected plants showed biomass values below the intersect of the two regression lines, indicating that for these accessions the effect of virus infection on seed weight was relatively smaller than on biomass (Fig. 3B).
To determine whether either one of these modifier loci might be responsible for the accession-specific effect of nrpd1a-8 on SI, markers tightly linked to these modifiers were used to analyze F2 progenies of the Col-0 nrpd1a-8[ SRKb] × C24 WT[ SRKb-SCRb] cross.
The regulation of these genes in response to As stress demonstrated the does-response and accession-specific effects.
The most dominating accession-specific effects in the phosphoproteome were found to comprise processes of membrane transport and trafficking, modulation of transcription factors and ubiquitination (Additional file 6: Table S4).
To filter out any line- or accession-specific effects, independent transgenic lines in the C24 background, line RS13 [ 20], and in the Col background, line G [ 6], were assayed.
Two-way analysis of variance was conducted to determine significant differences between treatments and among accessions with treatment (water) and accession as fixed effects and block as a random effect using PROC GLIMMIX of the statistical software SAS 9.2 (SAS Inc., Cary, NC, USA).
