Signalling pathway proteins tend to be up-regulated in CB4856 and in RILs compared to N2.

<p>Protein abundance was quantified by SRM. Identification of the true peak group was performed using the mProphet software, followed by protein significance analysis using intensity-based linear mixed-effects model implemented in MSstats. (A) Heat map showing differential abundance of 44 proteins in CB4856 and four empirically selected RILs relative to N2. Blue and red shades represent log₂ scaled fold changes, grey colour shows the fold change cut-off of 1.3 (~ 0.38 on log₂ scale) and number of asterisks represent BH corrected <i>P</i>-values. Black bands on the left side indicate proteins selected for subsequent pQTL mapping. Number of asterisks on top of each column represent BH corrected <i>P</i>-values from one sample t-test (H₀: μ = 0 and H₁: μ ≠ 0) on protein fold changes relative to N2; *<i>P</i> ≤ 0.05; **<i>P</i> ≤ 0.01; ***<i>P</i> ≤ 0.001; ****<i>P</i> ≤ 0.0001. (B) Tukey-style box plot of broad-sense heritability for the 44 proteins shown in panel A. Scatter points overlaid on the box plot represent the broad-sense heritability values for the individual proteins (solid black circles correspond to selected proteins). (C) Bar graph of selected proteins from panel A. Horizontal dashed lines represent the fold change cut-off of 1.3 (~ 0.38 on log₂ scale). Error bars represent SEM between three biological replicates.