Fig. 4

local-eQTL characterization by allele-specific expression reveals few cis-acting variants and a comparable distribution between cis- and non cis-eQTLs. a Schematic of the round robin design: isogenic parental lines (blue) were crossed to two different lines and heterozygote F1 female offspring (gray) were used for infection and further processing. b Distribution of the number of heterozygous crosses per eQTL in control (gray) and infected (orange) conditions. The distribution of cis-eQTLs (dark gray and dark orange) is not affected by the number of heterozygous crosses that are available to perform the calculations. c Number of eQTLs passing the data cutoff for cis-characterization (light green) and rejected (red) in control (19%) and infected (18%) conditions. cis-eQTLs are indicated in dark green with 9.7% and 7.5% of local-eQTLs in infected and control conditions respectively. d, e Correlation between local-eQTL p values (x-axis, −log10(Benjamini-Hochberg adjusted p value)) compared to cis-eQTL calculated p values (y-axis, −log10(Benjamini-Hochberg adjusted p value)). Vertical and horizontal lines represent the 0.05 cutoff in control and infected conditions. f Number of eQTLs passing the data cutoff for trans- characterization (light green) and rejected (red) in control (30.2%) and infected (31.2%) conditions. Trans-eQTLs are indicated in dark green with 6.6% and 9.3% of local-eQTLs in infected and control conditions, respectively