Fig. 2

Grh binding variation is primarily due to cis changes outside the Grh binding motif. A Histogram of the estimated Grh binding variation between Zhr and Z30 parental strains. Bars are colored based on above (light gray) or below (dark gray) a q-value of 0.05 for the parental difference. B Histogram of the estimated Grh binding variation between Zhr and Z30 hybrid alleles. Bars are colored based on above (aqua) or below (salmon) a q-value of 0.05 for the hybrid allele difference. C Scatterplot contrasting the estimated Grh binding variation between parents (x-axis) versus the estimated Grh binding variation between hybrid alleles (y-axis). Spearman’s rho displayed in the bottom right corner. D Pie chart showing the ratio of variable Grh-bound regions with and without a SNV in the local Grh motif. E For Grh motifs with sequence variation, scatterplot contrasting the difference in position weight matrix score between Zhr and Z30 genotypes (x-axis) versus the empirically estimated Grh binding variation between hybrid alleles (y-axis). F The SNV density per 500 bp contrasted between Grh-bound regions with and without evidence for Grh binding variation (q < or > 0.05, respectively). Wilcoxon rank sum test: p < 0.01