Fig. 3

Overlaps between the sets of DEGs identified from comparisons between the parents and the synthetics. The top left corners indicate the biological material and the variable being compared on the Venn diagrams. a: A diagram showing two sets of DEGs detected in grain transcriptomes of two synthetic generations, b: two sets of DEGs detected in leaf transcriptomes of two synthetic generations, c: two sets of DEGs detected in a hybrid and a synthetic leaf transcriptome, d: two sets of DEGs detected in leaf transcriptomes of reciprocal synthetics, e: two sets of DEGs detected in grain transcriptomes of reciprocal synthetics, f: three sets of DEGs detected in grain transcriptomes of different synthetic genotypes. Genotypes’ ID is shown in black in the centre of the circles. DEG counts of different fractions are shown in red, with two numbers for each overlap - the top one showing the number of DEGs with the same direction of gene expression change, and the bottom one followed by an exclamation mark the number of DEGs in contrasting directions. The red numbers outside of the Venn diagrams show over-representation of the intersection in respect to a count expected by chance. All overlaps have high statistical significance, according to exact hypergeometric probability with normal approximation (http://www.nemates.org/MA/progs/overlap_stats.html). In these calculations, the ‘total number of genes’ was the number of genes that are expressed (non-zero read counts) in both of the relevant DEG analyses