Distribution of nonsyntenic genes among different classes of genes. A, Proportion of nonsyntenic genes among nonadditively expressed genes (shaded) in the hybrids relative to all expressed genes (not shaded) in each of the four primary root tissues. B, Proportion of nonsyntenic genes among genes showing unexpected allelic ratios (shaded) in the hybrids relative to all expressed genes containing an SNP (not shaded) in each of the four primary root tissues. C, Proportion of nonsyntenic genes among differentially expressed genes [FDR ≤ 5%; |log2(FC)| > 1] (not shaded) between the four different genotypes B73 (B), Mo17 (M), B73xMo17 (BM), and Mo17xB73 (MB) in cortex, stele, elongation, and meristematic zone relative to all expressed genes in all genotypes (shaded). Significant differences (α ≤ 5%) compared with all expressed genes are indicated with an asterisk.