Figure 2.

DEGs and dosage-dependent expression pattern revealed by RNA-seq. (A) The distribution of DEGs between homozygous p1-ww714 and B73 plants identified by RNA-seq. Bars indicate the numbers of overexpressed (red) and underexpressed (blue) DEGs identified in the 14.6-Mb duplicated region (first bar), the remainder of chromosome 1 (second bar), and other chromosomes. (B) Ratios of chromosome 1 gene expression among three genotypes as determined by RNA-seq. Log₂ fold changes in transcript levels were plotted for pairwise comparisons among p1-ww714/p1-ww714, B73/B73, and p1-ww714/B73 sibling plants. Expression ratios are shown for all genes on chromosome 1. The gene copy-number ratios (log₂) of p1-ww714/p1-ww714 vs. B73/B73, p1-ww714/B73 vs. B73/B73, and p1-ww714/p1-ww714 vs. p1-ww714/B73 are 1, 0.585 and 0.415, respectively; these values are indicated as the solid red lines. The x-axis indicates the position of each gene in Mb on maize chromosome 1; the y-axis indicates the transcript level ratios (log₂) among the three tested genotypes. The segment duplicated in p1-ww714 (48.1–62.7 Mb) is indicated by the two green vertical lines; expression ratios of genes within this segment are indicated in blue. (C) Trans effects on unduplicated genes. Heat map of transcript ratios (log₂) of 90 DEGs unlinked with the duplicated region: 33 genes overexpressed (red) and 57 genes underexpressed (green) in p1-ww714/p1-ww714 vs. B73/B73. The transcript ratios were compared among B73/B73, p1-ww714/B73, and p1-ww714/p1-ww714 sibling plants as determined from mRNA-seq data.