Figure 4.
Dosage-dependent expression of small RNAs. Log2 fold changes in small RNA levels per 100-kb window were plotted for comparisons between (A) p1-ww714/p1-ww714 and B73/B73, (B) p1-ww714/p1-ww714 and p1-wwid1/p1-wwid1, (C) p1-ww714/p1-ww714 and p1-wwid1/p1-wwid1 and (D) p1-wwid1/p1-wwid1 and p1-wwid4/p1-wwid4. The x-axis indicates the position of each 100-kb window in Mb on maize chromosome 1; the y-axis indicates the ratios (log2) of small RNA level between the tested genotypes. Vertical lines (green) indicate the duplication borders. The numbers within two vertical lines represent the size of duplications. The thicker red lines indicate the twofold copy-number ratio between genotypes. (A) Expression difference between p1-ww714/p1-ww714 and B73/B73. p1-ww714 carries a 14.6-Mb segmental duplication (48.1–62.7 Mb), indicated by the two green vertical lines; log expression ratios of genes within this segment are indicated in blue. (B) Expression difference between p1-ww714/p1-ww714 and p1-wwid1/p1-wwid1. p1-wwid1 has a 3.3-Mb segmental duplication which is overlapped by the 14.6-Mb duplication of p1-ww714. The 3.3-Mb overlapped duplication is represented by the first two green lines. (C) Expression difference between p1-ww714/p1-ww714 and p1-wwid4/p1-wwid4. p1-wwid4 has a 400-kb segmental duplication which is overlapped by the duplication in p1-ww714. The 400-kb overlapped duplication is represented by the first two green lines. (D) Expression difference between p1-wwid1/p1-wwid1 and p1-wwid4/p1-wwid4. p1-wwid4 has a 400-kb segmental duplication which is overlapped by the 3.3-Mb duplication of p1-wwid1. The 400-kb overlapped duplication is represented by the first two green lines.