Fig. 2.

Preservation and divergence of gene coexpression networks between the hybrid and its parents underlying early shoot development (3–8 DAS). (A) Hierarchical cluster dendrogram showing consensus gene coexpression modules (CMs) among Arabidopsis ecotypes (Col-0, Per-1) and their F₁ hybrid. In the dendrogram, each leaf represents one gene, and each module below the dendrogram is labeled with one color. The red line above is the cut height (0.99) for CM identification. CM colors are labeled independent of the separately identified modules in each genotype. Genes not coexpressed in all three genotypes are marked in gray. (B) Differential eigengene expression patterns of CMs in the three genotypes across 3–8 DAS. Blue and red represent lesser and greater expression, respectively. (C) Heat map summarizing GO enrichment of genes in each CM. Color intensity represents the significance (−log₁₀[adjusted P value]) of GO term enrichment. (D) Heat maps of eigengene networks showing the relationships among CMs in each genotype.