Height, an important agronomic trait, relates to lodging resistance, harvest index, and yield potential. Height is also a major issue in developmental biology. Systematic identification and characterization of dwarf plants that show defects in height have basic and applied significance. In previous research, we analyzed the agronomic and physiological features of the dominant maize dwarf plant Dwarf11 (D11). However, transcriptomic specialization of D11 remains largely unknown. Here, we combined RNA-seq and co-expression analysis to survey the transcriptome dynamics of D11. A total of 306 significantly differentially expressed genes (DEGs) were identified, including 171 upregulated and 135 downregulated DEGs. Functional annotation, gene ontology (GO), and pathway enrichment analysis indicated that roles of DEGs were diversified, from organ size control, cell wall character, vascular tissue development, leaf morphology, chlorophyll metabolism, chloroplast function to sugar homeostasis. Functional associations of DEGs were further revealed by the co-expression analysis. Results presented here are informative for the elucidation of D11-involved regulatory network, and lay a foundation for candidate gene prioritization and D11 gene cloning.
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