Abstract
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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Acknowledgements
This work was supported by the National Natural Science Foundation of China (31571671 and 31201213), the National Key Research and Development Program of China (2016YFD0101002), the Priority Academic Program Development of Jiangsu Higher Education Institutions, and the Jiangsu Government Scholarship for Overseas Studies.
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Yijun Wang and Wenjie Lu contributed equally to this work.
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Figure S1
Correlations between biological replicates. Biological replicates showed high correlations (r > 0.94) in gene expression (JPEG 638 kb)
Figure S2
Gene ontology analysis of up-regulated differentially expressed genes (JPEG 105 kb)
Figure S3
Gene ontology analysis of down-regulated differentially expressed genes (JPEG 429 kb)
Figure S4
Shared differentially expressed genes between Zheng 58 and Mo17 populations (JPEG 102 kb)
Table S1
Primers used in this study (DOCX 17 kb)
Table S2
Sample statistics for RNA-seq and mapping (DOCX 15 kb)
Table S3
Information of all expressed genes in biological replicates of the wild-type and D11 (TXT 14557 kb)
Table S4
Information of differentially expressed genes in D11 relative to the wild-type (XLSX 66 kb)
Table S5
Differentially expressed genes revealed by RNA-seq and qRT-PCR (DOCX 16 kb)
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Wang, Y., Lu, W., Zhao, J. et al. Transcriptome Dynamics of Dominant Maize Dwarf Dwarf11 (D11) Revealed by RNA-seq and Co-expression Analysis. Plant Mol Biol Rep 35, 355–365 (2017). https://doi.org/10.1007/s11105-017-1028-0
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DOI: https://doi.org/10.1007/s11105-017-1028-0