Abstract
Light is the most important environmental cue signaling the transition from skotomorphogenesis to photomorphogenesis, thus affecting plant development and metabolic activity. How the light response mechanisms of maize seedlings respond to fluctuations in the light environment has not been well characterized to date. In this study, we built a gene coexpression network from a dynamic transcriptomic map of maize seedlings exposed to different light environments. Coexpression analysis identified ten modules and multiple genes that closely correlate with photosynthesis and characterized hub genes associated with regulatory networks, duplication events, domestication and improvement. In addition, we identified that 38% of hub genes underwent duplication events, 74% of which are related to photosynthesis. Moreover, we captured the dynamic expression atlas of gene sets involved in the chloroplast photosynthetic apparatus and photosynthetic carbon assimilation in different light environments, which should help to elucidate the key mechanisms and regulatory networks that underlie photosynthesis in maize. Insights from this study provide a valuable resource to better understand the genetic mechanisms of the response to fluctuations in the light environment in maize.
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Data availability
Sequence data from this article can be found in the National Center for Biotechnology Information Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra) under accession number SRP118761.
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Acknowledgements
This study was funded by the Young Scientists Fund of the National Natural Science Foundation of China (Grant No. 31701438) and the Science Foundation for Post Doctorate Research of the Ministry of Science and Technology of China (2018M633588).
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Shutu Xu, Dongwei Guo and Jiquan Xue conceived and designed the experiments. Shutu Xu, Xiaonan Gou, Wenxin Zhang, Ting Li and Jianzhou Qu performed experiments. Jianzhou Qu analyzed and interpreted the data. Jianzhou Qu and Shutu Xu wrote the paper and prepared figures and/or tables. All authors read and approved the final manuscript.
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438_2021_1761_MOESM1_ESM.tif
Supplementary Correlation of gene expression level across replicates. For each gene, the expression values were normalized by the log2(FPKM+1). The scale bar shows the degree of correlation between samples. The samples from seedlings under normal light condition (SNL), seedlings after four days of dark treatment (SDT) and four days after seedlings return to normal light (SRNL) (TIF 2312 KB)
438_2021_1761_MOESM2_ESM.tif
Supplementary Comparison of expression patterns of candidate genes by qRT-PCR and RNA-Seq. Histogram showing expression levels of candidate genes based on qRT-PCR (left). Boxplot showing expression levels of candidate genes based on RNA-Seq (right). The samples from seedlings under normal light condition (SNL), seedlings after four days of dark treatment (SDT) and four days after seedlings return to normal light (SRNL) (TIF 3827 KB)
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Qu, J., Gou, X., Zhang, W. et al. New insights into the response of maize to fluctuations in the light environment. Mol Genet Genomics 296, 615–629 (2021). https://doi.org/10.1007/s00438-021-01761-6
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DOI: https://doi.org/10.1007/s00438-021-01761-6