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Unveiling gibberellin-responsive coding and long noncoding RNAs in maize

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We report coding and long noncoding RNAs in maize upon phytohormone gibberellin stimulation.

Abstract

Plant hormone gibberellin (GA) orchestrates various facets of biological processes. Dissection the transcriptomic dynamics upon GA stimulation has biological significance. Feature of maize transcriptome in response to GA application remains largely elusive. Herein, two types of plants, one was with normal height, the other was GA-sensitive dwarfism, were selected from advanced backcross population for GA3 treatment with different concentrations. In control and GA3-treated plants, we identified a large number of coding and long noncoding RNAs (lncRNAs) through sequencing eight ribosomal-depleted RNA libraries. Transcripts encoding GA biosynthetic and metabolic enzymes KS, GA20ox, GA3ox, and GA2ox were significantly differentially expressed in GA3-treated samples. A total of 78 protein-coding transcripts were shared between GA3-treated normal height and dwarf plants. Shared transcripts encoding terpene synthase, MYB transcription factor, and receptor-like protein kinase were co-regulated with their corresponding partners. Out of identified lncRNAs, 22 and 34 significantly differentially expressed lncRNAs were responsive to GA application in normal height and dwarf plants, respectively. Shared GA-responsive lncRNAs were found in GA3-treated normal height and dwarf plants. Some lncRNAs corresponded to precursors of known miRNA, such as zma-miR528a and zma-miR528b. Multiple promising targets of significantly differentially expressed lncRNAs were discovered, including Lazy plant1 for auxin- and GA-mediated shoot gravitropism, bZIP transcription factor member for GA-controlled cell elongation. This study will improve our knowledge of GA-triggered transcriptome change and facilitate a comprehensive understanding of regulatory cascade centering on GA.

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (31571671), the National Key Research and Development Program of China (2016YFD0101002), the Key Research Program of Jiangsu Provincial Colleges and Universities (18KJA210002), the Innovative Foundation of Yangzhou University (2017CXJ063), the Science Foundation for Excellent Youth Scholars of Yangzhou University, the Priority Academic Program Development of Jiangsu Higher Education Institutions, and the Practicality and Innovation Training Project for College Students of Yangzhou University (x20160631, x20170646).

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Author notes

  1. Yijun Wang and Yali Wang contributed equally to this work.

Authors and Affiliations

  1. Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China

    Yijun Wang, Yali Wang, Jia Zhao, Jiayu Huang, Yining Shi & Dexiang Deng

  2. Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China

    Yijun Wang, Yali Wang, Jia Zhao, Jiayu Huang, Yining Shi & Dexiang Deng

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  1. Yijun Wang
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  4. Jiayu Huang
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Contributions

YJW conceived and designed the experiments. DD prepared the experimental materials. YLW, JZ, JH, and YS performed the experiments. YJW and YLW analyzed the data. YJW wrote the manuscript.

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Correspondence to Yijun Wang.

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The authors declare that they have no conflict of interest.

Electronic supplementary material

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11103_2018_788_MOESM1_ESM.png

Fig. S1 Structure of miRNA precursor. Significantly differentially expressed lncRNA TCONS_00051916 could be the miRNA precursor (PNG 17 KB)

Fig. S2 Antisense target of significantly differentially expressed lncRNA TCONS_00110864 (PNG 118 KB)

Fig. S3 Interaction network of target genes of significantly differentially expressed lncRNAs (TIF 243 KB)

Table S1

Primers used in this study (DOCX 14 KB)

Table S2 Information of significantly differentially expressed protein-coding transcripts (XLSX 91 KB)

11103_2018_788_MOESM6_ESM.xlsx

Table S3 Gene ontology enrichment analysis of significantly differentially expressed protein-coding transcripts (XLSX 11 KB)

Table S4 Functional annotation of shared GA-responsive protein-coding transcripts (XLSX 13 KB)

Table S5 Information of all identified lncRNAs and shared GA-responsive lncRNAs (XLSX 679 KB)

Table S6 Information of significantly differentially expressed lncRNAs (XLSX 15 KB)

Table S7 GA-responsive lncRNAs as precursors of miRNAs (XLSX 16 KB)

Table S8 Cis targets of significantly differentially expressed lncRNAs in D11 upon GA3 application (XLSX 10 KB)

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Wang, Y., Wang, Y., Zhao, J. et al. Unveiling gibberellin-responsive coding and long noncoding RNAs in maize. Plant Mol Biol 98, 427–438 (2018). https://doi.org/10.1007/s11103-018-0788-8

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  • DOI: https://doi.org/10.1007/s11103-018-0788-8

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