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Transcriptome-wide analysis of dynamic variations in regulation modes of grapevine microRNAs on their target genes during grapevine development

Plant Molecular Biology volume 84, pages 269–285 (2014)Cite this article

Abstract

MicroRNAs (miRNAs) play critical regulatory roles mainly through cleaving their target mRNAs or repressing gene translation during plant development. Grapevines are among the most economically important fruit crops with available whole genome sequences. Studies on grapevine miRNAs (Vv-miRNAs) are also widely available. However, studies on the regulation mode of Vv-miRNAs on their target mRNAs during grapevine development have not been studied well, especially at the transcriptome-wide level. Here, six small RNA and mRNA libraries from various grapevine tissues were constructed for Illumina and Degradome sequencing. Subsequently, we systematically analyzed the spatiotemporal variations in the regulation of the target genes of regulation of Vv-miRNAs. In total, 242 known and 132 novel Vv-miRNAs and 193 target mRNAs were identified, including 103 target mRNAs for known and 90 target mRNAs for novel miRNAs, were validated in one or more of the tissues examined. More than 50 % of novel miRNAs were expressed exclusively in the flowers and berries, where they cleaved their target genes in a tissue-specific manner, especially, the breadth of their cleavage sites in flower tissues. Moreover, six novel miRNAs in berries responded to exogenous gibberellin and/or ethylene under a quantitative real time RT-PCR analysis, which confirmed their regulatory functions during berry development. Up to 93.6 % of the known miRNAs were highly conserved in various tissues, where their expression levels exhibited dynamic variations during grapevine development. Significantly, some Vv-miRNA families had one key member that acted as the main regulator of their target genes during grapevine development.

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Acknowledgments

This work was supported by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), and the Graduate innovative training project in Jiangsu Province CXZZ11_0665 and CXZZ12_0284.

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The authors declare that they have no conflict of interests.

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Affiliations

  1. College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China

    Chen Wang, Xiangpeng Leng, Yanyi Zhang, Emrul Kayesh, Yanping Zhang, Xin Sun & Jinggui Fang

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  1. Chen Wang
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  2. Xiangpeng Leng
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  3. Yanyi Zhang
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  4. Emrul Kayesh
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  5. Yanping Zhang
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  6. Xin Sun
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  7. Jinggui Fang
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Correspondence to Jinggui Fang.

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Wang, C., Leng, X., Zhang, Y. et al. Transcriptome-wide analysis of dynamic variations in regulation modes of grapevine microRNAs on their target genes during grapevine development. Plant Mol Biol 84, 269–285 (2014). https://doi.org/10.1007/s11103-013-0132-2

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  • DOI: https://doi.org/10.1007/s11103-013-0132-2

Keywords

  • Grapevine
  • miRNA
  • mRNA
  • Regulatory mode
  • Dynamic variation