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Characterization of miRNAs responsive to exogenous ethylene in grapevine berries at whole genome level

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Abstract

MicroRNAs (miRNAs) are critical regulators of various biological and metabolic processes of plants. Numerous miRNAs and their functions have been identified and analyzed in many plants. However, till now, the involvement of miRNAs in the response of grapevine berries to ethylene has not been reported yet. Here, Solexa technology was employed to deeply sequence small RNA libraries constructed from grapevine berries treated with and without ethylene. A total of 124 known and 78 novel miRNAs were identified. Among these miRNAs, 162 miRNAs were clearly responsive to ethylene, with 55 downregulated, 59 upregulated, and 14 unchanged miRNAs detected only in the control. The other 35 miRNAs responsive to ethylene were induced by ethylene and detected only in the ethylene-treated grapevine materials. Expression analysis of 27 conserved and 26 novel miRNAs revealed that 13 conserved and 18 novel ones were regulated by ethylene during the whole development of grapevine berries. High-throughput sequencing and qRT-PCR assays revealed consistent results on the expression results of ethylene-responsive miRNAs. Moreover, 90 target genes for 34 novel miRNAs were predicted, most of which were involved in responses to various stresses, especially like exogenous ethylene treatment. The identified miRNAs may be mainly involved in grapevine berry development and response to various environmental conditions.

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Acknowledgments

This research was supported by projects funded by the Natural Science Foundation of China (NSFC) (No. 31301759), China Postdoctoral Science Foundation funded project (2013M531373), Postdoctoral Foundation of Jiangsu Province (1301116C), Special Program of China Postdoctoral Science Foundation (2014T70533), the Nanjing Agricultural University Youth Science and Technology Innovation Fund (KJ2013013), and the Fundamental Research Funds for the Central Universities of China (KYZ201411), and Jiangsu Agriculture Science and Technology Innovation Fund (JASTIF) [CX(13)5017].

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Authors and Affiliations

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

    Fanggui Zhao, Chen Wang, Jian Han, Xudong Zhu, Xiaopeng Li & Jinggui Fang

  2. College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China

    Fanggui Zhao

  3. Institute of Horticulture, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China

    Xicheng Wang

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  1. Fanggui Zhao
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  2. Chen Wang
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  5. Xiaopeng Li
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  6. Xicheng Wang
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  7. Jinggui Fang
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Correspondence to Chen Wang or Jinggui Fang.

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This article forms part of a special issue of Functional & Integrative Genomics entitled “miRNA in model and complex organisms” (Issue Editors: Hikmet Budak and Baohong Zhang).

Fanggui Zhao and Chen Wang should be considered co-first authors.

Chen Wang and Jinggui Fang are co-corresponding authors.

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Zhao, F., Wang, C., Han, J. et al. Characterization of miRNAs responsive to exogenous ethylene in grapevine berries at whole genome level. Funct Integr Genomics 17, 213–235 (2017). https://doi.org/10.1007/s10142-016-0514-z

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  • DOI: https://doi.org/10.1007/s10142-016-0514-z

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