3 Biotech

, 8:311 | Cite as

Identification of miRNAs and their targets in regulating tuberous root development in radish using small RNA and degradome analyses

  • Chen Liu
  • Xianxian Liu
  • Wenling Xu
  • Weimin Fu
  • Fengde Wang
  • Jianwei Gao
  • Qiaoyun Li
  • Zhigang Zhang
  • Jingjuan LiEmail author
  • Shufen WangEmail author
Original Article


High-throughput small RNA sequencing and degradome analysis were used in this study to thoroughly investigate the role of miRNA-mediated regulatory network in tuberous root development of radish. Samples from the early seedling stage (RE) and the cortex splitting stage (RL) were used for the construction of six small RNA libraries and one degradome library. A total of 518 known and 976 novel miRNAs were identified, of which, 338 known and 18 novel miRNAs were expressed in all six libraries, respectively. A total of 52 known and 57 novel miRNAs were identified to be significantly differentially expressed between RE and RL, and 195 mRNAs were verified to be the targets of 194 miRNAs by degradome sequencing. According to the degradome analysis, 11 differentially expressed miRNAs had miRNA-mRNA targets, and 13 targets were identified for these 11 miRNAs. Of the 13 miRNA-mRNA targets, 4 genes (RSG11079.t1, RSG11844.t1, RSG16775.t1, and RSG42419.t1) were involved in hormone-mediated signaling pathway, 2 gens (RSG11079.t1 and RSG16775.t1) were related to post-embryonic root development, and 1 gene (RSG23799.t1) was involved in anatomical structure morphogenesis, according to the GO function analysis for biological process. Target Genes participated in these processes are important candidates for further studies. This study provides valuable information for a better understanding of the molecular mechanisms involved in radish tuberous root formation and development.


Raphanus sativus Tuberous root Cortex splitting microRNA Degradome 



This study was supported by the Youth Foundation of Shandong Academy of Agricultural Sciences (2016YQN22, 2016YQN23), the National Key Research and Development Program of China (2017YFD0101806, 2016YFD0100204-27), and the Modern Agricultural Industrial Technology System Funding of Shandong Province (SDAIT-05-01).

Compliance with ethical standards

Conflict of interest

The authors declare that there is no conflict of interest regarding the publication of this article.

Supplementary material

13205_2018_1330_MOESM1_ESM.xlsx (11 kb)
Supplementary Table S1: qRT-PCR primers for 11 differentially expressed miRNAs and six target genes (XLSX 11 KB)
13205_2018_1330_MOESM2_ESM.xlsx (11 kb)
Supplementary Table S2: Analysis of sRNA reads from six sRNA libraries (XLSX 11 KB)
13205_2018_1330_MOESM3_ESM.xlsx (33 kb)
Supplementary Table S3: Known miRNAs identified in the six small RNA libraries (XLSX 32 KB)
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Supplementary Table S4: Novel miRNAs identified in the six small RNA libraries (XLSX 46 KB)
13205_2018_1330_MOESM5_ESM.xlsx (16 kb)
Supplementary Table S5: The differentially expressed miRNAs between RE and RL (XLSX 16 KB)
13205_2018_1330_MOESM6_ESM.xlsx (11 kb)
Supplementary Table S6: Classification of clean tags identified by degradome sequencing (XLSX 11 KB)
13205_2018_1330_MOESM7_ESM.xlsx (54 kb)
Supplementary Table S7: Targets of miRNAs identified by degradome analysis in radish (XLSX 54 KB)
13205_2018_1330_MOESM8_ESM.xlsx (12 kb)
Supplementary Table S8: Target mRNAs for differentially expressed miRNAs between RE and RL in radish (XLSX 12 KB)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Chen Liu
    • 1
  • Xianxian Liu
    • 1
  • Wenling Xu
    • 1
  • Weimin Fu
    • 1
  • Fengde Wang
    • 1
  • Jianwei Gao
    • 1
  • Qiaoyun Li
    • 1
  • Zhigang Zhang
    • 1
  • Jingjuan Li
    • 1
    Email author
  • Shufen Wang
    • 1
    Email author
  1. 1.Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables and FlowersShandong Academy of Agricultural SciencesJinanPeople’s Republic of China

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